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COVID rates tick down again in Houston

Jan 22nd, 2023
by Charles Kuffner.
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Always a good headline to read.

COVID-19 data from the Texas Medical Center this week suggests the current wave may be subsiding, though experts urge caution as a new, highly infectious variant continues to circulate.

The average number of daily hospitalizations in the medical center had been rising steadily for a month, but dropped last week by about 20 percent, from 182 to 146. Regional COVID hospitalizations also have dropped from a five-month high of 1,002 on Jan. 5 to 836 on Monday, according to the Southeast Texas Regional Advisory Council.

Most significantly, the viral load in the city’s wastewater — the most reliable indicator of future virus spread — dropped by about 34 percent last week, according to data published Tuesday.

“I would be very surprised if we saw this (trend) reverse at this point,” said Dr. James McDeavitt, senior vice president and dean of clinical affairs at Baylor College of Medicine.

Even with a hopeful outlook, researchers cautiously are eyeing the progress of XBB.1.5, which public health officials say is the most transmissible form of COVID yet. It quickly has become the dominant strain nationwide. The variant accounts for 80 percent of cases in the Northeast, according to the Centers for Disease Control and Prevention, though it has yet to beat out other infectious strains in Houston and much of the South.

Here’s that wastewater dashboard again. We’re still at a very high level compared to the July 2020 baseline, but at least we’re going in the right direction now. Hospitalization rate is the bigger concern, but again as long as we’re now trending downward, the overall picture is improving. There’s an argument to be made that we shouldn’t obsessively track each new alphabet-soup variant, at least not while they’re all about the same level of lethality. The fact that successive versions are more transmissible than their predecessors are just how viruses work. I’m not sophisticated enough to make a judgment about that, but I have limited my worry to the prospect of a deadlier strain.

There are still other things to worry about:

The United States has faced a triple threat of respiratory viruses over the past few months, with COVID-19, the flu and RSV driving infections and hospitalizations in the Houston area and elsewhere.

Each of the three are capable of causing mild to severe illness by themselves. But it’s also possible to contract more than one virus at a time — and a new study suggests a coinfection may lead to more severe illness in young children.

The term “flurona” became popular on social media last year as a surge in COVID-19 and the re-emergence of the flu caused a wave of infections. However, doctors were seeing patients — particularly young children — with coinfections before the pandemic, said Dr. Amy Arrington, medical director of the Special Isolation Unit at Texas Children’s Hospital.

“It’s not uncommon that we see younger kids getting co-infected,” she said. “I think a lot of parents today in Houston can say they feel like their child’s been sick for the past few months straight.”

Younger children might be more susceptible to coinfections because they haven’t been exposed to a respiratory virus before, Arrington said. They may be getting infected at daycare, or from an older sibling who picked up the virus at school.

Coinfections are uncommon, but doctors might be seeing them more frequently this fall and winter for a few reasons, said Dr. Luis Ostrosky, chief of infectious diseases at UTHealth Houston and Memorial Hermann Hospital.

The collision of COVID-19, the flu and RSV, as well as other respiratory viruses like rhinovirus and enterovirus, has created more opportunity for infection, he said.

“Tripledemic” was the word I heard. Fortunately, RSV and flu rates have been dropping as well. You can still get a flu shot, and for sure you can and should get your bivalent booster. Hell, I’m ready for whatever the next generation COVID booster is now. I’ll be among the first in line when that becomes available. You are your only real defense here, so do what you need to do.

It’s winter surge time again

Dec 22nd, 2022
by Charles Kuffner.
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Sorry to be the bearer of bad news, though I think you already suspected this.


COVID-19 cases are rising across Texas two weeks after the Thanksgiving holiday, echoing last year’s surge of the omicron variant.

There are more than 18,000 positive cases across the state this week, up from a little over 7,000 the week of Thanksgiving.

“Thanksgiving this year was kind of like PTSD,” said epidemiologist Katelyn Jetelina, author of Your Local Epidemiologist. “I think all of us epidemiologists were holding our breath, just to make sure this was going to be a regular Thanksgiving.”

While hospitalizations and deaths are still low thanks to COVID-19 vaccinations and the updated bivalent booster that targets omicron, cases have been steadily climbing since November.

The change this year, Jetelina said, is the combination of flu, RSV, and now COVID. The Texas Department of State Health Services reports the intensity of influenza-like illness has remained “very high” in the past few weeks, with an increase in the number of influenza outbreaks and more than 28,000 positive flu tests in the week ending in Dec. 3.

“RSV and flu are just back with vengeance,” she said. “We’re starting to get a sneak peek of what this new normal is.”

Other states, like New York, have issued a health advisory to encourage people to mask indoors while cases are high. Jetelina said it’s important to think about protecting the most vulnerable members of the community, like the elderly and folks who are immunocompromised.

“I’m going to have 90-year-old people at my house for Christmas this year,” she said. “That, to me, means I am wearing an N-95 mask in public everywhere I go the week before Christmas. It helps ensure I don’t miss the event because I’m sick, but it also helps break that transmission chain so I don’t bring it to my grandparents.”

She says it’s not too late to get vaccinated to protect against COVID and the flu.

“I’m tired, everyone’s tired, [but] the virus isn’t tired of us,” she said.

We saw this coming in October, and we know what a “tripledemic” is. The virus levels in the wastewater are high. You know what I’m going to tell you: Get your bivalent booster and your flu shot. Wear that mask in crowded indoor spaces. Isolate yourself if you feel sick. Think about the high-risk people in your life. We’re not in 2020 any more, and the current dominant strains are thankfully not as virulent as delta was. You really can do a lot to maximize your safety while giving up very little. But you have to actually do it.

I regret to inform you that “tripledemic” is a word

Dec 7th, 2022
by Charles Kuffner.
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The good news is that we may avoid it here in Houston.

A collision of three respiratory viruses — COVID-19, influenza and RSV — may not hit Houston as severely as other parts of the country, experts say, but pediatric hospitals are still preparing for a busy winter season with at least some virus overlap.

Texas Medical Center data published Tuesday shows early signs of another COVID wave, with an uptick in hospitalizations and the positivity rate, which jumped from 3.2 percent to 5 percent last week. COVID wastewater surveillance also offers a grim outlook, as the viral load rose for the fifth straight week, to 196 percent of the baseline set in July 2020. Newer variants make it difficult to predict the size and severity of the next wave of infections, experts say.

Meanwhile, RSV and flu, two respiratory viruses that commonly infect children, continue to circulate at high levels, weeks after patients began filling beds and prolonging wait times in Houston pediatric hospitals. Despite the ongoing strain, infectious disease experts believe Houston can avoid a so-called “tripledemic,” in which three simultaneous virus surges overwhelm hospital systems.

Statewide surveillance shows both RSV and flu have either peaked or declined.

“At least for us, here in Houston, the story that’s being written is we had this very early peak of flu and RSV and they’re starting to come down,” said Dr. Wesley Long, the medical director of diagnostic microbiology at Houston Methodist. “But then we’re probably going to see a winter speed bump of COVID.”

Dr. Melanie Kitagawa, medical director of the Texas Children’s Hospital pediatric ICU, said there are roughly 50 children admitted to Texas Children’s with RSV, or respiratory syncytial virus, which usually causes mild cold-like symptoms but can be severe for infants and older adults. That number has remained steady for at least a month, but flu admissions have been decreasing across the hospital system, she said.

Flu and RSV admissions have stayed at consistently high levels at Children’s Memorial Hermann for weeks, said Dr. Michael Chang, an infectious disease pediatrician at the hospital who is affiliated with UTHealth Houston.

Chang expects RSV to become more manageable before COVID ramps up. The percentage of positive RSV tests has dropped across the state since early October, from roughly 25 percent to less than 15 percent, according to the Texas Department of State Health Services.

For him, flu rates are more of a concern. Texas’ flu infection rate of 29 percent is among the highest in the nation, according to the Centers for Disease Control and Prevention.

“For flu, what I really worry about is that people have returned to normal behaviors, and vaccine uptake doesn’t seem to be really good,” he said. “From what I’ve seen of the new COVID numbers, we may see an unfortunate confluence of (COVID) and significant flu cases. But luckily I think we will avoid a full ‘tripledemic.’”

There are recent signs that the flu is waning as well.

See here for some background. We have milder winters here, so because we can still do stuff outside we can have a smaller winter effect from COVID. But the bottom line is the same as it always has been for minimizing the spread of these viruses. Get your COVID boosters, especially the bivalent booster. Get your flu shot. Keep wearing your facemask in crowded indoor spaces, and avoid such spaces where possible. You have the power and the choice to minimize your risk.

Is this just the calm before the next COVID wave?

Oct 17th, 2022
by Charles Kuffner.
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Things look good now, at least in the Houston area, but COVID never sleeps.

As the U.S. heads into a third pandemic winter, the first hints are emerging that another possible surge of COVID-19 infections could be on its way.

So far, no national surge has started yet. The number of people getting infected, hospitalized and dying from COVID in the U.S. has been gently declining from a fairly high plateau.

But as the weather cools and people start spending more time inside, where the virus spreads more easily, the risks of a resurgence increase.

The first hint of what could be in store is what’s happening in Europe. Infections have been rising in many European countries, including the U.K., France, and Italy.

“In the past, what’s happened in Europe often has been a harbinger for what’s about to happen in the United States,” says Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota. “So I think the bottom line message for us in this country is: We have to be prepared for what they are beginning to see in Europe.”

Several computer models are projecting that COVID infections will continue to recede at least through the end of the year. But researchers stress there are many uncertainties that could change that, such as whether more infectious variants start to spread fast in the U.S.

In fact, scientists are watching a menagerie of new omicron subvariants that have emerged recently that appear to be even better at dodging immunity.

“We look around the world and see countries such as Germany and France are seeing increases as we speak,” says Lauren Ancel Meyers, director of the UT COVID-19 Modeling Consortium at the University of Texas at Austin. “That gives me pause. It adds uncertainty about what we can expect in the coming weeks and the coming months.”

However, it’s not certain the U.S. experience will echo Europe’s, says Justin Lessler, an epidemiologist at the University of North Carolina who helps run the COVID-19 Scenario Modeling Hub.

That’s because it’s not clear whether Europe’s rising cases are related to people’s greater susceptibility to new subvariants they’ve not yet been exposed to. In addition, different countries have different levels of immunity.

“If it is mostly just behavioral changes and climate, we might be able to avoid similar upticks if there is broad uptake of the bivalent vaccine,” Lessler says. “If it is immune escape across several variants with convergent evolution, the outlook for the U.S. may be more concerning.”

In fact, some researchers say the U.S. is already starting to see early signs of that. For example, the levels of virus being detected in wastewater are up in some parts of the country, such in Pennsylvania, Connecticut, Vermont and other parts of the Northeast. That could an early-warning sign of what’s coming, though overall the virus is declining nationally.

“It’s really too early to say something big is happening, but it’s something that we’re keeping an eye on,” says Amy Kirby, national wastewater surveillance program lead at the Centers for Disease Control and Prevention.

But infections and even hospitalizations have started rising in some of the same parts of New England, as well as some other northern areas, such as the Pacific Northwest, according to Dr. David Rubin, the director of the PolicyLab at Children’s Hospital of Philadelphia, which tracks the pandemic.

“We’re seeing the northern rim of the country beginning to show some evidence of increasing transmission,” Rubin says. “The winter resurgence is beginning.”

As the story notes, we’re overall in a much better place because there’s a lot more immunity thanks to vaccinations and our previous high rate of infections. The COVID levels in wastewater here is low now, and while we’re hardly a leader in vaccinations, we at least have warmer winters so there are still plenty of opportunities to be outside, and fewer times where you have to be congregated inside. But also, not nearly enough people have had their bivalent boosters yet, and there are concerns about the flu season. So, you know, remain appropriately cautious – masking in places where you used to have to mask is still an excellent idea – and get those shots.

The wastewater is looking good now

Oct 8th, 2022
by Charles Kuffner.
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In terms of COVID levels, anyway.

The COVID-19 viral load in Houston’s wastewater has sunk to its lowest point in seven months as the city puts the latest wave, driven by the highly contagious omicron subvariant BA.5, in the rear view.

The wastewater levels are 71 percent of what the Houston Health Department detected during the July 2020 wave, which the city uses as a benchmark, according to Texas Medical Center data published Tuesday. The COVID hospitalization rate and positivity rate also continue to decline steadily.

Harris County last week dropped its COVID community level from “medium” to “low,” which recommends staying up to date on vaccinations and testing if you have symptoms. Scientists are looking to other countries for signs of what comes next.

“Our history has typically been a winter surge,” said Dr. Luis Ostrosky, chief of infectious diseases with McGovern Medical School at UTHealth Houston. “So let’s enjoy it while we can.”

Several new omicron off-shoots have been detected in the United Kingdom, India, Singapore, Denmark and Australia, according to the journal Nature. BA.5 continues to dominate cases in the United States, though one subvariant, BA.4.6, has gained some traction and now makes up roughly 12 percent of cases, according to the Centers for Disease Control and Prevention. Ostrosky urged people to get their updated booster shots, which better target omicron variants.

The dashboard is here, and you can see it as a graph here. COVID from the omicron wave peaked in the wastewater in July, but it was at almost ten times the level as it had been in July of 2020. It is now at 71% of the July 2020 levels, which is much better in so many respects. Get up to date on your boosters – I got my bivalent booster the other day – and get a flu shot (got one of those as well, at the same time), because there’s concern this could be a bad flu season. And even with these levels going down, hopefully for the foreseeable future, it’s still a good idea to wear a mask in crowded indoor spaces. Might help you avoid catching a winter cold, too.

Houston will monitor for monkeypox in the wastewater

Aug 7th, 2022
by Charles Kuffner.
1 comment

Seems like a good idea.

Houston will begin monitoring its wastewater for monkeypox in late August as cases of the blister-causing contagion continue to climb, health officials said.

Scientists will begin testing for the monkeypox virus in city sewage samples “starting in about three weeks,” Houston Health Department spokesperson Porfirio Villarreal said Thursday morning.

There are 152 cases in Harris County, 131 of those in Houston, the county’s Public Health Department reports. More than 6,300 Americans had tested positive for monkeypox as of Wednesday, nearly 500 of them in Texas. Many cases have been among gay and bisexual men, but the disease can be spread among anyone via close contact.

To collect the data, Houston scientists will take weekly samples from flushed wastewater at sewage treatment plants across the city. Once tested, the samples will give scientists a snapshot of which neighborhoods have the most monkeypox virus.

Health officials have used wastewater tracking to monitor COVID-19 levels in the city’s sewage since the beginning of the pandemic to understand how quickly the virus is spreading among the city’s two million inhabitants. The tracking project, a joint effort by Rice University and the Houston Health Department, offers clues to the severity of the pandemic that may be invisible in testing data.

We are familiar with the track-COVID-in-the-wastewater project, which has been a resounding success (and which is currently showing a decrease in the levels, praise be). Not clear yet if this data will show up on the same dashboard or if there will be a new one, but we’ll know soon enough. I’ll be on the lookout.

The latest COVID wave may be peaking in Houston

Aug 5th, 2022
by Charles Kuffner.
2 comments

Hopefully…

Texas Medical Center data released Tuesday suggests the latest wave of COVID-19 might have reached its peak in the Houston area, though several key metrics used to track the virus remain high.

The medical center’s weekly data report shows that COVID-19 hospitalizations, the positivity rate of coronaviruus tests and the amount of virus detected at the city of Houston’s wastewater treatment plants all trended downward for the second straight week. Those trends indicate the Houston area has likely crested the peak of a recent surge caused by the extremely contagious BA.5 subvariant, said Dr. James McDeavitt, executive vice president and dean of clinical affairs at Baylor College of Medicine.

“All the numbers are pointing to the fact that we’ve peaked maybe a week, a week and a half ago,” McDeavitt said. “I fully expect we will continue to trend down over the next several weeks.”

The line graphs from the TMC show a mountain range of peaks from prior waves of COVID-19, such as those caused by the delta and omicron variants. The latest BA.5 wave shows that after several weeks of steady climbing, the line is finally on the descent.

During previous waves, the virus did not pick up steam again after the numbers started to trend downward, McDeavitt said. He expects the same trajectory from BA.5.

It appears the current wave has at least reached a plateau, said Dr. Ashley Drews, an infectious disease specialist at Houston Methodist. The fact that the key metrics have stabilized is an encouraging sign, she said.

“We’re cautiously optimistic that things are turning in the right direction, and we’re going down,” Drews said.

[…]

During the week of July 25, TMC hospitals admitted an average of 219 patients with COVID-19 per day. That’s down from an average of 226 during the week of July 18, and 240 during the week of July 11.

However, the numbers remain much higher than they were before the emergence of BA.5. Three months ago, TMC hospitals admitted an average of 80 patients per day.

The good news is that the percentage of patients who need to be treated in an ICU remains lower than prior surges of COVID-19.

Last week, less than 14 percent of the 912 patients admitted with COVID-19 were treated in an ICU, according to TMC data. That’s lower than the percentage of patients treated in an ICU at the peaks of the omicron wave (17 percent) and the delta wave (22 percent).

[…]

The amount of virus detected at the city of Houston’s wastewater treatment plants, which has been a reliable indicator of community spread, also fell for the second straight week.

Wastewater loads reached an all-time high during the week of July 11, at 927 percent higher than a baseline established in June 2020. That fell to 774 percent during the week of July 18, and to 725 percent over the past week.

The amount of virus in the wastewater is still much higher than before the recent surge. Three months ago, it was less than 100 percent higher than the June 2020 baseline.

So, the data is starting to go in the right direction, which is good. But there’s still a lot of COVID out there, and all of the levels are still a lot higher than they were before the wave began, even if they never approached the heights of the previous peaks, and that’s bad. You should still be exercising caution, which is to say wearing your mask and avoiding indoor crowds if you can. And of course, get vaxxed and boosted as needed. We may be back on the downswing, but there’s no reason to believe we won’t trend up again at some point, and we’ve still got a ways to go to get to the lower levels we want.

The current state of the hospitals

Jul 21st, 2022
by Charles Kuffner.
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Worse than before, but not nearly as bad as before that.

A small but growing share of Houston healthcare workers are calling in sick with COVID, exacerbating long-running staffing issues at some hospitals amid the virus’s resurgence.

But despite spreading infections, medical leaders say the Houston-area healthcare system is managing this wave better than previous bouts with the virus, pointing to better therapeutics and fewer COVID patients requiring critical care.

Anecdotally, doctors say at least half of all COVID patients were admitted for reasons unrelated to the virus. While wastewater data reflects a soaring infection rate, daily new hospitalizations are climbing at a slower pace compared to the record-breaking omicron wave in January and February, according to Texas Medical Center data.

“I don’t anticipate we’re going to have major operational problems” among medical center hospitals, said Dr. James McDeavitt, executive vice president and dean of clinical affairs at Baylor College of Medicine.

The latest Texas Medical Center data, published Tuesday, show hospitalizations have nearly doubled over the last five weeks, from 121 in early June to 240 last week. In January, it took only five weeks for omicron to spark a nearly 600 percent increase in daily COVID hospitalizations, as admissions jumped from 74 to a record 515, according to TMC data.

Meanwhile, the increasing viral load detected in the city’s wastewater — 927 percent higher last week than July 2020 — appears to be as high as ever. Two weeks ago, the viral load was 843 percent of the July 2020 baseline. The citywide positivity rate also saw a slight increase from 29 percent two weeks ago to 31 percent last week, while the positivity rate in the medical center dropped slightly from 16.1 percent to 15.9 percent.

[…]

The number of sick hospital staff members reflects a small portion of the overall workforce at Houston hospitals. On Monday, Houston Methodist reported 402 staff members — 1.4 percent of all employees — had tested positive for COVID. Harris Health System said 245 staff members, or 2.4 percent of its workforce, had tested positive for COVID so far this July, compared to roughly 90 staff members throughout most of June.

Additionally, spokespeople for Memorial Hermann Health System, Texas Children’s Hospital and HCA Houston Healthcare say they are not experiencing major staffing issues or operational interruptions amid the current surge.

“Because of our vaccination and booster requirements, our staffing across hospitals is robust and fully intact,” said Dr. James Versalovic, chief pathologist at Texas Children’s Hospital. “I’m happy to say, we have prepared ourselves for this moment.”

More than two years into the pandemic, medical leaders now greet surges with more nuanced messaging, showing concern over rising infections and staffing struggles while assuring the public that hospitals are now better equipped to withstand rising infections.

Versalovic noted that Texas Children’s has seen its COVID population double over the last month. The 7-day rolling average of pediatric COVID patients is now more than 50 in the hospital system. He urged parents to seek out vaccinations as the start of school closes in.

On the one hand, this is basically good news. The hospitals are able to function without being overburdened, our overall vaccination level (and the good luck that this variant, however more contagious it is, isn’t particularly devastating) is helping keep levels in check, and while we’re worse off than we were a couple of months ago we’re much better off than we were in previous waves. One could argue that this is more or less what “endemic” looks like.

On the other hand, Stace is right. We’ve basically given up on trying to keep a lid on this thing – to be sure, there’s far less that governments can do now, thanks to a bunch of wingnut court rulings and Greg Abbott executive orders, but there are plenty of things we could be doing that we aren’t. A lot of leaders who should know better aren’t setting good examples. Even a milder form of COVID is potentially deadly to people with various comorbidities and risk factors, or who are immunocompromised in some way. Just having people mask up again as a matter of course would make all of their lives better, but we’re not doing that.

I’m definitely masking in indoor spaces again, but I’m also willing to be in indoor spaces, and to be among groups of people. I’ve mitigated some of my risk, but I’m engaging in riskier behavior than I had been before. It’s one part denial, one part pandemic fatigue, one part the perhaps naive hope that there will be another booster coming soon, and one part hoping that I’m being cautious enough. I don’t know what happens next if things do get worse from here. I very much hope I don’t have to find out.

Bexar County raises its COVID threat level

Jul 2nd, 2022
by Charles Kuffner.
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Hopefully not a sign of things to come.

Local health officials raised San Antonio’s COVID-19 risk level to high this week after warning of a “silent surge” just two weeks ago.

That surge continues, according to data from the city’s Metropolitan Health District, which is documenting an increase in new cases and hospitalizations.

As the July Fourth holiday approaches, San Antonio Metropolitan Health District chief Claude Jacob urged folks who will be getting together with friends and family to follow COVID-19 prevention strategies: “mask up in crowded indoor places, get tested if you have been exposed or have symptoms and stay up to date with COVID-19 vaccine and boosters.”

Dr. Bryan Alsip, chief medical officer at University Health, said the curve is starting to rise again, “but it’s not as steep an increase. It doesn’t look like the previous waves, not yet, so I think we have to wait and see how that turns out.”

The actual number of COVID-19 cases are suspected to be much higher than what is officially reported, as most people aren’t reporting positive home tests to any health authority.

Metro Health does not collect at-home test data, a spokeswoman said. Some rapid test kits include a way to report results through a mobile app, she noted, and urged everyone who uses a self-test to report positive results to their healthcare provider.

Alsip echoed Metro Health’s prevention strategies, noting that most people have stopped wearing masks. “Now that we know that the data support this high level [of transmission], while we’re in that higher risk timeframe, it would be a good additional layer of protection.”

He also warned that COVID-19 can now include a constellation of symptoms beyond the fever, cough and shortness of breath that characterized the disease at the beginning of the pandemic.

For the record, Harris County is still at Moderate threat level. Given the viral load in Houston’s wastewater these days, it’s not hard to imagine it going up. They key metric is hospitalizations, and that at least has remained at a sufficiently moderate level. It’s still the case that everyone needs to be vaxxed and boosted – kids under the age of five can now get vaccinated, and it looks like we’re getting an Omicron-specific booster later this year – and masking in indoor public places as well as anytime you may feel ill are still necessary. City and county governments can’t do much beyond exhort you to do the civic-minded thing, and for that matter the feds are pretty limited thanks to a bunch of sociopathic court rulings, so this is where we are. Do your part, if only for yourself, and we can make this be less bad than it otherwise would be.

Are we going to raise the COVID threat level again?

Jun 3rd, 2022
by Charles Kuffner.
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Maybe, but not yet.

Coronavirus infections are on the rise across Houston, wastewater tracking shows, even as fewer people seek testing two years into the pandemic.

Four months after the city saw record infection rates caused by the highly contagious omicron variant, new COVID-19 cases are once again climbing, according to data collected by Rice University and the Houston Health Department. The most recent sewage samples show increased viral loads at all but a few of the city’s three dozen wastewater treatment plants.

Citywide, the amount of virus particles detected in wastewater is up 242 percent above baseline, with an overall positivity rate of 14 percent. Both metrics increased by about a third over the previous samples, taken in early May. At the 69th street plant, serving much of the Inner Loop, officials said virus levels are 123 percent above baseline, with a 22 percent positivity rate.

Despite the uptick, health officials do not anticipate raising Harris County’s threat level to the highest level. The county’s threat level is currently set at moderate, signally a controlled level of COVID spread.

“Even though we see positivity rates going up, our hospital rates continue to remain low, said Dr. Erika Brown of the Harris County Health Department.

[…]

New of the rise in viral levels in the wastewater comes days after researchers at Houston Methodist reported new insight into how the omicron variant is mutating in Houston and across Texas.

Researchers demonstrated that two dominant sublineages of omicron have developed “unprecedented numbers” of spike protein mutations, leading to increased transmissibility. The mutations also enhance its ability to evade vaccines and the immune system.

This is a press release about the study in question; it’s from late April, which I’d classify as more than “days” ago, but whatever. The COVID levels in our wastewater continue to rise, but if the hospitals are still not seeing an increase in patients, then the threat level will stay where it is. I don’t know how long we can maintain this balance, but I sure hope it continues.

That press release is worth a read:

“One of the surprising findings in this study was that many mutations with critical roles in immune escape in previous variants of SARS-CoV-2 do not play the same roles in immune escape in omicron, and, in some cases, the effects of these mutations are completely reversed,” said Gollihar, who is the head of antibody discovery and accelerated protein therapeutics in Houston Methodist’s Center for Infectious Diseases. “The virus also appears to be stabilizing itself to allow for more mutations to evade our immune systems.”

He said this study is the first to systematically dissect each of the omicron mutations across the entirety of the spike protein. Previous studies miss contextual and long-range interactions across the protein.

“We developed a comprehensive map showing various mechanisms of immune escape by omicron that allows us to identify which antibodies retain neutralization activity against the virus,” Gollihar said. “This and future work will enable clinicians to make informed decisions about the use of monoclonal antibody therapy and aid in the development of next-generation vaccines.”

Having this new information about key features of omicron’s spike protein mutations and how they synergize, Gollihar and his team say it’s possible that the continuing accumulation of mutations may set the stage for greatly altering the equilibrium and stability of the spike protein in a way that allows for new, more virulent strains to develop. Understanding this evolution is critical, they say, to better inform future therapeutic targets and vaccine formulations, as the SARS-CoV-2 virus will continue to evolve with new variants inevitably arising and spreading.

Looking forward, they add, the strategy used in this study also will be applicable to future zoonotic outbreaks and other microbial pathogens, providing a powerful platform for investigating evolutionary trajectories of infectious agents and engineering appropriate and adaptable vaccines.

“We will continue to monitor the virus for changes in the spike protein and add new antibodies to test as they are discovered. Continuing to do so will allow us to design better probes for antibody discovery in hopes of engineering new therapeutics by finding potent neutralizing antibodies across all variants,” Gollihar said. “We have also recently expanded the platform to other pathogens where we hope to stay ahead of other potential outbreaks.”

I’m in awe of the work these folks have done and continue to do – I’m speaking of the researchers worldwide, not just these specific ones. We’re in a constant race with this virus, and so far we’ve been able to keep up. As above, I sure hope that continues, too. Stace has more.

Checking in again on the wastewater

May 27th, 2022
by Charles Kuffner.
1 comment

COVID levels keep creeping up.

After the U.S. death toll from COVID-19 hit 1 million deaths on Monday, new data shows numbers on the rise again.

The latest Houston Health Department wastewater results from May 9 show levels are now higher than they were in July of 2020.

The viral load on May 9 was 127 percent higher in comparison to July 6, 2020.

The July 2020 readings serve as a baseline for wastewater testing, since that was during the summer surge of cases.

The positivity rate in Houston is also now at 8 percent. At the end of March, Houston’s wastewater positivity rate was 2 percent.

Since the results are delayed, levels are likely higher now.

Houston Methodist is also reporting a rise in cases over the last two weeks.

[…]

“We have also seen our first cases of BA.4 and BA.5, which we will continue to monitor, since literature suggests these variants escape immunity from previous Omicron infection,” [Dr. Wesley Long of Houston Methodist] tweeted. “Vaccines are still our best defense against COVID-19 along with masking and distancing.”

Long also says while the wastewater levels are nearly 30 percent higher than the July 2020 surge, that the public shouldn’t be fearful, but shouldn’t ignore the trend either.

“The bottom line is, the amount of virus in the community is going up,” Long said. “That’s one thing we know for sure. I wouldn’t be worried, but I would be paying attention.”

There was a story in the Sunday print edition of the Chron about the Houston wastewater tracking, with a byline from the NY Times, but I could not find it online. Note that this KHOU story reports on the May 9 virus level in two different ways, saying that the viral load is “127 percent higher” and also that it is “nearly 30 percent higher”. The latter is correct – the Houston COVID dashboard says that the COVID load is “127% in comparison to the July 2020 level”, which is to say up 27%. Pay attention in those math classes, people.

At this point, until there is a new type of vaccine, we have what we’re going to get. I heard on the CityCast Houston podcast that the vax level in Harris County is about 67%, which is better than it used to be but still too low to really slow things down. What we can do is whatever we can to get the unvaxxed people in our lives to get the shots, and we can get boosted – one if we’re under 50, two if we’re over. Get your kids boosted, which also very much means getting them vaxxed in the first place – only about 30% of kids in this range have had two shots, which is just madness to me. Wear your masks when in indoor public places again, and avoid needless indoor public gatherings. You have to take care of yourself now, so do it. Until it gets worse – and I still hope it won’t – this is the best you can do.

UPDATE: The May 16 numbers are now on the dashboard, and they show that we are at 170% of the July 6, 2020 level. Not great!

Are we about to get more COVID in Houston?

Apr 29th, 2022
by Charles Kuffner.
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We could be.

New data from the Texas Medical Center shows COVID-19 cases have leveled off over the past week, but some trends suggest the Greater Houston area could be on the verge of seeing higher virus spread.

TMC hospitals reported an average of 351 new cases per day during the week of April 18, the same number it reported during the previous seven-day period. The number of new cases does not include anyone who used an at-home test and did not report a positive result.

Those numbers represent a significant decline from last month, when the hospitals were reporting an average of 2,592 new cases per day.

However, the effective reproduction rate – or the average number of people who will be infected by someone with COVID – increased to 1.0 last week, up from 0.82 one week earlier. The rate essentially measures how well collective behaviors like wearing masks and social distancing are slowing the spread of the virus, with any rate higher than 1.0 meaning that spread is increasing.

The amount of virus being detected at the city of Houston’s wastewater treatment plants has also increased to the highest rate since Feb. 7, according to data from the Houston Health Department. Twenty-one of the city’s 39 wastewater treatment plants saw an increase in viral load in samples that were collected and analyzed April 18. By comparison, 16 plants saw in increase in samples collected and analyzed one week earlier.

The TMC’s weekly update also shows new hospitalizations have increased to an average of 59 admissions per day during the week of April 18, up from 42 the week before. TMC hospitals admitted an average of 89 new patients per day last month.

The data isn’t strongly conclusive, but it’s also early in what could be a trend, and as we know with this virus once you really start to see an uptick, it’s already too late. On the other hand, lots of people have COVID antibodies now, and that plus the number of vaxxed people who haven’t had COVID is probably enough to mitigate any crazy spread, or at least to make it less harmful, at this time. But of course there are still plenty of high-risk people out there, and lots of kids haven’t been vaxxed, and no one wants to get even a mild case of COVID. So, you know, stay cautious. You can still wear a mask even if you don’t have to, and you can get that second booster if you’re eligible. It’s never a bad idea to minimize your exposure to this thing. Stace has more.

New variants being detected

Apr 18th, 2022
by Charles Kuffner.
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Got to keep an eye on that.

Two new omicron subvariants that health officials say are contributing to a COVID uptick in New York State have been identified in Houston, according to researchers at Houston Methodist.

Genome sequencing efforts within the hospital system have detected 83 cases of BA.2.12 and three cases of BA.2.12.1 — two sub-lineages of the dominant variant BA.2 — since the start of the year.

Local case numbers, however, are sitting at their lowest point in nearly a year, according to the Harris County Public Health COVID dashboard, which reports an average of 20 new cases per 100,000 people over the last seven days. That number was as high as 1,256 in mid-January, during the height of the omicron surge.

It’s a different story in New York, which has seen a 70 percent increase in new cases over the two weeks, from a daily average of 3,231 on March 13 to 5,467 on Thursday, according to the New York Times virus tracker.

[…]

Houston wastewater surveillance data show an increasing viral load at a growing number of the city’s treatment plants as of April 4, when samples were last collected.

The city’s wastewater dashboard shows 14 out of 39 total wastewater treatment plants experiencing an increase from the week before, compared to eight on March 28.

The wastewater data is here. As of April 4, the virus level was at 38% of where it was on July 6, 2020, which is the date when this collection project started and is used as the baseline. We’ll have to keep an eye on that of course, but we also have to consider infections versus hospitalizations and deaths. It makes sense to wear a mask in most indoor settings – I do, and plan to continue doing so for the foreseeable future – but it’s not clear yet that we need to do more than that. Other than get vaxxed and boosted, of course, which if you haven’t by now I don’t know what to say to you.

Here comes BA.2 in Houston

Apr 2nd, 2022
by Charles Kuffner.
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But don’t panic, it’s just a change in the virus composition, not an increase in viral load.

Houston is seeing an uptick in the number of BA.2 cases, with genome sequencing and wastewater testing picking up higher levels this week compared to last week.

The more contagious omicron subvariant was identified in 24 percent of patients who were sequenced at Houston Methodist, a jump from the 1 to 3 percent previously reported. BA.2 was also detected at six wastewater treatment plants on March 21 — the most recent day for which data is available — after the Houston Health Department last week said it had not been detected at any plants.

“Previously, we saw some indications of mutations consistent with BA.2 but were not confident in the determination at the time,” health department spokesman Scott Packard said in an email. “Retrospective analysis indicates BA.2 was likely in the wastewater in low levels starting in mid-to-late January.”

The recent data is the first indication of a significant rise in BA.2 in the Houston-area. Eventually, the subvariant is expected to become the dominant strain here, lining up with the nationwide rate, according to the health department.

[…]

In Houston, the average positivity rate over the last two weeks is 1.8 percent, down from the high 30s in the early January. Wastewater testing shows an increasing viral load at nine wastewater plants, while the remaining 30 are plateaued or decreasing.

“Although BA.2 appears to be more contagious than BA.1, the good news is that countries experiencing a spike in cases are not seeing a proportionate spikes in hospitalizations,” Packard said. “That means being up to date on vaccines (initial shots plus boosters) remains highly effective against serious illness, even with BA.2.”

As a reminder, you can see the Houston wastewater dashboard here. I don’t know how long we will be in this trough, but at least in the short term our vax level plus the sheer number of people who contracted the BA.1 version of omicron should help.

In the longer term, as immunity wanes and new variants pop up, it will be time for more shots. A fourth shot has now been authorized by the FDA for us old folks.

A second round of booster shots was greenlighted for everyone over the age of 50 by public health officials on Tuesday, kicking off the regulatory process for shots to likely be available in pharmacies this week.

Everyone 12 and older is already eligible for a booster shot five months after their initial vaccine series if they received an mRNA vaccine like Pfizer or Moderna, or two months after getting the Johnson & Johnson vaccine.

But for those over 50, determined to be a vulnerable age group, officials at the Food and Drug Administration and Centers for Disease Control and Prevention have decided the data on waning immunity justifies making another shot available four months after the first boost. And while anyone who meets that criteria can now get another booster, CDC Director Rochelle Walensky said it was “especially important” for those 65 and older and those 50 and older with underlying medical conditions.

“This is especially important for those 65 and older and those 50 and older with underlying medical conditions that increase their risk for severe disease from COVID-19 as they are the most likely to benefit from receiving an additional booster dose at this time,” Walensky said in a statement on Tuesday.

My niece is getting married in June in Washington state. I expect all of us who will be there for it and who are eligible for that booster will have gotten it by then. I ain’t messing around.

COVID may be down but it’s definitely not out

Mar 17th, 2022
by Charles Kuffner.
1 comment

Just a reminder, this pandemic hasn’t gone away. It’s less of a threat to us here right now, but it’s still very much a threat.

The evolution of the coronavirus is likely to produce dangerous new variants that escape built-up immunity and evade vaccines, according to a new study that may offer clues for the future of the pandemic.

In a searing condemnation of “misconceived and premature theories” about the demise of COVID-19, the authors — microbiologists at the European Commission and the University of Oxford — take aim at what they call the “persistent myth” that the virus will evolve to be benign.

That omicron caused relatively mild disease “has been enthusiastically interpreted to be a sign of the approaching end of the pandemic,” the authors write in the study, which was published Monday. “Yet the lower severity of omicron is nothing but a lucky coincidence.”

Instead, the microbiologists believe more severe strains could be on the way as the virus adapts to dodge natural immunity and vaccines. Analyzing the possibilities for how COVID may evolve in the coming months and years, they attempt to debunk the notion that omicron’s lessened severity represents a step towards normalcy.

“Omicron is not at all a good predictor for the future,” said Dr. Peter Markov, a scientist at the European Commission’s Joint Research Centre and lead author of the study.

Many viruses that plague human populations, including HIV and Hepatitis C, do not evolve to be less severe over time, Markov said.

You can find more details here. You know that BA2 omicron variant that’s already making case counts go up in Europe? We’re starting to see evidence of more infection in the US as well. In the wastewater, of course.

There’s a whole thread to read for that. The good news locally is that our wastewater virus levels are still trending down, as of March 7. That of course can change quickly. You know what the best protection from this is, of course.

That drum has been beaten to death, and yet the US as a whole and Texas and Harris County in particular are not great on getting shots in arms. Too many vaccinated people haven’t gotten boosters. Too many vax-eligible kids haven’t gotten theirs. The anti-vaxx crowd is as loud and obnoxious and dangerous as ever. And yet even with all that, we’re in a better position than some other places.

Another thread to read. An astonishingly small number of people over the age of 80 have been vaccinated in Hong Kong, which is absolutely getting slammed right now, and in China as well. That and a lack of immunity from prior exposures – this is their reward for suppressing the first waves of COVID so well – are the underlying factors. Our vax rate in Texas isn’t great, but so many people have been infected at least once that it helps make up the gap somewhat. But vax + booster is still by far the most effective protection against hospitalization and death. If the next variant is more effective at avoiding existing protections, or is more severe in addition to being more transmissible, we’re going to be in deep trouble. Hope for the best, make sure everyone in your circle is vaxxed and boosted, and stay vigilant. Stace has more.

The CDC gets in on the “track COVID in the wastewater” project

Feb 10th, 2022
by Charles Kuffner.
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Good to see.

U.S. public health officials are expanding their monitoring of Covid-19 in sewage, which has become a crucial early warning for surges of new cases.

The Centers for Disease Control and Prevention this week began sharing virus wastewater trends on its public-facing Covid data website. And the agency is in the midst of expanding the number of places from which raw sewage gets monitored for rising or falling waves of disease, adding hundreds of new sites in the coming months.

The U.S. struggle to track Covid in real-time has been one of the biggest frustrations of the pandemic. Early on, testing capabilities were only a fraction of what was needed. At-home tests, now more plentiful, mostly don’t get reported to health authorities. And even when local health departments and health care providers do get data, consolidating it for real-time analysis has been a challenge.

But with wastewater, the sewage – and the data it contains – keeps flowing.

Paying attention to that data can alert health officials to prepare medical surge teams, send out mobile testing units and to arrange for adequate supplies. It’s also a useful tool for health officials to help confirm what they’re seeing from other sources.

“The advantage wastewater surveillance has is that it’s not dependent on human behavior, beyond using the bathroom,” said Amy Kirby, program lead for CDC’s National Wastewater Surveillance System. “As the dynamics of the pandemic change, it remains an accurate measure.”

[…]

State and local health departments have been using, and publishing, the data since relatively early in the pandemic. The CDC has been monitoring it as well with Kirby’s program watching for SARS-CoV-2 signs in wastewater since 2020. Many cities track and publish the data on their own: Boston, Miami and dozens of others all make at least some data available.

To help get more places watching their wastewater, the CDC has convened working groups with state and local health officials who already use wastewater to track Covid levels. And they’re offering guidance and information sharing to help bring new sites online. As of Friday, the agency has begun posting wastewater data from 255 towns, cities, municipalities and other places.

The CDC has also contracted with a company called LuminUltra to collect wastewater data from 500 sites; about 200 are online so far. Kirby said the agency has identified hundreds more sites that it wants to enroll.

See here for another national tracking project. I also came across another dashboard, the Biobot Network of Wastewater Treatment Plants, which includes two Texas counties (Kaufman and Travis), though neither was up to date at the time. The CDC’s tracker is here. As the story notes, this is a macro view that can’t tell you how many people are sick, and it doesn’t cover all of the country, just places that are connected to sewer systems. But it’s a useful look at the data, which can tell you where the virus is going ahead of testing regimes, and we can use all the data we can get.

The wastewater is once again in our favor

Feb 5th, 2022
by Charles Kuffner.
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But there’s still a lot of room for improvement.

The latest samples of Houston’s flushed wastewater show diminishing traces of COVID-19 across the region — a promising sign that the highly contagious omicron variant is in retreat.

Hospital admissions are down. Fewer people are testing positive for the virus. And now, the amount of coronavirus in the sewage is falling at all but two Houston wastewater treatment plants. Samples taken from across the city show the virus is no longer proliferating as quickly as it was earlier in the omicron outbreak.

After rising to “unbelievable” heights with omicron’s arrival just weeks ago, the city’s viral load is now falling rapidly, said Loren Hopkins, chief environmental officer at the Houston Health Department.

The level of COVID present in the city’s sewage is now about one-third of that measured at the onset of the omicron peak in late December and early January.

“We had this huge rise to levels we had never seen before,” Hopkins said Wednesday afternoon. “It went up very fast and has been dropping very fast.”

But while the variant may be loosening its grip, levels of the virus remains high. According to sewage testing, there is about as much COVID circulating citywide now as there was during the post-holiday surge a year ago that sickened Houston residents by the thousands and overwhelmed area hospitals.

See here for more on the wastewater tracking project. This metric is in line with other data, but please note what that last paragraph says. I expect this trend to continue, but it’s not far enough down yet that if it were to hit a floor we’d be content with it. Please do continue taking all reasonable precautions. You can see that lovely COVID-in-the-wastewater dashboard here.

Have we reached peak omicron?

Jan 26th, 2022
by Charles Kuffner.
3 comments

I sure hope so (fingers crossed).

Omicron’s swift and sudden surge may have peaked, experts said Monday, but hospitals are likely to remain full in the coming weeks, with the highly contagious COVID-19 strain not expected to recede until March.

Two key metrics — transmission rate and wastewater tracking — indicate the variant may be loosening its grip on the Houston area.

Texas Medical Center records show positive case rates are declining. Around 9,000 people tested positive for COVID each day last week in the greater Houston area, down about 40 percent from the previous week, when the region averaged about 13,400 new cases daily, according to TMC data.

But hospitalizations and deaths lag behind new infections, so health care workers still have a challenging couple of weeks ahead, said Dr. David Persse, Houston’s chief medical officer. Intensive care units around Texas are at 92 percent capacity, among the highest levels recorded since the pandemic began.

“It appears that we may have hit a peak,” Persse said. “However, our numbers are still really really high. I hesitate for anyone hearing that we may have peaked to think that its over. It is far from over.”

[…]

Houston’s declining rate of transmission — a statistic used to gauge how likely an infected person is to spread their illness to others — offers some clues. The rate of transmission fell below 1.0 last week for the first time since mid-December, according to new TMC data. That means each infected Houstonian is spreading the virus to less than one other person.

The city’s wastewater offers another optimistic sign of omicron’s decline. The wastewater virus load last week was about half what it was in December, and appears to be falling precipitously from its all-time high recorded on Jan. 7, officials said.

As a reminder, the wastewater dashboard is here. It’s still high, but compare to January 3, and you’ll see how much better things look now. As noted, hospitalizations lag cases, and deaths lag hospitalizations, so while the number of people getting COVID may now be trending down, we’ll still see high levels of hospital bed usage, and a higher death rate for the time being. But at least there we can begin to see the end as well. Hang in there, and stay safe.

Here comes omicron

Dec 17th, 2021
by Charles Kuffner.
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Ready or not.

Houston is seeing early signs of another wave of COVID-19 infections, fueled in part by a fast-spreading omicron variant, as public health officials warn of a nationwide spike in cases as early as next month.

The daily average of positive cases in the Texas Medical Center more than tripled last week, from 232 to 721, and Houston Methodist on Tuesday recorded nearly five times the number of positive cases in its system compared to the previous week. Harris County Public Health on Tuesday reported 483 new cases, the highest single-day total in more than two months.

The number of omicron cases in Houston detected through genome sequencing is small but rising, with Houston Methodist reporting 54 samples of the new strain Wednesday, compared to 31 four days earlier. The variant now makes up roughly 32 percent of cases in the hospital system, up from 13 percent on Saturday. Traces of omicron are also being detected at a growing number of city’s wastewater treatment plants.

With little data available in what is considered the early stages of the new variant’s spread, experts are uncertain about the degree to which it could overwhelm the healthcare system — a critical question in the months ahead. They are, however, growing more confident of an imminent swell of sickness.

“We’re going to have a wave. I don’t doubt it at all,” said Dr. Rodrigo Hasbun, professor of infectious diseases with McGovern Medical School at UTHealth Houston. “It’s just the magnitude of it and the duration that’s in question.”

[…]

Throughout the pandemic, Houston’s wastewater treatment plants have been a reliable indicator of future local spread, usually preceding new infections by about two weeks. During the week starting Nov. 29, the city found traces of omicron in seven treatment plants. By the following week — the most recently available data — that number jumped to 25.

“We can see how quickly this variant is going to spread,” said Hasbun.

Early findings from South Africa suggest that omicron causes less severe disease than earlier strains, though several factors, such as the country’s younger population, cloud the data.

Some experts offer cautious optimism despite the bleak outlook.

Dr. Annamaria Macaluso Davidson, associate vice president of medical operations for Memorial Hermann Medical Group, is hopeful that pockets of highly vaccinated areas in the city and new COVID treatments arriving on the market will stave off a dire situation at hospitals.

Two new pills to treat less severe COVID infections could receive emergency use authorization by early 2022.

“We’ve got more tools at our disposal that I think are really promising, even if we’re facing another surge,” she said.

The latest developments highlight the urgent need for vaccinations and booster shots ahead of the Christmas holiday.

Well, we know about the wastewater data. There’s been an uptick in demand for the booster, but the total number of people who have had a third shot is still pretty small. What we know so far suggests that omicron can evade the immunity response better than delta can, and so even fully vaxxed people, or people with two shots who have also had COVID, can still get the omicron variant. But if they do, it will very likely be mild. Even lesser-strength immunization seems to mitigate the severity of omicron, and that plus the Pfizer pill is the reason for guarded optimism. You should still take all reasonable precautions. Get that booster, avoid large indoor gatherings, that sort of thing. We’re in a much better place than we were last spring. Just don’t be dumb about it.

A broader look at the Houston project to track COVID in wastewater

Dec 16th, 2021
by Charles Kuffner.
1 comment

The DMN tells me things I did not know about my current favorite public works project.

The [Houston] health department is conducting the wastewater surveillance for COVID-19 in partnership with researchers at Rice University and Baylor College of Medicine. Wastewater testing cannot identify individual people who have COVID-19, but it can identify neighborhoods with particular virus variants or relatively high virus loads.

Dallas County is not participating in similar wastewater surveillance to track the virus, said Dr. Philip Huang, director of Dallas County Health and Human Services. He said he doesn’t know of any other organizations or municipalities in North Texas that are operating similar programs.

While Dallas County previously considered using wastewater surveillance, the price of creating such a system was too high. “It’s actually quite expensive to set that up,” Huang said.

“After the 10-week survey, [the water district] discontinued its participation in the study due to inconsistent data that required continuous interpretation by local and state public health officials,” said Kathleen Vaught, public relations specialist at the water district.

Public health experts have long used wastewater samples to track the growth and spread of bacteria and viruses, like the poliovirus.

The Centers for Disease Control and Prevention began discussing the use of the tool to study COVID-19 in February 2020.

By September of that same year, the CDC and the U.S. Department of Health and Human Services launched the National Wastewater Surveillance System, also known as NWSS, to help state, tribal and local health departments track and respond to COVID-19.

[…]

Houston is the only Texas city to participate in the NWSS, although that could change as the program grows in the next month, said NWSS team lead and CDC microbiologist Dr. Amy Kirby. Data taken from Houston wastewater samples is submitted to a national database tracking similar data from nearly 400 utilities across the country.

The University of California, Merced’s Naughton Lab created and maintains a dashboard, called COVIDPoops19, to track global wastewater testing for the virus.

I just want to say that learning of the existence of a dashboard called COVIDPoops19 has improved my life in ways I could not have imagined. You can zoom in on Houston in this dashboard and click on the various icons to learn more; clicking on the icon for Baylor College of Medicine led me to the actual Houston dashboard for this, which I had not seen before. If you play around with the slider, which shows you what the viral levels were for past weeks, you can see that the inflection point for this year was the week of June 21 – levels had been dropping through June 7, then you saw a few upticks on June 14, and on the 21st it was all increases, and it got worse for the next few weeks. We’re on more of an upward trend right now (December 6 is the most recent date), but there are increases and decreases in the various locations. I’m going to be bookmarking this page. Anyway, if you want to know more about this project, there you go.

Yes, omicron was found in the wastewater

Dec 8th, 2021
by Charles Kuffner.
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In case you missed it.

Houston has detected the omicron variant of the virus that causes COVID-19 in eight of its wastewater treatment facilities, confirming the new strain is spreading in the city.

A Harris County resident was the first person in Texas to test positive for the variant Monday. She was fully vaccinated and did not report any recent travel history, officials have said.

City officials have been sampling wastewater facilities since last year, another metric to help the Health Department gauge the virus’s spread in Houston. People shed the virus through feces even if they are not symptomatic or have not tested positive, providing a truer picture than test results. It is also an early indicator, often presaging positivity rate and hospitalizations by weeks.

[…]

The city said the wastewater findings renew the need to get fully vaccinated and are cause for concern, but not panic.

“The Houston Health Department and Houston Water continue to do an exceptional job tracking the impact of the virus in our community,” Mayor Sylvester Turner said. “Vaccines help protect us, our loved ones, friends, and colleagues in the work environment. As the holidays approach, I encourage everyone to remain vigilant about their health and safety.”

See here and here for the background, and here for the Houston Health Department press release. I find it comforting to know that when all else fails, you can count on the wastewater treatment plants.

Our wastewater treatment plant is ready for omicron

Dec 4th, 2021
by Charles Kuffner.
1 comment

One small bit of reassurance in these uncertain times.

The Houston Health Department is testing the city’s wastewater for the new COVID variant, omicron, which experts say could soon be found in the U.S.

The department tests the city’s wastewater weekly for COVID strains. The most recent samples collected the week of November 22 show no trace of the omicron variant, officials said.

“Although our team has not detected Omicron in Houston, we should anticipate it arriving, and the health department is prepared to scale its operations as needed to respond,” Houston Mayor Sylvester Turner said in a release. “In the meantime, I encourage eligible Houstonians to get fully vaccinated.”

Much is still unknown about the new variant, including if it’s more transmissible, deadly or more bypasses vaccines.

“While we await data to show the level of threat from Omicron, it’s important to remember that vaccination is our best tool to reduce cases, prevent serious illness and death, and slow the emergence of new variants,” Dr. David Persse, chief medical officer for the City of Houston said. “If you are not fully vaccinated or if you are eligible for a booster, please do it now to protect yourself, your family, and our community.”

Note that the omicron variant is already here in the US, and it’s just a matter of time before it’s detected everywhere. The wastewater tracking project here has been a big success, and since the latest variant is detectable via PCR testing, it’s no surprise that we’ll have this method to track it. Let’s please all do our part to keep it at a low level.

A bit of good news in the wastewater

Sep 12th, 2021
by Charles Kuffner.
Comments are off for this post

I’ll take it where I can get it.

Community spread of coronavirus is on the decline from its recent summertime high, but experts warn that Labor Day gatherings and kids’ return to classrooms could bring a rash of new infections in the coming weeks.

The latest samples of Houston’s wastewater — a highly sensitive method for tracking coronavirus — show diminishing traces of the virus across the region, said Loren Hopkins, the Houston Health Department’s chief environmental science officer. The results indicate a slight drop in person-to-person spread.

“The positivity rates are still alarmingly high, the wastewater rates are still alarmingly high, but it may be trending down,” Hopkins said Wednesday.

The decline could be short-lived.

The holiday weekend and the start of school, which spurred record infections among children, will likely keep the Houston area in “plateau mode” for the foreseeable future, said Bill McKeon, CEO of the Texas Medical Center.

On Tuesday, the Texas Medical Center reported that the rate of transmission across the Houston area was 0.87; the average for the previous week was 0.99. Both figures landing below 1.0 is a good sign; any number above 1.0 means the virus is spreading through the community.

Still, McKeon urged caution. Tuesday’s low daily transmission rate of 0.87 could be artificially deflated due to low testing rates, he said, which commonly occur over holiday weekends.

“We are just coming out of the Labor Day weekend and we typically do not see the impact of holidays for one to two weeks,” McKeon said.

[…]

Houston’s coronavirus hospitalizations slowed by 2.3 percent in the past week, but remained only slightly lower than August’s record peak. As of Tuesday, 3,370 people were in area hospitals for COVID-19, down from the record high of 3,500 on Aug. 24, according to the Texas Department of State Health Services.

Ballooning school transmissions are another concern, experts said, especially in districts that do not have mask mandates. Student infections are rapidly rising across the state, with the total number of positive cases among public school students surging by 90 percent just a few weeks into the new school year.

“We need mask mandates to protect our school children from getting infected and bringing it home to Mom and Dad,” said Catherine Troisi, an epidemiologist at Texas Medical Center’s School of Public Health.

The wastewater had documented to surge, and it will be the leading indicator when there is a real decline. I hope people were cautious over the Labor Day weekend, but we’ll know soon enough what if any effect that had. As for mask mandates in the schools, it seems to be working pretty well for HISD. I keep saying, none of this is a mystery, we know what we need to do, we just have to do it.

Yes, the wastewater is also pointing to a COVID surge

Aug 22nd, 2021
by Charles Kuffner.
4 comments

In case you were wondering.

There is more COVID-19 in the city’s wastewater system now than at any time in the pandemic, city officials said Wednesday, the latest warning that the virus is spreading at an unprecedented rate.

Dr. David Persse, the city’s health authority, said there is more than three times as much virus in the system as there was last July. The volume also is higher than in January, during the most recent spike. Persse said that wastewater data, a precursor to other data points, show the surge will only grow worse in the coming weeks.

“We are at a level of virus in the wastewater that we have never seen before,” Persse said. “The wastewater predicts what we’ll see in the positivity (rate) by two weeks, which predicts what we’ll see in hospitalizations by about two weeks.”

[…]

The findings came during a news conference in which the city announced it will partner with Harris County and up to 17 school districts to vaccinate students over 12 and their families every Saturday in August, an effort they are calling “Super Saturday.” The inoculations will occur in school buildings throughout the region.

Persse described the state of the surge in stark terms, pointing to dire situations in area hospitals and rising cases and hospitalizations. The Lyndon B. Johnson Hospital declared an “internal disaster” Sunday night amid a nursing shortage and an influx of patients, circumstances officials said are occurring in other area hospitals, as well.

Texas Medical Center CEO Bill McKeon earlier this week said the region is “headed for dark times,” and the hospital system has exceeded its base intensive care capacity, opening unused wards to care for new patients.

“If you are currently unvaccinated, you need to consider that you represent a potential danger to yourself, and others, and most particularly your own family,” Persse said. “If you are not vaccinated… your chances getting through this without having to become either vaccinated or infected, is essentially zero.”

Just over 64 percent of Houstonians over 12 have received their first dose of the vaccine, according to city data, and 54.3 percent are fully vaccinated. The numbers among youth residents are more paltry, though: 28.1 percent of 12-17-year-old Houston residents are fully vaccinated, and 38.5 percent have received their first dose.

“If your child is 12 or older, stop and get them the shot,” said Houston ISD Superintendent Millard House II. “Increasing vaccination rates among our communities will help ease the worries of our families and their children returning to school.”

This is another one from earlier in the month, as things were really starting to get bad. We are familiar with this project, and it has been a big success. I just wish it had better news for us, but this is where we are. Getting more of those 12-and-older kids vaccinated would make a big difference as well, so I hope that effort is successful. We’re on our own, so we’d better act accordingly.

The COVID wastewater tracking project has been a big success

May 4th, 2021
by Charles Kuffner.
Comments are off for this post

This has been one of the best things to come out of this interminable and miserable COVID experience.

Lauren Stadler’s environmental engineering students always pose the same question at the beginning of a semester: “What happens to water in the toilet after you flush?”

Historically, humans have worked to quickly dispose and eradicate their own waste, which can carry diseases.

But an area’s waste creates a snapshot of who is there and what they’ve been exposed to, said Stadler, a wastewater engineer and environmental microbiologist at Rice University. She’s working with the Houston Health Department and Baylor College of Medicine’s TAILOR program to find SARS-CoV-2 in the city’s wastewater.

Stadler’s hunt has revealed variants in particular areas, heightening the city’s urgency to procure resources — COVID tests, informational meetings, advertising and now vaccine sites — in an effort to quash them before they proliferate.

“The beauty and challenge of wastewater is that it represents a pool of sample — we’ll never get an individual person’s SARS-CoV-2 strain, but a mixture of everyone in that population,” Stadler said. “We can find a population level of emergence of mutations that might be unique to Houston.”

[…]

Variant tracking has become an important part of the wastewater analysis process, Stadler said.

In February, the city and its research partners began seeing a quick emergence of the B.1.1.7 variant, which is now the dominant variant in the area. According to the Centers for Disease Control and Prevention, nearly 21,000 cases of the B.1.1.7 variant have been detected in nationwide.

Now that the team has gathered data and built a sustainable process, Stadler said they are using this information to forecast future pandemics. “Taking wastewater data, you can predict positivity rates and forecast infection burdens — it has this predictive power essentially. It’ll be very important to identify areas in the city experiencing increases in infection, and we can direct resources.”

The wastewater analysis team works with public works employees to collect weekly samples from nearly 200 sites across the city.

“I think they see this as a monitoring tool beyond the pandemic, and we see it as well,” Stadler said. “Hopefully, when SARS-CoV-2 is behind us, we will be able to monitor for an endemic virus, like flu. We can use wastewater monitoring to look for other viruses, bacterial pathogens and other pathogens of concern.”

See here and here for recent entries. I don’t have much to add, just my admiration for everyone involved and the knowledge they have gained. This was a simple and inexpensive innovation, and it will yield public health benefits for years to come. Kudos to all.

Finally, a bit of good COVID news

Jan 24th, 2021
by Charles Kuffner.
Comments are off for this post

Naturally, it comes from the wastewater.

Researchers who study sewage to monitor the pandemic are detecting less virus in Houston than they have in months, a positive signal that could indicate a forthcoming drop in new COVID-19 cases, doctors said.

The amount of viral load has declined at 28 out of 38 wastewater treatment plants across the city for the first time in five months, said Dr. Paul Klotman, president and CEO of Baylor College of Medicine. He announced the good news during a Friday video update.

“It’s actually a big drop,” Klotman said. “What that means is, in 7 to 10 days, I think we’re going to see a pretty dramatic drop in the number of new cases.”

[…]

Other indicators show signs of improvement. The Houston area’s R(t) value has dipped below 1 for the first time in weeks, meaning community spread is slowing. The test positivity rate for the Texas Medical Center hospital systems dipped from 13.2% last week to 12.7% this week, Klotman said, and the weekly average of COVID-19 hospitalizations is beginning to plateau.

See here, here, and here for the background. As we know, people shed virus in feces and urine, so tracking virus levels in wastewater is a pretty good tool for determining what the true status is and where hotspots are forming. If this is the start of a trend, we’ll see infection and hospitalization levels – not to mention deaths – start to decline rapidly in the next few weeks. Keep wearing your masks and avoiding indoor gatherings, as that’s been our best defense so far, and get that vaccine when you can.

It’s still not too late to prevent a big spike in COVID infections

Oct 31st, 2020
by Charles Kuffner.
Comments are off for this post

But it will be soon.

A rise in COVID-19 cases has health care officials and government leaders pleading with Houstonians: Act now to prevent, or at least minimize, a third wave of infections across Greater Houston.

“This feels a lot like late May, early June when we saw the early warning signs that things were beginning to increase,” Dr. Marc Boom, president and CEO of Houston Methodist, told the Chronicle on Tuesday, “and then things slipped out of our control.”

According to a Chronicle analysis, the seven-day rolling average for newly reported cases was 1,044.2 as of Monday in an eight-county Houston area. That’s the highest since Oct. 8. In the summer, the rolling average peaked July 17 at 2,432.7.

The rate at which the virus is spreading, called the reproduction rate, reached 1.18 across a nine-county Houston area as of Monday, according to the Texas Medical Center. A number below 1, which the Houston area did report for a few weeks, means the virus is burning out. A number above 1 means that virus spread is increasing. During the COVID-19 spike this summer, Houston’s reproduction rate was in the 1.5-1.7 range when things were getting out of control, Boom said.

Finally, the seven-day average for COVID test positivity rate was 4.2 percent for TMC hospital systems as of Monday. It had been 3.4 percent last month.

For the city, Mayor Sylvester Turner on Monday reported the positivity rate was 6.5 percent as of Oct. 21. Statewide, the positivity rate was 9.42 percent as of Monday.

[…]

Houston-area case increases are not as severe as in other parts of the country and state. In the U.S., 489,769 new cases have been reported since Oct. 20. There are surges in Wisconsin and other Midwest states. In El Paso, state health officials converted a convention center into a makeshift hospital to ease the crush of patients.

Still, Shreela Sharma, an epidemiologist at UTHealth School of Public Health, knows how quickly COVID cases can climb. And she said the number of new cases in the Houston region is roughly 40 percent higher than when the summertime peak began. That means if a third wave does occur, it would start with a higher baseline.

The time is now to wear masks, practice social distancing and wash your hands.

“Our window is right now,” she said. “We could rapidly lose that window over the next few weeks.”

Yes, that is the one piece of good news. We know how to get a handle on this, and we’ve been doing it all along. Wear your mask – yes, wear it while voting, too – maintain social distancing, and avoid indoor gatherings. This week’s colder weather excepted, we’re in much better shape to handle the winter than the northern climes, because for most of our winter it’s still perfectly amenable outside for activities and dining and whatnot. Again, just don’t be an idiot. Do the things that you know you need to do. The alternatives are so, so much worse.

One more thing:

Researchers with Houston’s Health Department will monitor the wastewater flushed from 60 schools and 15 senior living homes in the city for COVID-19 in hopes of catching outbreaks before they arise in clinical testing.

City council on Wednesday unanimously approved $11.5 million in federal COVID-19 spending. Included in that was $221,000 to buy the sampling equipment needed to expand the city’s existing wastewater testing program into K-12 schools in areas with high positivity rates.

People shed the novel coronavirus through feces, regardless of whether they experience symptoms. The samplers will be installed in manholes outside the schools, and researchers will analyze them, looking for the virus.

“It’s very granular,” said Dr. Loren Hopkins, the health department’s chief environmental science officer. “We don’t expect to see any positives at all, we expect to see nothing… If we see something in a school and we see it two days in a row, then we know someone in that school is shedding the virus.”

The department would then alert the school and deploy the more traditional, clinical testing, according to Hopkins.

Don’t laugh, this is an effective method of contact tracing. It’s already been used successfully by the city. Now, if there are people who can test wastewater to see if your poop has the COVID virus in it, you can damn sure keep wearing your mask.

We really can track COVID-19 through wastewater

Oct 4th, 2020
by Charles Kuffner.
Comments are off for this post

This is terrific news.

Researchers with the city, Rice University and Baylor College of Medicine were able to sniff out a potential second outbreak of COVID-19 at a homeless shelter in downtown Houston earlier this year by looking down its drains instead of in people’s noses, health officials said Thursday.

Quashing the resurgence at the Star of Hope Men’s Shelter earlier this year was one of the first successes of an effort to track the novel coronavirus through wastewater, city officials said Thursday. The initiative, one of several occurring around the country, attempts to spot outbreaks by sampling water at city treatment facilities, which could help officials tailor their testing and prevention efforts to specific neighborhoods.

To date, the results from testing wastewater largely have aligned with those from nasal swab testing, said Dr. Loren Hopkins, the city’s chief environmental science officer. That has increased the confidence that the wastewater sampling is accurate. The benefit, she said, is that wastewater tests produce quicker results.

“Ultimately, the goal is to develop an early warning system allowing the health department to identify the city’s COVID-19 hot spots sooner and put measures in place to the slow the spread of this virus,” Mayor Sylvester Turner said.

People shed the virus through feces, regardless of whether they experience symptoms. The city was able to detect the virus in the shelter by placing a sampler on the manhole outside the facility after its initial outbreak of COVID-19, the illness caused by the coronavirus.

The ability to home in on a single building still is limited, Hopkins said. City officials have deployed that strategy for the shelter and the Harris County Jail, and they are trying to acquire more equipment to expand the effort in the fall. The health department plans to begin testing long-term care facilities, for example.

[…]

So far, there has been a strong correlation between the viral load in the wastewater and the positivity rates by nasal tests, so the method has not unearthed large swaths of the virus that have gone undetected by tests. Still, that correlation has increased confidence that the wastewater analysis is accurate and can be used as a bellwether for future outbreaks.

From Sept. 7 to Sept. 14, for example, scientists found the virus was increasing in a statistically significant way in the communities served by the Tidwell Timber, Upper Brays and Forest Cove treatment plants, among others, while decreasing in District 23, White Oak and Homestead.

That information, coupled with the local positivity rate and other factors, helped the health department decide where to send strike teams to test people, conduct outreach and provide education about the virus. The city said the wastewater study has resulted in more testing at several congregant living centers.

See here and here for the background. This method is extra useful because it provides a more focused view of where the cases are clustering, and the testing is faster, so the response to the test results is also faster. If we are ever going to get a handle on this disease, especially before there’s a vaccine but also after one is available, it’s going to come from technology like this that gives a real-time and location-specific view of where the virus is happening. We should be rooting for this to ramp up as much and as quickly as possible. Kudos to all for making this happen. The Press has more.

When Houston is more like Austin

Aug 6th, 2020
by Charles Kuffner.
Comments are off for this post

In a climate sense. Which is to say, drier because of climate change.

A new study predicts that Texas’ climate is going to get drastically drier because of climate change. The journal Earth’s Future recently published the study looking at historical drought records, and it projected that the second half of the 21st century could be Texas’ driest of the last thousand years.

One of the study’s authors, Texas State Climatologist John Nielsen-Gammon, spoke with Texas Standard host David Brown on Tuesday about the future of the states’ climate and water supply.

“Conditions, on average, would be drier than we’re used to, and when we get extreme droughts, those will be drier as well,” he said.

Nielsen-Gammon said that could initiate a westward shift in the state’s climate – meaning, San Angelo’s climate becomes more like Midland’s; Houston’s climate becomes more like Austin’s, and so forth.

Reducing carbon emissions is the long-term solution to the problem that comes from a warming planet. But Nielsen-Gammon said that requires massive changes on a global scale that haven’t happened yet.

So Texans would be wise to prepare for drier conditions. And that includes planning for possible water shortages.

I’ve blogged about water issues and the challenges our state faces, as it sits at the crosswords of rapid growth, climate change, and a lot of people living in very dry places to begin with. Water conservation, wastewater recycling, desalinization, and on and on. The challenges we already face will be greatly exacerbated by climate change, and it’s going to change the state at a fundamental level.

The study highlighted a slew of looming problems for the state’s water supply. First, climate change will lead to even more megadroughts. In the latter half of the century, those droughts are likely to be worse than any of those previously on record.

“Our study shows that the drier conditions expected in the latter half of the 21st century could be drier than any of those megadroughts, depending on how you measure dryness,” lead researcher and A&M professor John Nielsen-Gammon wrote in a press release.

Second, the higher temperatures brought about by climate change will lead to more evaporation from the surface lakes that many parts of the state rely on. This problem will be particularly pronounced for Dallas, which relies entirely on surface water for its water supply, the study says.

Third, the state’s population is continuing to grow — from just under 30 million now to a projected more than 50 million in 2070 — meaning the demand for water will go up as the state gets drier.

“We’re warming up the atmosphere; that’s been happening and is projected to make the droughts more severe, but in cities like Austin, Dallas, Houston, the Rio Grande Valley and San Antonio, we know that populations are continuing to grow at a rapid pace,” said Jay Banner, a professor at UT-Austin who co-authored the study.

Merry Klonower, a spokesperson for the Texas Water Development Board, which offers water planning assistance to municipalities, said that each of 16 regional water planning areas throughout the state is required to take into account population projections for the next 50 years when making water supply decisions.

“And if there is a shortage, then the very next step is they have to determine how they are going to meet their water supply needs for that growing population,” she said. “So we have been doing this since the ’90s and it is a very robust process. So the state is well-prepared and is looking at future populations and water supply needs for municipalities.”

I’m sure we have been preparing and planning for years, but I’m also pretty sure we’ve been underestimating the scope of the problem all along. I mean, if we took it with an appropriate level of seriousness, we’d have a very different set of government leaders in place and would have had a much different set of priorities in this state. It’s still not too late to try to reduce the effects of climate change, but every day that passes is one day less we have for that, and one day closer to the future studies like this predict. What are we going to do about that?

The reopening metric we should be heeding

Jun 5th, 2020
by Charles Kuffner.
20 comments

From Twitter:

Here’s that link:

Abstract

We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. SARS-CoV-2 RNA was detected in all environmental samples and, when adjusted for the time lag, the virus RNA concentrations were highly correlated with the COVID-19 epidemiological curve (R2=0.99) and local hospital admissions (R2=0.99). SARS-CoV-2 RNA concentrations were a seven-day leading indicator ahead of compiled COVID-19 testing data and led local hospital admissions data by three days. Decisions to implement or relax public health measures and restrictions require timely information on outbreak dynamics in a community.

Introduction

The most common metric followed to track the progression of the COVID-19 epidemic within communities is derived from testing symptomatic cases and evaluating the number of positive tests over time.1 However, tracking positive tests is a lagging indicator for the epidemic progression.2, 3 Testing is largely prompted by symptoms, which may take up to five days to present4, and individuals can shed virus prior to exhibiting symptoms. There is a pressing need for additional methods for early sentinel surveillance and real-time estimations of community disease burden so that public health authorities may modulate and plan epidemic responses accordingly.

SARS-CoV-2 RNA is present in the stool of COVID-19 patients5-7 and has recently been documented in raw wastewater.8-10 Thus, monitoring raw wastewater (sewage) within a community’s collection system can potentially provide information on the prevalence and dynamics of infection for entire populations.11 When municipal raw wastewater discharges into treatment facilities, solids are settled and collected into a matrix called (primary) sewage sludge, which has been shown to contain a broad diversity of human viruses including commonly circulating coronavirus strains.12 Primary sludge provides a well-mixed and concentrated sample that may be advantageous for monitoring SARS-CoV-2. As viral shedding can occur before cases are detected, we hypothesize that the time course of SARS-CoV-2 RNA concentrations in primary sewage sludge is a leading indicator of outbreak dynamics within a community served by the treatment plant.

So in plain English, if you know what the level of SARS-CoV-2 is in your municipal wastewater, you will have a very accurate predictor of the new COVID-19 case rate in your community. And guess what? The city of Houston is tracking this very data. I don’t know if it’s being published anywhere, but it sure could shed some light on how things are really going around here. Other cities should be doing this as well – if they aren’t doing it already, they need to start – and that information should be collected and published at the state level as well. What are we waiting for?

From the “Shit happens” department

May 4th, 2020
by Charles Kuffner.
1 comment

I apologize, I couldn’t help myself.

City health officials and Rice University scientists have begun testing Houston wastewater samples for COVID-19, a process they hope will reveal the true spread of the new coronavirus as clinical testing continues to lag.

The city-led effort makes use of studies that show traces of the virus can be found in human feces. By testing samples of sewage collected at the city’s wastewater treatment plants, officials hope to uncover the scale of the outbreak in Houston and, perhaps, locate hotspots undetected by in-person tests.

“It’s an evolving field. We hope that it will help give us just more information on where the virus is and how much of it is out there,” said Loren Hopkins, a Rice University statistics professor who also serves as the health department’s chief environmental science officer.

[…]

For now, plant workers are collecting wastewater samples across a 24-hour period once a week, before sending them to Rice and health department officials who then analyze the samples for COVID-19, the illness caused by the new coronavirus.

If successful, the project will reveal COVID-19 trends over a span of weeks and months in certain areas of Houston and citywide, Hopkins said. Though less precise than directly testing people for the coronavirus, the analysis will produce case estimates that include people who lack symptoms, because asymptomatic people still shed the virus in their stool. And because workers at the treatment plants are collecting samples across a 24-hour period, the results may provide a more accurate snapshot than the number of positive in-person test results, Hopkins said, because that data is impaired by days-long delays in receiving results.

Where the data may prove especially useful, experts said, is in locations where wastewater samples indicate the virus has spread more widely than clinical testing has revealed. Officials can then direct more testing to those areas, including through a mobile unit that launched earlier this week.

This is an attempt to address the serious gap between our need for testing and our capacity for testing. We hope it will help identify trends and emerging hot spots more quickly and effectively. It’s something that’s not been done before, and who knows if it will work the way we want. It’s surely worth a try.

We have a consent decree

Jul 11th, 2019
by Charles Kuffner.
7 comments

It appears to be a done deal.

Houston would add $2 billion to its planned sewer system improvements over the next 15 years under a proposed deal with state and federal regulators that is expected to produce higher water bills as soon as next year.

The Environmental Protection Agency has long been concerned that Houston’s cracked, clogged or flooded sewer pipes spill waste into yards and streets hundreds of times each year, contaminating local streams in violation of the Clean Water Act. Eighty percent of area waterways fall short of water quality standards for fecal bacteria.

Rather than sue the city over these long-running problems, the EPA initiated negotiations nearly a decade ago, hoping to produce a “consent decree” specifying projects and procedures Houston would use to reduce spills by upgrading pipes, improving maintenance and educating the public on how to avoid clogging the city’s more than 6,000 miles of sewers, 390 lift stations and 39 treatment plants.

Mayor Sylvester Turner announced Tuesday that talks have been completed; his office expects the item to reach a city council vote as early as July 17.

“It’s good for the city of Houston,” Turner said. “I am proud to have resolved this long-standing problem in a way that will fix problems that have challenged our city for decades and will bring enhanced services to future ratepayers for decades to come.”

The deal would prioritize fixes in nine areas that experience voluminous spills during rainstorms. In an effort to reduce the more numerous spills that are a chronic problem when the skies are clear, the agreement would mandate a more aggressive schedule for assessing and repairing the city’s sewer system.

Houston also would commit to clean and inspect its 127,000 manholes and 5,500 miles of gravity-driven pipes every decade, to carry out more preventative cleanings in problem areas, and to emphasize its program to educate residents not to pour grease, oil and other fats down the drain.

[…]

It is unclear how much water bills would rise as a result of the federal decree. The city has begun a rate study that will incorporate the consent decree and other factors and suggest new rates to take effect in July 2020.

Some council members were told in preliminary briefings this spring that rates would rise about 4 percent in each year of the agreement, resulting in an increase of more than 70 percent by the end of the 15-year term, though Turner professed ignorance at that figure Tuesday. Other cities under comparable decrees, including San Antonio, will double their rates during their agreements.

Turner stressed that the projected overall cost of the deal is “substantially less” than the $5 billion to $7 billion the EPA was demanding in the Obama administration’s final year.

Despite the mayor holding a news conference to announce the agreement, the Turner administration considers the decree confidential, distributing it only to the elected council members and topping it with a memo that mentions fines for those who disclose its contents.

See here, here, and here for the background. I don’t understand the reason for keeping the decree secret. I’ll be happy if Council pushes back against that. As for water rates going up as a result, well, we should have been doing this a long time ago, and last I checked fixing broken things isn’t free. I’ll say again, how much is a lower level of fecal bacteria in your water worth to you? It’s worth a gradually increasing water bill to me.

We’re about to find out how much we’ll pay to fix Houston’s sewer system

Mar 13th, 2019
by Charles Kuffner.
1 comment

Be prepared.

Houston would ramp up spending on its sewer system by $2 billion over 15 years under a proposed deal with state and federal regulators that is expected to produce higher water bills as soon as next year.

The Environmental Protection Agency has long been concerned that Houston’s cracked, clogged or flooded sewer pipes spill waste into yards and streets hundreds of times each year, contaminating local streams in violation of the Clean Water Act. Eighty percent of area waterways fall short of water quality standards for fecal bacteria.

Rather than sue the city over these long-running problems, the EPA initiated negotiations six years ago, hoping to produce a “consent decree” specifying projects and procedures Houston would use to reduce spills by upgrading pipes, improving maintenance and educating the public on how to avoid clogging the city’s more than 6,000 miles of sewers.

Mayor Sylvester Turner’s staff now are briefing City Council members on the terms of the proposal, which could reach a council vote in April. The mayor said in a brief interview Friday he wanted to speak with all council members before discussing details of the deal publicly, but four people who received the briefings confirmed the deal’s length and projected cost. EPA officials declined to comment.

How much residents’ water bills would rise remains hazy. The city will soon begin a rate study, as it does every five years, that will incorporate the consent decree and other factors and suggest new rates to take effect in July 2020. Turner said rates would stay well within EPA guidelines designed to avoid burdening poor residents, though a 2016 Houston Chronicle analysis showed significant rate hikes would still comply with that framework.

Councilman Greg Travis said he was told the decree would add 4 percent to rates each year of the agreement, resulting in a more than 70 percent increase by the end of the 15-year term. It’s unclear whether that figure included assumptions about inflation and population growth, which drive automatic rate increases each spring. Some other cities under comparable decrees, including San Antonio, will double their rates during their agreements.

Still, the mayor stressed that the projected overall cost of the deal is “substantially less” than the $5 billion to $7 billion the EPA was demanding in the Obama administration’s final year. City officials made an anti-regulation argument to the Trump administration — “You cannot run our city from D.C., and you can’t impose on us costs that the people themselves have to bear” — and it succeeded, Turner told the West Houston Association at a luncheon last week.

“We’ll finally move forward with something that’s in the best interest of the city of Houston, something that will not cost us nearly as much, and something I believe will be the best deal that any city has received anywhere in the country,” Turner told the crowd.

See here and here for the background. This is what happens when maintenance is deferred for too long, though as noted in my earlier link, both Mayors White and Parker took steps to address the problem. Just please keep in mind that this is a problem of very long standing, and it’s one that affects us all, though it most definitely affects some more than others. And if you hear anyone complain about the forthcoming hike in water rates, please feel free to ask them what level of fecal bacteria in their water is acceptable to them, and how much they would pay to mitigate that.

Now how much would you pay to fix Houston’s sewer system?

Sep 24th, 2018
by Charles Kuffner.
5 comments

We may be about to find out.

Federal and state authorities sued the city of Houston over its long-running struggle to limit sewage spills on Friday, marking the beginning of the end of a years-long negotiation that could force the city to invest billions to upgrade its sprawling treatment system.

Houston’s “failure to properly operate and maintain” its 6,700 miles of sewer pipes, nearly 400 lift stations and 40 treatment plants caused thousands of “unpermitted and illegal discharges of pollutants” due to broken or blocked pipes dating back to 2005, the suit states. The city also recorded numerous incidents when its sewer plants released water with higher than allowable concentrations of waste into area waterways, the filing states.

The lawsuit by the Department of Justice on behalf of the Environmental Protection Agency and the Texas Commission on Environmental Quality wants a judge to force Houston to comply with the Clean Water Act and Texas Water Code — typical orders include upgrading pipes, ramping up maintenance and educating the public on how to avoid clogging city pipes — and to assess civil penalties that could reach $53,000 per day, depending on when each violation occurred.

[…]

The filing was spurred by the intervention of a local nonprofit, Bayou City Waterkeeper, which announced in July that it planned to sue the city over the same violations and which filed its own lawsuit on Friday mirroring the EPA’s claims. It states that the city has reported more than 9,300 sewer spills in the last five years alone.

“The city’s unauthorized discharges have had a detrimental effect on, and pose an ongoing threat to, water quality and public health in the Houston area and have caused significant damage to the waters that Waterkeeper’s members use and enjoy,” the nonprofit’s filing states.

Waterkeeper’s July announcement was required by the Clean Water Act, which mandates that citizens or citizen groups planning to sue under the law give 60 days’ notice, in part to allow the EPA or its state counterparts to take their own actions.

See here for the background. This has been going on for a long time, and the city has been in negotiation for a resolution to this. How much it will all cost remains the big question. The one thing I can say for certain is that no one is going to like it. As a reminder, consider this:

Upon taking office in 2004, former mayor Bill White locked utility revenues into a dedicated fund, raised water rates 10 percent, tied future rates to inflation, and refinanced the debt. That was not enough to prevent the debt mountain from risking a utility credit downgrade by 2010, when former mayor Annise Parker took office, so she passed a 28 percent rate hike.

Remember how much some people bitched and moaned about that rate hike? Get ready to experience it all again.

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