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Baylor College of Medicine

More COVID restrictions are about to happen in Harris County

Blame Greg Abbott and the virus, in whatever order you prefer.

Houston and its surrounding communities on Tuesday became the latest region to require new emergency restrictions after seven straight days of ballooning coronavirus hospitalizations.

The rollback, mandated under Gov. Greg Abbott’s emergency protocols, includes restaurants dropping to 50 percent occupancy from 75 percent, and bars that have not reclassified as restaurants closing immediately. The restrictions remain in place until the region drops below 15 percent COVID-19 hospitalizations for seven straight days.

As of Monday, the latest day of available data, the Houston region was at 19.9 percent, up from just over 13 percent a week earlier. Infections and hospitalizations have been rising steadily in recent weeks, following spikes in other parts of the state and amid holiday gatherings.

All but four of the state’s 22 hospital regions were over 15 percent as of Monday.

Texas Medical Center Hospitals in Houston announced earlier Tuesday that they were putting a hold on certain elective surgeries to save resources for coronavirus patients. Under the governor’s protocols, hospitals are required to postpone elective surgeries that would deplete COVID-19 resources.

“The best thing we can do is take this threshold as a wakeup call,” Harris County Judge Lina Hidalgo said in a news conference Tuesday afternoon. “This is the time to take this for the red alert that it is. We are only going to get through this if we are able to quickly stem the tide of hospitalizations.”

More here.

The rollback comes as Texas Medical Center hospitals already had begun deferring certain elective procedures or readying such a managed reduction strategy, the same one they deployed during the summer when patient censuses spiked. The reduction is not the wholesale delay of elective procedures all Texas hospitals invoked in the spring.

Hospital leaders said Tuesday their systems will continue some elective procedures but suspend those non-urgent cases whose demands on staff and space detract from resources better used to treat COVID-19 patients. Procedures such as mammography and colonoscopy will continue because they don’t tax needed hospital resources, for instance, but some procedures like heart catheterizations might be better delayed.

[…]

The surge of COVID-19 hospitalizations has been relentless. The number of admitted COVID-19 patients in the Houston region has increased for 13 straight weeks, and the 25-county area anchored by Harris County had more than 3,100 hospitalizations on Monday, the highest since July, the peak of the first wave in Texas.

Houston Methodist was just short of 700 COVID-19 patients on Monday. Methodist CEO Dr. Marc Boom emailed employees that if this trend holds the system will surpass its peak July numbers in a matter of days.

“This may well be among the most challenging few weeks we’ve experienced during this pandemic,” Boom wrote in the email to employees Monday. “Together, we will get through this, but it will be difficult.”

Dr. James McCarthy, chief physician executive at Memorial Hermann, said his system exceeded 800 patients and should eclipse July numbers by the third week in January. The system’s number of patients has increased three-fold over the last month, he said.

[…]

The COVID-19 positive test rate statewide is now at 20.53 percent. Methodist’s is nearly 32 percent.

Porsa said said Harris Health is about to enter Phase 3 of its surge plans, which involves closing some of its clinics in order to deploy its nurses and other staff at Ben Taub and Lyndon B. Johnson hospitals, both of which are near capacity. He said the leadership is currently determining which clinics to start with.

Hospital officials said they are encouraged that ICUs aren’t being overloaded with COVID-19. They said their staffs have gotten much better, thanks to better treatment options and nine months of experience with the disease, at getting patients discharged faster now compared to early summer.

But with the Houston area now averaging more than 3,300 new COVID-19 cases a day — compared to roughly 2,330 such cases at the pandemic’s height in July — it appears the peak won’t come before late January or February, hospital officials said. They also worry a more contagious strain — not yet identified in Houston but maybe already here — poses an even greater threat ahead.

“January and February are shaping up to be our darkest days, given these record numbers,” said William McKeon, CEO of the TMC. “Hospitals lag behind in feeling the effects of increases in cases so expect the numbers to keep going in the wrong direction before things get better.”

We’re already passing the levels we had seen at the worst of it in July, and we’re probably a few weeks out from hitting the peak this time around. Remember all this next year, when it’s time to vote for our state government.

More people in Houston than you think have had COVID

About one in seven, which is an awful lot.

Mayor Sylvester Turner

Nearly 1 in 7 Houstonians have been infected with the coronavirus, city officials announced Monday, the infection’s true prevalence according to a study of antibodies in blood samples taken from people at their homes.

The study, conducted by Baylor College of Medicine and the city health department, found 13.5 percent of people tested had antibodies to the virus in their blood in mid-September, about four times the number revealed through diagnostic testing at the time.

“Thank God a vaccine is on the way because without one, given these numbers, we would need five to six times the number of infections to achieve herd immunity,” said Dr. Paul Klotman, president of Baylor. “It would also mean five to six times the number of deaths.”

[…]

Dr. David Persse, the city’s health authority, said he wasn’t sure if the Houston antibody percentage “is good news or bad news.” He said “the takeaway is that the virus is more active in the community than we can otherwise tell.”

Klotman and some others said the percent of Houstonians infected was less than they had expected. The head of the Centers for Disease Control and Prevention last summer said the number of people who’ve been infected is likely 10 times higher than the number of confirmed cases, and one study found New York City was about 20 percent in late April.

The Houston finding suggests about 250,000 Houstonians had been infected as of Sept. 19, the last day blood samples were collected. Only 57,000 infections had been identified by traditional viral testing at that time.

Persse said it is nearly impossible to predict what the percentage will be in January, but Klotman said he believes it has grown appreciably in the past nearly three months.

The test identifies those who previously have been infected with the virus by the presence of antibodies, proteins the immune system makes to fight infections. It is not a diagnostic test that identifies people with active disease, COVID-19.

The study was done by city health employees calling households in randomly selected Census blocks and asking for volunteers to give a blood sample for testing. Harris County launched a similar effort next month, and the city of Houston will do another round in early 2021. I’ll be very interested to see how the three compare. So far, the antibodies people get for having and recovering from COVID-19 are known to last a few months, and beyond that it’s not fully clear how susceptible such a person is. This also shows the dire need for masking and social distancing, because there have been – and are, and will be – a lot of people walking around who don’t know they’re sick. They themselves may be fine, but they could wind up infecting others who won’t be. The vaccines will be a huge help, but we’re still a long way away from that blessed day. So yeah, please keep wearing your mask and avoiding indoor gatherings. The Press has more.

“On the cusp” of another COVID surge

The numbers are already trending up. You know what that means.

Cases of COVID-19 in parts of Texas surged to near catastrophic levels this summer as some hospitals were forced to put beds in hallways, intensive care units exceeded capacity and health officials struggled to stem the tide of the virus.

After peaking in late July and August, cases fell and leveled off in September, and the state’s seven-day positivity rate — or the proportion of positive tests — reached its lowest point since early June.

But health officials are now eyeing a worrying trend: New infections are rising again, and the number of patients hospitalized with COVID-19 is also ticking upward. The state reported 2,273 new cases Monday, and the seven-day average was up by 862 from the previous week. On Monday, at least 4,319 patients were hospitalized with COVID-19, far below the more than 10,000 in July, but that number has steadily risen during the last month.

“I’m no longer pondering if we’re going to see a surge,” said Dr. James McDeavitt, dean of clinical affairs at the Baylor College of Medicine. “We’re already seeing it.”

Eight months since Texas recorded its first case, experts say the state is more prepared to handle another wave, but they fear that if the state fails to control the outbreak, it could quickly spiral out of control.

“The question is whether it’ll be a modest surge, or something like we saw in July, or worse,” McDeavitt said.

[…]

At Houston Methodist, one of the region’s largest health care systems, medical staff were stretched thin this summer, said President Marc Boom. At its peak in July, the system’s staff treated nearly 850 patients with COVID-19 each day. Since then, Boom said, the medical community’s understanding of the virus has evolved, along with how to treat the disease.

Remdesivir, an antiviral medication, has shown promising results in minimizing the severity of illness, especially when administered shortly after symptoms develop. Houston Medical was the first hospital to use convalescent plasma, a therapy in which antibody-rich blood from people who have recovered from COVID-19 is administered to ill patients, Boom said.

“We’ve had tons of experience gained, better outcomes, shorter lengths of stay,” Boom said. “But this is still a serious illness.”

While health authorities are better equipped to deal with new spikes, including an adequate supply of protective gear and sizable quantities of drugs like Remdesivir, a fall surge could still be equally as taxing on hospitals, said Carrie Kroll, vice president of advocacy, quality and public health at the Texas Hospital Association. As colder weather forces people inside and families gather for the holiday season, the chances for transmission increase, she said.

“We certainly have been tested, and we know the beast that it is, and have shown that we were able to make it through those first two spikes,” Kroll said. “But we don’t want to test the limit by putting patients into hospitals.”

See here for the previous update. It’s getting bad all around the country, too. Just a reminder, the July surge was bad, and it took Greg Abbott way too long to react to it. In the meantime, various assholes have decided that it’s a good use of their time to sue everyone in sight to limit the government’s ability to respond to COVID-19. I have one small bit of local optimism in that Harris County has not backed down from being at the top threat level even as the numbers were improving. Our numbers are also trending up, but they’re not as bad as other places. Yet, anyway.

“The trends are going in the wrong direction,” said William McKeon, president of the Texas Medical Center. “You hate to see the sacrifices we made and the successes we achieved lost because people let their guard down.”

Dr. Marc Boom, president of Houston Methodist, said, “We’ve definitely turned the wrong corner. The numbers aren’t growing in an out-of-control fashion, but there’s no doubt we’re in a significant growth trend that we need to stop before the holiday season.”

[…]

The Houston numbers are well below those in other parts of the country, particularly the Midwest and the West. As of Monday, 16 states had added more COVID-19 cases the past week than in any other seven-day period.

The surge is even greater in Europe. There the total of new cases in the five most-affected countries — France, the United Kingdom, Russia, Spain and the Netherlands — was nearly 42 percent greater than the U.S. increase a week ago.

Nor does Houston’s increase compare to the Panhandle and El Paso. El Paso health officials Monday reported their highest number of COVID-19 hospitalizations since the pandemic began — 449 in one day — and said just seven of the city’s ICU beds were unoccupied.

Still, increases in Houston area’s key metrics since early October are cause for concern, said local health officials. Those provided by the Texas Medical Center include:

• The rolling average of 497 COVID-19 cases reported the week ending Sunday represents a 33 percent increase from late September, when the number was 373. It increased gradually the weeks in between.

• The number of COVID-19 patients admitted to TMC hospitals exceeded 100 last week, up from the 80s the previous week and 70s the week before that.

• The TMC COVID-19 test positivity rate, 3.4 percent early in October, has been at 3.9 percent the past week, an 8 percent increase.

• The so-called R(t), or reproduction rate, the rate at which the virus is spreading, did drop to 0.99 Tuesday, but that remains a 55 percent increase over the Sept. 29 rate of 0.64, when the spread was decreasing. The rate last week hit 1.14, which means the virus’ spread was increasing.

“We’re in a yellow zone, not a red zone”, is how one doctor put it. “COVID fatigue”, they say this is. I get that, but you can see what happens when we start to take this less seriously. Until there’s a widely available vaccine, wear your damn mask, stay out of crowded indoor spaces, maintain social distancing, and hope for the best. At least our mild winter weather means we can largely stay outside. It could be worse.

We really can track COVID-19 through wastewater

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.

How about some antibody tests?

That would be good.

After months of emphasis on diagnostic screening, contact tracing and research into possible treatments, Houston is about to deploy a new tool in the effort to contain COVID-19: antibody testing.

Baylor College of Medicine researchers last week presented evidence to school leadership that the blood test it developed to detect whether an individual has been infected with the coronavirus is highly accurate and ready for use in studies assessing the virus’ reach in the area. Such studies would provide the answer that hasn’t been ascertainable because of the shortage of diagnostic testing.

“This will tell us the severity of the disease based on prevalence, the number of people who have had the virus but do not show up in case counts because they were asymptomatic and weren’t tested,” said Dr. Paul Klotman, president of Baylor. “That’s needed to better understand how infections impact different Houston communities, the variations in those communities and the numbers in certain high-risk environments, like prisons and nursing homes.”

Klotman said he anticipates Baylor will partner with local health departments to determine optimal resource allocation — such as where to focus testing and contact tracing — based on the prevalence the studies find in communities.

A Baylor prevalence study based on antibody testing would put the Houston region among a handful of U.S. communities to conduct such research, which has found that more than 20 percent of people in New York City but only 4 percent of those in Los Angeles County have been infected. Klotman said he thinks Houston’s rate will be closer to the California number.

Such antibody testing, repeated over time, also would show the area’s progress toward herd immunity, the protection from a contagious disease that occurs when a high percentage of the population has either had the infection or been vaccinated. Experts say that percentage — there is no vaccine for the coronavirus yet — needs to reach at least 60 to 70.

There’s more, and you should read the rest. As a reminder, viral tests are to see who has the virus now, and antibody tests are to see who has had it in the past. Do not mix the two if you want to know the current case count. I would note that the Texas Tribune case tracker showed 10,921 infections in Harris County as of May 25. If that four percent guess is accurate, then given a county population of 4.7 million, the actual number of cases would be more like 188,000. That’s consistent, even a bit under, the typical antibody test experience, which winds up estimating the real infection count at about ten times the “official” count. And note that we’d have to have more than ten times that number to get close to the minimum threshold for herd immunity.

Anyway. I look forward to seeing what this can tell us. In conjunction with the wastewater testing, maybe we can finally get a clear local picture of this pandemic.

Typhus in Texas

One more thing to worry about, in case you needed it.

Strickland spent four days in a hospital receiving treatment and needed about a year to fully recover from the potentially fatal disease transmitted by fleas believed nowadays to be carried most abundantly by opossums and other backyard mammals that spread them to cats and dogs.

Between 2003 and 2013, typhus increased tenfold in Texas and spread from nine counties to 41, according to Baylor College of Medicine researchers

The numbers have increased since then.

Harris County, which reported no cases before 2007, had 32 cases in 2016, double the previous years’ numbers.

Researchers do not know why the numbers are increasing.

In any case, the infection is severe enough that 60 percent of people who contracted the infection during the 10-year period had to be hospitalized. Four died, one in Houston.

“We can now add typhus to the growing list of tropical infections striking Texas,” said Dr. Peter Hotez, founding dean of the National School of Tropical Medicine at Baylor and Texas Children’s Hospital, “Chagas, dengue fever, Zika, chikungunya and now typhus – tropical diseases have become the new normal in south and southeast Texas.”

[…]

It was Strickland’s bout with the disease, in 2009, that first got the attention of Dr. Kristy Murray, a Baylor associate professor of infectious disease who had taught about typhus in the Valley but had not heard of it in modern-day urban centers, despite a focus on the tropical diseases that have emerged in Texas in recent times.

In the ensuing years, Murray heard enough anecdotal evidence of an increase in cases from local doctors that she decided to look at state data, combing through case histories to document the numbers and spot trends.

Murray was struck by the results, published recently in the journal Emerging Infectious Diseases, which showed 222 cases in Texas in 2013, many in Houston, Austin and San Antonio. That was up from just 30 reported cases in 2003, all in the southern part of the state, in counties such as Hidalgo and Nueces where the disease has remained an issue over the decades.

Unlike many tropical diseases, which predominate in poor areas, the new cases of typhus were just as likely to be reported in more affluent areas, such as Bellaire and West University.

The highest rate of attack was in kids, 5 to 19 years old.

In 2016, according to the most recent state data, the number of Texas cases had risen to 364.

The study in question is here. Typhus, it should be noted, is not the same as typhoid fever, of Typhoid Mary fame. The study in question was published a couple of months ago, and there were a few stories on the same topic at the time. Country musician Bruce Robison had to cancel a few shows recently after he came down with typhus. It can be spread by fleas, so make sure your pets are getting treated. Common symptoms include fever, headache, and a rash, so be aware and take care.

No Rice-BCM merger

The longstanding merger talks between Rice University and Baylor College of Medicine have been terminated.

Rice President David Leebron and Baylor College of Medicine President Dr. William Butler gave no reason for the talks ending in their statement.

“Since we signed a memorandum of understanding in March of 2009, we have been in extensive discussions in an attempt to meet several conditions that both institutions considered to be essential for a successful merger,” said the statement, which was e-mailed to campus faculty, staffs and students. “We joined in a thorough and deliberate process that explored the many benefits and challenges a merger would entail. With the MOU due to expire this month, the leadership of both institutions decided it is in the best interests of both BCM and Rice University to strengthen the existing relationship without a formal merger.”

The announcement came just four months after Leebron and Butler hinted a deal might by in place by the end of January. In a joint statement in September, they said that the negotiating period had been extended through Jan. 31 and pledged “to work hard to bring our discussions to a successful conclusion over the next four months.”

But Baylor was never able to resolve Rice’s two big concerns — the medical school’s shaky finances and lack of a private adult hospital for its clinical faculty. Butler announced in December that talks had fallen through to make St. Luke’s Episcopal Hospital its partner again, some eight months after financial concerns prompted the school to shelve construction of its own hospital.

Given the tough budget situation at Rice this year, I’m sure those financial concerns loomed ever larger. For what it’s worth, most of the Rice students and alums I know were not favorable to the merger idea, and the initial reaction I’ve seen to its collapse is relief. Reaction on the Rice fan forum is a bit more varied. I think it would have been a plus for Rice to be affiliated with a medical school if it could have been made to work, but this is probably for the best. If the two schools do strengthen their existing relationship, perhaps most of the good that would have come out of a merger can still happen with less risk and disruption for all.

Senate panel approves budget

As you know, the Lege has one task they absolutely must do every biennium, and that’s pass a budget. The Senate Finance Committee has taken its first step towards doing that.

A two-year state budget that accepts federal stimulus money and increases spending by 7.3 percent, but hoards cash reserves, was approved by Senate budget writers today.

Counting federal funds, the Senate Finance Committee’s budget would spend $182.2 billion, up $12.5 billion over the current two year cycle.

“It’s a fairly significant increase in the overall budget,” said Finance Committee Chairman Steve Ogden, R-Bryan. “The committee worked hard to try and address many, many legitimate needs in state government, and we wouldn’t have been able to do it without the federal stimulus money.”

The panel approved the budget, 14-0. The full Senate is expected to act on it later this week.

A key goal of Senate budget writers was to protect the state’s “rainy day fund,” so that 2 1/2 -year old school property tax cuts won’t vanish after 2011. The committee left untouched some $9.1 billion expected in the rainy day fund by September 2011.

The reserve is expected to be used next session, when lawmakers will confront a yawning gap between the 2006 property tax cuts and offsetting new revenues from a revamped business tax and higher taxes on cigarettes and private transfers of used cars.

A 24-percent increase in federal funds helped the Senate panel balance the budget for 2010-2011.

So, thanks to stimulus funding, we can keep those irresponsible property tax cuts and not only not dip into the Rainy Day Fund, but also put aside enough money to pay for a further continuation of those cuts in the next session, when the piper was fixing to hand us a sizable bill for his services. My head is spinning.

In a brief discussion by the Finance Committee, Sens. Judith Zaffirini, D-Laredo, and Eddie Lucio, D-Brownsville, said they were voting for the budget with reservations.

Zaffirini said the panel should have heard testimony from experts before adopting a last-minute provision that would bar using any funds in the budget for embryonic stem cell research.

There’s a longer story on that here. Most of the arguments are familiar to people, since it’s basically the abortion issue one step removed, so I’ll just note this bit and move on:

Proponents of using embryos, who say they are obtained from fertility clinics and would be discarded anyway, said Texas stands to lose billions from a burgeoning biotech industry if it continues to create a hostile legal and regulatory climate.

A recent study by University of North Texas economists Bernard Weinstein and Terry Clower said the state could lose out on as many as 100,000 new jobs in the next five years if the state restricts embryonic research.

Yeah, no one’s ever really explained to me what’s supposed to happen to all those unused embryos at fertility clinics. Stay in the freezer forever, I guess. The Chron has a story on this as well, noting that researchers from Baylor College of Medicine, three University of Texas Health System academic health institutions and Rice University, including Norbel laureates Robert Curl and Ferid Murad, signed a letter to the Senate asking them to remove the Ogden rider. Anyway, moving on as noted to the House, where the Appropriations Committee was dealing with a different kind of kerfuffle.

House budget writers, spurred by a chairman angered by how Gov. Rick Perry helped steer a $50 million grant to the Texas A&M University System, voted Friday to strip Perry of one of the powers he used to make the grant happen.

The House Appropriations Committee put language in its proposed budget saying any transfers between the Texas Enterprise Fund and the Emerging Technology Fund must be approved by the 10-member Legislative Budget Board. The panel also said the budget board, made up of the lieutenant governor, House speaker and members of the House and Senate, must approve any grants from the two funds.

Perry uses the Enterprise Fund to attract businesses to the state and the Emerging Technology Fund to launch tech projects at universities working with the private sector. Current law says grants from those accounts must be approved by the governor, lieutenant governor and House speaker.

Friday’s move was a response to Perry’s announcement this week that he had transferred $50 million from the Enterprise Fund to the Emerging Technology Fund to pay for a grant to the Texas A&M University System for a new pharmaceutical manufacturing center.

But House Appropriations Committee Chairman Jim Pitts, R-Waxahachie , says that’s not how the state usually pays for buildings at universities.

Several members of the Appropriations Committee, including Pitts, praised the Texas A&M center, saying they were more concerned with the process than the result.

“We have a legitimate concern that funds (that) were dedicated for one purpose were moved to a fund with a completely different purpose with little or no input from the Legislature,” Pitts said.

There’s a reason a lot of us have called this a slush fund for the Governor. I suppose I should thank him for making that a little more obvious to some folks. This may well be a fine use of that money, but it sure would be nice to have something other than just Rick Perry’s say so.

One more thing:

The Appropriations panel also proposed putting $136 million into the Enterprise Fund and $77 million into the Emerging Technology Fund over the next two years — combined, more than $200 million less than Perry requested.

“Now is not the time to cut back on job creation programs,” Perry spokeswoman Allison Castle said.

Because Rick Perry’s priorities are sacrosanct. Other priorities can go hang, but what Rick Perry wants is untouchable. Got it.