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antibody tests

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.

A different kind of COVID tracking

Hope this works.

Harris County Public Health will survey residents for COVID-19 antibodies in an effort to determine how many people already have been infected with the novel coronavirus, the department said.

Beginning Sunday, health workers will visit randomly selected homes and ask residents to answer questions and provide blood samples.

Humans produce antibodies, proteins in the immune system, to fight infections from viruses and other pathogens. It can take days or weeks for antibodies to develop following exposure to the coronavirus, and it remains unclear how long they remain in an individual’s blood.

The Houston region has recorded 236,704 COVID-19 cases since the virus arrived here in March, according to a Houston Chronicle analysis, but health officials estimate this is only a fraction of the total number of infections.

Health officials hope the antibody tests will help the county determine how COVID-19 spread in certain communities, how transmission rates differ between neighborhoods, how effective containment strategies have been and how many residents contracted the virus but never exhibited symptoms.

“This survey is a very important way that local residents can help public health workers fight this virus,” Harris County Public Health Executive Director Dr. Umair A. Shah said in a statement. “By finding out how widespread the illness is, we can develop strategies that will help us control the spread of COVID-19.”

Participation in the program is voluntary, and only selected households are eligible. Teams of health workers wearing yellow vests will make their rounds from Nov. 15 through Dec. 15, from 8 a.m. to 5 p.m.

The point of this survey is to find the people who have COVID but didn’t know it and never got tested for it. This will help us know what the real level of infection is in the county, since the official stats are almost certainly too low. It may also help identify previously unknown hot spots, in the way that wastewater testing can do.

And speaking of official statistics:

Please wear your mask and stay socially distant, y’all. There’s only way one way out of this until that vaccine is ready.

We still suck at COVID data

I’m sure none of this is important.

The government’s official data on the coronavirus outbreak is startling: More than 4.6 million cases in the U.S. More than 440,000 in Texas. More than 70,000 in Harris County.

But those numbers don’t include all positive COVID-19 patients.

Texas, unlike 27 other states, excludes the results of increasingly popular, rapid COVID-19 tests from the numbers it reports publicly — obscuring the scope of the pandemic, records and interviews show. The antigen tests are used in doctor’s offices, hospitals and stand-alone clinics and deliver results in less than 30 minutes.

But conflicting guidance from the Texas Department of State Health Services created confusion among local health departments about what test results to report. A reliance on faxed test results has created a paper backlog that makes it impossible for the state to do its own tally.

And while there is no way to independently estimate the scope of the undercount, based on the 11 Texas counties that publish antigen tests results separately of their own accord, the state’s tally is short by at least tens of thousands of cases — but likely far more, a Houston Chronicle analysis found.

And the undercount is about to get worse. The federal government is rolling out a program to use thousands of antigen tests in nursing homes across the country — including Texas.

State Rep. Gina Hinojosa, D-Austin, who serves as vice-chair of the House committee that oversees the state’s public health agencies, said the lack of reliable data is hindering the overall COVID-19 response effort in Texas.

“The only way people will be inspired to act right without government mandates is if they have the information they need to make smart choices,” Hinojosa told the Chronicle. “And that has been just impossible to come by.”

The problem, apparently, is that the state considers a positive antigen test to be a “probable” positive for COVID-19, not a definite positive. I mean, I figure a couple of data geeks could work out a decent solution for this in less than a day’s work, so color me baffled by the confusion here. And if you’re confused for other reasons, please note that antigen tests are different from antibody tests, which determine if you have had COVID-19 in the past, and thus should be in a separate category. It would be nice if we could get this all straightened out. The Trib has more.

NBA sets a plan, MLB still working it out

Happening today.

The NBA is finalizing details of a plan which is expected to be approved by the league’s Board of Governors on Thursday, paving the way for a return from the coronavirus shutdown.

The board is poised to give the green light to commissioner Adam Silver’s return of basketball which would begin July 31 with a 22-team format, and end in mid-October with a champion being crowned, ESPN reported.

The plan requires support from three quarters of the league’s 30 teams in order to be approved.

The NBA suspended its season on March 11 because of the global COVID-19 pandemic.

The Milwaukee Bucks, Toronto Raptors, Boston Celtics, Miami Heat, Indiana Pacers, Philadelphia 76ers, Nets and Orlando Magic currently hold the playoff spots in the Eastern Conference.

The Los Angeles Lakers, Los Angeles Clippers, Denver Nuggets, Utah Jazz, Oklahoma City Thunder, Houston Rockets, Dallas Mavericks and Memphis Grizzlies occupy the postseason positions in the Western Conference.

Under the plan, each of the 22 teams will play eight regular-season games for seeding purposes for the postseason.

The 16 teams currently in the playoff picture will be joined by the New Orleans Pelicans, Portland Trail Blazers, Phoenix Suns, Sacramento Kings and San Antonio Spurs in the Western Conference.

In the East, the Washington Wizards are also included.

[…]

All games are expected to be within the confines of Disney’s ESPN Wide World of Sports Complex in Orlando Florida, with all teams remaining on site to minimise risk of COVID-19 outbreaks.

See here for the background. ESPN adds a bit more:

Life in the NBA bubble will be governed by a set of safety protocols. While players and coaches will be allowed to golf or eat at outdoor restaurants, they will also need to maintain social distancing, sources told ESPN’s Ramona Shelburne.

The NBA is planning to have uniform, daily testing for the coronavirus within the Disney campus environment, sources told ESPN. ESPN is owned by The Walt Disney Company.

If a player tests positive for the virus, the league’s intent would be to remove that player from the team to quarantine and treat individually — and continue to test other team members as they play on, sources said.

Employees at the Disney resort will have to maintain similar protocols. For example, no staff will be allowed into players’ rooms, and hallways will be carefully managed to avoid crowding, sources told Shelburne.

Weird, but the NBA had played the bulk of its season anyway, and the playoffs are always a different thing entirely. I just hope those employees at the Disney resort had someone thinking about their welfare as this deal was being hammered out. The Chron has more.

And then there’s MLB:

Major League Baseball has rejected the players’ offer for a 114-game regular season with no additional salary cuts and told the union it did not plan to make a counterproposal, sources confirmed to ESPN.

Players made their proposal Sunday, up from an 82-game regular season in management’s offer last week. Opening Day would be June 30, and the regular season would end Oct. 31, nearly five weeks after the Sept. 27 conclusion that MLB’s proposal stuck to from the season’s original schedule.

MLB told the union it had no interest in extending the season into November, when it fears a second wave of the coronavirus could disrupt the postseason and jeopardize $787 million in broadcast revenue.

While management has suggested it could play a short regular season of about 50 games with no more salary reductions, it has not formally proposed that concept. Earlier this week, multiple players told ESPN that they would not abide a shorter schedule, with one saying, “We want to play more games, and they want to play less. We want more baseball.”

See here for the previous update. If this sounds dire to you, let me refer you again to Eugene Freedman, who’s been around this block a few times.

Basically, it looks like the sides have agreed to the March deal, and now need to work out the safety and testing details, plus what to do if a player wants to opt out. Maybe the NBA getting set to start at the end of July will inspire them to agree on some version of their July 4 Opening Day season. Fingers crossed. The Chron has more.

MLB players make their counteroffer

Back to the owners.

The Major League Baseball Players Association delivered a return-to-play proposal to MLB on Sunday that includes a 114-game season, deferred salaries in the event of a canceled postseason and the option for all players to opt out of a potential 2020 season due to coronavirus concerns, sources familiar with the details told ESPN.

The proposal, which was the first from the union and came on the heels of an MLB plan that was loudly rejected by the players, comes at a seminal moment as baseball tries to become the first major American professional sport to return. Although the players expect the league to reject it, they hope it will serve as a bridge to a potential deal this week.

The 114-game season, which under the union’s proposal would run from June 30 to Oct. 31, is expected to be immediately dismissed by the league; MLB has proposed an 82-game season and suggested that the more games teams play this year, the more money they lose. The union remains steadfast that players should receive their full prorated salaries, while MLB’s plan included significant pay cuts that affected the highest-paid players the most but covered all levels.

The inclusion of potential deferrals in Sunday’s proposal was an acknowledgement by the players that amid the coronavirus pandemic and unrest around the country, cash-flow issues could prove problematic for owners. The deferrals would occur only if the playoffs were canceled, a concern the league has voiced, and would total $100 million. They would apply to players whose contracts call for $10 million-plus salaries and include interest to make them whole.

Deferrals could be part of any counter from the league, which had not officially responded to the union’s proposal Sunday. With the desire to start a season by the first week of July, both parties recognize that time is of the essence for a deal.

While MLB’s 67-page health-and-safety protocol draft included the ability for high-risk players — those with preexisting conditions or family members more susceptible to COVID-19 — to opt out of the season, the union’s proposal suggests that players can do so and receive salary. Players not deemed high risk would be able to opt out but would not receive salary.

See here for the background. I would recommend you read these Twitter threads about collective bargaining by Eugene Freedman for a better understanding of what the players are doing. As he describes there and in the latest Effectively Wild, the owners’ proposal to cut salaries and the players’ offer of a longer season are both basically non-starters unless the other side agrees to reopen the matter. Now that they have both asserted that they won’t open those matters, the real negotiations about health and safety can begin. At least, that’s the hope. If there’s going to be progress on this, it will probably happen this week, but you never know. Fangraphs has more.

UPDATE: Lookie here:

Now, maybe, we are getting somewhere.

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.

MLB’s latest startup proposal

The league still wants to stick it to the players.

Major League Baseball drew the ire of the players’ union Tuesday with an economic proposal that called for a significant cut in salaries that would affect all players and particularly the game’s highest paid, sources familiar with the proposal told ESPN.

The long-awaited plan, the first volley in an expected back-and-forth that will determine whether baseball returns in 2020, proposed a marginal salary structure in which the lowest-paid players would receive close to a full share of their prorated salary and the game’s stars receive far less than expected.

Players immediately bristled at the proposal, which includes an 82-game schedule that would begin in early July after a 21-day spring training, sources familiar with the plan said. Teams would play three exhibition games in the final week before starting a regular season that would finish Sept. 27.

The MLB Players Association is expected to reject the plan and counter in the coming days with a proposal that could include a longer season, according to sources.

The league’s proposal, which includes bonuses if postseason games are played, offers lower-salaried players a higher percentage of their expected wages and would give some of the game’s biggest stars a fractional cut of their salaries. The formula the league offered, for example, would take a player scheduled to make the league minimum ($563,500), give him a prorated number based on 82 games ($285,228) and take a 10% cut from that figure, leaving him with a $256,706 salary.

[…]

Although the proposal would keep a larger proportion of players close to their whole salaries — about 65% make $1 million or less and would receive more than 80% of their prorated salaries — players young and old objected to the plan, which they believe runs in contrast to a March agreement with the league that they believe legislated that players be paid full prorated salaries upon the return of baseball.

The league believes language in the deal calls for good-faith negotiations with the union about the economic feasibility of playing with no fans, which MLB expects to do upon a return. The league initially considered proposing a 50-50 revenue split with the players, citing massive losses due to the coronavirus pandemic. MLBPA executive director Tony Clark immediately rejected the idea, equating it to a salary cap.

See here for the background. Basically, this PR move by the owners is to stick to the highest-paid players, in an attempt to divide the union and make the players look as unsympathetic as possible to the public. I’ll outsource the analysis of this to Jay Jaffe, who sums it up as follows:

While this proposal does bear some resemblance to a progressive taxation scheme, the question that needs to be asked is why it’s the millionaires, whose careers have limited windows, bearing the brunt of the economic impact instead of the billionaire owners for whom annual profits — and for MLB, which has seen revenues grow for 17 straight years, there have been a whole lot of those — and losses pale in comparison to escalating franchise values. That’s without even considering the disproportionate risk the players are assuming by returning to play amid the pandemic. It’s not just their livelihoods that are at risk, it’s their lives. They can’t write those losses off.

Here’s a convenient timeline of the action so far, with some fact-checking as needed. By the way, while the owners as a whole are targeting the stars, one franchise is also sticking it to their minor leaguers, always a classy move. I’ll give a last word on this to Joe Sheehan:

More insidious, though, is the principle behind the plan. It’s asking Mike Trout to give money to Arte Moreno. Trout is rich; Moreno is wealthy. When Moreno had leverage, he paid Trout as little as he could. Now he’s asking Trout to give him back basically all the money Trout made in the first four years of his career.

Of course, any possibility of baseball or any other sport relaunching at this time is highly dependent on testing and keeping the players and coaches and umpires and staffers and everybody working at the stadiums COVID-free. Michael Baumann digs into what that means.

I asked Abdul El-Sayed, an epidemiologist and the former health commissioner for the city of Detroit, whether we know enough about COVID-19 to plan for games in October and November. “Yes, we do know enough about the virus,” El-Sayed says, “to know that we can’t make decisions five to six months in advance.”

One thing baseball has going for it compared to other major team sports—football, basketball, and so on—is that the actual gameplay isn’t particularly conducive to COVID-19 transmission. “An outdoor sport like baseball where [players are] not breathing heavily in each other’s faces seems like a good candidate for a sport that can return,” says Laura Albert, an associate professor of industrial and systems engineering at the University of Wisconsin whose research includes the optimization of emergency and public health systems.

While Albert isn’t worried as much about the in-game component of MLB’s plan to return in July, though, she has other concerns. Namely, even if the league prohibits sunflower seeds, tobacco, and spitting, there would still be plenty of scenarios during which a player with the virus could spread it to others. “There will be positive cases and there will be transmission between players,” she says. “And I anticipate it happening on airplanes and buses, in the locker rooms or bathrooms. It’s not totally clear how we can change those spaces to be safe if there’s a bunch of people using them.”

[…]

MLB’s return, whenever it happens, is already being heralded as a sign of things returning to normal. Indeed, as much as baseball fans miss the game itself, that touchstone to a more comfortable time is a huge reason why even a limited season is such an attractive proposition. But MLB has already accepted that if the league is going to have a prayer of making it to the World Series this year, the game won’t look, feel, or sound the same as it has in the past.

“Our lives are not going back,” Albert says. “They’re not returning to what they were like before, and there’s not one way we could really control the spread of COVID-19—there’s many things we have to do. And so it’s great that the leagues are embracing this. It’s not window dressing. I think it’s important for us to get used to these things.”

There’s a limit not only to what MLB and the MLBPA can do to ensure that the game is safe, but also to what they can know and predict. It will certainly be difficult for such a powerful industry to comprehend that idea, but it will be necessary for the baseball world to understand and embrace it. Given how COVID-19 works, the data on infection rate leaves investigators and public officials to work on a lag.

“We’re not dealing with linear dynamics here. That’s the hard part that I think is confounding so many of our best efforts to respond reasonably,” El-Sayed says. “You’re talking about exponential growth. Everything that we see today is information about the dynamics of the virus two weeks ago. And so all of a sudden you could be having exponential growth dynamics that only start showing up after it’s too late for you to act to stop them.”

As much as everyone is tired of having the course of the country and the economy determined on a fortnightly basis, [Thomas J. Duszynski, the epidemiology education director at the Richard M. Fairbanks School of Public Health at Indiana University–Purdue University Indianapolis] says that’s about as far ahead as we can responsibly plan right now. He’s open to the idea of MLB coming back—but only if the league is willing to stop the season if conditions change. “If they go down this road and start to play games, which personally I hope they do, and we see a shift in that science that says, ‘Hey, wait a minute, the disease is getting worse again,’ is MLB going to be able to pull this back?” he says. “Are they going to be able to shut it down and still survive?”

Both El-Sayed and Duszynski believe that it’s possible that a leaguewide infection could progress to the point where MLB simply can’t press on.

“God forbid a player dies because of this,” Dusynski says. “What kind of ripple effect would that have through Major League Baseball?”

I’m actually not that worried about a player dying. It could happen, but it would be unlikely. I’m much more worried about a coach, or an umpire, or a stadium staffer dying. Or a member of a player’s family, or a family member of one of these other groups. That could happen regardless – about 0.7% of players have already had COVID-19, per the MLB antibody study. Clearly, the risk is greater if the games are played. The players have the most leverage to assess and try to mitigate the risk to themselves and their families. I hope that’s sufficient for everyone else.

That’s not how you test

Oops.

Texas health officials made a key change Thursday to how they report data about the coronavirus, distinguishing antibody tests from standard viral tests and prompting slight increases in the state’s oft-cited daily statistic known as the positivity rate.

The positivity rate is the ratio of the confirmed cases to total tests, presented by the state as a seven-day rolling average. The Texas Department State of Health Services disclosed for the first time Thursday that as of a day earlier, it had counted 49,313 antibody tests as as part of its “total tests” tally. That represents 6.4% of the 770,241 total tests that the state had reported through Wednesday.

Health experts have warned against conflating the tests because they are distinctly different. Antibody tests detect whether someone was previously infected, while standard viral tests determine whether someone currently has the virus.

Now that DSHS is reporting the number of antibody tests, it has recalculated its daily positivity rates starting Tuesday to exclude such tests. That led to a 0.41 percentage-point increase in Tuesday’s rate and a 0.55 point increase in Wednesday’s rate, according to DSHS calculations.

DSHS acknowledged last week that it was reporting an unknown quantity of antibody tests as part of the “total tests” figure. Despite that, Gov. Greg Abbott incorrectly claimed Monday that the state was not “commingling” the numbers while promising the state would soon break out the antibody test count.

[…]

When public health agencies combine antibody testing figures with viral testing figures, “I want to scream,” said Seema Yasmin, an epidemiologist and director of the Stanford Health Communications Initiative.

Viral tests, usually taken from nasal swabs, can detect an active coronavirus infection. If a person’s biological sample is found to have traces of the virus’s genetic material, public health workers can order them to self-isolate and track down any of their contacts who may have been exposed.

Antibody tests “are like looking in the rearview mirror,” Yasmin said, because they may show if a person has recovered from a coronavirus infection. That can be useful for public health surveillance, but it does not offer much insight about where the virus is currently spreading. Another issue is that many antibody tests have been shown to have high rates of inaccuracy, she said.

“As an epidemiologist, this level of messiness in the data makes your job so much more difficult, and it misleads the public about what’s really happening,” Yasmin said. “We’ve been talking about the capacity for testing increasing over the last few weeks, but now we might have to tell the public that might not be true.”

And dumping antibody testing data into the pool of viral testing data brings the overall positivity rate down, reflecting “a deceptive misuse of the data,” analysts for the COVID Tracking Project wrote last week. That’s because the numbers may make it seem like the state has grown its testing capacity even if a state’s viral testing capacity remains flat.

“This is crucial as we need increased capacity for viral testing before reopening to identify active infections even in the pre-symptomatic or asymptomatic stages,” the analysts wrote.

To be fair, Texas is not the only state to have done this. Florida and Georgia have been accused of manipulating their data in other ways as well. The bottom line here is that we’ll never get our arms around this pandemic if we don’t have good data. The data is messy enough as it is, we surely don’t need to be making it worse.