This New COVID Wave May Be More Like a Flood

By Chas Danner

A lot of people will still be seeing the dreaded double line this summer. Photo: Justin Sullivan/Getty Images

A new COVID wave now fueled by four Omicron subvariants continues to drive up infections throughout the country. Though there are signs that the surge in the Northeast has begun to stabilize, infections are on the rise in other regions and the level of community transmission remains high across the vast majority of the country. There is also reason to worry that the current wave may not subside for a long time, particularly now that the two newest and most troubling Omicron subvariants, BA.4 and BA.5, may be starting to outcompete their predecessors. While previous nationwide surges in cases have mostly played out as single waves, this new one might be more like a flood. It could plateau, or dip and swell from that higher baseline across the coming weeks or even months.

Illustration: CDC/Map showing current community transmission across the U.S. as estimated by the CDC. (Red is bad.)

The BA.2.12.1 subvariant, which overtook BA.2 as the nation’s dominant strain last month, still makes up an estimated 62 percent of cases nationwide according to the CDC. BA.4 and BA.5 may be even more transmissible than BA.2.12.1, and it seems clear that they are better equipped to evade immunity induced by prior infection or vaccination. The CDC now estimates that the BA.4 and BA.5 account for a combined 13 percent (5.4 percent BA.4 and 7.6 percent BA.5) of U.S. cases, up from a combined 1.1 percent a month ago.

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Illustration: CDC Nowcast/CDC estimated variant proportions as of the week ending June 4.

The sister subvariants, which arrived in the U.S. in March, are on the rise across the country, but especially in some parts of the central U.S. and Southwest. It’s not yet clear whether or not BA.4 and BA.5 will overtake BA.2.12.1 in the U.S. but some COVID experts are predicting it will become dominant in the U.S. and globally, based on some preliminary studies. In recent lab research conducted by scientists at the Columbia University Vagelos College of Physicians and Surgeons, BA.4 and BA.5’s unique combination of mutations were found to equip them with a more than 4.2-fold advantage over BA.2 in escaping antibodies in people who have been vaccinated and boosted, whereas BA.2.12.1 only had a 1.8-fold advantage over BA.2 in that regard. The researchers also found that antibodies of vaccinated people who had breakthrough infections offered less protection against BA.4 and BA.5. That suggests, as previous research has, that BA.4 and BA.5 are going to cause a lot of breakthrough infections and reinfections, including among people who caught the original Omicron strain over the winter. That’s what has already happened in South Africa, where BA.4 and BA.5 fueled a wave of cases, despite most of the population having already had Omicron.

The ability of BA.4 and BA.5 to outcompete BA.2.12.1 will become clear very soon, now that they are starting to get a foothold in places like New York where the spread of BA.2.12.1 has been rampant. CNN additionally reports that data out of the U.K. found that the sister subvariants were spreading faster there than BA.2.12.1 was. “The betting favorite now suggests that BA.4 and BA.5 would be able to take out BA.2.12.1,” the assistant director of the University of Washington’s clinical virology laboratory, Dr. Alex Greninger, told CNN, adding that, “For the summer, going into the winter, I expect these viruses to be out there at relatively high levels.”

The good news across the board with all of the Omicron subvariants in the U.S. is that there is not yet evidence that any of these strains cause more severe illness than Omicron does. U.S. COVID hospitalizations have been trending up since the middle of April, including a 16 percent nationwide increase over the last two weeks, but the climb hasn’t been as steep as during previous waves. And while there has always been a lag time between hospitalizations and deaths, thus far COVID deaths haven’t trended up much at all. During the BA.4/5 wave in South Africa, hospitalizations rose but remained low compared with previous waves, and there wasn’t a substantial increase in the number of deaths from COVID there. Scientists have attributed those trends to the very high immunity levels among the population. In other words, while immunity from prior infection or vaccination may not protect well at all against catching BA.4 and BA.5, they may still protect very well against severe illness, particularly among people who have been vaccinated and boosted, or who have hybrid immunity from both vaccination and prior infection.

Still, though the U.S. may see nothing like the spike in hospitalizations and deaths the Omicron wave produced, the country could remain inundated with COVID infections for the foreseeable future — a sustained-spread summer, or as The Atlantic’s Yasmin Tayag has framed it: the “When will it end?” wave. And the level of infections may not drop off before what the Biden administration and many scientists have warned will be a large spike this coming fall or winter.

The other issue is that nobody really knows how many infections this wave is producing — and that will likely remain unclear, both for this and future waves. The wave is undoubtedly much larger than confirmed case counts indicate, since they don’t include all the unreported infections detected by now-ubiquitous at-home COVID tests. Hospitalization rates, COVID levels in wastewater, and test-positivity rates are now a better indicator of wave size than confirmed-case tallies, but each metric has its flaws and they don’t offer a complete picture.

According to the CDC’s community-transmission dashboard, which factors in both reported cases and test-positivity rates, more than 78 percent of U.S. counties are currently experiencing high community transmission of COVID, and nearly 11 percent are experiencing substantial levels of transmission. Some COVID experts have recently speculated that the number of new infections were between five to ten times higher than official case counts indicated. The real number could be even higher than that, according to a new (preprint) study from researchers at the CUNY Institute for Implementation Science in Population Health.

Focusing on the recent surge of infections in New York City, the researchers estimated that more than one in five adult New Yorkers — about 1.5 million people — likely had COVID at some point during the two weeks ending May 8. “It would appear official case counts are under-estimating the true burden of infection by about 30-fold, which is a huge surprise,” one of the study authors, CUNY ISPH epidemiology professor Denis Nash, explained to The Guardian. Furthermore, Nash added, the undercount may be even worse in other places without the relatively high access to testing that New Yorkers have. As he and the study’s other authors warn, the bottom line is that routine COVID surveillance, in its present form, isn’t up to the task of measuring the scope and scale of COVID surges, which denies scientists, politicians, and the public the accurate data needed to make informed decisions about risk and response. (Another alarming estimate from the study was that nearly 56 percent of the New Yorkers who had COVID were not even aware of the antiviral Paxlovid, and only 15 percent said they had received it, indicating a troubling lack of information about, and effective access to, one of the most powerful post-infection weapons we currently have against severe COVID-19.)

America isn’t flying totally blind through this wave, but leaders, public-health officials, scientists, and of course, the public, are stuck with an obstructed view. Even armed with more complete, timely information, it’s far from clear how fast or effectively local, state, and federal leaders would respond. And that’s assuming they are willing to respond much at all; it’s an election year, pandemic interventions are perceived to be politically toxic, and many Americans, now left to manage their individual COVID risk on their own, have dropped their guard and/or diverted their attention to other concerns.

Again, America may avoid the worst outcomes during this wave, namely overwhelming numbers of hospitalizations or a large spike in the number of COVID deaths — but nothing about this wave is good, either. Subvariants that appear to have the most immune escape yet seen during the pandemic are taking hold in a country where waning immunity was already undoubtedly a big problem. The expiration date of Americans’ immunity is still a mystery, as is what will happen after. U.S. booster uptake is among the worst in the developed world, including among seniors, who during Omicron and after have once again become the U.S. demographic disproportionally attacked and killed by COVID. How the wave plays out among the many Americans who remain unvaccinated who have survived previous infections remains to be seen, and the risk of reinfection, overall, also remains unclear. We don’t know if reinfections increase the risk of long COVID, either. And every infection, every reinfection, is another opportunity for the coronavirus to evolve more tricks up its sleeve. BA.4 and BA.5 might not wallop the U.S., but don’t bet on a similar or better outcome from BA.6 or whatever else comes next.

 

Why haven’t Covid cases started rising again in the U.S.?

 David Leonhardt

Grand Central Terminal in Manhattan last week.Hiroko Masuike/The New York Times

A new mystery

To many people’s surprise — including mine — new Covid-19 cases in the U.S. have not begun to rise. Over the past two weeks, they have held roughly steady, falling about 1 percent, even as the highly contagious BA.2 subvariant of Omicron has become the dominant form of Covid in the U.S.

Across much of Europe, by contrast, cases surged last month after BA.2 began spreading there, and many experts expected a similar pattern here. That hasn’t happened. “It has not taken off,” Michael Osterholm, a University of Minnesota epidemiologist, told me.

Chart shows 7-day averages as of April 4. | Sources: New York Times database; Johns Hopkins University

What’s going on? Today’s newsletter looks at four possible explanations.

1. More immunity

Even though the U.S. has a lower vaccination rate than Western Europe, this country may still have built up more immunity — thanks to our politically polarized response to the virus.

In liberal parts of the U.S., vaccination rates can be even higher than in Europe. In conservative communities, many Americans have been so dismissive of Covid that they have long been living almost normally. As a result, the virus has already swept through these communities, conferring at least some immunity on many people.

This laissez-faire approach has had horrible downsides. Covid death rates have been much higher in counties that voted for Donald Trump than those that voted for Joe Biden. But for people who survived a prior Covid infection, it does confer some immune protection, especially if it was recent.

“Most of Europe has been pretty Covid averse,” William Hanage, a Harvard epidemiologist, said on a recent episode of the “In the Bubble” podcast, “whereas parts of the United States have been quite Covid curious.” Hanage said that he still expected U.S. caseloads to rise soon. But, he added, “I don’t think it’s going to be as dramatic as Europe.”

If that’s correct, a preview is already visible in the Northeast, where cases have been rising lately, but not as steeply as in Europe.

Chart shows 7-day averages. | Source: New York Times database

One possible reason: There are not as many Americans vulnerable to infection. The earlier version of the Omicron variant seems to have infected about 45 percent of Americans, according to Andy Slavitt, a former Covid adviser in the Biden White House. That share appears to be higher than Europe’s.

2. Fewer tests

The shift toward at-home testing in recent months means that a smaller share of actual Covid cases may be showing up in the data that government agencies report and news organizations like The Times publish. The government data relies on laboratory tests.

Another potential factor depressing the volume of tests is reduced access for lower-income Americans. Some uninsured people now must pay for their own tests, and many testing clinics have closed.

All of which raises the possibility that Covid cases really are surging now, even if the data doesn’t show it.

Jessica Malaty Rivera of Boston Children’s Hospital told The Atlantic that the quality of current Covid data was “abysmal.” Dr. Scott Gottlieb, a former F.D.A. commissioner, told CNBC that he thought some parts of the country were “dramatically” underreporting cases.

This chart suggests that underreporting is a real issue. As you can see, official testing in several European countries increased as BA.2 spread, while testing in the U.S. has declined modestly.

Comparisons across countries are affected by different testing policies and reporting methods. | Source: Our World in Data

Still, the shortage of testing does not seem to be the only reason that cases have not surged in the U.S. Trends in Covid hospitalizations typically lag case trends by only about a week. And hospitalizations have continued to fall in the U.S., to their lowest level in more than two years.

3. Just wait

Even if high levels of immunity have kept cases from rising so far, the effect may not be permanent. Remember: About 45 percent of Americans were infected with Omicron, which leaves about 55 percent who were not. While many of those 55 percent may have had an earlier version of Covid, immunity can wane over time.

The current moment might be one of those times when we’re asking why cases have not begun to rise right as they begin to rise. “It may be too early to see a signal,” Jennifer Nuzzo, a Brown University epidemiologist, told me.

4. Another mystery

Throughout the pandemic, Osterholm — the Minnesota epidemiologist — has lamented that many scientists, journalists and laypeople exaggerate how much we actually know about Covid. His favorite example: The Alpha variant swept through Michigan and Minnesota last year and then largely died out, without causing case increases in other parts of the U.S. Another example: BA.2 has recently become the dominant variant in India, South Africa and some other countries without causing a spike in cases.

When I called Osterholm yesterday to ask why cases had not surged over the past few weeks, he simply said: “I don’t know, and I don’t think anybody really knows.”

Of all the variants, only the original Omicron was so contagious that it spread around the world in predictable ways, he said. Other versions of the virus have surged and receded in mysterious ways, much as a forest fire can die out without burning down an entire forest.

The bottom line: Cases still seem likely to rise, perhaps significantly, in the U.S. soon. But a new wave looks less certain than it did a few weeks ago. Regardless, the steps that can save lives in coming months remain the same: more vaccine shots, including boosters; and greater awareness of available treatments that offer extra protection for the vulnerable.

 

“Covid-19 need no longer control our lives”

 

 

Jim Lo Scalzo/Getty Images

• The White House has outlined an updated approach to the Covid-19 pandemic, almost exactly two years after the virus reached the US, causing mass economic shutdowns, lockdowns, hospital overcrowding, and nearly 1 million deaths to date in the US alone. President Joe Biden unveiled the plan on Wednesday, following his State of the Union address. [The White House]
• The National Covid-19 Preparedness Plan hinges on four components: testing to treat Covid-19, preparing for new variants, increasing global vaccination, and preventing economic and educational shutdowns. The White House’s new direction aims to adjust to a “new normal,” viewing Covid-19 as a background reality of life rather an overarching international crisis, as it’s been for the past two years. [The Hill / Peter Sullivan]
• “We’ve reached a new moment in the fight against Covid-19 where severe cases are down to a level not seen since July of last year,” Biden said during Tuesday’s State of the Union address. However, he stressed that although the new plan is aimed at making the crisis less acute, “we never will just accept living with Covid-19, we’ll continue to combat the virus, as we do other diseases.” [Reuters]
• The new plan will expand access to Covid-19 oral antiviral treatments such as Pfizer’s Paxlovid, distributing the treatment to pharmacies along with rapid tests so that people can start treatment immediately after testing positive. More than 1 million doses of the treatment will be made available this month, with more coming in April. [Axios / Caitlin Owens]
• All the new initiatives will require new funding from Congress, which will go toward increasing vaccine manufacturing capability; replenishing the national stockpile of tests, masks, and antiviral pills; and increasing monitoring capabilities to detect variants. [Al Jazeera]

 

New Research Points to Wuhan Market as Pandemic Origin

By Carl Zimmer and Benjamin MuellerUpdated Feb. 27, 2022

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NY TIMES

Scientists released a pair of extensive studies over the weekend that point to a large food and live animal market in Wuhan, China, as the origin of the coronavirus pandemic.

Analyzing a wide range of data, including virus genes, maps of market stalls and the social media activity of early Covid-19 patients across Wuhan, the scientists concluded that the coronavirus was very likely present in live mammals sold at the Huanan Seafood Wholesale Market in late 2019 and suggested that the virus spilled over into people working or shopping there on two separate occasions.

Members of the Wuhan Hygiene Emergency Response Team leaving the closed Huanan Seafood Wholesale Market on Jan. 11, 2020. Noel Celis/Agence France-Presse

The studies, which together span 150 pages, are a significant salvo in the debate over the beginnings of a pandemic that has killed nearly six million people across the world. The question of whether the outbreak began with a spillover from wildlife sold at the market, a leak from a Wuhan virology lab or some other event has given rise to pitched debates over how best to stop the next pandemic.

“When you look at all of the evidence together, it’s an extraordinarily clear picture that the pandemic started at the Huanan market,” said Michael Worobey, an evolutionary biologist at the University of Arizona and a co-author of both new studies.

Several independent scientists said that the studies, which have not yet been published in a scientific journal, presented a compelling and rigorous new analysis of available data.

“It’s very convincing,” said Dr. Thea Fischer, an epidemiologist at the University of Copenhagen, who was not involved in the new studies. The question of whether the virus spilled over from animals “has now been settled with a very high degree of evidence, and thus confidence.”

Map of Wuhan showing the location of the Huanan Seafood Wholesale Market.

Huanan Seafood

Wholesale Market

WUHAN

But others pointed to some gaps that still remained. The new papers did not, for example, identify an animal at the market that spread the virus to humans.

“I think what they’re arguing could be true,” said Jesse Bloom, a virologist at the Fred Hutchinson Cancer Research Center. “But I don’t think the quality of the data is sufficient to say that any of these scenarios are true with confidence.”

In a separate study published online on Friday, scientists at the Chinese Center for Disease Control and Prevention analyzed genetic traces of the earliest environmental samples collected at the market, in January 2020.

By the time Chinese researchers arrived to collect these samples, police had shut down and disinfected the market because a number of people linked to it had become sick with what would later be recognized as Covid. No live market animals were left.

Photos of animals for sale in the Huanan market.

Animals for sale in the Huanan market in 2019 and 2014, including raccoon dogs, Malayan porcupines and a red fox. Source: Michael Worobey et al., preprint via Zenodo. Photos taken by a citizen and posted to Weibo in 2019 (first three), and by Edward C. Holmes in 2014.

The researchers swabbed walls, floors and other surfaces inside the market, as well as meat still in freezers and refrigerators. They also caught mice and stray cats and dogs around the market to test them, while also testing the contents of the sewers outside. The researchers then analyzed the samples for genetic traces of coronaviruses that may have been shed by people or animals.

Although the Chinese researchers conducted their study over two years ago, it was not until Friday’s report that they publicly shared their results. They reported that the Huanan market samples included two evolutionary branches of the virus, known as lineages A and B, both of which had been circulating in early Covid cases in China.

These findings came as a surprise. In the early days of the pandemic in China, the only Covid cases linked to the market appeared to be Lineage B. And because Lineage B seemed to have evolved after Lineage A, some researchers suggested that the virus arrived at the market only after spreading around Wuhan.

But that logic is upended by the new Chinese study, which finds both lineages in market samples. The findings are consistent with the scenario that Dr. Worobey and his colleagues put forward, in which at least two spillover events occurred at the market.

“The beauty of it is how simply it all adds up now,” said Jeremy Kamil, a virologist at Louisiana State University Health Shreveport, who was not involved in the new studies.

Mapping Cases

Although the Huanan market was an early object of suspicion, by the spring of 2020 senior members of the Trump administration were promoting the idea that the new coronavirus had escaped from the Wuhan Institute of Virology, a coronavirus laboratory located eight miles away on the other side of the Yangtze River.

There’s no direct evidence that the new coronavirus, SARS-CoV-2, was present at the lab before the pandemic. Researchers there have denied claims of a lab leak.

But the Chinese government has come under fire for not being forthcoming about the early days of the pandemic.

The report from the Chinese C.D.C. about the Huanan market’s samples, for example, had remained hidden. Starting in June 2020, two newspapers, The South China Morning Post and The Epoch Times, reported on what they claimed were leaked copies of the report.

In January 2021, a team of experts chosen by the World Health Organization traveled to China to investigate. Collaborating with Chinese experts, the group released a report in March 2021 that contained previously undisclosed details about the market. They noted, for example, that 10 stalls in the southwest corner of the market sold live animals.

The report also noted that 69 environmental samples collected from the market by the Chinese C.D.C. had turned up positive for SARS-CoV-2. But the frozen meat and live animals had all tested negative.

A member of the Wuhan Hygiene Emergency Response Team inside the closed Huanan market on Jan. 11, 2020. Noel Celis/Agence France-Presse

Still, the W.H.O. left many researchers dissatisfied. Dr. Worobey and Dr. Bloom both signed a letter, along with 16 other scientists in May 2021, calling for more investigation into the origins of Covid — including the possibility that SARS-CoV-2 had escaped from a lab.

The W.H.O. experts had identified 164 cases of Covid-19 in Wuhan over the course of December 2019. Unfortunately, the cases were marked by fuzzy dots scattered across a nearly featureless map of Wuhan.

Dr. Worobey and his colleagues used mapping tools to estimate the longitude and latitude locations of 156 of those cases. The highest density of December cases centered around the market — a relatively tiny spot in a city of 11 million people. Those cases included not just people who were initially linked to the market, but others who lived in the surrounding neighborhood.

Spatial analysis of Covid cases in Dec. 2019.

Covid cases in Dec. 2019

Huanan Seafood

Wholesale Market

Concentration of Covid cases in Dec. 2019

WUHAN

2 MILES

Source: Michael Worobey et al., preprint via Zenodo The New York Times

The researchers then mapped cases from January and February of 2020. They drew upon data collected by Chinese researchers from Weibo, a social media app that created a channel for people with Covid to seek medical help. The 737 cases pulled from Weibo were concentrated away from the market, in other parts of central Wuhan with high populations of elderly residents, the study found.

Spatial analysis of Covid cases in Jan.–Feb. 2020.

Huanan Seafood

Wholesale Market

Concentration of Covid cases in Jan.–Feb. 2020

Source: Michael Worobey et al. The New York Times

These patterns pointed to the market as the origin of the outbreak, Dr. Worobey and his colleagues concluded. The researchers ran tests that showed it was extremely unlikely that such a pattern could be produced merely by chance.

“It’s very strong statistical evidence that this is no coincidence,” Dr. Worobey said.

But David Relman, a microbiologist at Stanford University, raised the possibility that these patterns might be just evidence that the market boosted the epidemic after the virus started spreading in humans somewhere else.

“The virus would have arrived in a person, who then infected other people,” he said. “And the neighborhood of the market, or the market itself, became a kind of a sustained superspreader event.”

Multiple Spillovers

Dr. Worobey and his colleagues argue against that possibility, pointing to signs of spillovers within the market itself.

The researchers reconstructed the floor plan of the Huanan market based on the W.H.O. report, the leaked Chinese C.D.C. study and other sources. They then mapped the locations of positive environmental samples, finding that they clustered in the area where live animals were sold.

Strikingly, five of the samples came from a single stall. That stall had been visited in 2014 by one of the co-authors of the new studies, Edward Holmes, a virologist at the University of Sydney. On that trip, he had taken a photograph of a cage of raccoon dogs for sale at the time.

The Huanan Seafood Wholesale Market in Wuhan, China.

XINHUA ROAD

Huanan Seafood

Wholesale Market

West Side

East Side

FAZHAN BLVD.

Diagram of the Huanan market.

Huanan Seafood Wholesale Market

West Side

Human cases of Covid-19

Coronavirus found in stall

Stall selling live mammals

Stall selling unknown meat

East Side

XINHUA ROAD

Photograph of raccoon dogs caged over birds in 2014.

Distribution of coronavirus samples in the Huanan market.

Huanan Seafood Wholesale Market

West Side

East Side

Distribution of positive coronavirus samples

in the market

Source: Michael Worobey et al. The New York Times; Satellite image via Google Maps

Another co-author, Chris Newman, a wildlife biologist at the University of Oxford, was part of a research team that documented a number of live, wild mammals for sale at the Huanan market in November and December of 2019, including raccoon dogs.

Dr. Worobey and his colleagues also carried out a new analysis of over 800 coronaviruses sampled from early Covid cases. They found that both Lineage A and Lineage B underwent separate bursts of explosive growth.

The most likely explanation for their results, they concluded, is that Lineage A and Lineage B each jumped on their own from an animal into different people, likely in November.

Both jumps, they said, could have happened at the Huanan market. In their analysis, Dr. Worobey and his colleagues found that the two earliest cases of Lineage A involved people who lived close to the market.

The Chinese C.D.C. study published on Friday revealed a Lineage A coronavirus on a glove collected when the market shut down.

“I think we’ve cracked this case,” said Joel Wertheim, a virologist at the University of California, San Diego, and a co-author of the new studies.

Dr. Bloom, however, questioned the idea that there had been two separate spillovers. He noted that the Lineage A glove sample from the market was collected some time after the virus had begun spreading in humans, raising the possibility that it had been brought into the market.

“I am especially unconvinced by the conclusion that there must have necessarily been two different spillovers in the Huanan Seafood Market,” Dr. Bloom said.

Workers in protective suits disinfect the Huanan market on March 4, 2020. Reuters

New evidence could still emerge. The Chinese government, for example, could release samples taken from Wuhan patients who came down with pneumonia in November 2019, noted Dr. Relman of Stanford.

Researchers could also learn more by looking at the genetic samples collected by the Chinese researchers. It’s possible that the samples included genetic material not just from viruses, but from animals at the market. Sharing the raw data could enable other scientists to investigate the potential spillover in more detail.

Kristian Andersen, a virologist at the Scripps Research Institute in La Jolla, Calif., and a co-author of the new studies, said it was important to figure out where the wild mammals for sale at Huanan came from, and to look for evidence of past outbreaks in those places. It’s possible, for example, that villagers at the sources of that wildlife still carry antibodies from exposures to coronaviruses.

“If I had to say what would be most helpful to do now, it would be those types of studies,” he said.