COVID-19 Data Dispatch

Category: Variants

  • The CDC is finally publishing wastewater data—but only ten states are well-represented

    The CDC is finally publishing wastewater data—but only ten states are well-represented

    This week, the CDC added wastewater tracking to its COVID-19 data dashboard. Wastewater has been an important COVID-tracking tool throughout the pandemic, but it gained more public interest in recent months as Omicron’s rapid spread showed the utility of this early warning system. While the CDC’s new wastewater tracker offers a decent picture of national COVID-19 trends, it’s basically useless for local data in the majority of states.

    Wastewater, as you might guess from the name, is water that returns to the public utility system after it’s been used for some everyday purpose: flushing a toilet, bathing, washing dishes, and so forth. In wastewater surveillance, scientists identify a collection point in the sewer system—either beneath a specific building or at a water treatment plant that handles sewage from a number of buildings. The scientists regularly collect wastewater samples from that designated point and test these samples for COVID-19 levels.

    When someone is infected with the coronavirus, they are likely to shed its genetic material in their waste. This genetic signal shows up in wastewater regardless of people’s symptoms, so a wastewater sample may return a positive result for the coronavirus earlier than other screening tools like rapid antigen tests. And, because wastewater samples are typically collected from public sewer networks, this type of surveillance provides information for an entire community—there’s no bias based on who’s able to get a PCR or rapid test.

    Scientists and organizations who utilize wastewater testing consider it an early warning system: trends in wastewater often precede trends in reported COVID-19 cases. For example, the coronavirus RNA levels identified in Boston’s wastewater shot up rapidly before Boston’s actual Omicron case numbers did, then also went down before case numbers did. Similarly, Missouri’s wastewater surveillance system—which includes genetic sequencing for variants—identified Delta cases last summer weeks before PCR testing did.

    Wastewater surveillance is also a popular strategy for colleges and universities, which can set up collecting sites directly underneath student dormitories. Barnard College, where I went to undergrad, is one school that’s employed this strategy. At one point in the fall 2021 semester, the college instructed students living in the Plimpton residence hall (where I lived as a sophomore!) to get individual PCR COVID-19 tests because the wastewater surveillance program had found signals of the virus under their dorm.

    Screenshot of the CDC’s new wastewater dashboard, retrieved on February 6.

    The CDC has been coordinating wastewater surveillance efforts since September 2020, Dr. Amy Kirby, team lead for the National Wastewater Surveillance System, said during a CDC media briefing on Friday. “What started as a grassroots effort by academic researchers and wastewater utilities has quickly become a nationwide surveillance system with more than 34,000 samples collected representing approximately 53 million Americans,” Kirby said.

    It’s a little unclear why it took the CDC so long to set up a dashboard with this wastewater data when surveillance efforts have been underway for a year and a half. Still, many researchers and reporters are glad to see the agency finally publishing this useful information. The dashboard represents wastewater collection sites as colored dots: blue dots indicate that coronavirus RNA levels have dropped at this site in the last two weeks; yellow, orange, and red dots indicate RNA levels have risen; and gray dots indicate no recent data. You can download data from a dropdown beneath the dashboard and on the CDC’s data portal site.

    “More than 400 testing sites around the country have already begun their wastewater surveillance efforts,” Kirby said at the media briefing. But she failed to mention that, out of these sites—the actual total is 471, according to the CDC dashboard—more than 200 are located in just three states: Missouri, Ohio, and Wisconsin. Missouri, with 80 sites, has a long-established system to monitor wastewater, through a collaboration between state agencies and the University of Missouri. Ohio has 71 sites of its own, while Wisconsin has 61.

    After these Midwest wastewater powerhouses, other states with a relatively high number of collection sites include North Carolina with 38, Texas with 35, New York with 32, Utah with 31, Virginia with 29, Colorado with 21, and California with 17. No other state has more than 10 wastewater collection sites, and 18 states do not have any wastewater collection sites at all.

    So, the CDC dashboard is pretty useful if you live in one of these ten states with a high number of collection sites. Otherwise, you just have to… wait for more sites in your area to get added to the dashboard, I guess? (Kirby did say during the media briefing that several hundred more collection sites are in development.) Even within the states that are doing a lot of wastewater surveillance, though, reporting is uneven at more local levels; for instance, many New York sites are concentrated in New York City and surrounding suburbs.

    In this way, biased wastewater surveillance coverage in the U.S. echoes biased genetic sequencing coverage, an issue I’ve written about many times before. (See the genetic surveillance section of this post, for example.) Some states, like California, New York, and others with high-tech laboratories set up for sequencing, have identified variants for a much higher share of their COVID-19 cases than states with fewer resources.

    The CDC gives wastewater treatment plants, local health departments, and research laboratories the ability to join its national surveillance network. But again, this is much easier for institutions in some places than others. Consider the resources available for wastewater sampling in New York City compared to in rural parts of the Midwest and South.

    In addition, for places that do have robust wastewater surveillance systems, there are some caveats to the data, the CDC expert told reporters. Data may be hard to interpret “in communities with minimal or no sewer infrastructure and in communities with transient populations, such as areas with high tourism,” she said. “Additionally, wastewater surveillance cannot be used to determine whether a community is free from infections.”

    If you’re looking for more wastewater data beyond the CDC tracker, here are two sources to check out:

    • Biobot’s Nationwide Wastewater Monitoring Network, which I included in last week’s Featured Sources: This wastewater epidemiology company collects samples from water treatment facilities across the country; their dashboard includes both estimates of coronavirus levels in the U.S. overall and estimates for specific counties in which data are collected. Biobot’s data are available for download on Github. (Interestingly, it seems that some of the counties included in Biobot’s dashboard are not currently included in the CDC’s dashboard; I’ll be curious to see if that changes in the coming weeks.)
    • COVIDPoops19 dashboard: This dashboard, run by researchers at the University of California Merced, provides a global summary of wastewater surveillance efforts. It includes over 3,300 wastewater collection sites tied to universities, public health agencies, and other institutions; click on individual sites to see links to dashboards, align with related news articles and scientific papers.

    More federal data

  • Other Omicron updates: Healthcare system, treatments, and more

    Other Omicron updates: Healthcare system, treatments, and more

    A new CDC analysis found that Omicron led to record hospitalizations, but lower levels of ICU admissions and other indicators of the most severe disease compared to past surges. Chart via CDC MMWR.

    While BA.2 has dominated the news cycle this week, we’re still learning more about—and seeing policy shifts due to—the original Omicron strain, BA.1. Here are a few major updates:

    • Omicron is causing 100% of new COVID-19 cases in the U.S. According to the CDC’s latest update of its variant prevalence estimates, Omicron caused more than 99% of new COVID-19 cases in the country for the second week in a row: there was a slight increase from 99.4% of new cases in the week ending January 15 to 99.9% in the week ending January 22. The remaining 0.1% of cases are caused by Delta. The CDC is not yet distinguishing between BA.1 and BA.2 in its estimates, but will likely start doing so in the coming weeks.
    • ICU admissions and other indicators of severe COVID-19 symptoms were lower during the Omicron surge than during previous surges in the U.S. The CDC released another round of studies presenting Omicron’s impact on the healthcare system last week, including this report focusing on disease severity. CDC researchers analyzed data from three hospital surveillance systems and an additional large database; while the peak of new COVID-19 cases was five times higher during the Omicron surge than the Delta surge, they found, the peak of hospital admissions was only 1.8 times higher. And ICU admissions, the average stay length for hospitalized COVID-19 patients, and death rates were all lower during the Omicron surge than in the Delta and winter 2020-2021 surges.
    • Pfizer and BioNTech have started a clinical trial of an Omicron-specific vaccine. Quickly after Omicron was identified, both Pfizer and Moderna started updating their vaccines for this variant and investigating whether such Omicron-specific shots would be necessary. Pfizer is now entering a new clinical trial with its Omicron-specific shot, along with its vaccine development partner BioNTech, according to Reuters. Trial participants will include about 1,400 people who received third doses from Pfizer’s current COVID-19 vaccine regimen three to six months earlier. Pfizer intends to study the Omicron-specific shot’s safety and effectiveness against this variant.

    • The FDA recommends that U.S. facilities stop using monoclonal antibody treatments that don’t work well against Omicron. Speaking of Omicron-specific drugs: the Food and Drug Administration (FDA) announced this week that the agency is limiting use of two monoclonal antibody treatments, made by Regeneron and Eli Lilly. Both treatments, which boost patients’ immune systems by providing them with lab-made antibodies, worked well at reducing severe symptoms for past variants but have less of an impact on Omicron infections. As a result, healthcare providers should “ limit their use to only when the patient is likely to have been infected with or exposed to a variant that is susceptible to these treatments,” the FDA says. A third monoclonal antibody treatment, along with other drugs (including Pfizer’s hard-to-find pill), do work well against Omicron.
    • Omicron has a short incubation period, so test timing is key. As I’ve written in the past, Omicron infections tend to move more quickly than infections with past variants: people can go from an exposure to symptoms within three days, rather than four or five. As a result, there’s less time to catch an infection before becoming contagious; but at the same time, rapid tests may give negative results in those early days of an infection, before patients have built up enough of a viral load for an antigen test to identify the infection. A recent New York Times article summarizes the science on how Omicron infections compare to past variants and provides recommendations on testing. For instance: “many experts now recommend taking a rapid test two to four days after a potential exposure,” and ideally testing twice about a day apart.
    • Some experts are optimistic that we could see a COVID-19 lull after Omicron surges. Last week, I shared a STAT News article explaining that, thanks to high levels of population immunity, the U.S. might have “a bit of a break from the Covid roller coaster” after our Omicron surge ends in the coming weeks. Despite BA.2 concerns, Dr. Hans Henri Kluge, WHO’s regional director for Europe, shared a similarly optimistic view in a statement last week. “The pandemic is far from over, but I am hopeful we can end the emergency phase in 2022 and address other health threats that urgently require our attention,” he said.

    More variant reporting

  • BA.2 FAQ: What you should know about this Omicron offshoot

    BA.2 FAQ: What you should know about this Omicron offshoot

    BA.2 has become the dominant strain in Denmark, one of the countries that sounded the alarm about this Omicron offshoot. Chart via the Pandemic Prevention Institute, posted on Twitter on January 26.

    An offshoot strain of the Omicron variant has been making headlines this week as it spreads rapidly in some European and Asian countries. While the strain, called BA.2 by virologists, has not yet been identified in the U.S. in large numbers, it’s already spreading here, too: scientists have picked it up in wastewater samples in some parts of the country.

    This strain clearly has a growth advantage over the original Omicron strain (also called BA.1), but it’s not cause for major concern at this point. Scientists are working to identify whether BA.2 has a higher capacity for breaking through immunity from past infection or vaccination; so far, early data suggest that it does not significantly differ from BA.1 on this front, though it may have a slight advantage.

    Here’s a brief FAQ on what we know about the strain so far.

    When and where did BA.2 emerge?

    I’ve been careful not to call BA.2 a “new strain” or a “new variant” here because it’s not actually new—at least, it’s not any newer than Omicron BA.1. When South African scientists first sounded the alarm about Omicron in late November 2021, BA.2 was already present among the country’s cases of this variant.

    In fact, a paper from South African scientists describing the Omicron wave in their country, published in Nature in early January, specifies that the earliest specimen of BA.2 was sampled on November 17; the earliest specimen of BA.1 was sampled on November 8. Around the same time, South African scientists also identified a third lineage, called BA.3—this one hasn’t yet become a cause for concern.

    Why are scientists concerned about BA.2?

    In the past couple of weeks, epidemiologists have identified that BA.2 is spreading faster in some countries than BA.1, the original Omicron strain. This means BA.2 has what scientists call a “transmission advantage” over BA.1: it is capable of getting from person to person fast enough that it may be able to outcompete BA.1.

    For example, in Denmark, BA.2 became the dominant strain in mid-January, taking over from BA.1. The takeover has coincided with an additional increase in COVID-19 cases in the country after Denmark’s Omicron wave initially appeared to peak a couple of weeks ago—but it’s hard to determine whether this second increase is solely due to BA.2 or also connected to an announcement that Denmark will end its COVID-19 restrictions on February 1.

    This past week, the World Health Organization (WHO) announced that investigations into BA.2, including its potential virulence and ability to escape prior immunity, “should be prioritized independently (and comparatively) to BA.1.” The WHO has yet to designate BA.2 as a separate variant of concern from BA.1, however; at the moment, both strains are still included under the Omicron label.

    https://twitter.com/PeacockFlu/status/1483770131419443201

    How does BA.2 compare to BA.1, the original Omicron strain?

    As I’ve explained in previous posts about the variant, Omicron has the most antigenic drift of any coronavirus variant identified thus far—meaning that it’s the most genetically different from the initial Wuhan version of the virus. Omicron BA.1 has about 60 mutations compared to the Wuhan strain, but BA.2 has even more: about 85 mutations, according to a recent Your Epidemiologist post.

    BA.2 is clearly more transmissible than BA.1, as we’ve seen from its rapid spread in countries including Denmark, the U.K., France, the Netherlands, India, and the Philippines. Scientists estimate that “BA.2 may be 30% to 35% more transmissible than BA.1,” STAT News reports.

    The question scientists hope to answer, then, is why BA.2 has this transmission advantage over BA.1. Do BA.2’s additional mutations lend it some adaptation in how it interacts with human cells, enabling faster spread? Or is BA.2 more capable of evading protection from past infection or vaccination compared to BA.1, leading it to cause more reinfections and breakthrough cases?

    While we don’t know the answers to these questions yet, early data are indicating that there’s no major difference in disease severity between BA.1 and BA.2. In other words, BA.2 isn’t more likely to cause severe symptoms.

    “There is no evidence that the BA.2 variant causes more disease, but it must be more contagious,” Danish Health Minister Magnus Heunicke said at a news conference last week, Reuters reported.

    Why do some articles call BA.2 a “stealth variant?”

    You might have seen some headlines referring to BA.2 as a “stealth variant” or a “stealth version of Omicron.” This is because of one major difference between BA.2 and BA.1: while BA.1 can be identified with a PCR test due to a key mutation that’s visible on PCR test results, BA.2 does not have this mutation.

    As a result, BA.2 can be more time-consuming for COVID-19 testing labs to identify: labs need to sequence a sample’s genome to identify this strain rather than simply look out for an indicator on a PCR test. It’s unclear how much of a difference this will make in the U.S.’s ability to track BA.2, however, as many labs across the country are already performing routine full-genome sequencing of coronavirus samples.

    How well do vaccines work against BA.2?

    So far, it seems like there is no significant difference in vaccine protection between BA.1 and BA.2, at least when it comes to severe symptoms—which makes sense, scientists say, given how well vaccines have worked against every major variant to emerge thus far.

    Early findings in this area come from the U.K., which designated BA.2 as a “Variant Under Investigation” (separate from BA.1) about a week and a half ago. This past Friday, the U.K.’s Health Security Agency released a report with information on BA.2, including how it compares to BA.1 or original Omicron.

    Overall, U.K. epidemiologist Meaghan Kall wrote in a Twitter thread summarizing the report, early evidence suggests that “BA.2 is no more immune evasive than Omicron,” though confidence in this statement is low. The report found that, for Brits who had received booster shots, vaccine effectiveness against symptomatic COVID-19 disease was 70% for BA.2 and 63% for BA.1. The confidence intervals on these effectiveness estimates overlapped, indicating that vaccines perform similarly against BA.2 and BA.1.

    When it comes to disease severity, Kall wrote, the U.K. doesn’t have enough data to compare BA.2 and BA.1; early data on this topic (suggesting BA.2 is not more severe) have come from Denmark and India.

    How will BA.2 impact the U.S.’s COVID-19 trajectory?

    BA.2 has already outcompeted BA.1 in some parts of Europe and Asia, and epidemiologists expect that countries like the U.K. and the U.S. could also follow this pattern—though it will likely be a longer, slower replacement process compared to the intense way Omicron pushed out Delta. A bigger unknown here is what effect this strain may have on case numbers, hospitalizations, and deaths.

    Countries and regions now passing the peaks of their Omicron BA.1 waves have extremely high levels of population immunity. As a result, people who are fully vaccinated with boosters and/or recently infected with Omicron BA.1 likely will have a lot of immune system protection against BA.2, though we don’t yet have good data on exactly how robust this protection is.

    So, could BA.2 cause the current downturn in U.S. COVID-19 cases to reverse? It’s possible, explains Andrew Joseph in a recent STAT News article. However, thanks to our high immunity levels, a further spike in cases could be “broadly limited to infections” rather than causing major increases in hospitalizations and deaths. In the coming weeks, we’ll get a better sense of how well prior Omicron infections protect against BA.2 and other key information that will inform our understanding of how this strain may change the country’s COVID-19 trajectory.

    Right now, COVID-19 experts are closely monitoring BA.2, but they’re not hugely concerned. As Dr. Jetelina put it in a recent Your Local Epidemiologist post, the bigger worry right now is that another variant could “pop out of nowhere” like Omicron did in November.

    More variant reporting

  • Omicron updates: Where will these massive case numbers leave us?

    Omicron updates: Where will these massive case numbers leave us?

    Omicron went from 1% of U.S. cases to nearly 100% of cases in about six weeks. Chart via the CDC, retrieved January 23.

    Major news items for this week include the potential peak of the U.S.’s Omicron surge and real-world data from the CDC on how well booster shots work against this variant.

    • Omicron is now causing nearly 100% of new COVID-19 cases in the U.S. The latest CDC estimates of variant prevalence put Omicron at 99.5% of new cases in the U.S. as of January 15, with Delta causing the remaining 0.5% of cases. I have to say, it’s incredibly striking not only how quickly Omicron outcompeted Delta (it went from 1% of new cases to nearly 100% in just six weeks), but also how both of these highly contagious variants have dominated the country so thoroughly that they’re now the only two variants present here at all. For comparison, Alpha only got to 70% of cases at its peak. These trends show how drastically both Delta and Omicron changed the trajectory of the pandemic.
    • While the U.S. may be peaking, massive numbers of people are getting infected. As I noted in today’s National Numbers, America’s Omicron wave may have peaked this week, with the country’s massive case growth appearing to turn around. Computational biologist Trevor Bedford wrote a recent Twitter thread about this peak, pointing out that a huge share of the U.S. population was infected with Omicron in the past month: “between 18% and 23% of the country was infected by Omicron by Jan 17, with the large majority infected in a span of just ~4 weeks,” he hypothesized. By mid-February, Bedford says, this number could be “36%-46%.”

    • The high infection numbers may give us “a bit of a break from the Covid roller coaster.” With so many people infected in such a short time, Omicron will have a huge impact on the “immunological landscape” of the U.S, Helen Branswell explains in a recent article for STAT News. Millions will have immunity from a recent infection, vaccination, or both; and Omicron’s unique biology may mean that people who caught this variant will be protected from other strains. As a result, the end of this wave may lead into “a bit of a break” from COVID-19, Branswell writes, with low case numbers for a few weeks or months. It’s hard to say whether this “break” will constitute the end of the pandemic, though—we don’t know how long post-Omicron immunity lasts.
    • Rapid at-home tests work well at detecting Omicron, though they’re far from perfect. As I’ve noted in past issues, there have been some questions recently about how well rapid antigen tests work at identifying Omicron infections. In a recent Your Local Epidemiologist post, Dr. Katelyn Jetelina walked through the data from several recent studies on this topic. The highlights: rapid tests likely won’t work well in the very beginning of an infection, so wait to test until five days after an exposure; if you test positive, trust the result; test repeatedly for higher accuracy; and, if you have the tests, wait for two negative results before coming out of isolation.
    • New CDC wastewater report shows how early Omicron was spreading in the U.S. The CDC published a report this week sharing findings from wastewater surveillance systems in a few states and localities. (Wastewater surveillance means the states are regularly testing samples from sewage to identify coronavirus levels coming from residents’, well, waste.) In New York City, Omicron was first detected in wastewater on November 21, the weekend before Thanksgiving. In California, Colorado, and Houston, Texas, the variant was detected in late November or early December.
    • An additional booster shot may not be enough to completely prevent Omicron infection, a small Israeli study suggests. Israel was one of the first countries to offer third vaccine doses to its residents, and now it’s also one of the first countries offering fourth doses. A new study presents the impact of these shots among about 270 healthcare workers. The additional doses produced more antibodies in the patients, but “this is probably not enough for the Omicron,” one of the study’s authors told Reuters—at least when it comes to completely preventing infection.
    • But: booster shots still reduce chances of infection significantly, compared to people who are unvaccinated. Another new CDC report published this week compares COVID-19 cases among vaccinated, boosted, and unvaccinated people in 25 U.S. jurisdictions. In late December, after Omicron started spreading widely, adults who were unvaccinated had a five times higher risk of COVID-19 infection compared to those who were fully vaccinated with a booster shot, the CDC found.
    • Booster shots also have a huge impact on risks of severe symptoms and hospitalization. One more CDC report released this week: scientists analyzed the impact of booster shots on emergency department visits and other hospitalization metrics in ten states. When both Delta and Omicron were the dominant variants in the U.S., the CDC researchers found, third doses had 94% efficacy rates in protecting people against COVID-related emergency department visits, and 82% efficacy rates in protecting against urgent care visits. Efficacy against hospitalization was also over 90%. In short: if you’re eligible for your booster, go get it!
    • Booster shots of Pfizer and Moderna vaccines could be critical for countries that used other brands. Last week, I shared a report that found 22 million mRNA vaccine doses are needed as booster shots in low-income countries, to protect the world against Omicron. This past week, a new study in Nature supported this report: a group of scientists in Hong Kong found that Pfizer doses are safe and highly effective booster shots for people who initially received the Chinese CoronaVac vaccine. The authors suggest that mRNA vaccines should be used as boosters in countries that originally distributed CoronaVac.
    • New research identifies a mutation that may contribute to Omicron’s super-contagiousness. A new study from the National Institutes of Health (NIH) found that a mutation present in the Alpha and Delta variants allows the coronavirus to more easily bind to human cells. When the coronavirus binds more easily, it can spread faster within the body; this rapid multiplication helps the virus quickly spread outside the body as well, increasing contagiousness. Though this study was done before the Omicron variant emerged, Omicron has this same mutation, explained lead author Dr. Lawrence Tabak in a post for the NIH Director’s Blog.

    More variant reporting

  • Omicron updates: Possible peaks, viral loads, vaccines

    Omicron updates: Possible peaks, viral loads, vaccines

    Has Omicron peaked in NYC? It sure seems like it, according to city data; screenshot retrieved from NYC Health dashboard on January 16.

    These update posts are getting shorter as time goes on, but we’re still learning about this variant! A few news items from this week:

    • Omicron is now causing almost 100% of new COVID-19 cases in the U.S. In the CDC’s latest variant proportions update, the agency estimated that 98% of new COVID-19 cases were caused by Omicron in the week ending January 8. The CDC also revised estimates for previous weeks, though the revisions were not as significant as they have been in the past—suggesting that the numbers are now fairly close to accurate, but will continue to be tweaked as more sequencing data come in.
    • Major Northeast hotspots appear to be peaking. Last week, I wrote that New York City’s Omicron wave seemed to have reached its peak. The trend has continued into this week: the new case rate and test positivity rate have both fallen consistently since peaking on January 3. Similarly, in Boston, the Omicron levels detected in the city’s wastewater have declined steeply since early January. The daily case rate is also going down in Washington, D.C., and in the Northeast region overall. Still, hospitals are still overwhelmed throughout the region, and it’s unlikely that cases will go down as quickly or as decisively as they went up.

    • New NYC report provides data on the city’s Omicron wave. Speaking of NYC: the city’s public health department recently put out a new report detailing the variant’s impact. The variant “has accounted for nearly all coronavirus samples sequenced in NYC” since Christmas, the report’s authors write. Also, while a smaller share of Omicron cases led to hospitalization compared to the Delta wave, more people have been hospitalized overall because of sheer case numbers. Unvaccinated New Yorkers, Black New Yorkers, and those over age 75 have been most likely to require hospitalization.
    • Real-world study suggests rapid at-home tests work well at detecting Omicron. A new study from the University of California, San Francisco, released this week as a preprint, analyzed rapid antigen tests’ capacity to detect Omicron by comparing rapid test results to PCR test results. The results: antigen tests correctly identified 95% of cases with high viral loads and 98% of symptomatic cases. In about one-third of the cases identified through PCR, patients tested negative on antigen tests; but this is in line with the tests’ accuracy for other variants.
    • Data from the NBA suggest Omicron’s viral load is pretty variable. Another new study posted as a preprint this week analyzed data from the National Basketball Association (NBA). The league’s regular testing policy allowed Harvard researchers to study viral loads in Omicron-positive patients, revealing that this variant had “lower peak viral load and more variable early viral growth durations than Delta,” according to one of the authors. In other words, some of the basketball players were highly contagious early into their Omicron infections, while others were less so; and the players had less virus in their bodies overall at the peak of their infections than in previous Delta infections. Also, a large number of the players were still contagious five days after they were diagnosed—which doesn’t bode well for the CDC’s new isolation guidance.
    • More confirmation that vaccinated people are protected from severe disease from Omicron. Another new study, this one published in Nature through the journal’s advance preview system for COVID-19 reports, confirms previous research about T cell response to Omicron. T cells are a key part of the immune system’s long-term memory apparatus; they help protect against severe symptoms and death. The study found that, in patients who were fully vaccinated (or, to a lesser degree, had a previous infection), T cells could recognize Omicron and protect people against its worst impacts.
    • Omicron adds urgency to the need to vaccinate the world—ideally, with mRNA vaccines. A report from advocacy groups PrEP4All and Partners In Health, written with scientists at Harvard, Columbia, and other institutions, found that 22 billion additional mRNA vaccine doses are needed to control the pandemic, now that Omicron has become the dominant variant in the world. The report specifies that mRNA vaccines are needed because other vaccine types are not capable of preventing Omicron infection, and likely are less effective against severe disease. “Future viral variants may become even more transmissible, immune evasive, and virulent than Delta or Omicron,” the report cautions.

    More variant reporting

  • Six more things, January 9

    Six more things, January 9

    If you test positive for COVID-19, here’s what the CDC says you should do. Graphic via the Maine health agency.

    Here are six other COVID-19 news items from the past week that didn’t quite warrant full posts:

    • The CDC made its COVID-19 isolation guidance even more confusing, somehow. On Tuesday, the CDC updated its isolation guidance again—and the new guidance is, kind-of a “dumpster fire,” as the headline on this article by The Atlantic’s Katherine J. Wu aptly puts it. The agency still isn’t requiring rapid tests to get out of isolation early, but it says you can test if you have one available. Also, wear a mask if you leave isolation after five days and avoid travel, restaurants, and other high-exposure activities. Wu’s article provides a good summary of the guidance (and criticism of that guidance), as does this Your Local Epidemiologist post from Dr. Katelyn Jetelina.
    • New reporting recipe explains how to explore “uncounted” COVID-19 deaths with CDC data. Last week, I shared a new investigative story from my team at the Documenting COVID-19 project that dives into unreported COVID-19 deaths in the U.S. Up to 200,000 deaths may have gone unrecorded thanks to a lack of training, standardization, tests, and other issues with death reporting. This week, the team published a reporting recipe aimed to help other journalists do similar stories in their states, cities, and regions. If you have questions about the project or recipe, you can reach out to us at info@documentingcovid19.io.
    • B.1.640.2, or the “IHU variant” from France, is not currently cause for concern. In the past few days, you might have seen headlines about a new variant called B.1.640.2 that was identified in France last November. The variant has a number of mutations, including some mutations that have also been identified in other highly-contagious variants, according to a recent preprint from French researchers. But it’s not currently a concern, say experts at the World Health Organization and elsewhere. This variant actually predates Omicron, and only 20 cases had been reported between early November and early January (compared to well over 100,000 Omicron cases in the same timespan). Omicron is the main variant we should be worrying about right now.
    https://twitter.com/sailorrooscout/status/1478130286072410118
    • “Flurona” means getting the flu and COVID-19 at the same time; it’s not a new mutant disease. Another buzzword you might’ve seen in headlines this week: “flurona,” a portmanteau of coronavirus and flu. Los Angeles and other places have recently reported cases in which a patient tests positive for both the flu and COVID-19 at the same time. While having two respiratory diseases at once is certainly unpleasant—and might lead to increased risk of severe symptoms—it’s not necessarily worth freaking out over. Roxanne Khamsi covered these potential coinfections in The Atlantic back in November 2021, writing: “Recent screening studies have found that 14 to 70 percent of those hospitalized with flu-like illness test positive for more than one viral pathogen.”
    • Senators call for HHS to answer key questions about COVID-19 testing. This week, Senators Roy Blunt (Missouri) and Richard Burr (North Carolina) wrote to Health and Human Services (HHS) Secretary Xavier Becerra requesting information on COVID-19 test spending. The Senators note that over $82.6 billion has been “specifically appropriated for testing,” yet the U.S. continues to experience dire shortages and delays for both PCR and rapid tests. The letter includes questions about Biden’s initiative to distribute 500 million rapid tests for free; little information has been shared about the initiative so far.
    • New meta-analysis estimates one in three COVID-19 patients have persistent symptoms for 12 weeks or more. In a meta-analysis, scientists compile results from a number of studies on the same topic in order to provide overall estimates for an important metric, like the risk of developing a particular condition. A new analysis from researchers at a Toronto hospital network and other co-authors examined the risk of Long COVID symptoms following a COVID-19 diagnosis, combining results from 81 studies. Their main findings: about 32% of patients had fatigue 12 weeks after their diagnosis, while 22% had cognitive impairment at 12 weeks; and the majority of those patients still had these symptoms at six months. (H/t Hannah Davis.)

    Note: this title and format are inspired by Rob Meyer’s Weekly Planet newsletter.

  • Omicron updates: the surge is here, but peaks might be in sight

    Omicron updates: the surge is here, but peaks might be in sight

    Antigenic drift posed by Omicron. Figure from Sanders et al., posted to Medrxiv on January 3.

    As the Omicron surge continues, we are still learning more about this variant. Here are the major updates from this week:

    • Omicron is now causing more than 90% of new cases in the U.S. In the latest update of the CDC’s variant proportions estimates, the agency found that Omicron caused 95% of new COVID-19 cases nationwide in the week ending January 1. The CDC also revised estimates for previous weeks, bringing us to 77% Omicron for the week ending December 25 and 38% Omicron for the week ending December 18. While these estimates continue to be based on weeks-old data, it the CDC now has enough sequencing information to make Omicron estimates with lower confidence intervals than it did a few weeks ago—suggesting that these numbers are closer to reality than the estimates we saw in December.
    https://twitter.com/jaspar/status/1478773556435730432

    • Omicron is causing the vast majority of cases in every state. Also included in the CDC’s variant proportions estimates: regional numbers. The latest figures estimate that, as of January 1, Omicron prevalence across the country ranges from 82% in the Northeast to 98% in New York/New Jersey and the Gulf states region (Texas, Louisiana, Arkansas, Oklahoma, and New Mexico). These numbers align with recent calculations from computational biologist Trevor Bedford based on sequences posed to the public repository GISAID. In short: Omicron is everywhere.
    • Evidence that Omicron is less likely to cause severe symptoms continues to mount. A combination of real-world hospitalization and lab data continue to suggest that Omicron is less likely to cause severe COVID-19 symptoms than past coronavirus variants. The hospitalization data: in Omicron hotspots, hospitalization numbers are not rising at the same rate as case numbers, nor are the numbers of patients who require intensive care or ventilators. “Despite steep rises in cases and patients, the number on ventilators has barely risen,” wrote Financial Times data journalist John Burn-Murdoch in a recent thread about U.K. data.
    • And the lab data: a growing number of studies show that Omicron is less capable of infecting patients’ lungs compared to past variants—meaning the worst respiratory symptoms are rarer. At the same time, people who catch Omicron after gaining immunity from vaccination and/or prior infection are protected against severe symptoms thanks to T cells and other aspects of immune system memory. Note that, however, we still don’t know about the risk of Long COVID following an Omicron case.
    • Still: U.S. Hospitals are now incredibly overwhelmed with Omicron and Delta cases. In the U.S. so far, the “decoupling” phenomenon (in which hospitalizations and ICU admissions don’t rise as fast as cases) has been less visible than in other countries hit by Omicron. Several states have already set hospitalization and/or ICU records during the Omicron surge. This is likely because many parts of the U.S. have lower vaccination rates than other countries like the U.K. At the same time, accounts from hospital workers show the toll that this surge is taking: “Thankfully the Covid patients aren’t as sick. BUT there’s SO many of them,” wrote NYC ER doctor Dr. Craig Spencer in a recent Twitter thread.

    • Omicron has more antigenic drift than any other variant. “Antigenic drift” is a virology term referring to the small mutations in virus genetic material that cause these viruses to change slowly over time. As I noted in early Omicron updates, this variant didn’t evolve out of Delta (as many experts were expecting) but rather showed up seemingly out of nowhere; it might have emerged from a part of the world with limited variant surveillance, an immunocompromised person, or even an animal host. We don’t know Omicron’s origin yet, but we now know that it is further apart, genetically speaking, from the original coronavirus than any other variant so far.
    • London’s Omicron surge may have peaked. According to U.K. data, both case numbers and hospital admission numbers have slowed in their increases, the Washington Post reports. “For the moment, we can probably say London appears to be over the worst,” U.K. hospital executive Chris Hopson said last week. Other U.K. health officials are more skeptical though, according to the Post: while case numbers are falling for teenagers and younger adults, London is still reporting increasing cases among seniors.
    • New York City also might be on the verge of peaking. Another tentative peak report: data from NYC’s health department suggest that case numbers might be starting to fall in the city. The citywide seven-day average for new cases fell from 3,261 per 100,000 people on January 2 to 2,754 per 100,000 on January 4, and NYC’s positivity rate is also trending down. Reduced COVID-19 testing over New Years and other reporting uncertainties are likely playing a role here, but still—NYC cases jumped right back up after Christmas, but haven’t yet jumped up after New Years. I am cautiously optimistic!
    • New research maps out South Africa’s intense Omicron wave. This recent study caught my eye when it was published in Nature this week through accelerated approval. Nearly 100 scientists in South Africa, Botswana, the U.S., Switzerland, the U.K., and other countries collaborated to analyze Omicron’s genetic makeup and the variant’s rapid spread through South Africa, including its ability to cause breakthrough cases and reinfect people who’ve previously had COVID-19. The paper is just one example of the immense collaboration that has taken place over the past month as scientists work to quickly understand this variant. Thank you, scientists!

    More variant reporting

  • FAQ: Testing and isolation in the time of Omicron

    FAQ: Testing and isolation in the time of Omicron

    After exposure to the coronavirus, someone may test negative on rapid antigen tests for multiple days before their viral load becomes high enough for such a test to detect their infection. Chart by Michael Mina, adapted by the Financial Times.

    As Omicron spreads rapidly through the U.S., this variant is driving record case numbers—and record demand for testing, including both PCR and rapid at-home tests. In other words, it feels harder than ever to get tested for COVID-19, largely because more people currently need a test due to recent exposure to the virus than at any other time during the pandemic.

    Also this week, the CDC changed its guidance for people infected with the coronavirus: rather than isolating for 10 days after a positive test, Americans are now advised to isolate for only five days, if they are asymptomatic. Then, for the following five days, people should wear a mask in all public settings. This guidance change has prompted further discussion (and general confusion) about who needs to get tested for COVID-19, when, and how.

    Here’s a brief FAQ, to help navigate this complicated testing-and-isolation landscape. In addition to the CDC guidance, it’s inspired by a recent question from a reader about testing and isolation following a positive PCR result in her family.

    What’s the difference between being infected and being contagious?

    As we think about interpreting COVID-19 test results in the Omicron era, it’s key to distinguish between being infected with the coronavirus and being actively contagious.

    • Infected: The virus is present in your body.
    • Contagious: The virus is present in your body at high enough levels that you can potentially spread it to other people.

    In a typical coronavirus infection, it takes a couple of days after you encounter the virus—i.e. breathe the same air as someone who was contagious—for the coronavirus to build up enough presence in your body that tests can begin detecting it. PCR tests can typically detect the virus within one to three days after an infection begins, while rapid tests may take longer.

    How do you use testing to tell if you’re infected and/or contagious?

    Timing is extremely important with coronavirus tests, and has become even more so with Omicron. If you learn about a recent exposure to the virus, you don’t want to get tested immediately after that exposure, since the test would not pick up a potential infection yet. Say you had dinner with a friend on Wednesday, and they tell you on Thursday that they just tested positive; you should wait until Friday or Saturday to get tested with PCR, or until Saturday or Sunday to get tested with a rapid at-home test. (And ideally, you would avoid interacting with other people while you wait to get tested.)

    PCR tests can detect the virus within a couple of days of infection. Rapid tests, which are less precise, generally can’t detect the virus until it’s at high enough levels for someone to be contagious. This can take time—though Omicron may have shortened the window between infection and becoming contagious to just three days, according to some early studies. A new CDC study released this week provides additional evidence here.

    This chart, an adaptation of a figure by rapid test expert Michael Mina published in the Financial Times, shows how someone could potentially test negative on rapid tests for multiple days after a coronavirus exposure, even though they are infected:

    When this person tests positive on a rapid test, the result indicates that they’ve become contagious with the virus. Then, it’s possible that the person may continue testing positive on PCR tests after they stop testing positive with antigen tests, because they are no longer contagious but continue to carry enough virus genetic material that a PCR test can pick it up.

    How do you get ahold of rapid tests, in the first place?

    In order to use rapid tests to tell whether you’re contagious with the coronavirus, you need to get some rapid tests! Here are a couple of suggestions:

    • Order online from Walmart: If you look at this website right now, Walmart will probably say that Abbott BinaxNOW rapid tests are out of stock. But if you leave the page open and refresh often, you may be able to snag some rapid tests right after Walmart restocks (which happens roughly once a day, I think). I like ordering from Walmart because they’re cheaper than other BinaxNOW vendors and ship quickly, usually within a week.
    • Order online from iHealth Labs: iHealth Labs is one rapid test manufacturer that’s grown in popularity recently, as an alternative to BinaxNOW. You can order up to 10 packs (with two tests each) directly from the manufacturer, and report test results in an app. In my experience, though, iHealth Labs is slower to ship than other distributors; an order I placed on December 22 is due to arrive two weeks later, on January 5.
    • Use NowInStock to see availability: This website tracks rapid test availability at a number of websites, including CVS, Walgreens, Walmart, Amazon, and others. It’s helpful to see your options for a number of different tests, but bear in mind that tests sold by third-party vendors (like Amazon) may be less reliable than those sold directly by pharmacies.
    • Follow local news: A lot of city and state governments have recently started making rapid tests available to the public for free, from D.C. libraries to Connecticut towns. I recommend keeping an eye on local news and government websites in your area to look for similar initiatives—or, if your area isn’t making rapid tests available, call your local representative and ask that they do!

    Why did the CDC change its guidance for isolation?

    As I mentioned above, the CDC recently changed its guidance for people who test positive for the coronavirus. If someone has no symptoms five days after their positive test result, they can stop isolating from others—but they need to wear a mask in all public settings.

    According to the CDC, the new guidance is “motivated by science demonstrating that the majority of SARS-CoV-2 transmission occurs early in the course of illness, generally in the 1-2 days prior to onset of symptoms and the 2-3 days after.” In other words, the CDC is saying that people are generally contagious for a few days after their symptoms start. After that, they’re less likely to infect others, so isolation may be less necessary—and good mask-wearing may be sufficient to prevent further coronavirus spread.

    Many experts are attributing the guidance chance to economic needs: as Omicron causes flight cancellations, closed restaurants, and other business disruptions, a shorter isolation period can help people get back to work more quickly. The recent isolation change follows a similar guidance change the previous week, which said healthcare workers could shorten their isolation periods if their facilities were experiencing staffing shortages.

    What are experts saying about the new guidance?

    Much of the commentary is not positive. While the CDC said the new guidance is “motivated by science,” the agency has failed to cite specific studies backing it up—though some such studies exist, as Dr. Katelyn Jetelina discusses in this Your Local Epidemiologist post.

    Generally, it does seem that most people—particularly vaccinated people—are no longer contagious five days after their symptoms start. (Reminder: five days after symptoms start could be seven to nine days into the infection period, since it takes time for the virus to build up in your body and cause symptoms.) But this is by no means guaranteed for everyone, as each person infected with the coronavirus has a unique COVID-19 experience.

    As a result, many experts have said that the CDC should have required negative rapid tests for people to leave isolation after five days. A negative rapid test would indicate that someone is no longer contagious, the argument goes, and they can then go back into the world. In the U.K., two negative rapid test results are required to shorten isolation from ten to seven days.

    However, for everyone in the U.S. to be able to rapid test out of isolation, the country would need a far greater supply of those tests than we currently have available. This Twitter thread, by epidemiologist Matt Ferrari, explains the challenges posed by limited rapid testing:

    Ferrari argues that the CDC guidance makes sense, given the information and resources currently available in the U.S., as well as the fact that simpler rules are easier to follow. Still, I personally would say that, if you have the rapid tests available to test out of isolation, you should.

    More Omicron reporting

  • Omicron updates: ‘mild’ cases can still mean a nasty surge

    Omicron updates: ‘mild’ cases can still mean a nasty surge

    Image
    Data from South Africa and the U.K. suggest that Omicron patients are less likely to require intensive hospital care than those infected with previous variants. Chart posted on Twitter by Paul Mainwood.

    It’s now been over a month since Omicron arrived in the U.S., and the variant’s impact is clear: January is about to be nasty. Here are the major updates from this week:

    • Omicron continues to cause the majority of new cases in the U.S., but the CDC revised its estimates down this week. On Monday, the agency updated its variant proportions estimates; according to the new data, Omicron caused 59% of new cases in the U.S. in the week ending December 25. Notably, this was lower than the previous week’s estimate of 73%. As I explained in a Twitter thread, the CDC’s variant proportions data are estimates with very wide confidence intervals, based on sequencing data that are reported with a lag of multiple weeks. And the agency’s slow pace of updates means that its estimates are unlikely to match the actual variant situation in the U.S. anyway. Still, the CDC data do tell us that Omicron is causing the majority of U.S. cases right now, and that it became dominant over Delta in under one month.
    • Outdoor concerts in Puerto Rico were a superspreading event for Omicron. Puerto Rico has been a pandemic success story, with one of the highest vaccination rates in the nation. But the territory is currently reporting record COVID-19 cases thanks to Omicron, with an increase of over 5,000% in the space of two weeks. One reason for the increase: a series of concerts by the Puerto Rican rapper Bad Bunny, which have now been connected to at least 2,000 cases according to Puerto Rico’s Office of Epidemiology. The concerts took place in an outdoor stadium, and audience members had to be vaccinated and wear a mask to attend. The high number of cases connected to this event indicates Omicron’s high transmissibility, even in outdoor settings.
    • South Africa’s Omicron wave continues to decline, and London may be seeing a similar pattern. Omicron cases have now been decreasing in South Africa for more than two weeks, with a 30% decline from December 18 to 25. The country’s leaders recently lifted a curfew from midnight to 4 AM, though public gatherings are still restricted to 1,000 people indoors and 2,000 outdoors. A similar decline may be starting in London, another major Omicron hotspot—though holiday reporting delays and high testing demand make it hard to say for sure.

    • Continued evidence that Omicron cases are more likely to be mild. Data out of South Africa continue to show that patients infected with Omicron have a lower risk of severe symptoms than those infected in past waves. One study, published this week in JAMA, finds that the country’s fourth wave has impacted younger patients with “fewer comorbidities, fewer hospitalizations and respiratory diagnoses, and a decrease in severity and mortality.” As I’ve written before, this is likely thanks to South Africa’s high prevalence of immunity from past infections. But a growing number of lab studies are also showing that Omicron may have inherent biological qualities that make it more mild, including a reduced capacity to infect lung cells compared to past variants.
    • It is worth noting, however, that mild, in the clinical sense, means that your case does not require hospitalization. A patient could have a high fever, become bed-bound for days, and even face Long COVID symptoms while still fitting the “mild disease” classification, as Nsikan Akpan discusses in this Gothamist article about his own experience with Omicron. Reminder: we still have next-to-no data on how Omicron may impact the likelihood of Long COVID.
    • Studies continue to indicate that vaccines protect against severe disease from Omicron, though protection against infection is less robust. A new preprint posted this week finds that “most of your T cell responses from vaccination or previous infection still recognize Omicron,” explained study author Wendy Burgers in a Twitter thread. T cells are a type of immune system cell that participates in long-term response; their recognition of Omicron means that vaccinated people are still well-protected against severe disease. At the same time, a new study set to be published in Nature found that vaccinated people who’d received two doses had limited protection against infection, while people with three doses or multiple doses and a prior infection were better protected.
    • Antibodies made during an Omicron infection could provide protection against Delta. In Omicron hotspots, people who recently caught Delta have been readily infected by the new variant. But an Omicron infection may lead to anti-Delta antibodies in your immune system, according to a new preprint from South African scientists who tested blood samples from Omicron patients in the lab. “The researchers found, unsurprisingly, that the patients’ blood contained a high level of antibodies potent against Omicron,” explained Carl Zimmer in the New York Times. “But those antibodies proved effective against Delta, too.” If other studies back up this finding, it could mean that regions with Omicron waves will be protected from Delta resurgence.
    • Pediatric hospitalizations are rising as Omicron spreads, but the variant is not necessarily inherently worse for children. In New York City, one of America’s Omicron hotspots, pediatric hospitalizations increased four-fold from the beginning of December through last week, according to the New York State health department. State leaders are encouraging parents to get their kids vaccinated, as less than one-third of children in the five to 11 age group had received at least one dose as of December 24. As the New York Times points out, low vaccination rates for young kids, combined with the sheer number of cases caused by Omicron, are likely to blame for this increase—rather than some inherent quality of Omicron making it more severe for children.
    • The Omicron surge will be bad in the U.S., but it may boost nation-wide immunity for a few months afterwards. I highly recommend reading through this story by STAT’s Megan Molteni, which walks through several potential scenarios for the Omicron winter surge in the U.S. Some highlights: while South Africa’s short wave is promising, it might not translate to the U.S.; the country will be “in a viral blizzard nationwide” for the next few weeks; massive numbers of Americans will be infected (though their cases may be mild and go unreported); the whole world may be in a similar situation; and those huge case numbers could translate to a lot of immunity in the future. “The thing Omicron will do, because it’s going to infect 40% of the entire world in the next two months, is it will raise population-wide immunity for a while,” Chris Murray, director of IHME, told STAT.

    More variant reporting

  • Omicron updates: A major surge is underway in the U.S.

    Omicron updates: A major surge is underway in the U.S.

    Within a week, Omicron has jumped from causing an estimated 13% of new COVID-19 cases in the U.S. to 73% of new cases. Chart via the CDC.

    The majority of new COVID-19 cases in the U.S. are now caused by Omicron, and a massive surge is underway. But there’s good news: the variant continues to appear less likely to cause severe disease than past coronavirus strains, and South Africa’s wave may have already peaked.

    Here are the highlights of Omicron news this past week:

    • Omicron is now causing the majority of cases in the U.S. Last week, I wrote that the CDC’s estimates of new COVID-19 cases caused by different variants were providing a delayed, incorrect look at Omicron in the U.S. This past Monday, the ramifications of that delay were made clear: the CDC updated its estimates, showing that 73% of new cases in the week ending December 18 were caused by Omicron. (The agency’s previous estimate: 3% of new cases.) The agency also updated its estimates for prior weeks, to 13% in the week ending December 11 and 1% in the week ending December 4. It’s important to note that, as Trevor Bedford points out in this STAT News interview, these numbers are estimates generated by CDC algorithms. New sequencing data are always reported with a lag, and the true share of cases caused by Omicron is almost certainly even higher by now.
    • The Yankee Candle Index shows a major rise in COVID-19 cases. One of the most common COVID-19 symptoms is loss of smell. As a result, COVID-19 surges in the U.S. tend to correspond with increases in one-star reviews of Yankee Candles, in which reviewers complain that they can’t smell their candles—a phenomenon known as the Yankee Candle Index. And in the past few weeks, those one-star Yankee Candle reviews have shot up again, to higher levels than even last winter. This SFGATE article provides a nice summary of the situation.
    https://twitter.com/zornsllama/status/1473575508784955394
    • In South Africa, Omicron cases continue to go down. COVID-19 case numbers in South Africa dropped by about 20% between December 15 and December 22, prior to any holiday reporting interference. Several South African scientists have said that the country appears to be “over the curve,” with similar case patterns observed in the Omicron hotspot of Gauteng. This news is puzzling for some researchers—and might be tied to insufficient testing and/or high numbers of mild and asymptomatic cases—but it still bodes well for Omicron outbreaks in other countries. London may be seeing the beginning of a case drop right now, as well.
    • It’s tough to say whether Omicron is more mild because of inherent biology or prior immunity. As the scientists studying Omicron in the lab continue to share their findings—and South Africa continues to see low numbers of cases requiring hospitalization—evidence is growing that Omicron seems to be less likely to cause severe disease than past variants. But scientists remain skeptical, as this recent piece in Science magazine explains. Some aspects of Omicron’s biology, like its reduced capacity to infect lung cells, may make it inherently less virulent. At the same time, vaccines and prior infections confer protection against severe disease, particularly in the form of T cells.
    • Omicron might be making people sick—and contagious—faster than past variants. Scientists call the gap between exposure to a virus and the beginning of symptoms the “incubation period.” For the original coronavirus, this period was five or six days, Katherine J. Wu writes in The Atlantic. For Omicron, it may be as short as three days. While it’s challenging to study incubation periods, Wu writes, early data indicate that Omicron makes people sick in less time than prior variants—thus shortening the time that we have to identify and stop infections. Her piece also discusses the implications that this shorter incubation period has for testing.

    • Oral swabs may be more accurate than nasal swabs in identifying Omicron infections. In the past few days, I’ve seen some discussion on Twitter about swabbing one’s throat in addition to one’s nose when rapid testing for a potential Omicron infection. One recent preprint from South Africa suggests that Omicron might cause more viral shedding in saliva and less in the nose than past variants, meaning tests that rely on samples from the throat could be more likely to catch Omicron infections than tests that rely on nasal swabs. If you’d like to try the saliva swab method yourself, this video from Public Health England is helpful.
    • Omicron protection from booster shots may be short-lived. In the latest Omicron briefing from the U.K. Health Security Agency, one finding stuck out: while booster shots provide additional protection against Omicron infection, this protection begins to wane several weeks after vaccination. “Updated vaccine effectiveness analysis shows mRNA boosters beginning to wane from one month (week 5-9) for Omicron, and as low as 30-50% effective from 10 weeks post-booster,” wrote Meaghan Kall in her Twitter thread summarizing the briefing. If you haven’t gotten your booster shot yet, definitely do so—the shots also increase protection from severe disease, and that doesn’t wane. But this finding suggests that Omicron-specific boosters may be needed in the coming months.
    • Antiviral pills for COVID-19 will soon be available, and they work against Omicron. This week, the FDA authorized two antiviral COVID-19 pills for emergency use in the U.S.: one pill made by Merck (about 30% effective against hospitalization and death in clinical trials), and the other made by Pfizer (about 90% effective). Both pills are designed to prevent severe disease in vulnerable adults, such as the immunocompromised, and both work well against Omicron infections—since they target pieces of the coronavirus outside of the heavily-mutated spike protein. While the pills require a positive COVID-19 test for prescription (a challenging task, as testing demand continues to increase), their authorization is still a source of hope as the variant spreads.
    • IHME predicts “enormous spread of Omicron,” but with most cases mild or asymptomatic. The Institute of Health Metrics and Evaluation (IHME) at the University of Washington has predicted that the U.S. could see 140 million new coronavirus infections between January and March 2022, with a peak of 2.8 million infections a day. That could amount to 60% of the U.S. getting infected, the IHME director told USA Today. Note, however, that the institute predicts infections, not reported cases; the modeling suggests that the vast majority of these cases will be mild or asymptomatic. This prediction is in line with estimates of existing COVID-19 immunity in the U.S.: for example, Trevor Bedford said that 80% to 90% of Americans currently have some degree of protection from vaccination or prior infection in the STAT News interview linked above.
    https://twitter.com/JuliaRaifman/status/1472972206246440971

    More variant reporting