COVID-19 Data Dispatch

Tag: SARS-CoV-2 variants

  • Delta updates: Disease severity, kids, boosters

    Delta updates: Disease severity, kids, boosters

    The states with the highest numbers of children in the hospital are also the states with the lowest vaccination rates, per CDC analysis.

    It’s been a minute since I last did a Delta variant update, and this seemed like a good week to check in. Here are a couple of major news items that I’ve seen, along with sources where you can read more.

    The Delta variant continues to be highly transmissible. On August 1, I wrote that an interaction of a few seconds is enough for Delta to spread from one person to another, when both people are unvaccinated and unmasked.

    All the new evidence that we have on Delta outbreaks backs up its incredible ability to spread. For example, in a California elementary school, an unvaccinated teacher spread the coronavirus to 12 out of the 24 students in her class, with students sitting closer to the teacher more likely to be infected. The classroom outbreak led to 27 cases in total, including the teacher—who worked for two days after first reporting her symptoms. All the cases were identified as Delta.

    Growing evidence points to Delta being more severe. A recent study in The Lancet from epidemiologists in the U.K. suggests that Delta causes severe disease more frequently than the Alpha variant (B.1.1.7). The researchers looked at hospitalization rates for British COVID-19 patients, finding that patients with Delta were twice as likely to require hospital care compared to those with Alpha. Delta patients were also younger, on average—though this could be conflated by high vaccination rates among British seniors.

    Commenting on this study in Your Local Epidemiologist, Dr. Katelyn Jetelina writes:

    This adds to the growing evidence that Delta is more severe. An early Scotland study found that the risk of hospitalization was nearly double than previous variants. An early Public Health of England technical report found this too. We also saw this in Singapore where Delta infection was associated with higher risk of oxygen requirement, ICU admission, or death.

    For kids, higher hospitalization rates are tied to community vaccination, not Delta severity. This Friday, the CDC released two reports on COVID-19 hospitalization in children.

    One major finding: out of all children with COVID-19 cases, the proportion of kids who have a severe case has not increased from previous surges to this current Delta surge. Prior to June 2021, about 27% of hospitalized COVID-19 patients under age 18 required ICU admission; in late June and July (during the Delta surge), that number was 23%. Also, the average hospital stay was shorter during the Delta surge than previously (1-4 days compared to 2-5 days). These statistics indicate that Delta isn’t more severe for kids—rather, we’re seeing cases in such high numbers that it drives up hospitalizations.

    According to the CDC’s other Friday report, hospitalizations among children (under age 18) were four times higher in states with low vaccination levels compared to states with high vaccination levels. In other words: vaccination is crucial not just to protect yourself from severe COVID-19, but to lower community transmission and protect young children who can’t yet be vaccinated.

    Evidence for boosters continues to be questionable. After the Biden administration announced that the U.S. plans to provide third vaccine doses to everyone who received Pfizer or Moderna’s vaccines, I wrote that evidence and transparency on this decision were lacking. The situation hasn’t changed much; while studies show that COVID-19 antibody levels decline several months after vaccination, many experts are not convinced that boosters are necessary for everyone at this point.

    If immunity is “waning,” why don’t we need extra shots? As usual, Katherine Wu at The Atlantic has a great article explaining the complexities here. Here’s a key paragraph from her piece:

    Defensive cells study decoy pathogens even as they purge them; the recollections that they form can last for years or decades after an injection. The learned response becomes a reflex, ingrained and automatic, a “robust immune memory” that far outlives the shot itself, Ali Ellebedy, an immunologist at Washington University in St. Louis, told me. That’s what happens with the COVID-19 vaccines, and Ellebedy and others told me they expect the memory to remain with us for a while yet, staving off severe disease and death from the virus at extraordinary rates.

    In short, though antibody levels may drop, that represents just one measurement of the immune system’s ability to fight COVID-19. Other parts of the immune system will remain ready to address the coronavirus for long after an individual is vaccinated—you just might be more likely to have an asymptomatic or mild case, rather than avoiding infection entirely. (One big caveat here: We don’t know much about the risk of Long COVID after vaccination.)

    In fact, both Rochelle Walensky (CDC director) and Janet Woodcock (interim head of the FDA) are reportedly “pushing back on the White House’s plan” for booster shots, saying they need more time to collect and review data. I, for one, hope all of their data — and discussions — are made public in the coming weeks.

    More variant news

    • Featured sources, July 18

      • COVID-19 resources by Evidence Aid: Evidence Aid is a U.K.-based nonprofit that provides evidence-based guidance for disaster response. The organization’s COVID-19 page includes plain-language research summaries about COVID-19 epidemiology, treatments, and more, available in several different languages.
      • Public Health England Technical Briefings on SARS-CoV-2 variants: While the CDC has not done the best job of providing data on variants and breakthrough cases, the U.K.’s public health agency is sequencing more cases than any other country—and providing detailed reports on the results of those efforts. These reports may be useful for anyone seeking to keep a close eye on Delta and other variants’ ability to beat our vaccines. (h/t Your Local Epidemiologist)
      • Excess mortality and COVID-19 deaths in 67 countries: Researchers from the University of Bologna (in Italy) analyzed the gaps between excess deaths and COVID-19 deaths in 67 countries, revealing the capacity of different national health systems to accurately identify COVID-19 cases. Their work was published this week in JAMA Network Open. (For more on excess deaths, see this CDD post about Peru.)
      • Characterizing long COVID in an international cohort: In another new paper, published this week in The Lancet, COVID-19 long-haulers from the Patient-Led Research Collaborative share the results of an international survey on long COVID-19. The findings indicate that the vast majority of long-haulers (over 90% of those surveyed) suffer from symptoms for at least 35 weeks.
      • COVID-19 Vaccine Acceptance and Hesitancy in Low and Middle Income Countries: One more new paper, this one published in Nature: an international group of researchers analyzed vaccine acceptance across several low- and middle-income countries (LMICs), the U.S., and Russia. They found much higher vaccine acceptance in LMICs (80%) compared to the U.S. (65%) and Russian (30%). The study data are available on GitHub.

      All featured sources
    • The Delta variant is taking over the world

      The Delta variant is taking over the world

      The Delta variant is now dominant in the U.S., but our high vaccination rates still put us in a much better position than the rest of the world—which is facing the super-contagious variant largely unprotected.

      Let’s look at how the U.S.’s situation compares:

      U.S.: Delta now causes 52% of new cases, according to the latest Nowcast estimate from the CDC. (This estimate is pegged to July 3, so we can assume the true number is higher now.) It has outcompeted other concerning variants here, including Alpha/B.1.1.7 (now at 29%), Gamma/P.1 (now at 9%), and the New York City and California variants (all well under 5%). And Delta has taken hold in unvaccinated parts of the country, especially the Midwest and Mountain West.

      Israel and the U.K.: Both of these countries—lauded for their successful vaccination campaigns—are seeing Delta spikes. Research from Israel has shown that, while the mRNA vaccines are still very good at protecting against Delta-caused severe COVID-19, these vaccines are not as effective against Delta-caused infection. As a result, public health experts who previously said that 70% vaccination could confer herd immunity are now calling for higher goals.

      Japan: The Tokyo Olympics will no longer allow spectators after Japan declared a state of emergency. The country is seeing another spike in infections connected to the Delta variant, and just over a quarter of the population has received a dose of a COVID-19 vaccine. I argued in a recent CDD issue that, if spectators are allowed, the Olympics could turn into a superspreading event.

      Australia: Several major cities are on lockdown in the face of a new, Delta-caused surge following a party where every single unvaccinated attendee was infected. Unlike other large countries that faced significant outbreaks, Australia has successfully used lockdowns to keep COVID-19 out: the country has under 1,000 deaths total. But the lockdown strategy has diminished incentives for Australians to get vaccinated; under 5% of the population has received a shot. Will lockdowns work against Delta, or does Australia need more shots now?

      India: Delta was first identified in India, tied to a massive surge in the country earlier this spring. Now, India has also become the site of a Delta mutation, unofficially called “Delta Plus.” This new variant has an extra spike protein mutation; it may be even more transmissible and even better at invading people’s immune systems than the original Delta, though scientists are still investigating. India continues to see tens of thousands of new cases every day.

      Africa: Across this continent, countries are seeing their highest case numbers yet; more than 20 countries are experiencing third waves. Most African countries have fewer genetic sequencing resources than the U.S. and other wealthier nations, but the data we do have are shocking: former CDC Director Dr. Tom Frieden reported that, in Uganda, Delta was detected in 97% of case samples. Meanwhile, vaccine delivery to these countries is behind schedule—Nature reports that many people in African countries and other low-income nations will not get their shots until 2023. 

      South America: This continent is also under-vaccinated, and is facing threats from Delta as well as Lambda, a variant detected in Peru last year. While Lambda is not as fast-spreading as other variants, it has become the dominant variant in Peru and has been identified in at least 29 other countries. Peru has the highest COVID-19 death rate in the world, and scientists are concerned that Lambda may be more fatal than other variants. Studies on this variant are currently underway.

      In short: basically every region of the world right now is seeing COVID-19 spikes caused by Delta. More than 20 countries are experiencing exponential case growth, according to the WHO:

      We’ve already seen more COVID-19 deaths worldwide so far in 2021 than in the entirety of 2020. Without more widespread vaccination, treatments, and testing, the numbers will only get worse.

      More international reporting

      • Breakthrough cases: What we know right now

        Breakthrough cases: What we know right now

        Washington is one of the states reporting high levels of detail about breakthrough cases. Screenshot via June 23 report.

        For the past few months, we’ve been watching the vaccines and variants race in real time. With every new case, the coronavirus has the opportunity to mutate—and many scientists agree that it will inevitably mutate into a viral variant capable of outsmarting our current vaccines.

        How will we know when that happens? Through genomic surveillance, examining the structure of coronavirus lineages that arise in the U.S. and globally. While epidemiologists may consider any new outbreak a possible source of new variants, one key way to monitor the virus/variant race is by analyzing breakthrough cases—those infections that occur after someone has been fully vaccinated. 

        In May, the CDC changed how it tracks breakthrough cases: the agency now only investigates and reports those breakthrough cases that result in hospitalizations or deaths. I wrote about this in May, but a new analysis from COVID Tracking Project alums and the Rockefeller Foundation provides more detail on the situation.

        A couple of highlights from this new analysis:

        • 15 states regularly report some degree of information about vaccine breakthroughs, some including hospitalizations and deaths.
        • Six states report sequencing results identifying viral lineages of their breakthrough cases: Nebraska, Arkansas, Alaska, Montana, Oregon, and Washington.
        • Washington and Oregon are unique in providing limited demographic data about their breakthrough cases.
        • Several more states have reported breakthrough cases in isolated press briefings or media reports, rather than including this vital information in regular reports or on dashboards.
        • When the CDC stopped reporting breakthrough infections that did not result in severe disease, the number of breakthrough cases reported dropped dramatically.
        • We need more data collection and reporting about these cases, on both state and federal levels. Better coordination between healthcare facilities, laboratories, and public health agencies would help.

        Vaccine breakthrough cases are kind-of a data black box right now. We don’t know exactly how many are happening, where they are, or—most importantly—which variants they’re tied to. The Rockefeller Foundation is working to increase global collaboration for genomic sequencing and data sharing via a new Pandemic Prevention Institute.

        Luckily, there is a lot we do know from another side of the vaccine/variant race: vaccine studies have consistently brought good news about how well our current vaccines work against variants. The mRNA vaccines in particular are highly effective, especially after one has completed a two-dose regimen. If you’d like more details, watch Dr. Anthony Fauci in Thursday’s White House COVID-19 briefing, starting about 14 minutes in.

        New research, out this week, confirmed that even the one-shot Johnson & Johnson vaccine works well against the Delta variant. The company reported that, after a patient receives this vaccine, blood antibody levels are high enough to beat off an infection from Delta. In other words, people who got the J&J shot do not need to rush to get a booster shot from an mRNA vaccine (a recent debate topic among some experts).

        Again, we’ll need more genomic surveillance to carefully watch for the variant that inevitably does beat our vaccines. But for now, the vaccinated are safe from variants—and getting vaccinated remains the top protection for those who aren’t yet. 

        More variant reporting

        • It’s time to worry about the Delta variant

          It’s time to worry about the Delta variant

          The Delta variant (also known as B.1.617.2) was first identified in India earlier this spring. It’s now known to spread more easily than any other variant found so far and evade immunity from a prior COVID-19 infection. Scientists are also investigating the variant’s potential to more easily cause severe disease—as well as links to a “black fungus” that has become a secondary epidemic in India.

          Harvard epidemiologist William Hanage called the variant “really, really anxiety-inducing,” STAT’s Andrew Joseph reports. (If you’d like to read more on the biology of this variant, Joseph’s article provides a useful overview.)

          The Delta variant was first identified in the U.S. in April. It’s making up a small fraction of new cases at the moment, but is spreading rapidly: from an estimated 1.3% of cases on May 8, to 2.5% of cases on May 22, to 6.1% of cases on June 5. The June 5 estimate comes from CDC’s Nowcast predictions, which extrapolate from the most recent available sequencing data (typically reported with a lag of two weeks or more.)

          The share of cases caused by this variant appears to be doubling every two weeks, which means that Delta could become the dominant variant here this summer. Some data suggest that domination could happen within a month—a dashboard run by the testing company Helix puts Delta at 10% of new cases as of May 31, suggesting an even faster transmission rate for the variant.

          Helix scientist Alexandre Bolze wrote on Twitter that Delta could become dominant “next week or next 2 weeks” based on these trends.

          Other variant trends also support Delta’s dominance. This variant, along with Gamma (or P.1, the variant first identified in Brazil), appears to be outcompeting other variants of concern in the U.S. Alpha (or B.1.1.7) has now plateaued at around 70% of U.S. cases, according to CDC data. The variants found in California and New York, both of which made up more than 10% of new cases earlier in the spring, are now declining.

          While the CDC is not yet publishing data on Delta’s prevalence in individual states, we can assume that state-by-state variant trends—especially in those states where Delta cases were first identified—are reflecting the variant’s rise on a national level.  

          Many experts are now looking at Delta’s spread in the U.K. as a portent for its spread here. The variant has become dominant in the U.K., thoroughly outcompeting Alpha, and is driving a new surge—even though over half of the British population has received at least one vaccine dose. In fact, the U.K. has delayed its full reopening plans by a month due to this case resurgence.

          The COVID-19 vaccines currently in use in both the U.K. and the U.S. do work well against Delta, especially the Pfizer and Moderna vaccines—and especially after a full two-dose regimen is complete. But anyone not yet vaccinated is highly vulnerable to this variant. In the U.K., the current case surge is driven by young adults and teenagers who aren’t yet eligible for vaccination.

          As physician and public health expert Vin Gupta put it: “Being unvaccinated on June 9, 2021 is much more risky to your own wellbeing than being unvaccinated on June 9, 2020.” And the longer one waits, the riskier this condition becomes.

          The Delta variant should serve both as an additional reason for those in wealthy nations who aren’t yet vaccinated to get their shots—and a reason for wealthy nations to share doses with the rest of the world.

          More variant data

          • New variant names from the WHO

            B.1.1.7. B.1.351. P1. B.1.671.2. It’s exhausting trying to keep up with emerging SARS-CoV-2 variants with names as inscrutable as these.

            But thankfully, we finally have a straightforward naming system: on May 31, the WHO announced a system using letters of the Greek alphabet. B.1.1.7 (first identified in the U.K. is now Alpha, B.1.351 (first identified in South Africa) is now Beta, and so on. You can find the complete list (so far) here. While there are an innumerable amount of SARS-CoV-2 variants, so far the WHO naming system only applies to “variants of concern” and “variants of interest.”

            While there have been non-place-related names for these variants for a while, colloquially they have been called things like “the U.K. variant” and “the South African variant” because most people won’t just toss “B.1.1.7” around in conversation. (I tried, and no one knew what I was talking about.) However, this is problematic for a few reasons. First, we don’t know for sure that B.1.1.7. originated in the United Kingdom — that’s just where they found it first. And for other countries, naming a coronavirus variant after them associates a dangerous stigma with that country (like how nicknaming the coronavirus “the China virus” earlier in the pandemic contributed to a rise in anti-Asian hate). According to WHO coronavirus lead Maria Van Kerkhove in an interview with STAT News, a country will be more likely to report a variant if the name of the variant will not be associated with the country name. 

            The WHO naming system is nice for now, but it’s not clear if it’ll catch on and become the norm or if it’ll just be yet another naming system in a crowded patchwork. It’s also unclear what will happen if we run out of Greek letters, but we certainly hope it doesn’t come to that. (Making this yet another reason to vaccinate the world.)

            More variant data

            • Featured sources, May 30

              • Cases and deaths among healthcare workers: A new addition to the CDC COVID Data Tracker this week: a tab reporting cases and deaths in doctors, nurses, and other healthcare personnel. The CDC is reporting both totals and new cases/deaths by week, though the data here likely represent only a fraction of the true counts of healthcare workers infected during the pandemic. Notably, the total death toll is only about 1,600—less than half of the healthcare worker deaths reported by The Guardian and KHN’s “Lost on the Frontline” project.
              • Health Equity Tracker: When the COVID Tracking Project (including the COVID Racial Data Tracker) ceased data collection in March, it became much more difficult to compare COVID-19 case counts by race and ethnicity across states. A new project from the Morehouse School of Medicine fills that gap—and does much more. The Tracker incorporates data from the CDC, the Census, and other sources to provide comprehensive information on which communities have been hardest hit by the COVID-19 pandemic. Read more about it in this STAT article.
              • Coronavirus variant lineages: I came across this source a few days ago while researching variant lineages, prompted by a question on Twitter. Phylogenetic Assignment of Named Global Outbreak Lineages (or PANGO Lineages, for short) is a software tool developed by a lab in the U.K. that allows users to submit and analyze coronavirus sequences. The specific page I’ve linked here provides a comprehensive, searchable list of all the coronavirus variants that scientists have identified. Very useful if you need to search up an older or less-well-known variant.
              • Unemployment Insurance Data Explorer: This tool from progressive think tank The Century Foundation allows users to explore, visualize, and download data on unemployment insurance distributed during the pandemic. The tool includes data broken out by state and goes back in time to 1971—valuable for historical analysis.

              All featured sources
            • Why did the CDC change its breakthrough case reporting?

              Why did the CDC change its breakthrough case reporting?

              Earlier this month, the CDC made a pretty significant change in how it tracks breakthrough cases. Instead of reporting all cases, the agency is only investigating and collecting data on those cases that result in hospitalizations or deaths.

              In case you need a refresher: “breakthrough cases” are those infections that occur after a patient is fully vaccinated (including both doses, if applicable, and the two-week waiting period after a final dose). These cases are rare—like, one in ten thousand rare. As I wrote back in April, it’s important to contextualize any reporting on these cases with their incredible rareness so that we hammer home just how effective the vaccines are.

              But just because breakthrough cases are rare doesn’t mean we shouldn’t pay attention to them. In fact, it’s critical to pay attention to these cases in order to monitor precisely how well our vaccines are working—and how new variants may threaten the protections those vaccines provide.

              As The Atlantic’s Katherine J. Wu explains:

              Breakthroughs can offer a unique wellspring of data. Ferreting them out will help researchers confirm the effectiveness of COVID-19 vaccines, detect coronavirus variants that could evade our immune defenses, and estimate when we might need our next round of shots—if we do at all.

              As I’ve discussed in past variant reporting, numerous studies have demonstrated that the vaccines currently in use in the U.S.—especially the Pfizer and Moderna vaccines—work well against all variants. That includes variants of concern, such as B.1.617 (from India), B.1.351 (from South Africa), and P.1 (from Brazil). But the vaccine efficacy rates for some of these variants are lower than that stellar 95% we saw in Pfizer and Moderna’s clinical trials. And some common therapeutic drugs don’t work well for patients infected with variants, too.

              As a result, scientists are concerned that, while the vaccines are working well now, they might not work well forever. Whenever the coronavirus infects a new person, it has the opportunity to evolve. And that continued evolution must be monitored. The first coronavirus variant able to evade our vaccines may emerge in a foreign country with a raging outbreak—but it may also emerge here in the U.S. Closely monitoring all breakthrough cases will help us find that dangerous variant.

              (Of note: A new, potentially-concerning variant was identified just last night in Vietnam; WHO scientist Maria Van Kerkhove described it as an offshoot of the variant from India, B.1.617, with “additional mutation(s).”)

              With that in mind, let’s unpack the CDC’s reporting change. When the vaccine rollout started, the agency was investigating all breakthrough cases that came to its attention—including those in patients with only mild symptoms, or with no symptoms at all. According to an agency study released this past Tuesday, the CDC identified 10,262 such breakthrough cases from 46 U.S. states and territories between January 1 and April 30, 2021.

              Keep in mind: By April 30, about 108 million Americans had been fully vaccinated. Dividing 10,262 by 108 million is where I got that “one in ten thousand” comparison I cited earlier. As I said: very rare.

              Starting on May 1, however, the CDC changed its strategy. Now, it is only tracking breakthrough cases that result in severe illness for patients, leading to hospitalization and/or death. The CDC says that this choice is intended to focus on “the cases of highest clinical and public health significance” rather than tracking down asymptomatic cases.

              In its May 25 report, CDC scientists said that 27% of the breakthrough cases identified before May 1 were asymptomatic. 10% of the infected individuals were hospitalized, though almost a third of those patients were hospitalized for a reason unrelated to COVID-19. Only 160 patients (less than 2% of the breakthrough cases) died.

              We need to take these numbers with a grain of salt, though, because the CDC has likely undercounted the true number of asymptomatic cases. Both clinical trials and studies on vaccine effectiveness in the real world have suggested that those people who get infected with COVID-19 after completing a vaccination regime are more likely to have mild symptoms, or no symptoms at all.

              Plus, the CDC is recommending that vaccinated Americans don’t need to get tested before traveling, if they have come into contact with someone known to have COVID-19, or for many of the other reasons that many of us got tested this past year. (The agency is still recommending that fully vaccinated people get tested if they’re experiencing COVID-19 symptoms, though.)

              As I wrote at Slate Future Tense last month, such guidelines are likely to drive down the number of COVID-19 tests conducted across the U.S. And this trend seems to be happening, so far: PCR tests dropped from their winter surge levels this spring, and are now dropping again. (Antigen and other rapid tests may be getting used more, but we don’t have any comprehensive data on them.)

              With that drop in testing—combined with the overall challenge of identifying asymptomatic COVID-19 cases outside of dedicated studies—it would be pretty damn hard for the CDC to track down all breakthrough cases. The agency’s focus on more serious cases instead may thus be considered a conservation of resources, directing research efforts and care to those Americans who get seriously ill after vaccination.

              But “a conservation of resources” is also a nice way of saying, the CDC made a lazy choice here. The agency has poured money into genomic surveillance over the past few months, sequencing over 20,000 cases a week (compared to a few thousand cases a week before Biden took office). In recent weeks, the Biden administration has announced renewed funding for public health and similar commitments to prioritizing scientific research. If the CDC wants to find and sequence breakthrough cases in order to identify vaccine-busting variants, there should be nothing stopping the agency.

              Or, as epidemiologist Dr. Ali Mokdad told the New York Times: “The C.D.C. is a surveillance agency. How can you do surveillance and pick one number and not look at the whole?”

              Out of those 10,262 cases that the CDC reported this week, only 5% had sequence data available—but the majority of those sequined cases were variants of concern, including B.1.1.7 and P.1. At The Atlantic, Wu reported that epidemiologists in some parts of the country are seeing more breakthrough cases tied to concerning variants, while others are seeing breakthrough case sequences that match the overall infections in the community.

              To me, this high level of unknowns and uncertainties mean that we need more breakthrough case reporting and sequencing, not less. And we need a national public health agency that commits to true surveillance, so that we aren’t flying blind when the coronavirus inevitably evolves beyond our current defenses.

              (P.S. Shout-out to Illinois, the one state that reports its own breakthrough case data.)

              More vaccine reporting

              • Sources and updates, November 12
                Sources and updates for the week of November 12 include new vaccination data, a rapid test receiving FDA approval, treatment guidelines, and more.
              • How is the CDC tracking the latest round of COVID-19 vaccines?
                Following the end of the federal public health emergency in May, the CDC has lost its authority to collect vaccination data from all state and local health agencies that keep immunization records. As a result, the CDC is no longer providing comprehensive vaccination numbers on its COVID-19 dashboards. But we still have some information about this year’s vaccination campaign, thanks to continued CDC efforts as well as reporting by other health agencies and research organizations.
              • Sources and updates, October 8
                Sources and updates for the week of October 8 include new papers about booster shot uptake, at-home tests, and Long COVID symptoms.
              • COVID source shout-out: Novavax’s booster is now available
                This week, the FDA authorized Novavax’s updated COVID-19 vaccine. Here’s why some people are excited to get Novavax’s vaccine this fall, as opposed to Pfizer’s or Moderna’s.
              • COVID-19 vaccine issues: Stories from COVID-19 Data Dispatch readers across the U.S.
                Last week, I asked you, COVID-19 Data Dispatch readers, to send me your stories of challenges you experienced when trying to get this fall’s COVID-19 vaccines. I received 35 responses from readers across the country, demonstrating issues with insurance coverage, pharmacy logistics, and more.

            • Source updates, May 16

              Two more important CDC data updates for this week:

              • Vaccine demographics, for the past 14 days and over time: This week, the CDC added a new category to its Vaccine Demographics page. Previously, the page allowed users to compare overall first dose and fully vaccinated rates for different race/ethnicity, age, and sex groups; now, you can also make those comparisons specifically for vaccinations in the last two weeks. For a time series view, check out the Vaccine Demographic Trends page, which shows vaccination rates over time—now available for race/ethnicity, sex, and age. The race/ethnicity view clearly shows that White and Asian Americans are getting vaccinated at higher rates than other groups.
              • Variant tracker “Nowcast”: Loyal CDD readers will already know that I love to drag the CDC for reporting their variant data with an enormous lag; often the most recent figures on the agency’s Variant Proportions page are a month old. Well, maybe somebody on their team is reading, because this week, the CDC added a new option to its variant dashboard that addresses this issue. Selecting “Nowcast On” (below the variant color bars) allows you to view prevalence estimates for the current week, in addition to the agency’s most recent week of data collection. A note below the dashboard explains that the “Nowcast” figures are based on modeling estimates that extrapolate from known proportions. For example, B.1.1.7 is known to cause 66% of U.S. cases as of April 24, but the “Nowcast” estimate puts it at 72% of cases as of May 8. This is actually pretty useful, thanks CDC!

              All featured sources
            • All variant data are weeks old

              All variant data are weeks old

              It takes three to four weeks for data on a variant COVID-19 case to be made public. I have been quietly stressing out about this fact for about a month, since I learned it from Will Lee, VP of science at the genomics company Helix.

              I talked to Lee for a recent Science News piece on the drivers and demographic patterns of the U.S.’s April rise in COVID-19 cases. During our conversation, he shared many details of Helix’s coronavirus sequencing process; most of this information was too technical for me to include in my Science News story, but in the COVID-19 Data Dispatch, I can get as technical as I want.

              Here’s an excerpt from our interview, following my question: What is the turnaround time for sequencing? How does it compare to getting a PCR test result?

              It is much, much slower. The median time from collection to [PCR] results, it’s varied quite a bit over time, but I think right now, for many labs, it’s less than 48 hours. And so what we do is, after the test result is done—we’re only picking from positive tests, obviously, for sequencing—so we would select the sample, probably somewhere on the order of two to three days after the sample is collected, after the test result is reported.  From then, I’d say there’s probably seven to ten days before the sequencing result is available…

              What happens is, we do the [PCR] test result, we send it out for sequencing. The turnaround time for sequencing—I’d say in a good case, it’s in the seven to eight day timeframe, sometimes it’s longer than that. There’s an additional holdback on the data before we make it publicly available, because the CDC wants to make sure that public health agencies have time to act on the information first, if it turns out [the case is] someone in their jurisdiction who’s identified to have a variant of concern. That’s potentially another week, depending on how fast they [the local public health agency] act.

              And then there’s additionally a lag for when you submit to somewhere like GISAID, and however long it takes them to do their review process and publish it. You add it all together, and you end up with something like 3-4 weeks [from test sample collection to sequence publication].

              So, let’s recap. Here’s what it takes to sequence and report a coronavirus variant case:

              1. PCR test: 1-2 days
              2. The testing company selects the positive test sample for sequencing: 1-2 days
              3. Genomic sequencing takes place: 7-10 days
              4. Local public health department gets notified, uses the sequencing results for contact tracing: Up to one week
              5. Sequence is submitted to a public repository: Possibly another 1-2 weeks

              When you add all this up, it’s no surprise that the most recent variant data on the CDC’s COVID Data Tracker are as of April 10, almost four weeks ago. I’m focusing on this process today because I believe the data lag is worth emphasizing. When you see a news report about B.1.1.7 or another variant, remember that the data took several weeks to get from test sample to newspaper.

              In other words, when the CDC tells us that B.1.1.7 now makes up about 60% of new cases in the U.S., remember that this number is a snapshot from a month ago. The true number as of today, May 9, is likely far higher.

              My interview with Will Lee inspired me to look at lag times for other common variant data sources. Let’s compare:

              • CDC’s Variant Proportions page, data from the national genomic surveillance program: Lag of 2-4 weeks, depending on how far away one is from an update when checking the page. (The CDC updates this page every two weeks.)
              • Helix’s Surveillance Dashboard, data from the company’s testing sites: Lag of 3-4 weeks. As of May 8, Helix is reporting B.1.1.7 sequence data as of April 15 and SGTF data as of late April. (SGTF, or S gene target failure, is a coronavirus mutation which usually indicates that a case is B.1.1.7-caused.)
              • Nextstrain dashboard, data from GISAID: Lag of 1-2 weeks. When I looked at Nextstrain’s coronavirus page yesterday, the most recent available sample sequences were collected on May 1 and the global variant frequencies chart ended at April 27.
              • CoVariants dashboard, data from Nextstrain/GISAID: Lag of 2-4 weeks, depending on the country. As of May 8, CoVariants reports data from the week of April 19 for some countries with more robust sequencing programs (U.S., U.K., etc.) and data from the week of April 5 for others.

              Nextstrain and CoVariants, both of which are powered by the public sequence repository GISAID, have more recent data than the CDC—likely because academic labs can submit sequences to GISAID without waiting on public health departments. Helix has a lag similar to the CDC’s because its partnerships require the company to submit sequences to public health departments before releasing the information publicly. Some state public health departments report variant data of their own, but this is often done in press releases rather than regular dashboard updates.

              Now, bearing in mind that the variant data are all weeks old, what are the most recent variant numbers for the U.S.? And why should we be worried about these variants?

              Here’s a status check on the major variants I’m watching:

              • B.1.1.7 (first identified in the U.K.): Causing about 60% of cases nationwide as of April 10. Among the states where the CDC reports variant data, it’s most prevalent in Tennessee (74%), Michigan (71%), Minnesota (68%), Georgia (65%), and Florida (63%). This variant is concerning because it spreads a lot more easily than older coronavirus variants; estimates range from 40% to 70% more transmissible.
              • B.1.526 (first identified in New York City): Causing about 12% of cases nationwide as of April 10. This variant is also likely more transmissible, but a recent CDC report suggests that it does not lead to more severe disease or increased risk for vaccine breakthrough cases. B.1.526 has yet to be classified nationally as a variant of concern, so the CDC isn’t publishing state-by-state data for it. (But if you live in NYC, check out this Gothamist article for ZIP code-level prevalence data.)
              • B.1.427/B.1.429 (first identified in California): Causing about 6% of cases nationwide as of April 10. I suspect the pair may be getting outcompeted by B.1.1.7, as it was representing closer to 10% of cases in a previous CDC reporting period—it’s more transmissible than the wildtype coronavirus, but not as transmissible as B.1.1.7 . This variant pair is most prevalent in California (38%), Arizona (28%), and Colorado (24%).
              • P.1 (first identified in Brazil): Causing about 4% of cases nationwide as of April 10. This variant has been tied to surges in Brazil and other South American countries; it’s more transmissible, associated with a higher death rate, and can reinfect patients who already recovered from COVID-19. While it currently represents a fairly small share of U.S. cases, computational biologist Trevor Bedford recently pointed out that P.1. “has been undergoing more rapid logistic growth in frequency” compared to other variants.
              • B.1.351 (first identified in South Africa): Causing about 1% of cases nationwide as of April 10. Soon after it was identified last December, the COVID-19 vaccines were shown to be less effective against this variant. But “less effective,” for the mRNA vaccines, is still pretty damn effective, as this recent study from Qatar demonstrates.
              • B.1.617 (first identified in India): Not yet represented in CDC data, but it’s been identified in several U.S. states over the course of April and May. This variant is strongly tied to India’s recent surge. While you may see it called a “double variant” because it has mutations at two key coding sequences, B.1.617 doesn’t actually have double the transmission bump or double the severity of older coronavirus variants, as explained here by epidemiologist Katelyn Jetelina.

              It’s also worth emphasizing that genomic sequencing is still not conducted evenly across the country. The CDC releases state-by-state variant prevalence data for states which have submitted more than 300 coronavirus sequences in a four-week period. As of April 10, only half of the states have met this benchmark; many states in the Midwest and South still aren’t represented in the CDC’s data.

              I am considering adding a variant data annotations page to the CDD website, in order to more consistently keep track of all the different info sources on these lineages. Would you use this page? What information would you like to see there? Shoot me an email (betsy@coviddatadispatch.com) or leave a comment here on the website to let me know.

              Support the COVID Data Dispatch

              More variant reporting