COVID-19 Data Dispatch

Tag: BQ.1 and BQ.1.1

  • National numbers, January 22

    National numbers, January 22

    While COVID-19 spread has dropped in recent weeks, according to Biobot’s wastewater surveillance, it is still at much higher levels than it’s been earlier in the pandemic.

    In the past week (January 12 through 18), the U.S. officially reported about 330,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 47,000 new cases each day
    • 101 total new cases for every 100,000 Americans
    • 24% fewer new cases than last week (January 5-11)

    In the past week, the U.S. also reported about 35,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 5,000 new admissions each day
    • 10.7 total admissions for every 100,000 Americans
    • 16% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 4,000 new COVID-19 deaths (560 per day)
    • 49% of new cases are caused by Omicron XBB.1.5; 40% by BQ.1 and BQ.1.1 (as of January 21)
    • An average of 150,000 vaccinations per day (CDC link)

    National COVID-19 metrics continue to suggest that the U.S. is coming out of its holiday surge, though some parts of the country may face increased transmission as the Omicron variant XBB.1.5 spreads.

    Official COVID-19 case numbers and new hospital admissions both reported declines this week, according to the CDC (of 24% and 16% respectively, compared to the prior week). Biobot’s wastewater surveillance data also show a decline, with coronavirus concentration at a similar level to mid-November 2022, just before Thanksgiving.

    This trend is fairly consistent across states and regions, according to case and hospitalization data from the latest HHS Community Profile Report. However, Biobot’s regional and county-level data suggest that COVID-19 spread is in a plateau or even starting to increase in some parts of the South and Midwest regions.

    Hospitalizations for the flu and RSV are following a similar pattern to COVID-19, according to a new CDC dashboard that reports on all three illnesses together. Almost all states reported moderate or low levels of influenza-like activity in the week ending January 14, very different from the patterns we were seeing a few weeks ago. The only areas still reporting high influenza-like activity are California, North Dakota, New Mexico, Texas, Puerto Rico, New York City, and Washington D.C.

    All of this is good news, suggesting that the worst of this winter’s respiratory virus surges may be behind us. But COVID-19 is still spreading across the country at fairly high levels, reflecting the high baseline that the U.S. has faced ever since new Omicron subvariants started to hit in spring 2022.

    We also need to continue watching XBB.1.5, the latest and most contagious version of Omicron. This subvariant caused about half of new cases in the U.S. in the last week, according to CDC estimates. It’s most prevalent in the Northeast but is quickly gaining ground in the Southeast and other regions. (And the BQ lineages that currently dominate these regions can spread quickly, too.)

    In the coming weeks, we’ll see how much XBB.1.5 (and any other variants) contribute to increased transmission in these regions. Meanwhile, COVID-19 deaths went up recently as the holiday surge took its toll: more than 500 people have died from COVID-19 every day in the last two weeks. Deaths are always the most delayed—and the most tragic—metric.

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  • National numbers, December 18

    National numbers, December 18

    Biobot’s wastewater surveillance data suggest that COVID-19 spread is trending down in the West coast and plateauing in other regions. Data as of December 15.

    In the past week (December 8 through 14), the U.S. reported about 460,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 65,000 new cases each day
    • 139 total new cases for every 100,000 Americans
    • 3% fewer new cases than last week (December 1-7)

    In the past week, the U.S. also reported about 35,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 5,000 new admissions each day
    • 10.7 total admissions for every 100,000 Americans
    • 2% more new admissions than last week

    Additionally, the U.S. reported:

    • 2,700 new COVID-19 deaths (390 per day)
    • 69% of new cases are caused by Omicron BQ.1 and BQ.1.1; 5% by BF.7; 7% by XBB (as of December 17)
    • An average of 250,000 vaccinations per day (CDC link)

    After a significant post-Thanksgiving spike, COVID-19 transmission in the U.S. appears to be in a high plateau, according to trends in cases and wastewater. Official case counts stayed fairly steady this week compared to the week following the holiday, according to the CDC, while wastewater data from Biobot show coronavirus concentrations leveling out.

    COVID-19 hospital admissions are similarly at a high plateau: about 5,000 new people with COVID-19 were admitted to hospitals every day last week, per the CDC. That’s a 2% increase from last week.

    Going beyond the national trends, though, we see that some places are experiencing dips in COVID-19 spread while others are spiking. In Boston, for example, wastewater data suggest that COVID-19 is at its most prevalent since the surge in early summer. Across the country in Los Angeles, coronavirus levels in wastewater are trending down after increasing through November.

    New York and New Jersey had the highest official COVID-19 case rates in the last week, according to the latest Community Profile Report, followed by Illinois, California, and Rhode Island. But these data may be more a product of which states still have somewhat-available PCR testing than actual case comparisons.

    And even in places where COVID-19 is declining, the combined threat of this virus, flu, and RSV is still putting a lot of strain on healthcare systems. Take Los Angeles: while it might not be seeing record COVID-19 cases, the city currently has fewer free hospital beds available than at any other point in the pandemic, per reporting by the Los Angeles Times.

    Flu might be peaking in some parts of the country, Helen Branswell wrote in STAT on Friday, based on CDC data. But it’s still early in the typical flu season, and hard to tell how COVID-19 and the flu (and RSV) might impact each other.

    As we gear up for another week of holiday travel and gatherings—and as highly contagious Omicron subvariants, the BQs and XBB, continue to outcompete other versions of the virus—this is an important time to take all possible safety precautions.

    That includes getting your flu shot and the new Omicron-specific COVID-19 booster, which further CDC studies have shown is highly effective at preventing hospitalization. And it includes masking, testing before and after events, and gathering outdoors (or otherwise improving ventilation) to reduce your risk of spreading all kinds of viruses.

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  • National numbers, December 11

    National numbers, December 11

    The CDC’s influenza-like illness map shows that the vast majority of the country is facing either high or very high levels of respiratory disease.

    In the past week (December 1 through 7), the U.S. reported about 460,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 66,000 new cases each day
    • 140 total new cases for every 100,000 Americans
    • 50% more new cases than last week (November 24-30)

    In the past week, the U.S. also reported about 34,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 4,800 new admissions each day
    • 10.3 total admissions for every 100,000 Americans
    • 14% more new admissions than last week

    Additionally, the U.S. reported:

    • 3,000 new COVID-19 deaths (430 per day)
    • 68% of new cases are caused by Omicron BQ.1 and BQ.1.1; 6% by BF.7; 4% by BN.1;  5% by XBB (as of December 10)
    • An average of 300,000 vaccinations per day

    It’s now undeniable that Thanksgiving led to a jump in COVID-19 spread: officially-reported cases went up 50% this past week compared to the week of the holiday, following the trend that we first saw in wastewater data. Hospital admissions for COVID-19 also continue to go up.

    As always, it’s important to remember that official case counts are significantly underreported, due to dwindling access to (and interest in) PCR testing. So, the CDC’s estimate of 66,000 new COVID-19 cases each day likely amounts to over a million actual new infections each day. And that’s adding to the surges of flu, RSV, and other respiratory viruses already going strong.

    “Levels of flu-like illness, which includes people going to the doctor with a fever and a cough or sore throat, are at either high or very high levels in 47 jurisdictions,” CDC Director Dr. Rochelle Walensky said at a media briefing last Monday. That “flu-like illness” metric, shown on the CDC’s flu dashboard, is primarily used as an estimate of flu cases, but in our era of under-testing it likely includes COVID-19 and other viruses with similar symptoms.

    Dr. Walensky said that current hospitalizations for flu are the highest they’ve been in a decade for this time of year, indicating that the U.S. is having a bad flu season earlier in the winter than usual. According to Inside Medicine, flu hospitalizations actually overtook COVID-19 hospitalizations for the first time in the pandemic recently; though this trend could reverse as COVID-19 spreads more.

    The flu surge could peak and give us a milder January, or it could continue to go up from here—it’s currently hard to say. Flu vaccination rates have been low this year, which doesn’t help. CDC officials highlighted the benefits of both the flu vaccine and the updated COVID-19 booster shots at their briefing on Monday.

    Those updated COVID-19 boosters offer better protection against Omicron infection than prior vaccines, as real-world data has demonstrated. That should include protection against BQ.1 and BQ.1.1, the descendants of Omicron BA.5 that are currently causing the majority of cases in the U.S.—about 68% of new cases in the week ending December 10, per the CDC. XBB, the BA.2 subvariant that led to surges in Asian countries, is on the rise.

    Last week, wastewater data from Biobot showed a steep increase in COVID-19 spread. This week, the company’s dashboard suggests that this surge may have already peaked in some parts of the country. Was Thanksgiving the start of a major winter wave, or was it more of a holiday blip? Future weeks of data will help answer this.

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  • National numbers, December 4

    National numbers, December 4

    All four major regions of the country are reporting increased coronavirus levels in their wastewater, per Biobot. Data as of November 28.

    In the past week (November 24 through 30), the U.S. reported about 303,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 43,000 new cases each day
    • 92 total new cases for every 100,000 Americans
    • 1% fewer new cases than last week (November 17-23)

    In the past week, the U.S. also reported about 29,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 4,200 new admissions each day
    • 9.0 total admissions for every 100,000 Americans
    • 18% more new admissions than last week

    Additionally, the U.S. reported:

    • 1,800 new COVID-19 deaths (250 per day)
    • 63% of new cases are caused by Omicron BQ.1 and BQ.1.1; 6% by BF.7; 5% by BN.1;  6% by XBB (as of December 3)
    • An average of 200,000 vaccinations per day

    If the U.S. wasn’t at the start of a COVID-19 surge before Thanksgiving, we’re certainly in one now. While official case counts have stagnated, wastewater surveillance indicates that the country is seeing about 1.5 times the coronavirus transmission that we had three weeks ago, according to data from Biobot.

    All four major regions of the country are experiencing clear upward trends in COVID-19 spread, per Biobot, with no sign of peaking; this is the first time there’s been a unified national increase since mid-summer. Individual metropolitan areas from Boston, to the Twin Cities in Minnesota, to Los Angeles, are reporting major upticks.

    The current difference between wastewater surveillance trends and case trends further confirms what I’ve been saying for months: case data simply are no longer that helpful for seeing early warnings of surges, as few people seek out PCR testing compared to earlier points in the pandemic. If you don’t already have a good place to see wastewater data for your community, put some pressure on your local officials to make this information available.

    The U.S.’s new increase in transmission can likely be attributed to travel and gatherings over the Thanksgiving holiday, combined with newer, more-transmissible versions of Omicron. Lineages BQ.1 and BQ.1.1 caused almost two-thirds of new cases in the week ending December 3, according to CDC estimates, while XBB caused about 6% of new cases.

    XBB has been spreading intensely in some Asian countries, and experts are watching to see how it competes with the alphabet soup of subvariants already circulating in the U.S. So far, it is most prevalent in the Northeast, per the CDC.

    In addition to wastewater trends, new hospital admissions for COVID-19 went up this week: about 18% more patients were admitted to hospitals around the country in the week ending November 30 compared to the prior week. These patients are entering a hospital system already overwhelmed by flu, RSV, and other respiratory viruses.

    As epidemiologist Caitlin Rivers noted in her newsletter last week: “The cumulative hospitalization rate for influenza is already on par with where we would expect to be in December or January.” And that virus continues to spread further, with most of the country experiencing high or very high levels of influenza-like activity.

    COVID-19 and these other viruses might not seem like a big deal thanks to vaccines and treatments, but they can still have very severe consequences. For example, New York City just reported that three children died of COVID-19 in recent weeks. And the risk of Long COVID remains, too.

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  • National numbers, November 27

    National numbers, November 27

    BA.5 sublineages BQ.1 and BQ.1.1 are now the dominant variants in the U.S., while newer lineage XBB has made an appearance. Chart via the CDC.

    In the past week (November 17 through 23), the U.S. reported about 310,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 44,000 new cases each day
    • 93 total new cases for every 100,000 Americans
    • 8% more new cases than last week (November 10-16)

    In the past week, the U.S. also reported about 24,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 3,400 new admissions each day
    • 7.2 total admissions for every 100,000 Americans
    • 0.2% more new admissions than last week

    Additionally, the U.S. reported:

    • 2,600 new COVID-19 deaths (380 per day)
    • 57% of new cases are caused by Omicron BQ.1 and BQ.1.1; 7% by BF.7; 3% by BN.1;  3% by XBB (as of November 26)
    • An average of 300,000 vaccinations per day

    Nationwide, reported COVID-19 cases went up last week: the CDC reports 8% more cases in the week ending November 23 than in the week ending November 16. Wastewater monitoring also suggests a pre-Thanksgiving uptick, according to Biobot, while new hospitalizations have been at a plateau.

    All eyes will be on wastewater data in the next couple of weeks, to look for potential spread after Thanksgiving travel and gatherings. We likely won’t see any immediate spikes in case data thanks to the data delays that always happen after holidays, but wastewater surveillance is less susceptible to these delays (and less biased by behavioral patterns). To look for wastewater data in your community, see the COVID-19 Data Dispatch’s resource page.

    Any outbreaks we see in the coming weeks will likely be driven by newer coronavirus variants, combining forces with holiday behavior. Omicron subvariants BQ.1 and BQ.1.1 caused about 57% of new COVID-19 cases in the week ending November 26, according to CDC estimates; the BQ lineage is more transmissible than its parent variant, BA.5, though it has not caused major case spikes in the U.S. yet.

    The CDC’s latest variant update also provides estimates on XBB, a subvariant that evolved from BA.2 and that has caused new surges in some Asian countries. XBB caused about 3% of new cases in the last week, the agency estimates, with higher prevalence in the Northeast and West coast. Health officials are closely watching XBB due to the many mutations on its spike protein, but it’s unclear whether this subvariant alone could cause a new surge.

    As we watch for new COVID-19 outbreaks, healthcare systems—especially children’s hospitals— across the country are already facing intense pressure from the flu, RSV, and other respiratory viruses. Many states, particularly on the East coast and in the South, continue to report very high levels of influenza-like activity, according to the CDC. 

    If you took part in a Thanksgiving gathering over the last few days: this week, you should look out for any respiratory symptoms and consider getting a PCR test, if you can. If possible, get a test that will check for COVID-19, the flu, and RSV at once. Make sure any disease spread stops with you!

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  • National numbers, November 20

    National numbers, November 20

    Data from the CDC indicate that much of the country is seeing high flu levels. Chart as of November 12.

    In the past week (November 10 through 16), the U.S. reported about 280,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 40,000 new cases each day
    • 86 total new cases for every 100,000 Americans
    • 3% fewer new cases than last week (November 3-9)

    In the past week, the U.S. also reported about 24,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 3,400 new admissions each day
    • 7.3 total admissions for every 100,000 Americans
    • 1% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 2,200 new COVID-19 deaths (320 per day)
    • 50% of new cases are caused by Omicron BQ.1 and BQ.1.1; 8% by BF.7; 5% by BN.1;  2% by BA.2.75 and BA.2.75.2 (as of November 19)
    • An average of 400,000 vaccinations per day

    Nationwide, reported COVID-19 cases and new hospital admissions are still in a plateau; both metrics declined very slightly this week after rising slightly last week (declining by 3% and 1%, respectively).

    While we have yet to see as clear of a fall/winter surge as we did in the last two years, infection levels are still quite high. Evidence for this comes from wastewater data, which doesn’t rely on people getting PCR tests; trends from Biobot suggest that viral transmission is at a similar level to late October/early November of last year, when Delta was still the dominant variant.

    Biobot’s data also indicate that the West coast region is now seeing a notable uptick in COVID-19 spread, taking over from the Northeast (which has been a regional hotspot since September). Wastewater testing sites in cities like Los Angeles is reporting significant transmission spikes in the last couple of weeks.

    The West coast, like the Northeast, has been a hotspot for newer Omicron subvariants BQ.1 and BQ.1.1, according to CDC estimates. Nationwide, the BQ lineage caused about half of new cases in the last week—solidly outcompeting its parent lineage, BA.5. And there are several other Omicron subvariants spreading, including two lineages from BA.2, BF.7 and BN.1.

    With all these new variants circulating and colder weather throughout the country, why haven’t we seen a significant jump in COVID-19 spread? It’s possible that the U.S. has enough prior immunity from vaccinations and past infections to prevent a big surge, White House COVID-19 coordinator Ashish Jha said at the STAT Summit last week.

    I hope Jha is right, but I personally remain skeptical. Way too few people have received the new booster shots that protect against Omicron variants, while we’re heading into several weeks of holiday travel and gatherings—with fewer COVID-19 protections than in the last two years.

    At the same time, the U.S. is dealing with flu and RSV surges. About a dozen states, plus New York City and Washington, D.C., reported “very high” levels of influenza-like activity in the week ending November 12, according to the CDC. And the country’s RSV wave continues at high intensity, though it might be reaching its peak.

    These two respiratory diseases may be less severe than COVID-19 at an individual level (especially accounting for the burden of Long COVID), but they can still put intense pressure on healthcare systems—especially those focused on treating children. Wearing a mask, avoiding indoor crowds, improving ventilation, and other measures can protect against all three diseases.

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  • Sources and updates, November 13

    • Updated booster doses by state: This week, the CDC started reporting how many people have received the bivalent, Omicron-specific boosters by state, including state-level data for several demographic groups (over age 5, over 12, over 18, and over 65). The numbers are low: Vermont and Washington, D.C. have the highest booster rates as of November 9, with 21% and 20% of their populations receiving the bivalent shots, respectively. In about half of states, less than 10% of the population has received an updated booster. (H/t Jason Salemi.)
    • Additional data suggests new boosters work against BQs: Speaking of the updated booster shots, a recent preprint from researchers at Emory University, Stanford University, and the NIH found that the new boosters produced several times more neutralizing antibodies against subvariants BQ.1.1 and BA.2.75.2 compared to the older vaccines. This was a small lab study and hasn’t yet been peer-reviewed, but it follows similar evidence from other research suggesting that the new boosters do provide additional protection against the most concerning variants currently circulating in the U.S. (See last week’s post.) If you haven’t gotten a bivalent booster yet, now is a good time!
    • More evidence that masks in schools prevent COVID-19 spread: Another notable new study this week, published in the New England Journal of Medicine: a group of researchers from Boston institutions examined the differences in COVID-19 case numbers between public school districts that kept mask requirements in place during spring 2022, and those that lifted their requirements upon a statewide policy change in February. Overall, ending required masking led to “an additional 44.9 COVID-19 cases per 1,000 students and staff” during the remainder of the semester, the researchers found. The study demonstrates that masks are still a useful public health strategy to reduce illness—and risk of Long COVID—in schools.
    • Paxlovid may reduce Long COVID risk: When Paxlovid first became available earlier in the year, some Long COVID patients reported that the drug helped alleviate their symptoms. A new study from Ziyad Al-Aly and his team at the Veterans Affairs St. Louis healthcare system provides evidence behind the anecdotal reports, finding that veterans treated with Paxlovid had a 25% lower risk of long-term symptoms, based on their electronic health records. The study has received some criticism (and has not yet been peer-reviewed); to me, it provides motivation for actual clinical trials examining Paxlovid’s use for treating Long COVID. RECOVER is running one such trial, but it won’t start until early 2023.
    • Estimating COVID-19 infections from wastewater: And one more study that caught my attention this week: researchers at the University of Florida used a modeling technique called a “mass balance equation” to estimate how many people in Gainseville, Florida were sick with COVID-19 based on the virus’ concentration in wastewater. Using about one year of wastewater data (May 2020 to May 2021), the researchers were able to accurately predict actual infections with an error of just 1%. Translating wastewater data into useful information for public health action has been a major challenge for the growing field, so I was glad to see this study providing a potentially-useful method.

    All featured sources
  • National numbers, November 13

    National numbers, November 13

    COVID-19 hospitalizations have risen slightly in recent weeks, indicating the start of a fall/winter surge, according to CDC data.

    In the past week (November 3 through 9), the U.S. reported about 290,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 41,000 new cases each day
    • 88 total new cases for every 100,000 Americans
    • 6% more new cases than last week (October 27-November 2)

    In the past week, the U.S. also reported about 24,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 3,500 new admissions each day
    • 7.4 total admissions for every 100,000 Americans
    • 5% more new admissions than last week

    Additionally, the U.S. reported:

    • 2,300 new COVID-19 deaths (340 per day)
    • 44% of new cases are caused by Omicron BQ.1 and BQ.1.1; 8% by BF.7;  2% by BA.2.75 and BA.2.75.2 (as of November 12)
    • An average of 400,000 vaccinations per day

    We are beginning to see the impacts of colder weather and new variants this week, as both official COVID-19 cases and new hospital admissions went up slightly: increasing by 6% and 5% from the prior week, respectively.

    Wastewater monitoring similarly shows an uptick in coronavirus transmission at the national level, according to Biobot’s dashboard. The Northeast still has the highest virus concentration, but other regions of the country are catching up—particularly the West coast, which reported a significant increase in the last two weeks.

    About half of the wastewater surveillance sites included on the CDC’s national dashboard reported increases in coronavirus transmission over the two-week period ending November 7, with 30% of sites reporting increases of at least 100%.

    Omicron BQ.1 and BQ.1.1 are likely a major source of increased virus spread. These two strains—subvariants of BA.5 that are even more contagious—now account for 44% of new cases in the week ending November 12, according to CDC estimates. New variants tend to have an impact on transmission when they reach about 50% prevalence, so we will likely see more BQ-driven spread in the weeks to come.

    The New York/New Jersey region continues to report the highest amounts of BQ.1 and BQ.1.1: these variants represented about 60% of new cases in the last week. These two states also reported some of the highest (official) case rates in the country last week, along with Puerto Rico, New Mexico, and North Dakota, per the latest Community Profile Report. Cases and hospitalizations in New York City, often a bellwether for the rest of the country, are rising again.

    At the same time, the U.S. is seeing an early and intense flu season. Most of the country’s Southeast region (from Virginia to Mississippi) reported the highest possible levels of influenza-like activity in the week ending November 5, according to the CDC. Flu, COVID-19, and RSV are all straining hospitals as we head into the holiday season.

    The new, Omicron-specific booster shots provide enhanced protection against the latest variants, but uptake remains very low—as shown by new CDC data providing vaccinations by state. Only 10% of the eligible population has received one of the new shots, as of November 9.

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  • National numbers, November 6

    National numbers, November 6

    Despite significant undercounting of COVID-19 cases, the CDC’s Community Transmission Levels (based on case rates and test positivity) are high enough to suggest the majority of the country should be masking. Data here are as of November 2.

    In the past week (October 27 through November 2), the U.S. reported about 270,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 39,000 new cases each day
    • 83 total new cases for every 100,000 Americans
    • 5% more new cases than last week (October 20-26)

    In the past week, the U.S. also reported about 23,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 3,300 new admissions each day
    • 7.0 total admissions for every 100,000 Americans
    • 1% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 2,500 new COVID-19 deaths (360 per day)
    • 35% of new cases are caused by Omicron BQ.1 and BQ.1.1; 9% by BF.7;  4% by BA.2.75 and BA.2.75.2 (as of November 5)
    • An average of 400,000 vaccinations per day

    Continuing a trend from the last few weeks, nationwide COVID-19 cases and hospitalizations are still at plateaus or trending very slightly downward. We aren’t clearly in a fall surge yet, but concerning newer Omicron subvariants are rising—along with other respiratory diseases.

    National wastewater trends are also still suggesting plateaus or downturns in coronavirus transmission, according to Biobot’s dashboard. The Northeast’s wastewater saw a major drop in coronavirus concentration over the last couple of weeks while other regions are at high, but steady levels.

    As always, it’s important to remember that official case data are significantly undercounted. True infections are likely around 20 times higher than reported cases, though even that factor is difficult to estimate at this point in the pandemic.

    Despite the undercounting, the CDC’s Community Transmission Levels (based on case rates and test positivity) suggest that 75% of U.S. counties are experiencing “high” or “substantial” coronavirus spread. If we had more accurate data, that number would likely shoot up to 100%. In other words, even today’s seemingly-low and underestimated case numbers are still high compared to earlier periods of the pandemic.

    Newer versions of the Omicron variant will likely drive continued COVID-19 spread this fall. BQ.1 and BQ.1.1 have emerged as the most competitive subvariants and are quickly taking over from their parent lineage, BA.5. These two subvariants caused about 35% of new cases in the U.S. in the week ending November 5, according to the CDC’s estimates, while BA.5 caused 39%.

    The BQs are most prevalent in the Northeast, especially New York and New Jersey: these subvariants caused over 50% of new cases in the NY/NJ region last week, according to the CDC. These two states and Connecticut also had the highest per-capita COVID-19 hospitalization rate last week, per the HHS Community Profile Report.

    As hospitals around the country brace for a winter COVID-19 surge, they’re already dealing with high transmission of the flu. Flu hospitalizations have not been as high as they are this season since 2010-2011, the CDC reports. Last week, Washington D.C., Tennessee, South Carolina, and Alabama reported influenza-like illness rates so high that the CDC needed a new map color to express it.

    Even if COVID-19 isn’t (yet) surging in your community, this is a good time to stock up on high-quality masks and rapid tests, and plan holiday gatherings that will keep friends and family members safe. Your Local Epidemiologist has a helpful guide for the latter.

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  • National numbers, October 30

    National numbers, October 30

    BA.5 caused just under half of new COVID-19 cases nationwide in the last week, according to CDC estimates. But we have yet to see a new subvariant clearly take over.

    In the past week (October 20 through 26), the U.S. reported about 270,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 38,000 new cases each day
    • 81 total new cases for every 100,000 Americans
    • 2% more new cases than last week (October 13-19)

    In the past week, the U.S. also reported about 23,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 3,200 new admissions each day
    • 6.9 total admissions for every 100,000 Americans
    • 1% more new admissions than last week

    Additionally, the U.S. reported:

    • 2,600 new COVID-19 deaths (380 per day)
    • 27% of new cases are caused by Omicron BQ.1 and BQ.1.1; 8% by BF.7;  3% by BA.2.75 and BA.2.75.2 (as of October 29)
    • An average of 400,000 vaccinations per day

    The national COVID-19 picture continues to be somewhat murky, thanks in part to poor-quality data. Both nationwide cases and new hospital admissions trended slightly upward in the last week (by 2% and 1%, respectively); this could reflect the beginnings of fall surges in some places, but it’s hard to say for sure.

    Wastewater data from Biobot continue to suggest the Northeast is seeing more COVID-19 transmission than other parts of the country, though this region reported a decrease in viral levels over the last two weeks. Other regions are reporting plateaus in transmission, according to Biobot.

    One reason we’re not seeing a definitive national surge yet could be that the newest iterations of Omicron have yet to fully dominate the country. BA.5 caused just under half of new COVID-19 cases nationwide last week, according to the CDC’s latest estimates, but the remaining half of cases were driven by a variety of new lineages: BQ.1, BQ.1.1, BA.4.6, and BF.7 all contributed over 5%.

    When one of these subvariants (likely BQ.1.1) outcompetes the others, we will likely see a clearer picture of its impact on transmission. Also worth noting: XBB, the subvariant spreading quickly in Singapore and other Asian countries, has been identified in the U.S.—though its prevalence is too minimal to show up in the CDC’s estimates, at this point.

    New York is a hotspot again: the state has a higher prevalence of BQ.1 and BQ.1.1 than other parts of the country, and some experts are concerned about rising COVID-19 hospitalizations here. In New York City, official cases have remained relatively stable for the last few weeks even as hospitalizations are going up, suggesting how continued low testing may make cases even less useful as a metric to watch.

    This isn’t the only region seeing the start of a fall surge, though. The Twin Cities area in Minnesota reported a major spike in wastewater this week, with viral prevalence the highest it’s been since the original Omicron surge. Some counties in the South and West coast are showing similar warnings, according to Biobot’s dashboard.

    And COVID-19 isn’t the only respiratory virus wreaking havoc right now, as we’ll discuss more in this issue. Places like NYC are seeing rising hospitalizations from the flu and RSV, placing additional strain on an already-overburdened healthcare system. Even if the coronavirus doesn’t have a drastic surge this winter, we could still see a lot of respiratory infections.

    more national numbers