Writing (56)
No, 73% of US COVID-19 cases aren’t Omicron yet: how the press got it wrong

Something extremely odd happened this afternoon.  The press, including the New York Times, the Washington Post, CNN, the Wall Street Journal, USA Today, and Axios, reported that the CDC had announced that 73% of US COVID-19 cases were now being caused by the Omicron variant, and major public health gurus like Ashish Jha, Eric Topol, Florian Krammer, Eric Feigl-Ding, and Scott Gottlieb circulated the reports at face value. But that’s not really what’s happening.  There was some kind of b

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Breaking data: Omicron evades immunity to spread explosively, but is less transmissible than Delta; vaccines still help

Since my previous post about Omicron just eleven days ago when the news first broke of its existence, we've learned what the deal is, thanks to amazing feats of rapid research on a number of fronts by scientists coordinating around the globe and working around the clock.  Although much remains to be learned, the broad brushstrokes about what Omicron is and what's going to happen, things we didn't know eleven days ago but will still be true and important months from now, have emerged. Here's

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The new Omicron strain of COVID-19 could be really bad, and we may not know how bad for weeks

A new COVID-19 variant has been identified with some very concerning features. Dubbed Omicron, it’s rapidly spreading in the southern region of Africa and an increasing number of countries around the world, and the news has rocked government policy and financial markets over the last two days. Despite the drama, however, we don’t yet know very much about just how bad Omicron is, and the range of possibilities remains very wide. So I'm going to break down this rapidly evolving situatio

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Full approval of the Pfizer vaccine will legalize off-label dosing for kids, boosters

Update, 08/23/2021, 3 PM Eastern: In the hours since the publication of this piece, both the FDA and the American Academy of Pediatrics have come out strongly against off-label dosing of children below 12 years old with the Pfizer vaccine.  Acting FDA Commissioner Janet Woodcock described it as a matter of "great concern."  The AAP's announcement came as something of a surprise given the AAP's previously stated stance in favor of approval of the vaccine for kids based on data already in han

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COVID-19 and the Delta variant: what you need to know in August 2021

Like many of you, we’ve been enjoying a summer with small slices of normality. But, as we predicted, things are quickly getting worse again --- some areas are already at the worst levels they’ve been in the entire pandemic --- as the Delta variant and bad actors within our society continue to do damage. This post brings you up to speed on what’s changed and what you need to know. Summary: The vaccines work and all available data says they are safe. Anyone who tells you otherwise

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The numbers on COVID-19 spread in the USA are extremely heartening right now, despite the ongoing high levels of cases and deaths, because they are falling so fast. Right now, only three states have rising numbers, and the estimate of nationwide R from the friendly folks over at epiforecasts.io has plunged all the way down to .84, which corresponds to a halving time of only sixteen days. This data includes time from several weeks of school being open in person. At this rate, if R just stays where it is, we will hit a pandemic-era low in cases some time between Thanksgiving and Christmas, and keep dropping from there. And there is, so far, still no sign of a successor strain to Delta. The latest data continues not to show any other variant threatening to spread more efficiently than Delta, which now makes up 99.9% of US cases. Remember Mu? Last week no laboratory in the USA sequenced any cases of Mu. And we’re about to have the power to make big strides toward pushing R down by boosting adults and vaccinating children, approvals for which are likely coming in just a few weeks. Vaccinating children, especially, will take a large percentage of the population that can still spread COVID-19 off the table, and a majority of parents say they intend to vaccinate their kids swiftly after approval. Right now there’s a little bit of a cargo cult thing going on in the media, where people take it as read that there will be another big surge this winter in the USA, because they overestimate the seasonality effect of COVID-19 (which appears to be pretty modest) and as a mindless imitation of the thing they have seen actual experts do, where you point to a chart and say “aha, a surge is coming.” They’re doing things like “with Delta, and kids going back to school, we’ll see a major surge,” not realizing that those things already happened and we’re not seeing a surge. But in reality, it appears far from clear there will be one. In fact, if we swiftly vaccinate the majority of children and boost the majority of vaccinated adults, and don’t see a major new strain, I’d say it’s probably impossible. There is a future. We can vaccinate everyone, kill the virus, and end the pandemic. And, although too slow and imperfectly, and with a portion of the population choosing to vaccinate themselves by getting COVID-19, that is what we are doing. It can’t happen fast enough.

Yes, in the sense that it’s harder.  The calculations about the herd immunity threshold from my articles late last year and earlier this year are still true, but Delta lowers the transmission efficacy of the vaccine and increases R0, raising the threshold.  This is why you’ve seen Delta grow, even as Alpha and the wild type and so on have been nearly exterminated in the USA.  We did get herd immunity to those strains! There have been some panicked discussions from some experts saying that herd immunity is not possible with Delta; this comes from the fact that with some efficacy numbers and R0 numbers, herd immunity is not attainable even with 100% vaccination or infection. I don’t think this is likely to be true with Delta in the long run, however.  I could easily be wrong (as I mentioned, many experts don’t agree), but I don’t think so.  For one, we see some countries getting control of Delta outbreaks without a lot of containment; India is an example of this right now, with society still largely open and cases and deaths down tenfold despite only a third of people vaccinated.  But also, the reduced vaccine efficacy with Delta is unlikely to persist for that long, since Delta-adapted vaccines are already in Phase 2 trials and should be coming this year.  We have every reason to believe that a Delta vaccine will be as effective against Delta as the original vaccine is against the wild type. So, my best guess is, herd immunity is harder but we do still get there.


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The numbers on COVID-19 spread in the USA are extremely heartening right now, despite the ongoing high levels of cases and deaths, because they are falling so fast. Right now, only three states have rising numbers, and the estimate of nationwide R from the friendly folks over at epiforecasts.io has plunged all the way down to .84, which corresponds to a halving time of only sixteen days. This data includes time from several weeks of school being open in person. At this rate, if R just stays where it is, we will hit a pandemic-era low in cases some time between Thanksgiving and Christmas, and keep dropping from there. And there is, so far, still no sign of a successor strain to Delta. The latest data continues not to show any other variant threatening to spread more efficiently than Delta, which now makes up 99.9% of US cases. Remember Mu? Last week no laboratory in the USA sequenced any cases of Mu. And we’re about to have the power to make big strides toward pushing R down by boosting adults and vaccinating children, approvals for which are likely coming in just a few weeks. Vaccinating children, especially, will take a large percentage of the population that can still spread COVID-19 off the table, and a majority of parents say they intend to vaccinate their kids swiftly after approval. Right now there’s a little bit of a cargo cult thing going on in the media, where people take it as read that there will be another big surge this winter in the USA, because they overestimate the seasonality effect of COVID-19 (which appears to be pretty modest) and as a mindless imitation of the thing they have seen actual experts do, where you point to a chart and say “aha, a surge is coming.” They’re doing things like “with Delta, and kids going back to school, we’ll see a major surge,” not realizing that those things already happened and we’re not seeing a surge. But in reality, it appears far from clear there will be one. In fact, if we swiftly vaccinate the majority of children and boost the majority of vaccinated adults, and don’t see a major new strain, I’d say it’s probably impossible. There is a future. We can vaccinate everyone, kill the virus, and end the pandemic. And, although too slow and imperfectly, and with a portion of the population choosing to vaccinate themselves by getting COVID-19, that is what we are doing. It can’t happen fast enough.

Yes, in the sense that it’s harder.  The calculations about the herd immunity threshold from my articles late last year and earlier this year are still true, but Delta lowers the transmission efficacy of the vaccine and increases R0, raising the threshold.  This is why you’ve seen Delta grow, even as Alpha and the wild type and so on have been nearly exterminated in the USA.  We did get herd immunity to those strains! There have been some panicked discussions from some experts saying that herd immunity is not possible with Delta; this comes from the fact that with some efficacy numbers and R0 numbers, herd immunity is not attainable even with 100% vaccination or infection. I don’t think this is likely to be true with Delta in the long run, however.  I could easily be wrong (as I mentioned, many experts don’t agree), but I don’t think so.  For one, we see some countries getting control of Delta outbreaks without a lot of containment; India is an example of this right now, with society still largely open and cases and deaths down tenfold despite only a third of people vaccinated.  But also, the reduced vaccine efficacy with Delta is unlikely to persist for that long, since Delta-adapted vaccines are already in Phase 2 trials and should be coming this year.  We have every reason to believe that a Delta vaccine will be as effective against Delta as the original vaccine is against the wild type. So, my best guess is, herd immunity is harder but we do still get there.

Sure.  🙂 I said “all” because that was the information I had at the time.  I wrote before the Lancet article saying otherwise was published. Despite this information, the vast majority of early cases still have the link, and our sources in China (posts upcoming) have told us that testing of surfaces in the market showed significant amounts of coronavirus.  It’s not necessarily the case that every early case will show a link, both because 1) not every wild animal sold for food in Wuhan went through the one market, 2) not every single person will be candid about their history when speaking to doctors, and 3) not every transmission link to the market is legible.  If the disease began spreading earlier than we previously thought, then this point is reinforced, although the Lancet paper only pushes that date back 7 days relative to previous reports. Any analysis of a “first case” has to be interpreted in light of our degree of confidence about which case actually was first.  With estimates of the ascertainment rate (percentage of cases known to authorities) in the early epidemic down in the single digits, we can’t have that confidence. Although the situation is messy, the market origin hypothesis continues to be a clear leader.  And the people who say “no market origin” aren’t accounting for the facts.  The Lancet paper only says that they found no epidemiological link between the first known case and subsequent cases, not that he had no exposure to the seafood market.  And they say that 14 of the first 41 patients were not directly exposed to the market, not that they were not indirectly exposed, e.g. in the identified family cluster.  And that’s why the Lancet paper’s discussion teaches toward the market hypothesis. There’s a lot of noise out there, but the signal is still clear.