SARS-CoV-2 Update for Jan 31st
The situation in the United States continues to improve but absolute levels of cases and hospitalizations remain high. Daily vaccination numbers are increasing but need further increases.
The over-arching situation remains the same; it’s a race between vaccinations and variants. Daily vaccinations continue to increase and are at an all-time high of 1.34 million shots per day. 30.5 million total vaccination shots have been given and Bloomberg estimates that 7.5% of Americans have received their first dose and 1.7% have received their second dose.
This vaccination rate, while above previous expectations, needs further increases. Only 61.2% of distributed vaccinations have been administered. Until our supply is constrained (>85% of shots administered), we need to be vaccinating faster. At the current pace, it would take approximately one year to vaccinate 80% of Americans, image credit to Nate Silver.
Fortunately, there continues to be only positive news on vaccine development. This week saw the announcement of two positive Phase III trials for new vaccines, Johnson & Johnson’s and Novavax's.
Let’s focus on Johnson’s and Johnson’s. This trial took place in the United States, Latin America, and South Africa (so we have direct evidence of it’s quality against multiple variants). In these locales, the vaccine showed 72%, 66%, and 57% effectiveness, respectively. While these numbers are less than ideal, a vaccine’s effectiveness is measured by it’s ability to prevent infection. Infections are not optimal (obviously) but the more important quality is whether a vaccine can prevent severe disease and death. In the Johnson & Johnson trial, individuals were 100% protected from deaths (at 28-days post vaccination) and they were 100% protected from severe disease (at 49-days post vaccination). A vaccine that isn’t perfect at preventing infection but does prevent severe disease and death is still “a fantastic result,” according Dr. Scott Gottlieb. Even better, this vaccine only requires a single dose. Results summarized below by Dr. Akiko Iwasaki.
There are now five effective vaccines in the Western world, summarized below by Dr. Eric Topol. All are highly effective against the ‘original’ strain as well as B.1.1.7 (the ‘British variant’). Importantly, we now have evidence that the two new vaccines are effective against B.1.351 (the ‘South African' variant), though at reduced levels. This emphasizes both the quality of the current vaccines and the critical importance of administering them as rapidly as possible. Evolution is a continuous process. In 2020, we had one main strain that produced four concerning variants. In 2021, we have all four of those variants experiencing evolutionary pressures. The simplest and quickest way to limit viral evolution is to limit the total number of infections. The simplest and quickest way to limit total number of infections is population-wide vaccination.
Viral genomic surveillance is ongoing and changes by the day. So far, the P.1 (the ‘Brazilian variant’) has been identified in Minnesota (importantly, the patient has recently traveled to Brazil). More concerning is the identification of community spread (i.e. no history of travel) of B.1.351 (the ‘South African variant’) in both South Carolina and Maryland.
There is direct evidence that at least some of the new variants can cause a resurgence in even the hardest hit areas. If interested, I highly suggest this article published in The Lancet about the experience of Manaus, Brazil, which is currently experiencing a surge of cases despite 76% of the population having tested positive for antibodies (against the ‘original’ strain) in October 2020. A summary of the concerning variants is below.
There have been 26,076,032 total confirmed cases of COVID-19 in the United States. The seven-day average of daily cases continues to decline and is now 154,092. While this is a steep decline from peak daily cases, it is still ~3x the peak of the summer wave.
Testing remains inadequate but the situation is improving. We’ve reached a new all-time high in daily testing at 1.72 million tests per day. This is reflected in the positivity rate, which has now fallen to 8.8%.
Just as with cases, hospitalizations continue to rapidly decline but absolute levels remain high. There are 97,561 Americans currently hospitalized with COVID-19, the first time it’s been sub-100,000 since December 1st. 19,130 Americans are in the ICU with COVID-19.
Unfortunately, deaths are not resolving as quickly as cases and hospitalizations. Last week, 21,848 Americans died from COVID-19 and there have been 439,536 confirmed deaths in the United States. All available evidence suggests this number should be considered a minimum. For one example of this, a report from the Attorney General of New York estimates that New York State has undercounted nursing home deaths by as much as 50%. Most countries in the world report a gap between confirmed COVID-19 deaths and total excess deaths. A least some portion of this difference should be considered unconfirmed COVID-19 deaths.
Finally, our simple model of total United States immunity suggests 88.5 million Americans carry some immunity against SARS-CoV-2. Remember, this is a simple model [(confirmed deaths/0.6%) + (total vaccinations/2)] that doesn’t take into account a few factors (unconfirmed deaths, 1st vs 2nd doses of vaccination, the lag between vaccination and immunity, etc.). For now, it remains roughly accurate. Dr. Yougang Gu’s more complex modeling suggests 97 million Americans carry immunity. His full ‘Path to Herd Immunity’ page can be found here.
110M and 220M Americans having immunity are the estimated numbers for partial-herd and full-herd immunity (based on a total American population of ~330M). While full-herd immunity will greatly suppress case counts, it is likely that pandemic will not be fully resolved until 80-90% of the population carries immunity.
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