Weekly coronavirus-related chat, questions, and minor updates - week of May 16

The Covid Capitulation (Eric Topol)

The real number of cases is likely at least 500,000 per day, far greater than any of the US prior waves except Omicron. The bunk that cases are not important is preposterous. They are infections that beget more cases, they beget Long Covid, they beget sickness, hospitalizations and deaths. They are also the underpinning of new variants.

Meanwhile, the CDC propagates delusional thinking that community levels are very low (as my friend Peter Hotez called the “field of greens”) while the real and important data convey that transmission is very high throughout most of the country. Not only does this further beget cases by instilling false confidence, but it is conveniently feeding the myth that the pandemic is over—precisely what everyone wants to believe.

As of last week, 43% of new cases were attributable to BA.2.12.1 and this subvariant had reached dominance (>50% of cases) in only one region of the country. BA.2.12.1 is out-competing BA.2 with its 25% higher transmission rate, which foretells its further rise to dominance across the US in the days and weeks ahead.

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[…] 40-50% of Americans were infected with BA.1 (or BA.1.1) and without added protection from vaccination, they will be vulnerable to BA.2.12.1 infections. It is further worth mentioning that the Omicron-specific booster vaccines in the hopper, thought to be due out in July, are BA.1 directed and may not provide strong protection against BA.2.12.1 or whatever new Omicron subvariant (or not Omicron related) we will be dealing with this summer. It remains to be seen whether BA.4/BA.5 can outcompete BA.2.12.1, with the former now at low levels in the US.

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Prior to Omicron we could, with a booster, assume there was well over 90-95% vaccine effectiveness vs severe disease. It is clear, however, from multiple reports, including the UK Health Security Agency and Kaiser Permanente that this level of protection has declined to approximately 80%, particularly taking account the more rapid waning than previously seen. That represents a substantial drop-off: instead of a gap or “leak” of 5%, it is about 4-fold at 20%. And we don’t yet know how well vaccines are still holding up with the BA.2.12.2 and BA.4/BA.5 variants.

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Not only are [Omnicron variants] providing further seeding grounds for more variants of concern, but that path is further facilitated by tens of millions of immunocompromised people around the world, multiple and massive animal reservoirs, and increased frequency of recombinants—the hybrid versions of the virus that we are seeing from co-infections. As difficult it is to mentally confront, we must plan on something worse than Omicron in the months ahead.

State of Affairs: May 16 (Your Local Epidemiologist)

South Africa. The BA.4/5 subvariant leader continues to report exponential growth in cases and hospitalizations, although decoupling between the two metrics continues to widen. Death counts are at their lowest levels since the beginning of the pandemic and, thus far, high levels of BA.1 Omicron immunity are keeping deaths down. It will be important to continue to watch, as death counts are lagged.

Australia and New Zealand. Two other Southern Hemisphere countries entering the winter season, Australia and New Zealand, are getting hammered with infections. Deaths have begun to increase, but thanks to their successful vaccine campaign during lockdown, cumulative deaths remain incomparably low. (Side note: We are seeing the comeback of flu down in Australia, which is always an early sign of what is to come in the fall for the U.S.)

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Cases are increasing in all states. If we assume uniform testing behaviors (and thus underreporting) across states, our case leader is Puerto Rico, which is getting hammered with infections but recently reached their peak. This is followed by Rhode Island and Massachusetts. Interestingly, if we compare U.S. states to 195 countries, 18 of them would currently be among places with the highest new cases per capita in the world.

Case accelerations are not regional, but occurring across the country. The acceleration leader is Mississippi (+224%) followed by Missouri (+211%), Utah (+169%), South Carolina (+152%), Arizona (+134%), and Louisiana (+131%). To me, the lack of regional patterns is a sign of a true national wave.

The current surge is at least partially due an increase in reinfections, as Omicron is getting better and better at dodging our first line of defense. The CDC's last update on reinfections was in January, but the story is very clear among local jurisdictions tracking this data closely. In Colorado, for example, 82% of reinfections have occurred since Omicron with the majority among unvaccinated. Starting in March 2022, North Carolina reported an increase in reinfections. In Indiana and Idaho, reinfections account for 12-18% of reported cases.

Hospitalizations are also increasing with a +23% change in the past 14 days. It will be very interesting to see how the rate soon changes (or doesn’t change) as hot spots move to less vaccinated parts of the U.S. As seen in the graph below from New York City, there continues to be a large discrepancy between unvaccinated and vaccinated.

Unfortunately, severe disease is not the only outcome. While evidence continues to show that vaccinations reduce risk of long COVID by ~50%, the most recent UK Health Security report found even those boosted aren’t spared. Among the triple vaccinated, 8-9% of people report long COVID (at least 4 weeks) after their first infection; 5-6% are reporting activity-limiting symptoms. There doesn’t seem to be a statistical difference between variants.

She gives a source for the estimate of 500k US cases a day. It’s this graph from the IHME at the University of Washington. There is large uncertainty in that projection, which isn’t displayed by default, but you can turn it on. I haven’t looked into how this is calculated.

Out of curiosity have any younger folks here gotten their second booster? I'll be traveling for work in early June and after reading everything am interested in a second booster if they will give me one.

US residents can order another set of 8 free COVID tests through the USPS. (Direct link to the order page)

Also, I haven’t been following things as closely as I used to. Is there any evidence that the current rise in cases is linked to fading immunity from prior infection/vaccines?

CDC urges older Americans to get Covid booster shots as hospitalizations soar again (CNBC)

The Centers for Disease Control and Prevention this week urged older Americans to get a Covid booster shot to increase their protection against the virus amid another surge in hospitalizations, particularly among those 70 and older.

“Over the past few weeks we’ve seen a steep and substantial increase in hospitalizations for older Americans,” CDC Director Dr. Rochelle Walensky told the public health agency’s committee of independent vaccine experts during a public meeting on Thursday.

Only 43% of people ages 65 and older have received a vaccine dose in the past six months and just 38% of people ages 50 to 64 have done so, Walensky said.

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Walensky said people ages 50 and older should get a fourth Covid shot, and those 12 and older with weak immune systems should get a fifth shot.

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Hospitalizations have increased 25% among those 70 and older over the past week, with more than 1,500 people in the age group admitted with Covid per day on average as of Tuesday, according to CDC data. The U.S. is reporting more than 100,000 new Covid infections per day on average, an 18% increase over the week prior, as more transmissible omicron variants weep the U.S.