Coronavirus Tidbits #261, Sept 3, 2023


First, there is now a Resources Page here for the most commonly asked questions I'm getting.

Happy to continue to answer your questions/concerns as best I can, so don't be shy about that.


US Hospital Admissions 15,067

(August 13 to August 19, 2023)

Trend in Hospital Admissions

+18.8% in most recent week.  Jul 21, 2023Aug 19, 2023


% Due to COVID-19.  1.7%

(August 13 to August 19, 2023)

Trend in % COVID-19 Deaths

+21.4% in most recent week

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Upcoming new Covid vaccine booster

see Drugs and Vaccine section

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Limited data suggest rising global COVID-19 activity

Though case reporting doesn't accurately reflect COVID-19 activity because of decreased testing and reporting, the number reported over the past month increased by 63%, with increased cases reported in three regions, the World Health Organization (WHO) said in its latest weekly update yesterday.

During an online Q and A session today, Maria Van Kerkhove, PhD, the WHO's technical lead for COVID, said the latest update is the WHO's final weekly report as it transitions to monthly reporting.

[This is colossally stupid. Cases are going up and the reporting is going down. Who designed this x for deniability?]

Over the past month, only 44% of countries reported any cases to the WHO,...Of the 19 countries that regularly report data on hospitalization for COVID, eight reported increases of 20% or more compared to the previous month:

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Study helps explain SARS-CoV-2 variants' rapid spread

"The omicron variants that have become dominant over the past year, such as BQ.11 and XBB.1.5, have  for the receptor on host cells, angiotensin-converting enzyme 2, and they are able to fuse with the  and invade much more efficiently than previous SARS-CoV-2 omicron variants," Veesler said.

They have also been able to reinfect people who had been infected by earlier variants and break through the immune protection of vaccines designed to protect against the earlier variants. These reinfections and breakthrough infections are possible because the new variants can evade antibodies induced by exposure to the earlier variants, Veesler and his colleagues found. Such antibodies, called neutralizing antibodies, prevent infection by quickly clearing an invading virus before it can become established.

However, the researchers also found that previous infection or vaccination did help to generate antibodies that recognized some of the proteins found on newer variants. These antibodies successfully activate  that eradicate infection by killing and eliminating infected cells.

This  may explain why previous exposure to earlier variants or vaccination against them appears to reduce the risk of serious illness, hospitalization, and death with reinfection by a newer variant, Veesler said.

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BA2.86, aka "Pirola" and FLip variants

recently-dominant XBB.1.5, now BA.2.86, which emerges from BA.2 with a long branch, with over 30 spike mutations of unobserved evolution.

There is some unanticipated cross-reactivity of XBB.1.5 antibodies, which forecasts better for the new booster
     --@BenjMurrell and @EricTopol
The more immediate concern than BA.2.86 now are the FLip combo variants of #SARSCoV2... Together, but not alone, the spike binds more avidly to ACE2, the cell receptor for the virus...this FLip combo mutation also leads to further reduction of neutralizing antibodies. This certainly suggests this evolution of the virus will be more troubling than EG.5.1

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CIDRAP: High levels of 2 blood-clotting proteins may portend post-COVID brain fog "One in eight patients receives their first ever neurological or psychiatric diagnosis within 6 months following COVID-19,"
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Clotting proteins linked to Long Covid’s brain fog

Study of unvaccinated people hospitalized with COVID-19 bolsters theory that blood clots may contribute to cognitive problems months later


Along with physical fatigue, “brain fog” has become one of the best known manifestations of the condition known as Long Covid. Yet it’s still unclear why some people infected with SARS-CoV-2 develop cognitive problems—which can include trouble concentrating and remembering—and others don’t. Now, a large study of people hospitalized with COVID-19 early in the pandemic has identified two proteins involved in blood clotting, fibrinogen and D-dimer, that are associated with cognitive deficits up to 1 year postinfection.

The findings, published today in Nature Medicine, are an “important advance” for scientists’ understanding of how Long Covid develops, says Steven Deeks, a physician-scientist at the University of California, San Francisco (UCSF), who was not involved in the work. Combined with previous research, the study supports the theory that blood clots triggered during the acute stages of viral infection could lead to lingering symptoms such as brain fog. Deeks cautions, however, that the study’s focus on unvaccinated people who had severe COVID-19 may limit relevance for the wider population; many people with Long Covid had milder initial infecti—they aren’t represented in the research.

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COVID infection risk rises the longer you are exposed — even for vaccinated people

Rigorous evidence shows that significant contact with a person with SARS-CoV-2 is more likely to lead to transmission than a short encounter.

Nature  Anil Oza   30 August 2023

Prolonged exposure in close proximity to someone with COVID-19 puts people at high risk of catching the disease, even if they’ve had both the disease and vaccinations against it, a study1 shows.

The study, published this month in Nature Communications, reveals that the greater a person’s exposure to SARS-CoV-2, the more vulnerable they are to infection, regardless of their vaccination status. This relationship has long been suspected, but the study is one of the first to document it.

The findings point to the importance of masking, improved ventilation and other measures that reduce exposure to the virus, says Akiko Iwasaki, an immunobiologist at Yale University in New Haven, Connecticut, who was not part of the study.

The finding “just makes intuitive sense,” she says. “But now there’s evidence that these [measures] are probably going to be important to help the vaccine-mediated immunity work for you.”

Close contacts

Scientists have speculated since the start of the pandemic that the likelihood of SARS-CoV-2 infection correlates with the amount of virus that a person is exposed to. But verifying this relationship has been difficult because of the challenges in quantifying how much time people spend in close contact with others, and in tracking infections after such contact.

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Native Americans at outsized risk of severe COVID-19, death

An observational study published yesterday in PNAS Nexus reveals that American Indian/Alaska Native (AI/AN) COVID-19 patients were three times more likely to become severely ill than their White or Hispanic peers and had more than double the risk of in-hospital death—despite being younger and having fewer chronic conditions.

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NIH Research: SARS-CoV-2 can cause lasting damage to cells’ energy production


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Long Covid:

was on to explain the complexities of this illness so well! We talked about #LongCovid’s mechanisms (incl viral persistence, blood vessel damage), stigma, & urgency for clinical trials *now*
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Experts encourage US states to create legislation aimed at improving indoor air quality in public spaces 

 Model State Indoor Air Quality Act as a legal framework for states and localities to implement legislation to allow for IAQ inspections and publicly posted monitoring results, actions that will lead to improved IAQ in public buildings.

The model act provides a comprehensive framework for states to create legislation aimed at improving IAQ by:

  • Setting up a state advisory council to set standards appropriate for states' needs.
  • Requiring indoor air quality be measured and the results posted publicly.
  • Establishing a system for people to report health impacts potentially caused by bad air and for the state to investigate these reports and order necessary fixes.

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Nightmare TB outbreak in Kansas:

CDC Details Multidrug-Resistant #TB Outbreak in an Unlikely Spot - Rx needed 26 weeks of bedaquiline, pretomanid, linezolid, and moxifloxacin (BPaLM).


global sequencing #SARSCoV2 down to 1% of what it was 2 years ago,

-- @EricTopol 8/29

Drugs and Vaccines:

The new XBB.1.5 monovalent booster, to be available in ~2 weeks, appears to elicit a good immune response vs EG.5.1 and FL.1.5.1
    @EricTopol. 9/1
there is very close alignment between XBB.1.5 and EG.5.1 except for 2 new mutations in the latter: F456L and Q52H. Accordingly, the new Covid booster should be very effective vs severe Covid. On the other hand, the BA.5 spike has more than 15 different mutations than either of the newer variants, which not only reflect further evolution of the virus, but also how poorly aligned that bivalent BA.5 booster is with the virus circulating now. Even with FLip gaining traction, we’d be far better off with the new XBB.1.5 monovalent booster than what we have now.
 The FLip double whammy exploits 2 ways at once with tighter binding to the receptor and incremental immune evasion.
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Should I wait until October for my shot?

While scientists evaluate the effectiveness of the updated COVID vaccines, the CDC urges people to get their shots this fall to reduce the risk of  and hospitalization.

"It may not be as good as if we had a specific vaccine designed for that variant with its mutations," but the updated vaccines should offer some decree of cross protection immunity, Dionne says.

While there was an uptick in COVID cases this summer, winter is when the illness typically spreads widely as people gather indoors and for holiday celebrations.

"COVID does not have the same seasonality as flu, where we see very little in the summer," Dionne says.

"But it does seem to have a degree of seasonality where we do see more cases in the winter, which probably has to do with the increased risk of transmission," he says.

To time vaccinations to achieve full effectiveness in advance of holiday gatherings that start in November, both Dionne and Maniar say people might want to wait to be vaccinated until later in October, just before Halloween.

It typically takes about two weeks to get a full vaccine response, although it may be shorter for a booster, Dionne says. "A week or two weeks is probably on the safer end to have that full antibody response."

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Many say that it is better to get the Covid vaccine in the same arm as previously.
You can also get the flu shot and new RSV vax at the same time.
Monoclonal antibodies won't work against the Omicron strains--which are now the only ones circulating
Paxlovid should still work
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Data show that immunity induced by vaccines, prior infection or both (hybrid) protects against SARS-CoV-2 infection when viral exposure is low to moderate.
Prior infection, vaccination, or both provided significant protection against infection when the exposure was moderate (index case was within their cellblock) or low (no exposure was documented in cellblock co-residents) against Delta or Omicron. (4/)
However, when the viral exposure was intense (with infected cellmate - exposure is 24/7), none of these groups had enough immunity to protect against infection with Delta or Omicron virus. (5/)
These findings suggest that protection conferred by prior infection and vaccination is dependent on the cumulative viral exposure dose. An important question for the future is to determine how much the viral load vs. duration of exposure plays a key role. (6/)
If the protection is indeed dose-dependent, coupling non-pharmaceutical interventions with vaccination would be beneficial because the non-pharmaceutical intervention (masking, ventilation, etc..) reduces viral exposure, resulting in improved levels of conferred protection. (7/)
Their findings suggest the “need for layered interventions to mitigate SARS-CoV-2 spread, especially within dense settings, such as congregate settings, and in settings where prolonged contact is likely, such as households with infected people.” An important message to end thread.
   --Akiko Iwasaki   @VirusesImmunity 8/27


 “Air Quality Is The Issue of Our Time.”

Gift article

--Linsey Marr, and convo w Eric Topol:

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Wear a respirator, not a cloth or surgical mask, to protect against respiratory viruses

Epidemiology/Infection control:

Nearly half of phones tested during pandemic carried COVID-19 virus, finds systematic review

Almost half of mobile phones tested at the height of the pandemic were contaminated with the SARS-CoV-2 virus, bolstering a theory that the devices supercharged the spread of COVID-19.

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Nosocomial (Hospital-acquired) infections:

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North Carolina: “43 staff members who either work directly at the new Scarborough Center or come in and out for work are sick, and 26 staff members are COVID positive.” h/t @MeetJess
   --@LauraMiers   Aug 26
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The CDC wants to weaken masking and infections controls when tuberculosis increased 5% among all ages and 26% in American children 0-4 last year.
   -- @LauraMiers   Aug 21
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We've summarized the literature supporting airborne transmission of COVID-19 & several other respiratory pathogens. Guess what? #COVIDisAirborne #FluisAirborne #SARSisAirborne #MERSisAirborne Live version of table & refs:
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@MeetJess   Aug 29
Covid Outbreak Prompts Restrictions At Hawaii’s Largest Prison
So far 58 prisoners have tested positive. H/t ⁦
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@MeetJess   Aug 29
COVID-19 outbreak reducing hours at Montague hospital emergency department
We would rather reduce hours in an emergency department than REINSTATE MASKS to reduce outbreaks. What in the fk are we doing anymore?
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@luckytran   Aug 30
People often say COVID cases are rising but there are far fewer cases than any other time. Wastewater shows that's false. There are far more cases now than the first summer of the pandemic, and this year's pattern is ominously similar to the lead up to the huge Omicron surge.
Show this thread
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@gwladwr   Aug 31
Covid hospitalisations in Wales... In the week ending 27 August 2023 at least 47% were the result of hospital acquired (nosocomial) infection.
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@19joho   Aug 31
In the past week, covid has closed schools in: Texas, Kentucky, Tennessee, Indiana, and now Oklahoma. The “open schools” bros don’t care. Cause schools were an excuse for them to bash Democrats and teachers unions.
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@MeetJess   Sep 1
As COVID-19 cases slowly rise again, 1 in 4 nursing homes in N.J. report an outbreak This boils my blood ⁩

Tips, general reading for public:






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Here's a great set of tips on how best to write legislators -- what they pay attention to, and more: (from @watermelonpunch)
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Researchers are trialing Paxlovid for LongCovid patients 5 months after we learned variants are already developing resistance to Paxlovid, and fewer than 5% of infected Americans have been able to access Paxlovid.
   -- @LauraMiers   Aug 26
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Commenting on Mandy Cohen:
"Things look so much rosier when illuminated by gaslight."
   --@CthulhuKnows  8/28
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”Ending routine masking in #hospital settings is dangerous move” -

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Great thread by Martha Linoln, aka @heavyredaction
They’ve gone under the radar—but “We’re in a different/a better place” are admin talking points, sometimes used in parallel to “we have the tools.” Jha, Walensky, Becerra, Murthy, Biden, and the WH press secretary have all invoked the idea of being in a better/different place
For example, here is one set of comments about being in “a better place” by Joe Biden on Jan 19, 2022—in the middle of the Omicron wave, with 144,441 people hospitalized with COVID per WH data on Jan 18 (21,111 of whom had been hospitalized on that day alone)
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In the genre of “another brick in the wall,” it is now officially institutionalized and being socially normalized to coerce children to attend school while unwell, just as their parents are expected to labor through illness. Inhumane and unsustainable.
Before 1965, married couples in the United States did not have the legal right to use birth control. A wife needed her husband's permission to purchase any kind of contraception. 1965 was also the year “The Pill” became available.
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@MarkJacob16   Sep 1
Forced-birth extremists in Texas are passing laws banning use of public roads to take someone out of state to get an abortion. Don't let anyone tell you the right wing promotes personal freedom. It's quite the opposite.
(Free WaPo article)
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Horseshoe Crab Blood in Drug Safety Testing? It May Not Be Needed Much Longer

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@SDonziger   Aug 26
Incredible that dozens of countries are consideringmaking "ecocide" an international atrocity crime with the same legal force as genocide. This is one of my 5 recommended legal reforms that can be key in saving the planet. Stunning progress by the @EcocideLaw campaign.
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@SDonzige   Aug 29
In a huge win for the planet, 18 jurists from the UN have found that children can sue their own countries over climate change under a treaty called the Convention on the Rights of the Child. Children are now leading a powerful global shift in the law on climate
Little by little, courts and legal experts are beginning the long process of truly holding the fossil fuel industry accountable for its destruction of the planet. Here's one way students and youth are leading a global paradigm shift in the law:
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FDA/Drug expirations:
@propublica   Aug 26
It turns out that the FDA, the agency that helps set drug expiration dates, has long known the shelf life of some drugs can be extended, sometimes by years. In fact, the federal government has saved a fortune by doing this.
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@mehdirhasan  8/29
Second-biggest owner of Twitter is executing a man for his tweets. Silence from the owner of Twitter, who is a self-styled ‘free speech absolutist.’ Not even a “concerning”.
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@tomaskenn   Aug 27
DeSantis, who has given billions in corporate tax giveaways to his special interest donors, is saying that he is counting on people dying early to not pay them Social Security and Medicare.
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North Carolina:
@SIfill_   Aug 30
Do not ignore this. The NC Judicial Commn is investigating a Black woman Supreme Court judge b/c of her publicly stated support for diversity. The Commn is pursuing a complaint that her statements undercut the public’s confidence in Judge Earl’s impartiality! She’s fighting back.

Feel good du jour:

Comic relief:

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