PlagueWatch 2020-23 - Coronavirus

[sagegrouse]

This article in the Sunday NY Times talks about the efforts -- personal intervention and widespread sequencing analysis -- that is going on in South Africa in effort to find Covid variants.

Even one HIV-positive person not taking antiretroviral medications can become a long-term brewery for variants in COVID, and S. Africa has a huge number of HIV-positive persons (8 million, or 13 percent).

The sequencing analysis directs the human investigators to find the source of variants within the population.

There is much more in the article. This is an eye-opening account and would appreciate others' opinions on it.

[MChambers]

This article in the Sunday NY Times talks about the efforts -- personal intervention and widespread sequencing analysis -- that is going on in South Africa in effort to find Covid variants.

Even one HIV-positive person not taking antiretroviral medications can become a long-term brewery for variants in COVID, and S. Africa has a huge number of HIV-positive persons (8 million, or 13 percent).

The sequencing analysis directs the human investigators to find the source of variants within the population.

There is much more in the article. This is an eye-opening account and would appreciate others' opinions on it.

Great article. Thanks for sharing.

It is eye-opening. The article seems to assume that the omicron variant originated in South Africa, but that hasn't been proven yet. It may be that it originated somewhere else, traveled to South Africa, and was detected there because of South Africa's strong detection capabilities. Unfortunately, the US is not doing a very good job on detection of variance, to put it politely.

[cato]

Great article. Thanks for sharing.

It is eye-opening. The article seems to assume that the omicron variant originated in South Africa, but that hasn't been proven yet. It may be that it originated somewhere else, traveled to South Africa, and was detected there because of South Africa's strong detection capabilities. Unfortunately, the US is not doing a very good job on detection of variance, to put it politely.

It has not been proven yet, but I read last week an analysis by a doctor is South Africa that proposed this exact possibility: that Omicron originated in a person with untreated HIV. One reason was that the types of mutations were somehow similar to what they have seen in other cases where they know that SARS-Cov-2 mutated in someone with untreated HIV.

As for US sequencing, my understanding is that the US is doing a much better job than even 6 months ago. The speed with which the first detected omicron cases in the US went from the patient testing positive to sequencing to confirmation was a testament to confirmation was reassuring.

[JasonEvans]

Interesting early data from the SAfrican hospital at the center of Omicron: https://www.statnews.com/2021/12/04/...h-africa-data/

Strikingly, most hospitalized patients who tested positive for Covid did not need supplemental oxygen. Few developed Covid pneumonia, few required high-level care, and fewer still were admitted to intensive care. The report included an analysis of 42 Covid patients in the hospital on Dec. 2 which showed that most were actually hospitalized for other medical reasons; their infections were only detected because hospitals are testing all incoming patients for Covid. Many did not have respiratory symptoms. And the average length of hospital stay was 2.8 days, far shorter than the average of 8.5 days recorded in the region over the past 18 months, the report said.

I've also heard some reports that the vaccinated seem to be recovering from Omicron faster and that they are not experiencing serious symptoms. That said, it is abundantly clear that Omicron spreads really, really fast... like leaving Delta in its dust fast. That's scary.

https://www.voanews.com/a/south-afri...-/6340912.html

Unvaccinated people are particularly susceptible to omicron, as are individuals who have not been exposed to COVID-19 before, disease specialist Sanne said.

“At this time, we think about 75% to 80% of hospitalizations are unvaccinated," he said. "It could be as large as 40% of the population that has not yet either been vaccinated or had a previous infection with coronavirus up until now,” he noted. “So, we have a large pool of people who can still present with overwhelming infection and severe disease,” he said.

Since detection of the variant was first announced in southern Africa last month, scientists have been hoping that most cases would be mild.

Health authorities say omicron is re-infecting some people who have been vaccinated, but mostly their symptoms are not severe.

One of the country’s top epidemiologists, Salim Abdool Karim, told VOA that current vaccines should provide “good protection” against omicron.

[Bluedog]

Interesting early data from the SAfrican hospital at the center of Omicron: https://www.statnews.com/2021/12/04/...h-africa-data/



I've also heard some reports that the vaccinated seem to be recovering from Omicron faster and that they are not experiencing serious symptoms. That said, it is abundantly clear that Omicron spreads really, really fast... like leaving Delta in its dust fast. That's scary.

https://www.voanews.com/a/south-afri...-/6340912.html

Sounds like we'll nearly all be getting it at some point (bad news), but that early data suggests if you're vaccinated, it's not too much of a concern for severe illness (good news). I frankly see that as good news overall although if quarantine procedures on close contacts are still in the same spot, we're going to be seeing a LOT of class/school closures perhaps in the upcoming months....But as someone posted above, perhaps a super transmissible but not very severe variant will help us get out of this thing as it won't be the health crises from other variants (maybe)....until the next variant.

[Skydog]

If Omicron really is much milder than previous variants it may turn out to be the best vaccine of all. Of course it is waaay too early to tell but it seems possibly true. Wouldn’t it be great to get some good Covid news for a change?

[Bluedog]

I got the Pfizer booster this weekend after having received the two doses of Moderna in the spring, and my side effects from the booster were MUCH less than dose #2. Sore arm and a little headache/tired from booster which was greatly preferred to fever/chills/body ache/sore arm/headache after dose #2. Not scientific, but was happy with that outcome and feel more protected now. Don't know if it was the lower dosage/change in manufacturers or what but from studies, that combo produced 11x antibody levels compared to MMM which produced 10x (where the third M was 100 micrograms in the study, while Moderna's booster ended up being 50 micrograms, so probably would have been less I'd imainge), so am happy with my choice I guess from a protection/side effect perspective. Obviously, 11x vs. 10x is certainly negligble.

[MChambers]

I got the Pfizer booster this weekend after having received the two doses of Moderna in the spring, and my side effects from the booster were MUCH less than dose #2. Sore arm and a little headache/tired from booster which was greatly preferred to fever/chills/body ache/sore arm/headache after dose #2. Not scientific, but was happy with that outcome and feel more protected now. Don't know if it was the lower dosage/change in manufacturers or what but from studies, that combo produced 11x antibody levels compared to MMM which produced 10x (where the third M was 100 micrograms in the study, while Moderna's booster ended up being 50 micrograms, so probably would have been less I'd imainge), so am happy with my choice I guess from a protection/side effect perspective. Obviously, 11x vs. 10x is certainly negligble.

Maybe Pfizer's shots have a smaller microchip?

[Dr. Rosenrosen]

Maybe Pfizer's shots have a smaller microchip?

I think it just has smarter AI embedded. So it knows how to avoid all forms of detection.

Maybe this also explains the global microchip shortage. Hmmm…

[budwom]

Got to playing with some numbers today (dangerous) as Vermont rose to the second highest per capita case count in the country, per the CDC website. Florida now sits second from the bottom in case counts.
Did it turn out to be unwise for Vermont to lock down as much as it did during most of the pandemic?
Probably not...while case counts are very high here, deaths are not at horrible levels...on a per capita basis, it would appear that Florida's more hands off approach resulted in about 4.4x the number of deaths on a per capita basis.

Meanwhile the VT gov is saying that we test at far greater rates than almost every other state....he claimed (IIRC from his press conference) that Vermont is testing the most in the country, and the tenth place state only tests 1/3 as much as VT, so that's his current claim...nonetheless, we just hit a high for hospitalized patients, and patients in the ICU. Back under the bed for me.

[Section 15]

Got to playing with some numbers today (dangerous) as Vermont rose to the second highest per capita case count in the country, per the CDC website. Florida now sits second from the bottom in case counts.

The line it is drawn
The curse it is cast
The slow one now
Will later be fast
As the present now
Will later be past
The order is rapidly fadin'
And the first one now
Will later be last
For the times they are a-changin'

[Bluedog]

...while case counts are very high here, deaths are not at horrible levels...on a per capita basis, it would appear that Florida's more hands off approach resulted in about 4.4x the number of deaths on a per capita basis.

While I agree with you, you'd have to control for demographics. Methinks Florida attracts a decent number of retirees and older folks more than Vermont. And you'd of course also have to control for vaccination levels/education/other factors as well to isolate public policy approach impacts. Age is just such a huge risk factor that can distort the numbers and Florida has a lot of older people...(and is more diverse than Vermont from a racial/socioeconomic perspective as well).

[cato]

Got to playing with some numbers today (dangerous) as Vermont rose to the second highest per capita case count in the country, per the CDC website. Florida now sits second from the bottom in case counts.
Did it turn out to be unwise for Vermont to lock down as much as it did during most of the pandemic?
Probably not...while case counts are very high here, deaths are not at horrible levels...on a per capita basis, it would appear that Florida's more hands off approach resulted in about 4.4x the number of deaths on a per capita basis.

Meanwhile the VT gov is saying that we test at far greater rates than almost every other state...he claimed (IIRC from his press conference) that Vermont is testing the most in the country, and the tenth place state only tests 1/3 as much as VT, so that's his current claim...nonetheless, we just hit a high for hospitalized patients, and patients in the ICU. Back under the bed for me.

Good luck and stay safe. Which I suppose is applicable to everyone these days.

[House P]

While I agree with you, you'd have to control for demographics. Methinks Florida attracts a decent number of retirees and older folks more than Vermont. And you'd of course also have to control for vaccination levels/education/other factors as well to isolate public policy approach impacts. Age is just such a huge risk factor that can distort the numbers and Florida has a lot of older people...(and is more diverse than Vermont from a racial/socioeconomic perspective as well).

Florida may attract more old folks than Vermont, but Vermont isn’t exactly overflowing with younger folks. Consider the following.

States Ranked by Oldest Median Age
1. Maine - 45.1
2. New Hampshire - 43
3. West Virginia - 42.9
4. Vermont - 42.8
5. Florida - 42.4

States Ranked by Percent of Population Aged 65 and Older
1. Maine - 20.6%
2. Florida - 20.5%
3. West Virginia - 19.9%
4. Vermont - 19.4%
5. Delaware - 18.7%

[Bluedog]

Florida may attract more old folks than Vermont, but Vermont isn’t exactly overflowing with younger folks. Consider the following.

States Ranked by Oldest Median Age
1. Maine - 45.1
2. New Hampshire - 43
3. West Virginia - 42.9
4. Vermont - 42.8
5. Florida - 42.4

States Ranked by Percent of Population Aged 65 and Older
1. Maine - 20.6%
2. Florida - 20.5%
3. West Virginia - 19.9%
4. Vermont - 19.4%
5. Delaware - 18.7%

Wow I didn't realize upper New England was comprised of so many older folks. Interesting. Thanks for sharing.

[Bostondevil]

Florida does, however, have more diabetics. Florida is 17th with 11.8% diabetics in the adult population while Vermont is 46th at 8.0%

Florida is only slightly more obese than Vermont. Florida rank 42, 28.4% of population with BMI over 30, Vermont rank 46 with 26.3%.

Vermont is number 1 in percent of total population vaccinated at 74% (that number includes kids). Florida is 19th with 62% vaccinated. That's going to explain most of the difference. Unvaccinated people are at least 10 times more likely to die from covid than vaccinated people. It might be a higher risk, but with delta, it's not lower. Perhaps it will be lower with omicron.

[MChambers]

YLE has an update on omicron today. She says the first in vitro study on vaccine effectiveness shows that omicron definitely has enhanced ability to escape immunity, but she is optimistic that boosters will help protect against it. It also looks to be extremely transmissible. Hard to reach any conclusions yet on severity of disease. The possibility of breakthrough infections and the transmissibility mean that even if omicron causes less severe disease, healthcare facilities could be overwhelmed again by the large number of cases.

As usual, she explains everything very clearly and in a balanced way. Read all about it here: https://yourlocalepidemiologist.subs...g-some-answers

[budwom]

Wow I didn't realize upper New England was comprised of so many older folks. Interesting. Thanks for sharing.

yes, we are a geezer state...all in all I think our approach was worked with regard to deaths, but the hospitals are pretty full right now, again primarily with the unvaccinated.

[JasonEvans]

Pfizer says Omicron does partly evade its vaccine, but that if you have gotten a booster, you are well protected: https://www.cnn.com/2021/12/07/healt...udy/index.html

Tests in lab dishes using samples from 12 people who had been fully vaccinated with Pfizer's vaccine showed the Omicron variant could evade the immune protection built by the vaccine -- but not completely.

"I thought this news was very positive. I expected worse," Sigal said in a telephone interview. The mutations that characterize the Omicron variant, he said, looked like they could allow it to evade the immunity offered by vaccines to a greater extent.

But the experiment indicates it doesn't. "This is not a variant that has completely escaped," he said. "It certainly escapes. It is certainly bad. But it looks to me like there are ways of dealing with it."

Sigal's team used human lung cells for the tests. Blood from the six volunteers who had been infected and then vaccinated was better able to neutralize the virus, they reported in a study submitted to an online preprint site. It has not been peer reviewed.

"Previous infection, followed by vaccination or booster, is likely to increase the neutralization level and likely confer protection from severe disease in Omicron infection," Sigal's team concluded.

[ClemmonsDevil]

yes, we are a geezer state...all in all I think our approach was worked with regard to deaths, but the hospitals are pretty full right now, again primarily with the unvaccinated.

In retrospect we probably should have told the unvaccinated that they needed to get vaccinated. Our bad.