Lunchtime Pandemic Reading, 23-June-2021
Detective work
Lunchtime pandemic reading.
Standard disclaimer: this is a roundup of informative pieces I've read that interest me on the severity of the crisis and how to manage it. I am not a qualified medical expert in ANY sense; at best I am reasonably well-read laity. ALWAYS prioritize advice from qualified healthcare experts over some person on Facebook.
This is also available as an email newsletter at https://lunchtimepandemic.substack.com if you prefer the update in your inbox.
You are welcome to share this.
---
Nothing in the cloud is ever deleted. "The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH's Sequence Read Archive. I recover the deleted files from the Google Cloud, and reconstruct partial sequences of 13 early epidemic viruses. Phylogenetic analysis of these sequences in the context of carefully annotated existing data suggests that the Huanan Seafood Market sequences that are the focus of the joint WHO-China report are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2's bat coronavirus relatives."
Source: https://www.biorxiv.org/content/10.1101/2021.06.18.449051v1
Commentary: This is an impressive bit of digital detective work. At the insistence of the government of China, it appears that most data from early on in the pandemic was deleted or destroyed. An enterprising scientist found that the data was deleted from the app the community uses, but not the underlying storage mechanism, and was able to recover some of the deleted data that hints more at the origins of COVID-19.
The pre-print paper emphasizes there was no scientific reason to delete the data; political interference is suspected, and the actions of the government of China indicate that it had something to hide. There's no smoking gun here, but it's certainly suspect and does nothing to engender trust by the scientific community in that government.
Read the whole paper. It's a worthwhile read.
---
Delta will dominate the USA. "White House chief medical advisor Dr. Anthony Fauci said Wednesday the delta variant now accounts for roughly 20% of newly diagnosed cases in the U.S. and will become the dominant Covid strain in the nation in a matter of weeks.
“It just exploded in the U.K. It went from a minor variant to now more than 90% of the isolates in the U.K.,” Fauci said on NBC’s “TODAY” show. Fauci said the variant has a doubling time of about two weeks and currently accounts for 20% of the isolates in the U.S., which are newly diagnosed infections. “So you would expect, just the doubling time, you know, in several weeks to a month or so it’s going to be quite dominant, that’s the sobering news.”
The variant, which first emerged in India, has quickly swept across the globe. World Health Organization officials said Monday that delta has been found in at least 92 countries. Dr. Mike Ryan, head of WHO’s emergencies programs, said the variant is the fastest and fittest coronavirus strain yet, and it will “pick off” the most vulnerable people, especially in places with low Covid-19 vaccination rates.
At a White House Covid briefing Tuesday, Fauci called the variant the greatest threat to U.S. efforts to contain the pandemic. Fauci said the current vaccines in the U.S. are effective at protecting most people against the delta and other variants. CDC Director Dr. Rochelle Walensky said the delta variant is “hyper” transmissible, and she urged people to get vaccinated.
Studies suggest it is around 60% more transmissible than the alpha variant that emerged in the U.K. last fall and was already more contagious than the original strain that emerged from Wuhan, China, in late 2019.
Dr. Barbara Taylor, an associate professor of infectious diseases at UT Health San Antonio, said she’s worried the U.S. will likely see a lot of the delta variant in the summer and fall.
“We’re all pretty concerned about it,” she said. “It looks like it’s more transmissible, it looks like it can reinfect people who’ve already had Covid. It looks like it causes more severe disease and in some settings, it appears it has increased mortality.”
She said it’s especially worrisome for people who haven’t been vaccinated yet and adds “a lot of urgency” to vaccination efforts both in the U.S. and globally."
Source: https://www.cnbc.com/2021/06/23/delta-covid-variant-fauci-says-delta-accounts-for-20percent-of-new-cases-in-us.html
Commentary: Delta isn't playing around. Get vaccinated if you haven't already and it's available in your area, and if you are vaccinated, continue observing precautions where possible. Wear a mask indoors and any place there's crowds or poor ventilation. And if you have anyone in your household that is not vaccinated, behave as though no one in your household is vaccinated.
---
One shot + previous COVID. "Studies of two SARS-CoV-2 mRNA vaccines suggested that they yield ∼95% protection from symptomatic infection at least short-term, but important clinical questions remain. It is unclear how vaccine-induced antibody levels quantitatively compare to the wide spectrum induced by natural SARS-CoV-2 infection. Vaccine response kinetics and magnitudes in persons with prior COVID-19 compared to virus-naı̈ve persons are not well-defined. The relative stability of vaccine-induced versus infection-induced antibody levels is unclear. We addressed these issues with longitudinal assessments of vaccinees with and without prior SARS-CoV-2 infection using quantitative enzyme-linked immunosorbent assay (ELISA) of anti-RBD antibodies. SARS-CoV-2-naı̈ve individuals achieved levels similar to mild natural infection after the first vaccination; a second dose generated levels approaching severe natural infection. In persons with prior COVID-19, one dose boosted levels to the high end of severe natural infection even in those who never had robust responses from infection, increasing no further after the second dose. Antiviral neutralizing assessments using a spike-pseudovirus assay revealed that virus-naı̈ve vaccinees did not develop physiologic neutralizing potency until the second dose, while previously infected persons exhibited maximal neutralization after one dose. Finally, antibodies from vaccination waned similarly to natural infection, resulting in an average of ∼90% loss within 90 days. In summary, our findings suggest that two doses are important for quantity and quality of humoral immunity in SARS-CoV-2-naı̈ve persons, while a single dose has maximal effects in those with past infection. Antibodies from vaccination wane with kinetics very similar to that seen after mild natural infection; booster vaccinations will likely be required."
Source: https://pubs.acs.org/doi/10.1021/acsnano.1c03972
Commentary: Those individuals who have already had COVID-19 don't see any substantial benefit in two doses of vaccine. The antibody response appears to be the same as COVID-19 + one shot. The danger here is whether or not someone knows they had COVID-19 or not. Unless you received a positive test in the past, assume that you have not had COVID-19 and fulfill the full vaccine regimen.
---
A reminder of the simple daily habits we should all be taking.
1. Wear the best mask available to you when you'll be around other people, even after you've been vaccinated. Respirators are back in stock at online retailers, too. Wear an N95/FFP2/KN95 that's NIOSH-approved or better mask if you can obtain it. If you can't get an N95 mask, wear a surgical mask with a cloth mask over it.
2. Get vaccinated as soon as you're able to, and fulfill the full vaccine regimen. Remember that you are not vaccinated until everyone you live with is vaccinated. If you received an adenovirus vaccine (J&J/AstraZeneca), consider gettings an mRNA single shot booster (Pfizer/Moderna).
3. Wash/sanitize your hands every time you are in or out of your home.
4. Stay home as much as practical. Minimize your contact with others and avoid indoor places as much as you can; indoor spaces spread the disease through aerosols and distance is less effective at mitigating your risks.
5. Get your personal finances in order now. Cut all unnecessary costs.
6. Replenish your supplies as you use them. Avoid reducing your stores to pre-pandemic levels in case an outbreak causes unexpected supply chain disruptions.
7. Ventilate your home as frequently as weather and circumstances permit, except when you share close airspaces with other residences (like a window less than a meter away from a neighboring window).
8. Masks must fit properly to work. Here's how to properly fit a mask:
---
Common misinformation debunked!
There is no basis in fact that COVID-19 vaccines can shed or otherwise harm people around you.
Source: https://www.reuters.com/article/factcheck-covid19vaccine-reproductivepro-idUSL1N2MG256
There is no mercury or other heavy metals in the Pfizer mRNA vaccine.
Source: https://www.technologyreview.com/2020/12/09/1013538/what-are-the-ingredients-of-pfizers-covid-19-vaccine/
There is no basis in fact that COVID-19 vaccines pose additional risks to pregnant women.
Source: https://www.nejm.org/doi/full/10.1056/NEJMoa2104983
There is no genomic evidence at all that COVID-19 arrived before 2020 in the United States and therefore no hidden herd immunity:
Source:
There is no evidence SARS-CoV-2 was engineered, nor that it escaped a lab somewhere.
Source: https://www.washingtonpost.com/world/2020/01/29/experts-debunk-fringe-theory-linking-chinas-coronavirus-weapons-research/
Source: https://www.nature.com/articles/s41591-020-0820-9
Source: https://www.nationalgeographic.com/science/2020/05/anthony-fauci-no-scientific-evidence-the-coronavirus-was-made-in-a-chinese-lab-cvd/
Source: https://www.smh.com.au/national/are-we-ignoring-the-hard-truths-about-the-most-likely-cause-of-covid-19-20210601-p57x4r.html
There is no evidence a flu shot increases your COVID-19 risk.
Source: https://www.factcheck.org/2020/04/no-evidence-that-flu-shot-increases-risk-of-covid-19/
Source: https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa626/5842161
---
Disclosures and Disclaimers
I declare no competing interests on anything I share related to COVID-19. I am employed by and am a co-owner in TrustInsights.ai, an analytics and management consulting firm. I have no clients and no business interests in anything related to COVID-19, nor do I financially benefit in any way from sharing information about COVID-19.
---
A common request I'm asked is who I follow. Here's a public Twitter list of many of the sources I read.
https://twitter.com/i/lists/1260956929205112834
This list is biased by design. It is limited to authors who predominantly post in the English language. It is heavily biased towards individual researchers and away from institutions. It is biased towards those who publish or share research, data, papers, etc. I have made an attempt to follow researchers from different countries, and also to make the list reasonably gender-balanced, because multiple, diverse perspectives on research data are essential.
This is also available as an email newsletter at https://lunchtimepandemic.substack.com if you prefer the update in your inbox.