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 a qualified healthcare provider who knows your specific medical situation over advice from people on the Internet.
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Wash your hands. "Interesting preprint demonstrating Omicron having more environmental stability compared to other variants & maintaining infectivity for longer.
Air matters, but maybe more fomite transmission with Omicron than previously thought?
Handwashing still (read: always) important."
Source: https://www.biorxiv.org/content/10.1101/2022.01.18.476607v1
Source:
Commentary: So, mask up and wash your hands. Really no different than we've been doing. What's interesting is that this preprint conflicts with a recent study showing that SARS-CoV-2 does very poorly at surviving in the air past 20 minutes. Neither study conflicts with the general advice to wear a mask, wash your hands, and get vaccinated and boosted.
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Long COVID (clinically called post-acute sequelae of COVID-19) is demonstrating unusual predictive markers. "Post-acute sequelae of COVID-19 (PASC) represent an emerging global crisis. However, quantifiable risk-factors for PASC and their biological associations are poorly resolved. We executed a deep multi-omic, longitudinal investigation of 309 COVID-19 patients from initial diagnosis to convalescence (2-3 months later), integrated with clinical data, and patient-reported symptoms. We resolved four PASC-anticipating risk factors at the time of initial COVID-19 diagnosis: type 2 diabetes, SARS-CoV-2 RNAemia, Epstein-Barr virus viremia, and specific autoantibodies. In patients with gastrointestinal PASC, SARS-CoV-2-specific and CMV-specific CD8+ T cells exhibited unique dynamics during recovery from COVID-19. Analysis of symptom-associated immunological signatures revealed coordinated immunity polarization into four endotypes exhibiting divergent acute severity and PASC. We find that immunological associations between PASC factors diminish over time leading to distinct convalescent immune states. Detectability of most PASC factors at COVID-19 diagnosis emphasizes the importance of early disease measurements for understanding emergent chronic conditions and suggests PASC treatment strategies."
Source: https://www.cell.com/cell/fulltext/S0092-8674(22)00072-1#relatedArticles
Commentary: This is the second time in two weeks that Epstein Barr has made the news; it's the virus responsible for mononucleosis. If SARS-CoV-2 can reactivate the effects of mono, that's bad news for anyone who has the genetic markers for multiple sclerosis activation. All the more reason to get vaccinated and boosted.
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Omicron BA.2 is different than BA.1. "This is a completely reasonable request about what recent UK (and other) data means for the pandemic, and in particular BA.1 and BA.2 (let alone BA.3 which, yes, is a thing). Here goes 1/n
BA.1 and BA.2 (leaving 3 aside for this) are *both* omicron. They are deep branching cousins within the lineage, separating almost a year ago (phylogenetic types don't at me, this is in general terms) 2/n
Now they can be distinguished using this neat property of one of the diagnostic tests. BA.1 has a mutation which means some tests produce a weird characteristic result called Spike Gene Target Failure or SGTF. Most other circulating viruses (including Delta and BA.2) don't 3/n
As it happens, SGTF was also a property of alpha, about a year ago. Changes in the proportions of cases with that property were an early sign of alpha taking over. Later, we saw the proportion of SGTF results dropping as delta (which did not share that property) became common 4/n
It's like successive variants are distinguished by easily detected fashion choices, as if they were Gen Z rejecting millennials' skinny jeans (and millennials rejected the 90s). That is the context for this 5/n
So - BA.1 which has been the great majority of omicron so far produces a SGTF result. BA.2, doesn't. Therefore when you see the proportions of tests returning SGTF falling away, that suggests BA.2 is increasing 6/n
BA.2 has been increasing in Denmark which has good genomic epi - though no.s of recently sequenced samples relatively small, so any bias towards checking out odd results (non-SGTF) matters. No idea if that has actually been contributing @K_G_Andersen? 7/n
This is the context in which evidence BA.2 is increasing in the UK, which has a lot of infections as well as very good surveillance, is significant. Huge numbers of BA.1 infections have been dropping but have reached a plateau for now. Not predicting which way that will go 8/n Image
Probably not helped by this. Note that infection control in schools, never especially serious in the UK, was recently scaled back. There *are* ways to reduce transmission in schools to minimal though not zero levels if resources are available 9/n
Am I worried? Well any rapidly transmitting lineage is serious because of the disruption it can cause. The severity of BA.2 is yet to be established. My expectation is that it is less serious in those with more prior immunity 10/n
BA.1 and BA.2 are both omicron, but they are pretty different. It remains to be seen what degree of immunity each will generate to the other. This is what I am watching for and what will matter for the future of the pandemic (as well as whether delta becomes extinct) 11/n
Finally, is BA.2 serious? Yeah. But BA.1 was serious. There's a balance between jumping at every curve ball the virus throws us and keeping a cool head. We'll understand more soon. For now, remember that the best thing you can do especially if you're older, is get boosted. END "
Source:
Commentary: We've got several new generations of Omicron - the OG, BA.1, plus BA.2 and BA.3, and now a new generation seen in San Diego, BA.1.1. Because of its rapid spread and high infectivity, it's mutating quickly - and changing characteristics. Mask up.
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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 people you don't live with, 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. Verify your mask's NIOSH certification here: https://www.cdc.gov/niosh/npptl/usernotices/counterfeitResp.html
3. Get vaccinated as soon as you're able to, and fulfill the full vaccine regimen, including boosters. Remember that you are not vaccinated until everyone you live with is vaccinated. If you received an adenovirus vaccine (J&J/AstraZeneca), consider getting an mRNA single shot booster (Pfizer/Moderna) if available. If it's available, choose Moderna as your first choice for both vaccine and booster, Pfizer as your second choice. However, remember than any vaccine is better than no vaccine.
4. Wash/sanitize your hands every time you are in or out of your home.
5. Stay out of indoor spaces that aren't your home and away from people you don't live with 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.
6. Aim to have 3-6 months of living expenses on hand in case the pandemic gives another crazy plot twist to the economy.
7. Replenish your supplies as you use them. Avoid reducing your stores to pre-pandemic levels in case an outbreak causes unexpected supply chain disruptions.
8. 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).
9. Masks must fit properly to work. Here's how to properly fit a mask:
10. If you think you may have been exposed to COVID-19, purchase a rapid antigen test. This will detect COVID-19 only when you're contagious, so follow the directions clearly. https://amzn.to/3fLAoor
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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
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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.
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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.