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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Omicron and Delta recombinant variation detected. "UK reports Delta Omicron recombination, this time it's the real thing.
I will try to answer 3 questions here:
1.Was this expected?
2.Is this the report from Cyprus?
3.Should we be concerned?
1.Was this expected? Yes.
Recombination occurs when a cell is infected with 2 variants.
when 2 variants are in high # & % recombination is more likely to be visible. it is likely to occurred during the Δ times, but if AY.4 recombined with AY.3, that's gonna be hard to spot
For example:
When α rose and mostly replaced B.1.177 in the UK, XA (recombinant of those 2) detected.
When Delta rose and replaced α, XC detected.
And now – UK spotted some Δ-ο recombination.
2. Is this the report from Cyprus? No!
Those were just Δ sequences (Complete Δ, no breakpoint), from different AY lineages, that had ~2-3 mutations that also appeared in o.
Δ sequences with additional mutations like these found long before o emerged.
Should we be concerned? Hard to say (but probably not).
Recombination is just another tool in the evolutionary toolbox of the virus. Like mutations that accumulate in a chronic infection, reverse zoonosis or even genetic drift from transmission in the community.
Recombination is not the combination of mutations from both parents. Each variant contributes a part, but the complementary part disappears. For example, the unsuccessful BA.3 is a recombinant of BA.1 and BA.2 (which are causing the main part of the pandemic right now).
Remember - The cases of α - B.1.177 ,Δ-α and now ο-Δ found in countries with high levels of 🧬. That may be attributed to those being really rare phenomena.
Successful Variants defined as VOC / VUI / VUM originated a lot from places with low 🧬 such as SA, India and Peru."
Source: https://www.gov.uk/government/publications/sars-cov-2-variants-of-public-health-interest/sars-cov-2-variants-of-public-health-interest-11-february-2022
Source:
Commentary: The more cases of COVID-19 there are, the more chances the virus has to merge with previous successful versions of itself and develop more robust capabilities, such as faster spread and immune evasion. The only way to stop new variants is to stop spread.
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Good news for immune compromised kids? "UK immunocompromised paediatric patients were at no increased risk of severe COVID-19.
Only 4/38 PCR detected infections were admitted to hospital. None had acute severe COVID-19 or died.
Increasing age and immunodeficiency increased reporting of SARS-CoV-2 infection. Worsening of fever, cough and sore throat were associated with reporting SARS-CoV-2 infection.
Serology results suggest there was a proportion of SARS-CoV-2 infections undetected by PCR."
Source: https://www.sciencedirect.com/science/article/pii/S016344532100548X
Commentary: This report effectively says that there's no major difference in outcomes for kids who are immune compromised versus those who are not for contracting COVID-19, which is a silver lining. That said, get your kids vaccinated and boosted to improve their chances even more, if eligible.
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Prior infection has lost protection against Omicron. "The effectiveness of previous infection in preventing reinfection was estimated to be 90.2% (95% confidence interval [CI], 60.2 to 97.6) against the alpha variant, 85.7% (95% CI, 75.8 to 91.7) against the beta variant, 92.0% (95% CI, 87.9 to 94.7) against the delta variant, and 56.0% (95% CI, 50.6 to 60.9) against the omicron variant (Table 1). Sensitivity analyses confirmed the study results, as expected for this study design, which is robust regardless of the approach that is used to control for vaccine-induced immunity.4 An additional analysis that was adjusted for the interval since previous infection also confirmed the study results (Table S4).
Among the patients with reinfection, progression to severe Covid-19 occurred in one patient with the alpha variant, in two patients with the beta variant, in no patients with the delta variant, and in two patients with the omicron variant. None of the reinfections progressed to critical or fatal Covid-19. The effectiveness with respect to severe, critical, or fatal Covid-19 was estimated to be 69.4% (95% CI, −143.6 to 96.2) against the alpha variant, 88.0% (95% CI, 50.7 to 97.1) against the beta variant, 100% (95% CI, 43.3 to 100) against the delta variant, and 87.8% (95% CI, 47.5 to 97.1) against the omicron variant. (For the delta variant, the calculation of the 95% confidence interval is clarified in a footnote in Table 1.) Limitations of the estimations (e.g., the relatively young population of Qatar) are discussed in Section S1."
Source: https://www.nejm.org/doi/full/10.1056/NEJMc2200133
Commentary: 56% effectiveness against COVID-19 is very, very low. That means that prior infection, which used to be almost as good as a vaccination, is no longer the case by itself. Omicron changed the game and now everyone needs a shot, whether or not you had prior COVID.
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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.