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.
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Household transmission on the rise. "In this updated systematic review and meta-analysis of 87 studies representing 1 249 163 household contacts from 30 countries, the estimated household secondary attack rate was 19%. An increase in household transmission was observed over time, perhaps owing to improved diagnostic procedures and tools, longer follow-up, more contagious variants, and different study locations.
These findings suggest that the household remains an important site of SARS-CoV-2 transmission, and recent studies have generated higher household secondary attack rate estimates compared with the earliest reports; more transmissible variants and vaccines may be associated with additional changes in the future."
Source: https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2783544
Commentary: If someone in your household is infected, there's a good chance you will be too - and with Delta, those chances are increased. Mask up, and if you suspect a problem, get tested.
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Strain drift. "One of the most important things I was looking for in reporting on #SARSCoV2 evolution was a way of making sense of all the virus variants, putting them in some framework.
And one of the most useful things I found for that is this antigenic map.
In its first year #SARSCoV2 spread in mostly naive people and it made big jumps in infectiousness: D614G, Alpha, Delta.
“This virus has gone up three notches in effectively a year”, @edwardcholmes told me.
Think of it this way:
The virus spent the last year getting better at spreading in humans.
Now needs to get better at spreading in partly protected humans.
Several researchers told me that we are now at tipping point with evolutionary pressure moving more towards immune evasion.
So one of the big questions for the coming months is how much #sarscov2 can evolve to evade our immunity.
Well let’s look at the variants so far and this is where that antigenic map really helps me visualize things.
So how do we read the map?
The colored dots are different variants of #SARSCoV2.
The further apart two dots are the worse antibodies elicited by one variant neutralize the other variant in the lab
The unit as you move from one line to the next is essentially a two-fold drop in neutralization
One thing the map makes clear is that immune evasion is not black or white.
Yes, these variants have moved, so they are “escaping immunity” but it’s gradual. As @jbloom_lab told me: “Immune escape conjures this catastrophic failure of immunity when it is really immune erosion.”
Delta has moved further from the original virus than Alpha showing it can better evade immunity. But not “in the way people think of an escape in slightly cartoonish terms,” @ArisKatzourakis told me. “It shows the possible beginning of a trajectory and that’s what worries me.”
It’s also interesting to note that Beta has moved furthest away from the original virus on the map. It is the virus variant that is most “immune escapy” so far.
Yet, as you can see in this diagram showing the frequency of variants Delta is still outcompeting it.
It suggests some tradeoff between immune escape and infectiousness (as is thought to be the case in other viruses).
Essentially Beta may “pay” for its immune escape by being a bit worse at spreading. That could suggest future variants that escape even better are less infectious.
So one of the biggest questions for the next months will be where on this antigenic map new variants fall.
It’s important to remember that there are likely some boundaries to where and how far the virus can move.
Let’s hope it cannot move very far or fast…"
Source:
Commentary: This is really interesting science and something we'll have to pay attention to. As new variants emerge to escape immune responses, will they keep their infectivity or need to trade off? Of the current VOCs, Beta is the one I'm paying attention to. It has been outcompeted by Delta but spreads very differently, more like a flu. Our vaccines work against it, however.
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Vaccines work. "The emergence of SARS-CoV-2 antigenic variants with increased transmissibility is a public health threat. Some variants show substantial resistance to neutralization by SARS-CoV-2 infection- or vaccination-induced antibodies. Here, we analyzed receptor binding domain-binding monoclonal antibodies derived from SARS-CoV-2 mRNA vaccine-elicited germinal center B cells for neutralizing activity against the WA1/2020 D614G SARS-CoV-2 strain and variants of concern. Of five monoclonal antibodies that potently neutralized the WA1/2020 D614G strain, all retained neutralizing capacity against the B.1.617.2 variant, four also neutralized the B.1.1.7 variant, and only one, 2C08, also neutralized the B.1.351 and B.1.1.28 variants. 2C08 reduced lung viral load and morbidity in hamsters challenged with the WA1/2020 D614G, B.1.351, or B.1.617.2 strains. Clonal analysis identified 2C08-like public clonotypes among B cells responding to SARS-CoV-2 infection or vaccination in 41 out of 181 individuals. Thus, 2C08-like antibodies can be induced by SARS-CoV-2 vaccines and mitigate resistance by circulating variants of concern."
Source: https://www.cell.com/immunity/fulltext/S1074-7613(21)00345-9#.YRuvoatJ3Y0.twitter
Commentary: This is an interesting piece that effectively says even though antibody resistance has waned, vaccines still trigger enough common antibodies that they suppress severe illness and death across all the current variants. Get vaccinated!
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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. 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 permitted.
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.