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.
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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It's all about how much you take in. "COVID-19 presentation varies widely between individuals, ranging from asymptomatic to life-threatening infection. Several host and viral factors have been shown to influence disease penetrance and severity. In addition, the infectious dose has also been speculated to have a role. Dabisch et al. show in a SARS-CoV-2 challenge study of 16 cynomolgus macaques that the infectious dose indeed influences symptom development and seroconversion. They used aerosolized virus at different concentrations and found that low doses could lead to seroconversion and virus replication in the respiratory tract without symptom development, such as fever, whereas higher doses produced fever, which suggest that low infectious doses might be associated with asymptomatic infection."
Source: https://www.nature.com/articles/s41579-021-00634-4
Commentary: This is why superspreader events are so deadly - there's a LOT of virus in the air, and the more you take in, the more severe your case. This is also why masks work - you take in less and less virus the better your mask is. Want to avoid illness? Filter out as much virus as you can by wearing the best mask available to you. It's also why we say any mask is better than no mask, and any accredited, authorized vaccine is better than no vaccine.
It also means if you have to choose risks, choose them based on how much infected air you're at risk of inhaling.
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Plasma antibodies wane and Delta can escape some of them. "Information concerning the longevity of immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) following natural infection may have considerable implications for durability of immunity induced by vaccines. Here, we monitored the SARS-CoV-2 specific immune response in convalescent coronavirus disease-2019 (COVID-19) patients up to 15 months after symptoms onset. Methods: The levels of anti-spike and anti-receptor binding domain antibodies and neutralizing activities were tested in a total of 188 samples from 136 convalescent patients who experience mild to critical COVID-19. Specific memory B and T cell responses were measured in 76 peripheral blood mononuclear cell samples collected from 54 patients. Twenty-three vaccinated individuals were included for comparison. Findings: Following a peak at day 15-28 post-infection, the IgG antibody response and plasma neutralizing titers gradually decreased over time but stabilized after 6 months. Plasma neutralizing activity against G614 was still detected in 87% of the patients at 6-15 months. Compared to G614, the median neutralizing titers against Beta, Gamma and Delta variants in plasma collected at early (15-103 days) and late (9-15 month) convalescence were 16- and 8-fold lower, respectively. SARS-CoV-2-specific memory B and T cells reached a peak at 3-6 months and persisted in the majority of patients up to 15 months although a significant decrease in specific T cells was observed between 6 and 15 months. Conclusion: The data suggest that antiviral specific immunity especially memory B cells in COVID-19 convalescent patients is long-lasting, but some variants of concern, including the fast-spreading Delta variant, may at least partially escape the neutralizing activity of plasma antibodies."
Source: https://www.biorxiv.org/content/10.1101/2021.10.08.463699v1
Commentary: This is a pre-print, so caveat emptor. What's going on here is that natural immunity in B cells is durable, but T cell immunity fades over time. This explains why Delta is so tricky - it can infect the vaccinated (but not harm them nearly as much). Thus, the logical conclusion is to not spread Delta in the first place by masking up always around people you don't live with.
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Thoughts about flu from Dr. Marion Coopmans: "Ok, a tweetorial for the most frequently asked question of this period for all virologists: what will flu do.
I was asked to present how we look at flu in the coming season. First question: what will the COVID 19 pandemic “do” in fall. Restrictions to reduce circulation have really had an impact on flu circulation as well. Look at the global flu surveillance data
Then question: what happens if there is a two year gap in flu circulation? What does that do to population immunity? This study looked at waning of protective antibodies over time, and estimates 25% reduction over 2 years in unvaccinated individuals.
A specific question is what the role of children will be. There is a large group of young children that has not yet experienced flu. This is measurable, reduced antibodies to some seasonal respiratory viruses in children April 2020 and April 2021 (Sikkema et al)
Next question: what is the infection attack ate in a typical flu season (obviously if there are no measures in place for COVID) . This study estimates 1/5 in children and 1/10 in adults
Uncertain; we have seen substantial excess mortality in the oldest age groups that also are at highest risk for severe flu. Will that result in lower flu impact in the same group?
Then there is the question: which strains will circulate. This is assessed based on surveillance data but there is a gap there too, globally. On the other hand, without much virus circulation, one does not expect a lot of drift, so that works for us I think
So in all, many uncertainties. We do see that flu circulation is starting in Europe, so should be prepared"
Source:
Commentary: You know what works to prevent flu?
Masks.
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A long and useful thread on COVID-19 data. "NEW: people obsess over vaccine uptake stats, eagerly comparing one country to others to see which has jabbed the highest share of its population, but what if I told you many — perhaps most — of those stats are wrong?
Time for a thread on bad Covid data and how it can cost lives
Let’s start with the most obvious sign of the problem:
In several European countries, the share of elderly people who have been vaccinated exceeds 100%.
To state the obvious, this is not possible.
But it’s not just a funny quirk, it has big implications.
In reality these countries won’t have reached 100%, so there are tens of thousands of unvaxxed elderly that are invisible, and no-one is going to visit someone to make sure they’re jabbed if they think everyone is jabbed.
And this is critically important, because due to their far greater vulnerability, jabbing the last few elderly people will save far more lives than jabbing far larger numbers of kids.
So what’s going on?
It all comes down to population data. In short, most governments don’t know how many people live in their country, so they estimate
Censuses are usually every decade, so right now, ~9 yrs on from the last one in many cases, the estimates are especially shaky
So what we’re really seeing when vaccine uptake exceeds 100%, is a country discovering it has more people that it thought it did.
But what that means is there could still be thousands of unvaccinated people out there.
When the US decennial census landed last month, it showed there were fewer white people than estimated, and more Asian & Hispanic people.
The result: white vax uptake higher than thought, but there are more unvaxxed Asian and Hispanic people than realised
And sticking with the US, it gets worse:
In Florida, vaccine uptake may have been hugely over-stated in official CDC figures, because people who were vaccinated while visiting Florida in winter but usually live elsewhere, have been counted in Florida’s vaccine coverage data.
In Miami-Dade, vax coverage among over-65s exceeds 100% in *more than half of all zipcodes*, in some cases passing 200%.
This is the "snowbird" effect: thousands of older folks went south to Miami in winter, got jabbed, then returned north
At the state-level, this causes a major discrepancy:
According to CDC data, just 3.7% of people aged 65+ have not yet had any vaccine dose.
But Florida’s department of health, which only includes Florida residents, says 12% of the elderly are still unprotected. More than 3x.
Again, this may just feel like a curious quirk, but it’s a matter of life or death.
As @redouad put it to us, "if we take a step back and imagine this as a new disease and we say that 10 per cent of the population is susceptible vs five per cent, that’s a huge difference"
And that’s exactly what played out in Florida.
If we trust CDC data, when Delta hit FL its elderly were as well-protected as those in Maryland. Just 10% unvaxxed.
But if we use residents only, its vulnerable elderly pop was twice as big — more like Georgia.
What happened next?
FL had a brutal wave, setting records for deaths. It looked much more like Georgia than Maryland, whose Delta wave has been much more muted.
As Miami Beach mayor @MayorDanGelber put it, the official data created a false sense of security in Florida, quite possibly contributing to people behaving less cautiously.
And the population denominator issue isn’t just a problem for vax uptake.
Here in England, anti-vax activists have been circulating data published by @UKHSA which appears to show case rates are higher among fully-vaxxed people than among the unvaxxed 🚨❓
But once again, this is due to misleading population data. NIMS — the system used by UKHSA — is known to double-count large numbers of working-age adults.
The result is NIMS thinks there are far more unvaxxed people than there are, pushing unvaxxed case rates artificially low.
When you use the @ONS’ population estimates, which — while still just that, estimates — don’t suffer the same double-counting flaw, it turns out that in all of those age-groups, the unvaxxed are actually much more likely to get Covid than the vaxxed, as we would expect.
There are still quirks — among the most elderly, the roles are reversed and ONS almost certainly overstates the population size, pushing unvaxxed case rates too low — but the persistent use of NIMS data, known to produce these misleading outcomes — is puzzling, to put it mildly.
And to conclude, here are 5 key take-aways:
1) National vax uptake figures could be out by ~2-5% in many cases, and among some subgroups the discrepancies will be much greater
2) So please stop eagerly saying country X is beating country Y because its uptake is 2-3% higher
3) Be especially careful when countries use markedly different denominators. e.g English stats are usually published using NIMS denominators (so will under-state uptake), while Scotland uses ONS (and is known to over-state uptake, at least in some age-groups).
4) Pay very careful attention to methodology and footnotes. Does the data you’re looking at include residents-only, or could it suffer from Florida’s snowbird problem?
And finally
5) Small errors in uptake rates can have huge impacts. The difference between 85% vaxxed and 95% vaxxed is better expressed as 15% vulnerable vs 5% vulnerable, i.e triple the death toll. "
Source:
Commentary: A good, thorough read on COVID data and things to keep in mind as you hear about COVID statistics.
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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.