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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The Delta wave may be abating for now until the fall. "It looks like we're about at the peak of the Delta SARS-CoV-2 wave in the US (figure based on @CDCgov data). A thread on current circulation patterns and the impact of Delta. 1/14
This inflection point in case loads at the country-level is due to decline in some states (such as FL and LA) and growth in others (such as OH and WV). Figure shows cases per 100k population on a log axis to emphasis state-level growth and decline. 2/14
Using previously described method to split cases by variant frequency, we see a striking pattern in which most states have a moderate spring wave comprised of a mix of Alpha and other variants, but show a large Delta wave in the summer. 3/14
If we take the starting point for the US Delta wave at June 15th, we have a cumulative ~6.4M cases between Jun 15 and Sep 3, and if we assume 2.7 infections per reported case, we arrive at ~17.3M infections up to this point during the Delta wave. 4/14
Assuming there are approximately another 17.3M infections on the other side of the Delta peak (which may not be the case), we arrive at roughly 34.6M Delta infections in the US wave, which is pretty close to my forecast ~36M infections on June 30. 5/14
Globally, we see that Delta is nearly dominant everywhere in the world except South America (nextstrain.org/ncov/gisaid/gl… showing distribution of samples from July 1). 6/14
Delta appears competitive with endogenous South American variants Gamma, Lambda and Mu (nextstrain.org/ncov/gisaid/so…) and I expect it will displace existing variation in the comings weeks. 7/14
This suggests that it will only take roughly 1 year for the emergence of Delta in late 2020 to (near) fixation in the global SARS-CoV-2 viral population. This "selective sweep" is extremely rapid commensurate with Delta's large jump in viral fitness. 8/14
In comparison, seasonal influenza H3N2 sees new strains appear and take 2-5 years to sweep through the global viral population (bedford.io/papers/bedford…). Having a new SARS-CoV-2 variant sweep in ~1 year is remarkable, especially given continued reductions in global travel. 9/14
Although PANGO has designated sub-lineages AY.1 to AY.25 of B.1.617.2 (Delta), this has been for purposes of epidemiological tracking (pango.network/new-ay-lineage…) and so far no striking sub-lineages of Delta have emerged. 10/14
However, there is a split in Delta diversity with one sub-clade bearing ORF1a mutations L1640P, P2287S, V2930L (among others) and the other bearing ORF1a A3209V (nextstrain.org/ncov/gisaid/gl…). The sub-clade with ORF1a L1640P et al is gaining in frequency, but pace has been slow. 11/14
At this point, it seems highly likely that the next impactful variant will emerge as a sub-lineage from within Delta diversity, bearing additional mutations on top of Delta's mutations. Consequently, I would urge that the regulatory process for vaccine updates begin. 12/14
Although Delta has had relatively small impacts on neutralization titers (perhaps 6-8X reductions) and vaccine effectiveness (perhaps 10-20% reductions), with a newly reduced viral diversity, a vaccine update to a basal Delta virus seems like an easy win. 13/14
Even if current impact of Delta on vaccine effectiveness is minor, updating the vaccine strain should provide a buffer against further viral evolution relative to continuing with a Wuhan-like vaccine strain. 14/14
Follow up #1: Replies have questioned the statement about this being the "peak" of the Delta wave. Fundamentally, what's going on is this: the large Delta wave has immunized a fraction of the US population (roughly 5% so far) on top of vaccination.
Follow up #2: Current population immunity + current behavior results in Rt of ~1. Vaccination and Delta imposed immunity will continue and further reduce Rt, while school term forcing, seasonality and waning immunity will act to increase Rt.
Follow up #3: I would guess that school term forcing won't be enough to flip Rt above 1, but school term + seasonality + waning may well be enough to do so. This would suggest case loads picking up again later in the fall, but I'd expect some decrease in the intervening weeks."
Source:
Commentary: A Delta-based booster would be a logical jump to make, targeting the mutations in Delta's protein spike. Doing so would substantially enhance the efficacy of vaccines, which are still mostly targeted at the virus as it was in January of 2020. A lot has changed since then.
Note that school being in session is flagged as a likely reason for the wave not subsiding faster. Schools are going to be messy.
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"The independent emergence late in 2020 of the B.1.1.7, B.1.351 and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three “501Y lineages” coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favoured convergent mutations at 35 genome sites: mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition."
Source: https://www.cell.com/cell/fulltext/S0092-8674(21)01050-3
Commentary: SARS-CoV-2 is mutating in somewhat predictable ways, at least in terms of fitness. This has two outcomes. First, it will continue to improve at transmission and possibly immune evasion as long as there are willing hosts - aka unvaccinated people - and eventually may acquire mutations that can substantially negate vaccines. Second, the mutations that improve the virus are all occurring in a predictable region, which means a comprehensive vaccine that stymies many future mutations is theoretically possible. Let's hope we get to the latter before the former.
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Kids are making up more COVID-19 cases. "Research is beginning to reveal that the reason children have fared well against COVID-19 could lie in the innate immune response — the body’s crude but swift reaction to pathogens. Kids seem to have an innate response that’s “revved up and ready to go”, says Herold. But she adds that more studies are needed to fully support that hypothesis.
The emergence of the Delta variant has made finding answers more urgent. Reports suggest that in the United States and elsewhere, children are starting to make up a larger proportion of reported infections and hospitalizations. These trends might be due to Delta’s high transmission rate and the fact that many adults are now protected by vaccines."
Source: https://www.nature.com/articles/d41586-021-02423-8
Commentary: Kids' innate immunity is still holding the line for now, but Delta's increased transmission means that the odds of it mutating to negate that advantage increase with every new case. The only way to stop that is to vaccinate everyone eligible and for everyone to use NPIs like masks and ventilation.
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Texas adds 50,000 new cases among students in two weeks. "Texas schools have amassed more than 50,000 confirmed coronavirus cases in students in just a couple of weeks. More than a dozen school districts have closed temporarily as a result of the disease, and Texas is a leader in child deaths from COVID-19 with 59 as of Sept. 3.
But state leaders have spent weeks of the surge pushing through controversial bills around abortion, voting restrictions and bail reform while Gov. Abbott has been fighting local governments over their efforts to stem the spread of the disease.
Hospitals across the state are running low on pediatric intensive care unit beds. Texas' Department of State Health Services says only 81 of them remain — and just a couple hundred more regular ICU beds are available in the state of 29 million people.
Portugal and other Texas members of the advocacy group the Committee to Protect Health Care called on the governor to rescind his executive order barring local governments from mandating masks in schools. They are just a few of the many healthcare workers and local governments frustrated by the state’s lack of action on preventing the spread of COVID.
State officials recently admitted the bans were unenforceable by them, leaving it to local district attorneys. But the continued litigation and threats to school districts has left confusion and patchwork of policies that many doctors see as exacerbating the COVID surge."
Source: https://www.houstonpublicmedia.org/articles/news/politics/2021/09/03/407791/doctors-say-texas-leaders-failed-to-stop-covid-19-from-spreading/
Commentary: At this point at least in the USA, parents and schools seem to have largely given up attempting to protect kids at a systemic level. Thus, if you are a parent of a kid that is unvaccinated, the onus falls to you to keep your kid as safe as possible. That means:
- Making sure they've got an N95 or better mask and that they wear it properly from the moment they leave home to the moment they get home
- Making sure you're testing, if you can manage either scheduling or the cost of home tests, on a regular and frequent basis
- If practical, withdraw your kids from schools and go remote until they are eligible for vaccination
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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.