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.
You are welcome to share this.
---
SARS-CoV-2 B.1.1.7 reaches America's shores. "The first reported US case of the highly-infectious Covid-19 variant that emerged in the UK has been confirmed in the state of Colorado.
The patient, a man in his 20s with no recent travel history, is currently in isolation.
State health officials said they were working to identify contacts and other potential cases of the new variant.
It came as US President-elect Joe Biden criticised the Trump administration's distribution of vaccines.
He said the programme was falling behind schedule.
The US has recorded more than 19 million infections and more than 337,000 deaths from coronavirus, the highest figures in the world.
The new variant is considerably more transmissible than previous strains but not necessarily any more dangerous for those infected, experts say.
US health officials said last week that they believed it was already in circulation in the country.
In a statement on Tuesday, Colorado governor Jared Polis said the infected patient was in isolation in Elbert County near Denver.
Public health officials were carrying out "a thorough investigation", he said, and no infections had been discovered among close contacts so far.
Cases of the new variant have been appearing around the world. The first two known infections on the North American continent came to light in Canada at the weekend."
Source: https://www.bbc.com/news/world-us-canada-55479590
Commentary: It is likely that it's been here for some time. The question is, how fast is it spreading?
---
Another modeled analysis of B.1.1.7. "Background: The emerging B.1.1.7 SARS-CoV-2 lineage has proliferated rapidly in the U.K. Here we use a combination of daily local SARS-CoV-2 incidence data and weekly genomic surveillance data from COG-UK to infer its infection dynamics and parameters during English national lockdown from November 5 to December 2 2020.
Methods: A hierarchical Bayesian model is used to jointly model lineage-agnostic spatiotemporal SARS-CoV-2 PCR test data and genomic sequencing data of the B.1.1.7 lineage. This analysis infers the total and lineage-specific temporal incidence in each local authority and estimates the historic basic reproductive ratio R for new and other SARS-CoV-2 lineages per local authority.
Findings: We find strong and consistent evidence that B.1.1.7 proliferated (R>1) during the English lockdown in 86% (215/246) of lower tier local authorities with an average R value of 1.26. At the same time other lineages contracted (R<1) at an average R value of 0.86 in most regions, leading to 81% (200/246) of regions showing B.1.1.7 proliferation while other lineages diminished.
Implications: The emerging B.1.1.7 SARS-CoV-2 lineage spreads faster than its predecessors. It continued to grow during a lockdown in which other lineages shrank. These analyses suggest that stricter measures are required to contain the B.1.1.7 lineage."
Source: https://virological.org/t/lineage-specific-growth-of-sars-cov-2-b-1-1-7-during-the-english-national-lockdown/575
Commentary: What's important here that previous studies didn't highlight as well are the controls - the existing strains of SARS-CoV-2 that didn't do as well during lockdown, showing that it's not a change in distancing or mask usage. The new variant spread more easily, even when other strains were not faring quite as well.
More testing and genomic evidence is needed before B.1.1.7's transmissibility is confirmed as hard fact, but every indication thus far suggests that to be the case. If I had to guess - and it's guessing, so take it with a grain of salt - that lax measures which stopped regular COVID-19 like barely competent mask usage (hello people not wearing a mask over their nose) do not impede the B.1.1.7 strain nearly as much.
That suggests that it's more efficient at landing and infecting people, so wear your mask properly and in general, wear the best mask available to you whenever you're out of your home.
---
Relative humidity matters. "Our central observable here is the relative viral load, i.e. the amount of virus carried by an individual droplet normalized to the total amount of virus in the ensemble of droplets. To connect the relative viral load to the probability of infection, further information is needed: what is the cumulative viral load emitted with the entire population of droplets by an infected individual, and what is the infectious dose of SARS-CoV-2? A comprehensive revision of the state of knowledge on this complex issue is beyond the scope of the present work. However we note that while epidemiology and virology are clearly at the front line in the fight against COVID-19, knowledge on the disease itself must be coupled to the physics of droplet production, transport and evaporation. We hope that our work will raise awareness about these less appreciated unknowns of the problem.
Finally, our results show that a single rule for social distancing may not be adequate to protect individuals in different environments. The relative humidity of the environment has a particularly dramatic effect, with all droplets evaporating to their dry nuclei under sufficiently dry conditions, and all droplets remaining liquid under sufficiently wet environmental conditions. Provided science advances on the key issues identified above, the strategy employed in the current study can actively contribute to outline a revised notion of social distancing underpinned by scientific evidence."
Source: https://www.nature.com/articles/s41598-020-80078-7
Commentary: Part of the reason COVID-19 - and most respiratory viruses - do well in the winter is the cool, dry air. Dry air makes virus particles weigh less, so they stay in the air longer because they're smaller and lighter.
Be sure to humidify your residence to at least 40% relative humidity through any normal conventional means like running a humidifier, airing your laundry to dry indoors on a line, leaving the bathroom door open during showers, and putting bowls/dishes of water on old-fashioned radiators.
When out and about, wear the best mask available to you, ideally an N95 or better if you know you'll be breathing air indoors. If you've only got a cloth mask and you're concerned about increased transmissibility, wet it down with diluted hydrogen peroxide (1% strength, so 2 parts water to 1 part drugstore peroxide) before donning it and re-moisten as needed.
---
80 days to evasion in a laboratory setting from a pre-print. "To investigate the evolution of SARS-CoV-2 in the immune population, we co-incubated authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The plasma fully neutralized the virus for 7 passages, but after 45 days, the deletion of F140 in the spike N-terminal domain (NTD) N3 loop led to partial breakthrough. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed at day 80 by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. Computational modeling predicts that the deletion and insertion in loops N3 and N5 prevent binding of neutralizing antibodies. The recent emergence in the United Kingdom and South Africa of natural variants with similar changes suggests that SARS-CoV-2 has the potential to escape an effective immune response and that vaccines and antibodies able to control emerging variants should be developed."
Source: https://www.biorxiv.org/content/10.1101/2020.12.28.424451v1
Commentary: This pre-print from GSK has not been peer-reviewed, but comes from a reputable company. In this laboratory test, they were able to watch SARS-CoV-2 adapt within 80 days to evade neutralizing antibodies. That's concerning because the speed of vaccine rollout is going to be much slower than 80 days, so we might need the vaccine manufacturers to repeatedly pivot to deal with major changes in the virus over time if vaccination drags on long enough.
What needs to happen is a massive, fast wave of vaccinations, enough to put out the fires in hotspots and squash COVID-19's ability to mutate quickly enough to evade a vaccine. If we parcel out vaccines slowly, we give the virus that much longer to adapt to it, and as this laboratory test shows, it doesn't need years and years to make an adaptive change - less than 3 months.
When it's your turn for vaccination, go get it. Don't wait. Help be part of the real herd immunity by taking the vaccine and then continuing to adhere to protective measures like wearing masks - because if a variant does emerge that's resistant, you'll want your mask as your backup plan.
---
A reminder of the simple daily habits we should all be taking.
1. Wash/sanitize your hands every time you are in or out of your home for any reason. Consider also spraying the bottoms of your shoes with a general disinfectant (alcohol/bleach/peroxide) when you return home. Remember that cleaners are NEVER to be ingested or injected. If you come in physical contact with others, wash your clothing upon returning home.
2. Always wear the best mask available to you when out of your home and you'll be around other people. Respirators are back in stock at online retailers, too.
3. Stay home as much as possible. Minimize your contact with others and maintain physical distance of at LEAST 6 feet / 2 meters, preferably more. Avoid indoor places as much as you can; indoor spaces spread the disease through aerosols and distance is less effective at mitigating your risks.
4. Get your personal finances in order now. Cut all unnecessary costs.
5. Replenish your supplies as you use them. Avoid reducing your stores to pre-pandemic levels in case an outbreak causes unexpected supply chain disruptions.
6. 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).
---
Common misinformation debunked!
There is no mercury or other heavy metals in the Pfizer mRNA vaccine. https://www.technologyreview.com/2020/12/09/1013538/what-are-the-ingredients-of-pfizers-covid-19-vaccine/
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/
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
---
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.