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.
---
New variants cropping up in Africa. "At the end of 2020, the Network for Genomic Surveillance in South Africa (NGS-SA) detected a SARS-CoV-2 variant of concern (VOC) in South Africa (501Y.V2 or PANGO lineage B.1.351)1. 501Y.V2 is associated with increased transmissibility and resistance to neutralizing antibodies elicited by natural infection and vaccination2,3. 501Y.V2 has since spread to over 50 countries around the world and has contributed to a significant resurgence of the epidemic in southern Africa. In order to rapidly characterize the spread of this and other emerging VOCs and variants of interest (VOIs), NGS-SA partnered with the Africa Centres for Disease Control and Prevention and the African Society of Laboratory Medicine through the Africa Pathogen Genomics Initiative to strengthen SARS-CoV-2 genomic surveillance across the region.
Here, we report the first genomic surveillance results from Angola, which has had 21 500 reported cases and around 500 deaths from COVID-19 up to March 2021 (Supplemental Fig S1). On 15 January 2021, in response to the international spread of VOCs, the government instituted compulsory rapid antigen testing of all passengers arriving at the main international airport, in addition to the existing requirement to present a negative PCR test taken within 72 hours of travel. All individuals with a positive antigen test are isolated in a government facility for a minimum of 14 days and require two negative RT-PCR tests at least 48 hours apart for de-isolation, whilst all travelers with a negative test on arrival proceed to mandatory self-quarantine for 10 days followed by a repeat test. In March 2021, we received 118 nasopharyngeal swab samples collected between June 2020 and February 2021, a number of which were from incoming air travelers (Supplemental Fig S1). From these, we produced 73 high quality genomes (>80% coverage), 14 of which were known VOCs/VOIs (seven 501Y.V2/B.1.351, six B.1.1.7, one B.1.525), 44 of which were C.16 (a common lineage circulating in Portugal), and twelve of which were other lineages (Supplemental Fig S2). In addition, we detected a new VOI in three incoming travelers from Tanzania who were tested together at the airport in mid-February. The three genomes from these passengers were almost identical and presented highly divergent sequences within the A lineage (Figure 1A & 1B). The GISAID database contains nine other sequences reported to be sampled from cases involving travel from Tanzania, two of which are basal to the three sampled in Angola
This new VOI, temporarily designated A.VOI.V2, has 31 amino acid substitutions (11 in spike) and three deletions (all in spike) (Figure 1C & 1D). The spike mutations include three substitutions in the receptor-binding domain (R346K, T478R and E484K); five substitutions and three deletions in the N-terminal domain, some of which are within the antigenic supersite (Y144?, R246M, SYL247-249? and W258L)4; and two substitutions adjacent to the S1/S2 cleavage site (H655Y and P681H). Several of these mutations are present in other VOCs/VOIs and are evolving under positive selection."
Source: https://www.krisp.org.za/publications.php?pubid=330
Commentary: This is why we must not make distinctions between rich and poor countries. Wherever there are people, we need vaccines to stem the pandemic. Otherwise, some countries will be unending reserves of new mutations, making the overall fight that much more difficult.
We are, whether some folks want to admit it or not, one human race and we are literally all in this together.
---
Long COVID and vaccination. "In late January, Griffin reached out on Twitter: “I have now heard from several people with Long COVID who feel significantly improved after getting vaccinated. Would love to hear from more people with Long COVID about their experience with vaccination.” The response was meagre and mixed: some said yes, some no. He repeated the call a few weeks later, this time posing the question to Akiko Iwasaki, a professor of epidemiology and immunobiology at Yale University, to see if she had any theories on why this was happening.
Iwasaki is one of the leading researchers investigating the puzzling phenomenon that is long Covid. She has three theories that could explain what is happening in the bodies of long Covid sufferers, and how the vaccine might be alleviating the persisting symptoms the condition causes.
Firstly it may be that there is a viral reservoir somewhere in the body where the virus is replicating but it can’t be located because it is inaccessible by nasal swabs. The vaccines may be stimulating T cells and antibodies that then eliminate that viral reservoir. Secondly, Iwasaki suggests, the persisting symptoms could be attributed to some remnants of the virus hiding somewhere in the body, causing a similar kind of inflammatory response – like a viral ghost. Vaccine-induced immunity may wipe out the viral ghost. Finally, long Covid could be chalked up to an autoimmune response induced by the infection, in which T cells or B cells, or both, are reacting out of place, and the vaccine may be diverting these cells.
It may also be that the vaccine is stimulating the innate immune response, and the short-lasting inflammation that causes could be diverting the immune cells causing long Covid. “I haven’t ruled in or ruled out any of those possibilities yet, because I think the data [are] too early,” she says. “These numbers are still very small. So even though it’s statistically significant, we need to see if this holds up in a larger scale study.” She emphasises that these theories are not mutually exclusive, so diagnosing what people have, and then giving them the appropriate treatment, will be key going forward. “We cannot treat long Covid as one disease, because they may be driven by different things.”
Despite the growing number of long-haulers telling their stories of a post-vaccination recovery, concrete evidence is still lacking. And anecdotal evidence based on personal observations or opinions – doesn’t prove what’s really going on."
Source: https://www.wired.co.uk/article/covid-19-long-haulers-vaccine
Commentary: This is VERY interesting. I will defer to Dr. Iwasaki's hypotheses because she's vastly more qualified to speak to the possibilities than I am, but I do think it's very interesting. This is a tricky virus, and the idea of a ghost in the system or hidden reservoirs of virus makes a ton of sense. It also reinforces the idea that what immunity people get from the virus itself may be haphazard, so vaccination is recommended for everyone.
---
A COVID pill? "Pfizer Inc has started an early-stage U.S. trial of an oral COVID-19 antiviral therapy that could be prescribed to patients at the first sign of infection, the company said on Tuesday.
The drugmaker, which developed the first authorized COVID-19 vaccine in the U.S. with Germany’s BioNTech SA, said the antiviral candidate showed potent activity against SARS-CoV-2, the virus that causes COVID-19, in lab studies.
Pfizer’s candidate, named PF-07321332, is a protease inhibitor that prevents the virus from replicating in cells.
Protease inhibitors have been effective at treating other viral pathogens such as HIV and hepatitis C virus, both on their own and in combination with other antivirals, the company said.
Pfizer believes this class of molecules may provide well-tolerated treatments against COVID-19, as currently marketed therapeutics that work on the same lines have not reported safety concerns.
The company is also studying an intravenously administered antiviral candidate in an early-stage trial in hospitalized COVID-19 patients.
“Together, the two (oral and intravenous candidates) have the potential to create an end-to-end treatment paradigm that complements vaccination in cases where disease still occurs,” Pfizer’s Chief Medical Officer Mikael Dolsten said in a statement."
Source: https://www.reuters.com/article/us-health-coronavirus-pfizer-antiviral/pfizer-begins-early-stage-study-of-oral-covid-19-drug-idUSKBN2BF22P
Commentary: Let's hope this pans out - another tool in the toolbox in the fight against it. This would be especially useful in areas where vaccine shortages persist, a way to dampen the impact while more vaccine is eventually brought in.
---
A reminder of the simple daily habits we should all be taking.
1. 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. 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. Get vaccinated as soon as you're able to.
3. Wash/sanitize your hands every time you are in or out of your home for any reason.
4. 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.
5. Get your personal finances in order now. Cut all unnecessary costs.
6. Replenish your supplies as you use them. Avoid reducing your stores to pre-pandemic levels in case an outbreak causes unexpected supply chain disruptions.
7. 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).
8. Masks must fit properly to work. Here's how to properly fit a mask:
---
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.