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.
---
Commentary:
Should X be re-opened? (where X is the office, a school, etc.) Here's a simple test. We know that air needs to be changed out very frequently to reduce the probability of infection, either cleaned with HEPA filtration or exchanged with outside air. So take any room you want to study, and light something - a cigarette, incense, etc. - in that room for 30 seconds. Then leave the room and come back in 5 minutes. If you can still smell what you lit on fire, the room is not safe for people without high-quality masks. If the air is clear, then you're in good shape.
This makes intuitive sense, too. Light a cigarette or incense outside for 30 seconds, leave that spot, and come back in 5 minutes. Do you smell anything at that spot? Probably not - which is why outdoors is substantially safer than indoors.
If you're a parent concerned about school, ask your school administration if YOU can do this test in one of the classrooms. If the room fails, then you know that you need to either keep your kids home or make sure they wear N95 masks, properly fitted, during school and not take them off for any reason inside the school.
---
COVID breaks healthcare safety. "The profound changes wrought by COVID-19 on routine hospital operations may have influenced performance on hospital measures, including healthcare-associated infections (HAIs). We aimed to evaluate the association between COVID-19 surges and HAI and cluster rates.
Central line-associated blood stream infections (CLABSI), catheter-associated urinary tract infections (CAUTI), and methicillin-resistant Staphylococcus aureus (MRSA) bacteremia increased as COVID-19 burden increased. There were 60% (95% CI, 23-108%) more CLABSI, 43% (95% CI, 8-90%) more CAUTI, and 44% (95% CI, 10-88%) more cases of MRSA bacteremia than expected over 7 months based on predicted HAIs had there not been COVID-19 cases. Clostridioides difficile infection was not significantly associated with COVID-19 burden. Microbiology data from 81 of the hospitals corroborated the findings. Notably, rates of hospital-onset bloodstream infections and multidrug resistant organisms, including MRSA, vancomycin-resistant enterococcus and Gram-negative organisms were each significantly associated with COVID-19 surges. Finally, clusters of hospital-onset pathogens increased as the COVID-19 burden increased.
COVID-19 surges adversely impact HAI rates and clusters of infections within hospitals, emphasizing the need for balancing COVID-related demands with routine hospital infection prevention."
Source: https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab688/6346721#.YRFRvtleAvY.twitter
Commentary: Simply put, when resources are under strain, EVERYTHING gets worse. Overall quality of care suffers. Convince everyone you know that's not vaccinated to get vaccinated if they can. It helps everyone!
---
An excellent explanation video of the lineage of viruses - and the fact that SARS-CoV-2 has a common ancestor that's over 40 years old.
Source:
Commentary: This was a fascinating watch, and I learned quite a lot about the different ways viruses evolve.
---
In the USA, hospital admissions of 0-17 year olds in the pandemic is at an all-time high.
Source: https://covid.cdc.gov/covid-data-tracker/#new-hospital-admissions
Commentary: As has been mentioned elsewhere, the pandemic is now largely a pandemic of the unvaccinated. The single largest group? Kids under 12 years old. This is why it's so important to protect them until vaccines are available for them. Keep them away from others, and mask up yourself so you don't carry COVID-19 to them, even if you're asymptomatic.
Remember that vaccination is at household level. If one person in your house isn't vaccinated, behave as though no one is vaccinated. You are vaccinated only when everyone you live with is also vaccinated and protected from harm.
---
COVID-19 study showing earlier emergence of the virus may be seriously flawed. "SARS-CoV-2/COVID-19 in Italy in September 2019: the most important finding yet on the origin of the pandemic*.
A thread. 1/24
The study, led by Dr. Elisabetta Tanzi, also includes heavy-hitters of molecular evolution @sergeilkp and Sudhir Kumar. I greatly admire both but respectfully disagree with their conclusions here and feel it is important to explain why. 2/
Dr. Tanzi led an earlier study claiming to find evidence of SARS-CoV-2 in a boy in Northern Italy who presented with measles symptoms in Nov 2019. 3/
Although that paper claims that her lab was "designated SARS-CoV-2 RNA-free", my correspondence with her indicates that that was not the case. A positive control from a local patient was used, presumably to develop the in-house nested PCR approach used. 4/
Nested PCR is super-sensitive. It involves a first-round amplification of a PCR-product, then a second-round amplification of a subregion of that amplified PCR product. 5/
Especially true when a positive control is amplified before or at the same time you screen an "unknown" sample. 6/
Although not mentioned, I assume a positive control was used the validate the assay. 7/
They report SARS-CoV-2 RNA in 11/44 cases from the "pre-pandemic" period, Aug 2019-Feb 2020. The earliest in Sept 12, 2019, plus 6 in Oct, 1 in Nov. 8/
(They also report SARS2 RNA in 2/12 such cases from Mar 2020-Mar 2021 who had also tested negative for SARS2.)
Crucially, in each "pre-pandemic" case that yielded SARS2 RNA spanning the three mutations characterizing the spring 2020 Italian outbreak, they were present. 9/
A23403G/D614G 10/
In other words, instead of some ancestral genome, as might be expected for samples collected months before the earliest ones in Dec 2019 in Wuhan, they have highly derived genomes typical of what was circulating in Northern Italy in spring 2020. 11/
I have published a study, with Joel Wertheim, @suchard_group, @LemeyLab @jepekar and others that indicates that the B.1 variant jumped from China to Italy on or around Jan 28 2020. 12/
The German lineage B virus was just *one* mutation different than the Italian one. 13/
Sure enough, I *just* noticed that one does: hCoV-19/Zhejiang/HZ103/2020 EPI_ISL_422425.
Indeed, B lineage viruses with the full progression to B.1 were present in PRC by Jan 2020... 14/
C3037T + A23403G/D614G; and
C3037T + A23403G/D614G + C14408T.
That makes Fig. 2 from Tanzi et al quite nonsensical. The figure portrays a stepwise evolution of the B.1 lineage in Italy, with B.1. present by Oct 2019. 15/
Both options strike me as *much* less likely than a nested-PCR false positive. 16/
What are the chances of hitting 11 true positives without a single one yielding a qRT-PCR positive result? 17/
But they are derived from viruses that were circulating in China that already possessed high affinity for hACE2. 18/
Not just that: those key mutations in the genomic data indicate that they are extremely "fit" B.1 viruses! Those are the ones that rapidly displaced almost all the other lineages around the world! 19/
Presence of the virus in Italy in June-Aug 2019, as proposed, also flies in the face of molecular clock estimates calibrated over and over again at about 2 changes per genome per month. 20/
A study I co-authored with Joel Wertheim, who led the work, @jepekar, @niemasd and Konrad Scheffler uses that molecular clock, plus realistic epidemiological parameters, to infer an origin of the Wuhan/Hubei outbreak in October 2019 at the earliest. 21/
The idea that a derived, B.1, variant was present in Italy in Sept 2019, but remained unnoticed for some 6 months, also flies in the face of epidemiological data – e.g. a doubling time of 2-5 days in the absence of mitigation efforts. >35 doublings = millions of infections. 22/
"We find very, very few people who do not develop neutralizing antibody titers of at least 20....They provide no numbers on the semi-quantitative Eurimmun serology assay....This seems really dubious to me." 23/
The Chinese government is keen to assert that the pandemic started outside China. I fear this study will play right into that narrative. 24/24"
Source:
Commentary: It seems clear from Dr. Worobey's analysis that something did go wrong with the study showing earlier emergence of SARS-CoV-2. I'd still bank on emergence in late 2019 in China, and 2020 for most of the rest of the world - and certainly nothing earlier than the fall of 2019.
---
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. Get your personal finances in order now. Cut all unnecessary costs.
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
---
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
---
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.
---
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.