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.
You are welcome to share this.
---
This week is Amazon Prime Day. If you travel a lot or have to be in at-risk places, consider grabbing a CO2 meter. These tools tell you how well-ventilated a place is. Outdoor air is about 400 ppm CO2. Anything more than double that indoors and you've got a place that isn't well-ventilated.
---
Worst yet. "The pandemic is a relentless race against Mother Nature. Waves of infection took millions of lives, and only highly effective vaccines prevented even more deaths. Now, the coronavirus is speeding up once again, mutating, evading immunity and still on the march. The arrival of subvariant BA.5 should be a reminder that the finish line in this race is nowhere to be seen.
What’s BA.5? This is the latest subvariant of omicron, which stormed the planet late last year and caused a huge wave of infection. As of now, BA.5 and a closely related variant, BA.4, account for about 70 percent of all infections in the United States, according to estimates by the Centers for Disease Control and Prevention, based in part on modeling. These two newcomers are easing out an earlier variant, BA.2.
The obscure names should not hide the punch of BA.5. Eric Topol, professor of molecular medicine at Scripps Research, says that BA.5 “is the worst version of the virus that we’ve seen.” He adds, “It takes immune escape, already extensive, to the next level, and, as a function of that, enhanced transmissibility,” well beyond earlier versions of omicron. There has not been a marked increase in hospitalizations and deaths, he reports, because there is so much immunity built up from the winter omicron wave. But there are aspects of this new variant very much worth keeping an eye on as the United States remains stuck at an uncomfortably high plateau of pandemic misery. And the new variants are driving a case surge in Europe.
At the core of the BA.5 difference is its biology. Evolution has given it more fitness, a term that incorporates its ability to transmit, grow and evade immunity; the variant shows “marked difference from all prior variants,” reports Dr. Topol. One way it does so is by evading the body’s immune system, and BA.4 and BA.5 together are “the most immune-evasive variants” seen in multiple studies to date."
Source: https://www.washingtonpost.com/opinions/2022/07/07/worst-virus-variant-just-arrived-pandemic-is-not-over/
Commentary: BA.5 is no joke. It packs a dual punch: it's more immune-evasive AND it's better at infecting cells than its predecessors. Right now your best bet is vigilant masking, assuming you've gotten all your vaccines and boosters.
---
The answer is in wastewater. "As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission."
Source: https://www.nature.com/articles/s41586-022-05049-6
Commentary: With testing being a hot mess in many places due to rapid antigen testing, wastewater is the easiest way to determine population-level infectivity. Any time I'm traveling somewhere, checking local wastewater surveillance numbers tells me what's really happening in that locale if the data is available.
---
As fewer people mask, you need better masks worn properly. "SARS-CoV-2 spreads via droplets, aerosols, and smear infection. From the beginning of the COVID-19 pandemic, using a facemask in different locations was recommended to slow down the spread of the virus. To evaluate facemasks’ performance, masks’ filtration efficiency is tested for a range of particle sizes. Although such tests quantify the blockage of the mask for a range of particle sizes, the test does not quantify the cumulative amount of virus-laden particles inhaled or exhaled by its wearer. In this study, we quantify the accumulated viruses that the healthy person inhales as a function of time, activity level, type of mask, and room condition using a physics-based model. We considered different types of masks, such as surgical masks and filtering facepieces (FFPs), and different characteristics of public places such as office rooms, buses, trains, and airplanes. To do such quantification, we implemented a physics-based model of the mask. Our results confirm the importance of both people wearing a mask compared to when only one wears the mask. The protection time before the healthy wearer has an infection risk of 50% reduces by 80% if only one wears the facemask instead of both people. The protection time is further reduced if the infected person starts to cough or increases the activity level by 85% and 99%, respectively. Results show the leakage of the mask can considerably affect the performance of the mask. For the surgical mask, the apparent filtration efficiency reduces by 75% with such a leakage, which cannot provide sufficient protection despite the high filtration efficiency of the mask. The facemask model presented provides key input in order to evaluate the protection of masks for different conditions in public places. The physics-based model of the facemask is provided as an online application."
Source: https://www.medrxiv.org/content/10.1101/2022.07.05.22277221v1
Commentary: This is a critical study. It demonstrates that anything less than an N95 mask is basically ineffective these days at providing serious protection from COVID for more than a minute or two.
---
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. P100 respirators are back in stock at online retailers, too and start around US$40 for a reusable respirator. 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, including boosters. 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 available. If it's available, choose Moderna as your first choice for both vaccine and booster, Pfizer as your second choice. However, remember than any vaccine is better than no vaccine.
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, or you know, a global war breaks out.
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 several rapid antigen tests and/or acquire them from your healthcare provider or government. 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.