Lunchtime Pandemic Reading, 16-June-2021

Delta upgraded to VOC

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.

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CDC upgrades Delta to a variant of concern. "The B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.427 (Epsilon), B.1.429 (Epsilon), and B.1.617.2 (Delta) variants circulating in the United States are classified as variants of concern."

"BREAKING—CDC now officially declares #DeltaVariant a “variant of concern”—because much more transmissible (50% faster than #B117, 2x than original strain), more severe (2.5x hospitalization risk than B117, 4x original) & 1 dose vaccine evasive. #COVID19"

Source: https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

Source:

Commentary: Delta spreads 2x faster and is 4x more dangerous. The CDC upgrade means it's in the USA in enough concentration to be gaining momentum. Three things you should do:

1. If you received J&J or AstraZeneca as your vaccine, consider getting a Pfizer or Moderna booster.

2. If you have kids under the age of 12 or someone in your household who is not fully vaccinated, resume wearing masks in indoor places so you don't accidentally carry Delta home, even if you're fully vaccinated.

3. If you are eligible for vaccination and have not done it, please go do it.

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Shit happens, and that's a good thing. "The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective."

Source: https://www.nature.com/articles/s41598-020-69869-0

Commentary: Tracing disease outbreaks in sewage is a fantastic investment to make, especially for cities - and not just for COVID-19. It should be something we implement for all known diseases. Why? It's proven, it's something that can scale to the municipal level, and it does not in any way infringe on any one individual's privacy. These tests reveal things like mosquito-borne illnesses, bacterial infections, even the kinds of foods in diets based on the kinds of bacteria present.

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An example. "In some ways, this was an old routine for the scientists. Halden is director of the Center for Environmental Health Engineering at the Biodesign Institute. His lab had been analyzing the city’s wastewater for nearly two years. In 2018, they started fishing out molecular fingerprints of different kinds of opioids consumed across the city. The next year, they got a National Institutes of Health grant to use that monitoring network to track influenza. But when SARS-CoV-2 emerged that winter, they quickly pivoted to testing for the new coronavirus instead.

It took his team a few months to hone their methods but by April they were bringing more of the city’s seven sewersheds online each week. They filtered and spun down the samples, then loaded them into a desktop polymerase chain reaction, or PCR, machine. Inside, short strings of synthetic DNA swirled, grabbing onto any matching bits of SARS-CoV-2 they encountered, and giving off a fluorescent glow when they did. As the machine recorded any glimmers, it beamed the readout to a nearby computer. More light meant more virus, represented on the computer screen as a series of curves, one for each sewershed where samples had been collected: hundreds of thousands of toilet flushes captured in a spray of spidery arcs.

Two of them caught Halden’s eye. Today was the first time they were analyzing samples from Area 3. Located in the southwest corner of Tempe, Area 3 is shaped a bit like a giant amoeba eating a milk jug. That jug is the town of Guadalupe, and all of its sewage flowed into Area 3. Tempe utility workers were also sampling at the points where the pipes changed municipalities, so they could isolate the contribution of Guadalupe’s sewage from Area 3’s.

When Halden looked at the curve for Area 3, it showed a gradual incline, barely enough virus to be detectable. In contrast, the curve for Guadalupe shot straight up into the millions of copies per liter. Those numbers meant Covid-19 was already spreading through the community. If they’d only looked at Area 3, they would have missed it completely. “Area 3 is much bigger, so this significant signal from this small community was very quickly being drowned out,” said Halden.

He alerted Rosa Inchausti, Tempe’s then-director of strategic management and diversity, who was coordinating the wastewater testing pilots. In early May, she called Molina with a warning and an offer to share the data Halden’s team had collected.

“Just by chance, it was the little nugget we were looking for,” said Molina.

With Covid testing then limited, she was blinded to the virus spreading through her community and she had struggled to get health officials in the region to pay attention to her pleas for information. But armed with the wastewater data Tempe was offering, Molina was finally able to marshal the resources her town needed to fend off the virus."

Source: https://www.statnews.com/2021/06/16/sewage-sleuths-helped-an-arizona-town-beat-back-covid-19-for-wastewater-epidemiology-thats-just-the-start/

Commentary: With effective wastewater surveillance, we can get ahead of future pandemics and epidemics without substantially straining public health resources - it's far easier to collect wasterwater samples than to test hundreds of thousands or even millions of people.

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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 other people, 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. 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.

3. Wash/sanitize your hands every time you are in or out of your home.

4. Stay home 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.

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:

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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.