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.
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Commentary: In the global war effort, we are about to cross a threshold - almost a billion doses of vaccine administered. This will go down in history as one of the biggest public health efforts in human history. We have never before administered this much medicine, this fast, to so many people, and with such positive results.
It makes you wonder what else we could accomplish as a species if we put our minds and backs to it.
Source: https://www.bloomberg.com/graphics/covid-vaccine-tracker-global-distribution/
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A positive mystery: breakthrough cases are REALLY low. "Last week, the Centers for Disease Control and Prevention reported that more than 5,800 out of 75 million fully vaccinated people in the U.S. have been infected with COVID-19. Of these “breakthrough cases,” 396 were hospitalized and 74 people died. The CDC defines a breakthrough case as someone who gets sick, either symptomatically or asymptomatically, 14 or more days after full vaccination. A few headlines about the report implied, rather irresponsibly, that the breakthroughs happened because the vaccines didn’t work. CNN, for instance, put it this way: “So far, 5,800 fully vaccinated people have caught Covid anyway in US, CDC says.”
The reality is that breakthrough cases are normal and expected after vaccination. That’s because none of the three vaccines available in the U.S. (or, indeed, anywhere else) is 100 percent effective at preventing disease from COVID-19. The Pfizer/BioNTech vaccine, for instance, is 95 percent effective. That’s impressively high, but a few breakthrough infections, hospitalizations, and deaths are still expected to occur in people who get the vaccine. (One slightly confusing thing about investigating breakthrough infections is that research is using the term differently. There’s the CDC’s definition of an infection two weeks after full vaccination. But some studies have also investigated breakthrough infections in people who have received only one vaccine dose, like Viterbo. Other research addressing infections after vaccination doesn’t use the term breakthrough at all.)
“If it were 95 percent protection, you would expect 5 percent of the [75] million people who’ve been vaccinated not to be protected,” said Barry Bloom, a professor of public health and an immunologist at the Harvard T.H. Chan School of Public Health on a press call on Friday. The same logic applies to the Moderna vaccine, which is 94 percent effective, and the Johnson & Johnson vaccine, which was 72 percent effective in a U.S. trial. In fact, the number of breakthrough COVID cases was “less than I expect,” said Bloom. “Far less.” Of the 75 million vaccinated people in the U.S., the 5,800 breakthrough cases represent just 0.0075 percent."
Source: https://slate.com/technology/2021/04/covid-19-vaccine-breakthrough-infections-cdc-data.html
Commentary: This is why we all advocate, even after vaccination, that you still wear a mask and practice preventative measures. That said, these numbers are crazy low. 75 million people with a vaccine that's 95% effective should yield 3.75 million people who still get COVID-19 after vaccination. Instead, we've had 5,800. Now, perhaps some of that is due to testing and the fact that the vaccine makes COVID-19 less serious - so much so that perhaps the cases which are occurring are asymptomatic, or people who've been vaccinated simply stop bothering to get tested. That said, it's still amazing. The vaccines not only work, they REALLY work.
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We may have hit peak vaccinations. "Daily U.S. vaccinations have peaked
Now under 3M/day rolling avg
Doubt we'll get back above 3M again
Why?
Vaccine avid folks have gotten their shot
Its now the ground game
Reaching those with less access
Reaching those who have questions
It'll be hard. Its so important"
Source:
Commentary: This is indeed the hard part, convincing people who are hesitant or uninformed to go get vaccinated. What can you do? Keep encouraging everyone you know to get vaccinated. The vaccines are safe and effective. Share selfies when you get vaccinated. Share, like, and comment on the photos your friends post. Make sure you amplify their content, so that everyone possible sees that vaccination is safe and effective.
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Sequencing is picking up. "When variants of concern were first identified in late Dec, the US was not where it needed to be in terms of genomic surveillance. However, with considerable ramp up by the CDC, state labs and academic groups, we now have a remarkable genomic surveillance system. 1/14
My favorite metric for genomic surveillance is the number of cases that have been sampled, sequenced and shared publicly to @GISAID in the previous 30 days. By incorporating both sequencing volume and turnaround time, it tells you how much is known about current circulation. 2/14
Throughout the fall, the US had just 100-300 genomes available that were sampled, sequenced and shared in the previous 30 days. 3/14
However, with investments in sequencing capacity, the US had rapidly increased this count, ramping from 100-300 in Dec 2020 to over 30,000 in April 2021. This is a remarkable achievement and I'm no longer worried about novel variants escaping detection in the US. 4/14
This increase in sequencing has been driven by the CDC and by non-CDC groups (mostly academic labs and state lab health departments). 5/14
Much attention has focused on proportion of cases sequenced, where in the past 30 days the US has sequenced about 1.7% of cases, behind countries such the UK (30%), Switzerland (5%) and Germany (2.5%). Data from gisaid.org/index.php?id=2…. 6/14
However, for variants in particular, analysis focuses on frequency, where we particularly care about variants that are increasing rapidly in frequency across different geographies. 7/14
In this case, having a very large volume of sequences with good turnaround time should be sufficient to characterize variants while they're still at low frequency. 8/14
With ~30,000 genomes in the past 30 days, we can reliably catch variants at a 0.02% frequency threshold in the US (geometric distribution with 99% probability of detection). Again, this is remarkable. 9/14
Other countries have also been increasing sequencing throughput in response to the emergence of variants of concern and we see the US now matching sequencing throughput of the UK and the rest of Europe when considered separately. 10/14
However, SARS-CoV-2 variants are emerging throughout the world and only focusing on improving genomic surveillance within national borders is short sighted. The primary goal of this surveillance is to be to able to formulate vaccine updates with sufficient lead time. 11/14
Work by South African and Brazilian scientists to quickly identify and share data on B.1.351 and P.1 did the world an enormous favor. 12/14
Sequencing throughput has been increasing in Africa and South America, but now lags behind the US and Europe due to recent national investments in sequencing capacity in the US and Europe. 13/14
International investment is incredibly important here. I'd so much prefer an additional 1000 genomes from South America or Africa to an additional 10,000 from the US or Europe. 14/14 "
Source:
Commentary: It's pretty astonishing how fast things changed for genomic sequencing in the United States. Once the new administration took office, it was like putting rocket boots on. We will need to sustain sequencing efforts around the world to make sure we detect new variants as they occur. That means continued testing and sequencing.
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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, 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.
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:
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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
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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.