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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Dr. Angela Rasmussen on the new mink variant of SARS-CoV-2.
"So you may have heard concerns about the mink variant of #SARSCoV2 that was discovered in Denmark and is leading to the decision to cull all farmed minks in the country.
This should not be a cause for panic.
Denmark Will Kill All Farmed Mink, Citing Coronavirus Infections
Government officials said on Wednesday that a mutation in the virus could interfere with vaccine effectiveness in humans.
https://www.nytimes.com/2020/11/04/health/covid-mink-mutation.html
This is another example of sharing data by press release, and on its face, it sounds alarming:
-People got infected with it
-People mounted weak antibody responses
-Danish public health official said that this strain would interfere with vaccine efficacy
OH NO SOUNDS BAD
There is no data available to support any of these statements so it's hard to evaluate them. However, we know a few other things that may mitigate concerns a bit.
In the Netherlands, there were big mink farm outbreaks earlier this year.
The Dutch mink farms were likely the result of anthroponotic transmission (from humans to minks). At least 2 people are thought to have then contracted SARS-CoV-2 zoonotically (from minks to humans). So it's not surprising that there were cases in Denmark.
Ferrets, which are related to minks, are used as an experimental model of COVID-19 (well, more like a model of SARS-CoV-2 infection, because ferrets don't get very sick). So it's not shocking that minks are susceptible to infection.
So far there have not been any data demonstrating that COVID-19 caused by mink-derived variants is substantially different from human-derived variants. "Weak" antibody responses are seen in mild or asymptomatic COVID-19 cases too.
Now let's get to the most worrisome claim, that the mink-derived viruses will render vaccines less effective. This suggests that replication in the mink selected for mutations in critical regions of SARS-CoV-2 antigens, probably the spike protein.
However, without knowing what those mutations are, it's unclear what the implications are for vaccines. Unless the mutations are in regions of spike (called neutralizing epitopes) that are important for antibody neutralization, that's just speculation.
Even if there are mutations in known neutralizing epitopes, it's still speculation. You can use all the fancy computational and structural modeling tricks in your toolbox to predict the functional effect of a mutation but you won't actually know until you test it experimentally.
And furthermore, RNA viruses like SARS-CoV-2 are always mutating. It's normal and expected. We already know that any mutation, whether from a human- or mink-derived variant, can occur in an important epitope.
Mutations are changes in the RNA genome. When these occur in a part of the genome that encodes a viral protein, it can result in a different amino acid being inserted in that protein than the amino acid that was originally encoded. That can affect antibody binding to that epitope
Antibodies are exquisitely specific and sometimes even a single amino acid substitution can abrogate antibody binding. Thus a mutation in a key epitope could mean that vaccines raised against one variant will elicit antibodies that don't protect against variants w/ the mutation.
But they haven't shown what mutations the mink-derived variants have acquired, so who knows? Mutations arise in human-derived viruses too, so the moral of the story is that we need to conduct robust surveillance for all circulating SARS-CoV-2 isolates to look for escape variants.
So there's no reason to be extra concerned about these mink variants without evidence otherwise. We should review the data objectively when available and we should continue and expand genomic surveillance.
The thing I'm most concerned about was not really addressed by the Danish authorities: spillback into a new reservoir species. If SARS-CoV-2 starts circulating in wild animals, then we risk future outbreaks caused by zoonotic transmission from exposure to these new reservoirs.
I'm already very concerned that SARS-CoV-2 could become established in cats. Cats are susceptible to infection and there are millions of feral cats in the US (and millions more globally). If cats become an established reservoir, we may be stuck with SARS-CoV-2 for years to come.
In this regard, it's good that the Dutch mink industry is shutting down entirely by 2021. Hopefully other countries will follow suit. Mink farming is also unnecessary and cruel, so there's little upside for continuing the practice if it's also a spillback risk.
But I really wish that the trend of science by press release would stop. There's no reason why the genomic data couldn't be shared, which would allow the scientific community to evaluate these claims. It's hard to communicate risk when you haven't seen the data.
ADDENDUM: Yes I know the difference between Dutch and Danish. When I said the Dutch mink industry is shutting down by 2021, I was referring to mink farming in the Netherlands. It's not clear to me that mink farming in Denmark is ending for good after the animals are culled."
Source:
Commentary: Dr. Rasmussen and others have highlighted this new mutation, but as many have pointed out, we are overwhelmed with the current version of the virus. No need to borrow trouble - and there isn't much of a survival advantage right now for many mutations because the current version of the virus is spreading so easily and well. Mutations really surface only when a survival advantage comes from a mutation that makse an adaptation more viable than the original. The D614G mutation gave SARS-CoV-2 more infectivity, making it easier to spread - that's the last major mutation that gave it a substantial advantage.
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"The United States on Wednesday recorded over 100,000 new coronavirus cases in a single day for the first time since the pandemic began, bursting past a grim threshold even as the wave of infections engulfing the country shows no sign of receding.
The total count of new infections was at least 107,000, according to a New York Times database. Twenty-three states have recorded more cases in the past week than in any other seven-day stretch.
Five states — Colorado, Indiana, Maine, Minnesota and Nebraska — set single-day case records on Wednesday. Cases were also mounting in the Mountain West and even in the Northeast, which over the summer seemed to be getting the virus under control.
North and South Dakota and Wisconsin have led the country for weeks in the number of new cases relative to their population. But other states have seen steep recent increases in the last 14 days.
Daily case reports in Minnesota, on average, have increased 102 percent over that time, while those in Indiana have risen 73 percent. For months, Maine had among the lowest levels of transmission anywhere in the country, but new cases there have more than tripled. In Wyoming, new cases are up 73 percent, while in Iowa they have more than doubled.
Deaths related to the coronavirus, which lag behind case reports, have increased 21 percent across the country in the last two weeks.
Hospitals in some areas are feeling the strain of surging caseloads. More than 50,000 people are currently hospitalized with Covid-19 across the country, according to the Covid Tracking Project, an increase of roughly 64 percent since the beginning of October.
Dr. Anthony S. Fauci, the country’s top infectious disease expert, predicted in June, when new cases were averaging roughly 42,000 a day, that the rate would eventually reach 100,000 a day if the pandemic were not brought under control. His blunt assessments of the country’s failure to control the virus drew attacks from Trump administration officials, including the president, who called him alarmist.
In an interview on Friday, Dr. Fauci told The Washington Post that the country would most likely hit the 100,000 mark soon.
“We’re in for a whole lot of hurt,” he said.
Dr. Fauci said that the country “could not possibly be positioned more poorly” as winter approaches and colder temperatures lead people to gather indoors."
Source: https://www.nytimes.com/live/2020/11/05/world/covid-19-coronavirus-updates
Commentary: Other than having people willfully going around and licking others, Dr. Fauci is correct. America and Europe are in a terrible position right now, just before winter and holidays, as is much of the Northern Hemisphere.
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Rapid tests struggle with asymptomatic infections. "As the number of coronavirus cases in the United States exceeds 9.2 million, experts continue to call for an enormous scale-up of testing among both the healthy and the sick — a necessary measure, they have said, to curb the spread of an infection that can move swiftly and silently through the population.
One strategy has involved the widespread use of rapid tests, which forgo sophisticated equipment and can return results in minutes. Purchased in bulk by the federal government and shipped nationwide, millions of these products have already found their way into clinics, nursing homes, schools, athletic teams’ facilities and more, buoying hopes that the tests might hasten a return to normalcy.
But a new study casts doubt on whether rapid tests perform as promised under real-world conditions, especially when used in people without symptoms.
In a head-to-head comparison, researchers at the University of Arizona found that, in symptomatic people, a rapid test made by Quidel could detect more than 80 percent of coronavirus infections found by a slower, lab-based P.C.R. test. But when the rapid test was used instead to randomly screen students and staff members who did not feel sick, it detected only 32 percent of the positive cases identified by the P.C.R. test.
Quidel’s tests are authorized for use only in people with symptoms, but their use in those who are asymptomatic has been strongly encouraged by the federal government. In September, the White House announced detailed plans to purchase and distribute 150 million rapid antigen tests manufactured by another company, Abbott.
“This is really valuable data that has been hard to come by,” said Dr. Benjamin Mazer, a pathologist at Johns Hopkins University who was not involved in the study. “But 32 percent is a very low sensitivity. I’m surprised by how low that is.”"
Source: https://www.nytimes.com/2020/11/02/health/coronavirus-testing-quidel-sofia.html
Commentary: A 32% accuracy rate is below that of a flip of a coin. Looks like we still have a long way to go on testing.
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A reminder of the simple daily habits we should all be taking.
1. Wash/sanitize your hands every time you are in or out of your home for any reason. Consider also spraying the bottoms of your shoes with a general disinfectant (alcohol/bleach/peroxide) when you return home. Remember that cleaners are NEVER to be ingested or injected.
2. Always wear a mask when out of your home and if going to a high risk area, wear goggles. Respirators are back in stock at online retailers, too.
3. 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.
4. Get your personal finances in order now. Cut all unnecessary costs.
5. Replenish your supplies as you use them. Avoid reducing your stores to pre-pandemic levels in case an outbreak causes unexpected supply chain disruptions.
6. Participate in your local political process. For Americans, go to Vote.org and register/verify your vote.
7. Ventilate your home as frequently as weather and circumstances permit.
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Common misinformation debunked!
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.