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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A thread from Trevor Bedford of Bedford Labs on the new variants. "After a ~2 month plateau from mid-Nov to mid-Jan, the US #COVID19 epidemic has undergone a steady week after week decline and is now back to daily case counts last seen in late October. A thread on what we might expect going forwards. 1/13
Working with case counts from @COVID19Tracking and Rt estimates from epiforecasts.io, I'm showing US confirmed cases broken out by state alongside transmission rate as measured by Rt through time. 2/13
Generally, Rt > 1 in Nov and Dec corresponding to rising cases and drops below 1 in Jan corresponding to falling cases. We've seen a steady decline in Rt from Nov to Feb. Thus, current decline is not a sudden shift in circumstance, but resulted from reaching Rt < 1. 3/13
The US fall/winter epidemic is illustrated here as a series of twice monthly snapshots with bubble size representing per-capita case counts in a state and bubble color representing Rt, where red indicates growing epidemics and blue represents declining epidemics. 4/13
This shows "inflation" in Nov and Dec followed by "deflation" starting mid-Jan. The Dakotas and surroundings show a similar trajectory to other states, but were ahead of the curve with an epidemic peak in Nov. 5/13
Solely based on continued improvements to seasonality and continued increase in population immunity due to natural infection and vaccination I'd expect this trend to largely continue and the US fall/winter surge to be brought further under control. 6/13
However, the rapid take-off of B.1.1.7 will push against these gains. The trajectory of B.1.1.7 in the UK decently fits a simple logistic growth model with a growth rate r of 0.07 per day as assessed using SARS-CoV-2 genome data from @GISAID. 7/13
A similar rate of growth of B.1.1.7 is observed in Denmark and Switzerland with Denmark reaching ~20% B.1.1.7 frequency and Switzerland reaching nearly 20% B.1.1.7 frequency at the end of January. 8/13
Recent work from @genesareclever, @gkay92, @K_G_Andersen and colleagues looking at B.1.1.7 in the US (medrxiv.org/content/10.110…) estimated a similar rate of frequency increase, which suggests B.1.1.7 will reach 50% frequency in the US by perhaps late March. 9/13
However, current prevalence differs across states and B.1.1.7 may become dominant in some areas of the US earlier than other areas. 10/13
It's not clear to me at this point whether biological increase in transmissibility of B.1.1.7 will "win" against further improvements to seasonality and immunity in ~6 weeks time at the end of March. 11/13
Increased transmissibility of B.1.1.7 will certainly stretch out circulation of COVID-19 and make it harder to bring under control relative to the non-B.1.1.7 scenario, but I'm not sure at this point how much of a spring B.1.1.7 wave to expect. 12/13
I do think this will become clear shortly as we observe what happens in countries like Denmark and Switzerland or states like Florida which are farther along on their B.1.1.7 trajectories relative to the US as a whole. 13/13"
Source:
Commentary: This is important: B.1.1.7 will become the dominant strain until the next mutation that offers survival advantage, but Dr. Bedford's models are looking at logistic growth models that indicate it may not spread any faster than current strains. If nations can stay the course and vaccinate quickly, we may still be able to blunt the overall impact of the new strains.
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"Life expectancy in the United States fell by a full year in the first six months of 2020, the federal government reported on Thursday, the largest drop since World War II and a grim measure of the deadly consequences of the coronavirus pandemic.
Life expectancy is the most basic measure of the health of a population, and the stark decline over such a short period is highly unusual and a signal of deep distress. The drop comes after a troubling series of smaller declines driven largely by a surge in drug overdose deaths. A fragile recovery over the past two years has now been wiped out.
Thursday’s data gives the first full picture of the pandemic’s effect on American expected life spans, which dropped to 77.8 years from 78.8 years in 2019. It also showed a deepening of racial and ethnic disparities: Life expectancy of the Black population declined by 2.7 years in the first half of 2020, slicing away 20 years of gains. The life expectancy gap between Black and white Americans, which had been narrowing, is now at six years, the widest it has been since 1998.
“I knew it was going to be large but when I saw those numbers, I was like, ‘Oh my God,’” Elizabeth Arias, the federal researcher who produced the report, said of the racial disparity. Of the drop for the full population, she said, “We haven’t seen a decline of that magnitude in decades.”"
Source: https://www.nytimes.com/2021/02/18/us/covid-life-expectancy.html
Commentary: The last time life expectancy declined this much was 1942 - during the middle of World War 2. That illustrates the severity of the pandemic - that its impact is similar to that of a major world war.
After the pandemic, we're also going to have to contend with COVID long-haulers, people who are affected for substantial, possibly life-long COVID-19 impacts. Reforming healthcare to be more equitable will need to be a serious long-term priority in the United States if the impact of the pandemic in the long-term is to be minimized.
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There was no flu season.
Source: https://www.cdc.gov/flu/weekly/index.htm
Commentary: As predicted by some folks like Michael Coley, the flu simply isn't as infectious as COVID-19, so as we suppressed COVID-19, we nearly wiped out the flu. Let's hope that in the years to come, the lessons and practices we've learned from COVID-19 help us also mitigate future flu seasons.
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"The Pfizer-BioNTech Covid-19 vaccine loses some potency against the coronavirus variant that first appeared in South Africa, researchers reported Wednesday, based on lab experiments.
What the findings mean for how well the vaccine will protect real people from the variant, called B.1.351, is hard to tell. But clinical data from three other vaccines — those from AstraZeneca, Novavax, and Johnson & Johnson — have already shown the shots are not as powerful at blocking symptomatic Covid-19 cases caused by B.1.351 as by other forms of the virus.
In the new study, which was published Wednesday in the New England Journal of Medicine, researchers from Pfizer, BioNTech, and the University of Texas Medical Branch examined how well blood taken from people who had received the companies’ shot fought off a virus engineered to have the key mutations found in B.1.351. They reported that there was about a two-thirds drop in neutralization power against the variant compared to other forms of the SARS-CoV-2 coronavirus.
It can be difficult to extrapolate what such lab experiments mean for what happens if someone who received the vaccine is exposed to the variant. For one, these experiments only look at how one arm of the immune system, called neutralizing antibodies, responds to the modified virus. The vaccines generate a range of immune fighters, including other types of antibodies and T cells, so it’s possible that overall people retain more of their defenses in fending off the virus. It’s also possible that even though neutralizing antibodies don’t work as well against the variant, they can still mount enough activity to have an impact.
Moreover, vaccines that are less effective against B.1.351 or other variants that may emerge may still protect people from getting severe Covid-19; it’s just that they’re not as powerful against milder disease.
But based on the available data, some experts fear that the immunity elicited by vaccines won’t last as long against B.1.351 as against other variants, and that the immunizations won’t be able to drag down transmission of B.1.351 as well as they appear to be limiting the spread of other variants."
Source: https://www.statnews.com/2021/02/17/pfizer-biontech-vaccine-less-potent-against-coronavirus-variant/
Commentary: The good news is that the two major mRNA platforms - the Pfizer and Moderna vaccines - are easily adapted to new strains. Clearing regulatory hurdles for updates to them will take the longest, and is something that folks like Dr. Scott Gottlieb have been urging - an expedited regulatory process to get variations of the vaccine into the marketplace as quickly as possible to stop new strains from gaining a foothold.
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Cold snap, hot virus. "In the wake of the winter storm that plowed through Texas, power outages have plagued the state. An unexpected consequence is that Texas could now be facing another covid-19 spike resulting. With hundreds of thousands losing heat and electricity, many Texans have flocked to crowded hotels and shelters, or have been forced to seek heat and shelter in the homes of friends and relatives that still have power.
Conditions favoring spread of SARS-CoV-2 are only worsening. Grocery store lines are longer than ever. Many hotels are full—with reported instances of price gouging given the growing demand, driving people into increasingly crowded conditions. It is unlikely that physical distancing can be reasonably maintained amid these crowded conditions, making it a matter of time before the risk of viral transmission rises to dangerous levels. Moreover, Texas has pushed back against mask mandates and physical distancing measures despite the gravity of the covid-19 pandemic, which means a surge now stands to be all that much worse.
This deteriorating situation clearly has far reaching implications, and Texas' leaders have not taken effective action—more inclined to blame the situation on the Green New Deal (which has yet to be implemented) than enacting policies that could actually help the immediate situation. To make matters worse, the delivery of hundreds of thousands of vaccines will be delayed by the storm.
The Texas crisis is just the latest example of our country's need to invest in infrastructure, disaster preparedness, and to take climate change seriously. Preventing emergencies like this takes foresight, time, and effort. But once they've occurred, gaining immediate control of the consequences becomes impossible."
Source: https://brief19.com/2021/02/18/brief/will-texas-storm-cause-a-covid-19-spike
Commentary: Infrastructure is one of the things that America has invested in poorly compared to other peer nations on the world stage. The consequences of that lack of investment become more clear with every new crisis, from pandemics to polar vortexes. Is there waste in government? Unquestionably. There's waste any time human beings are involved. But underinvestment is not the same as smart spending, and America as a whole is paying a high price for chronic underinvestment.
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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. 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.
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.