“We think of ourselves like the National Weather Service, but for infectious diseases”

Let’s talk about the weather and infectious disease
washingtonpost.com/health/2022/04…
1/ Hundreds of people die of weather related incidents every year, but thanks to the National Weather Service, we’ve made significant progress, particularly in heat related deaths Weather Related Fatality and Injury Statistics
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weather.gov/hazstat/

Why we need a COVID Moon Shot, 1st gen vaccines reduce severe disease and death, but infection/contagion not so much. Even highly vaccinated countries like Israel and Denmark continue to see surges with each new VOC (that’s BA.2 emerging in the upper right in the US)
1/ Memory B cells and affinity maturation protect us against severe systemic spread, but variants like delta and omicron reproduce rapidly in the nose before we can do affinity maturation and ramp up plasma cell populations
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The bioethics Catch-22. Quality improvement is encouraged, but publishing the results is considered research and subject to a whole different set of rules. Let’s consider a scenario
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https://twitter.com/jeremysussman/status/1490687520820142081

A hospital’s usual bandage and dressing supplier had supply chain issues so the hospital ordered supplies from a different vendor. A few months later, it’s time to reorder, and the QI team is asked should we go back to the original or keep using the new supplier?
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Where are we on the pandemic? There has been a change in strategy at several levels in the US. First and importantly, the CDC now acknowledges airborne spread of COVID. It took the CDC and WHO way too long, but the CDC has come around
1/ Second, the US is moving away from mandating lousy masks that protect others to a making good quality masks available to those who want to protect themselves. This is driven by several factors.
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A big problem with our pandemic response: binary thinking. You’re vaccinated or unvaccinated, masked or unmasked, locked down or free to do whatever you want. That’s not how the real world works
1/ Even infection is not binary. It’s not just you have the virus or you don’t. How much you were exposed to can make a big difference in the severity of the disease you experience. It’s true for every virus studied, assume it’s true for SARS-CoV-2
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Omicron and evolution to milder disease: viruses themselves don’t evolve to be milder, but we as a species may have evolved mechanisms to limit the severity of disease following infection of tissues/sites that support rapid viral spread
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https://twitter.com/statesdj/status/1477092023068987394

Why would we evolve mechanisms to limit the severity of disease following infection of tissue, e.g. nasopharynx, that support rapid spread? That’s easy, species that didn’t are no longer in existence
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Not looking good for the hope that delta + S:Y145H is just a founder effect or fluctuation, its prevalence continues to increase in the UK, now up to ~8%. Only a matter of time before this hits the US and rest of the globe Translating into plain English, what's this mean? Delta is a variant of SARS-CoV-2. AY4 is a subvariant derived from delta and AY4 S:Y145H is a subsub variant in which the spike gene (S) is mutated from a tyrosine (Y) at position 145 to a histidine (H)
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Let’s talk about Provincetown. There has been a lot of discussion about a recent COVID outbreak in Barnstable County, MA which is where P-town is located. Why all the excitement? And what does it mean for you?
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cdc.gov/mmwr/volumes/7… Provincetown was once a whaling port and Portuguese fishing town, but it morphed into a party mecca many years ago, and with mask mandates ended and everyone ready to party after a year of lockdown, I’m pretty sure this past 4th of July was a wild scene
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We’re thinking all wrong about the variants. The prevailing narrative is that each new variant comes to dominate because it’s more transmissible than previous variants. A better view may be that it’s immune escape driving viral diversity
1/ If it was just transmissibility, older viruses would continue to spread, even if somewhat more slowly, but that’s not what’s happening. Older variants are declining in absolute case count suggesting that there is competition between variants
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ncbi.nlm.nih.gov/pmc/articles/P…

@trvrb @LongDesertTrain @CT_Bergstrom Perhaps influenza (or any endemic virus) isn’t a good model. It depends on availability of susceptible hosts. A highly transmissible variant in one season would deplete the pool of available hosts in the next so endemic pathogens stabilize at moderate levels of transmission 1/ @trvrb @LongDesertTrain @CT_Bergstrom OTOH SARS-CoV-2 is in a transient phase and has yet to become endemic. ~All naive humans are susceptible so the immediate selective pressure is to maximize transmissibility
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Some push back on the notion that NIH spent hundreds of billions of dollars on basic research and therefore owns mRNA vaccine technology and has “march in” rights to dictate the use of pricing of this technology @RESachs @Dereklowe
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https://twitter.com/cmrherder/status/1337032693595463680

The fundamental contract underlying academic publication is that you publish your findings in return for recognition of priority, but once you have published others are free to use and build on your work. It’s practice established in the time of Newton and honored ever since
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Despite the catchy headline, the mandate of the CDC is far broader than pandemics, and the problems at the CDC precede COVID-19. But yes, the response to the COVID-19 pandemic was deeply flawed and systemic
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nytimes.com/2020/06/03/us/… Vaccination is a key public health responsibility, and the US does well on influenza vaccination of the elderly, but we are middle of the pack on childhood vaccination rates
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data.oecd.org/healthcare/inf…

Let’s talk about Fall Semester. Colleges and universities have to make some big decisions soon
1/ And it won’t affect just students. For example, the University of Michigan #GoBlue has 46,000 students but it also has 25,000 faculty and staff. While students may be mostly young, many faculty and staff are in vulnerable age groups
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cupahr.org/wp-content/upl…

Epidemiologists and economists say we need millions if not tens of millions of tests/day to convince people it's safe to re-open the economy, e.g. this Harvard study estimates we'll need 20 millions tests per day ethics.harvard.edu/Covid-Roadmap
1/ Nobel Laurette Paul Romer’s @paulmromer simulations say we need to test everyone in the US every two weeks, or about 25 million tests per day paulromer.net/covid-sim-part…
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The explosive growth seen in early outbreaks within community may be a result of highly exposed individuals rapidly spreading to their many connections. As we re-open we may see slower spread because many of the highly connected people are now immune 1/

https://twitter.com/mlipsitch/status/1258829527150735361

But it’s important note that this phenomenon only applies after the virus has been spreading in the community for a while. As the people of Albany Georgia learned, it only takes one individual in the wrong setting to trigger a large outbreak 2/

Let’s get real on test/trace/isolate. We have ~30k new testing confirmed cases per day. That mean we actually have ~300k new cases per day. Contact tracking is a lot of work, and BLS says we only have about 56 community health workers
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bls.gov/oes/2018/may/o… First let’s define the problem. Figure shows the amount of virus being shed from the day of onset of symptoms. For both mild and severe cases, it’s already decreasing when symptoms start
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nature.com/articles/s4159…

Let’s talk testing, specifically the coronavirus test we really need and essentially no one is talking about. What we need is a fast, low cost field test for highly contagious people, and tests like this exist, in fact they’ve been around quite a while
1/ Full disclosure. I am an exec in a biotech company, and my company is developing tests for SARS-CoV-2. I try to keep my posts objective, but obviously I believe that this is an important issue and that the solutions we are pursuing have merit
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That 1 in 5 New York City residents has already been infected with SARSCOV2 is a very dark cloud, but there may be a silver lining. It has to do with epidemics and social networks
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cnbc.com/2020/04/23/new… Epidemics spread through social contacts. The most connected people spread the virus most quickly, but they also tend to get infected earliest
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royalsocietypublishing.org/doi/full/10.10…

Let’s stop with the “It’s just a bad flu” stuff. NYS serology data shows a 13.9% infection rate across NYS, 21% in NYC. That means ~20k deaths (15k confirmed) among 2.7M infected statewide for a 0.74% infected fatality risk (IFR) 1/
cnbc.com/2020/04/23/new… The CDC says the number of symptomatic cases of flu in the US range from 10 to 45 million (avg 28.6M) but serology shows only ~25% of people infected with flu have symptoms so in typical year ~100M people get the flu 2/
ncbi.nlm.nih.gov/pmc/articles/P…

If you’re hoping a vaccine is going to be a knight in shining armor saving the day, you may be in for a disappointment. SARSCOV2 is a highly contagious virus. A vaccine will need to induce durable high level immunity, but coronaviruses often don’t induce that kind of immunity 1/ There’s a nice preprint just out on antibody responses to SARSCOV2. Lots of people don’t develop much of an IgM response and the IgG response fades noticeably after just two months 2/ medrxiv.org/content/10.110…

Good discussion of the COVID19 epidemic and the imporance of hygiene and social distancing. Actually may be even more important than they suggest. Let me explain: 1/
thelancet.com/pb-assets/Lanc… 2/ The spread of virus stops when enough people have acquired immunity. If R0 is fixed, this happens when the fraction of the population infected is 1-1/R0. In the case of SARSCOV2, R0 is ~2.5 which means about 60% of the population gets infected before viral spread ends