One small note about these trials. It's often assumed that vaccines are only a proxy for immune response to natural infection. However, there's nothing that prevents vaccines from inducing better, more durable protection than natural infection. 3/8
Here, I'm showing a trimmed down figure from Jackson et al (nejm.org/doi/full/10.10…) detailing phase 1 immunogenicity results from the Moderna vaccine. I've trimmed this to show only the relevant dosage that was chosen for the ongoing phase 3 trial. 4/8
You can see that at 36 days after the 2nd dose, titers for binding and neutralization are often substantially higher in vaccinated individuals than individuals recovered from COVID-19 infection (labeled as "convalescent"). 5/8
We see a similar picture for Pfizer / BioNTech in Walsh et al (nejm.org/doi/full/10.10…). I've trimmed this figure to show only relevant dosage and vaccine construct (full spike protein rather than just receptor binding domain). 6/8
Again, titers for both binding and neutralization are often substantially higher in vaccinated individuals after two doses than in recovered individuals (labeled as "HCS"). 7/8
Although it remains to be seen whether these efficacy numbers hold up with time (
), I'm really optimistic about these vaccines. I just hope we can hold off the epidemic for a bit longer to allow time to roll them out to the population. 8/8
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The #COVID19 epidemic is rapidly growing throughout the US. What happens now? Here I try to make some predictions, but mostly try to explain how I think about the epidemic. 1/14
The US just reported ~170,000 cases in a day. However, there hasn't been a sudden increase in transmission. This is the same exponential growth process going on for weeks now. Rt has ticked up from a US average of ~1 in August to ~1.15. Data from rt.live. 2/14
This increase in Rt can be ascribed to seasonality of the virus. Seasonality of respiratory pathogens is (incredibly) not well understood but is thought to be due to a combination of indoor crowding and increased stability of viral particles in drier winter air. 3/14
A brief update on our work with the sequencing of the White House #COVID19 outbreak. Since posting on Nov 1, groups from all over the US have shared an additional 2798 #SARSCOV2 viral genomes via @gisaid and additional connections have emerged. 1/9
This sequencing has revealed additional viruses circulating in Virginia and collected between Aug and Oct that fall alongside the WH lineage, as well as three viruses from Michigan collected in Oct that are closely related to sequences from the White House outbreak. 2/9
These three viruses from Michigan possess 1 differentiating mutation and the two White House-associated viruses also possess 1 differentiating mutation. A molecular clock analysis places their common ancestor in Aug or Sep. Interactive figure at nextstrain.org/community/blab…. 3/9
After posting about sharply rising #COVID19 cases Friday, there were multiple replies to the effect of "but deaths aren't going up". As should be obvious to most at this point, (reported) deaths lag (reported) cases. This thread investigates. 1/8
There is a lag between when a case is diagnosed and when the individual may succumb to their disease and there is a further lag between date of death and when the death is reported. 2/8
Here, I compare state-level data from @COVID19Tracking for cases and deaths and find that a 22-day lag maximizes state-level correlations. 3/8
I know that everyone has been (justifiably) distracted by other things, but the #COVID19 epidemic in the US is looking pretty dire with 125,552 confirmed cases reported Friday by @COVID19Tracking. 1/10
Confirmed cases have continued to tick up across the US, though with the Midwest and Mountain West contributing to most of the recent increase. Data from @COVID19Tracking. 3/10
Separately, I wanted to address the question of "why do this?" with regards to sequencing of infections involved in the White House #COVID19 outbreak. 1/10
Although the origins of the White House outbreak were characterized as "unknowable", viral genome sequencing can offer important clues to how infections in a cluster are connected to each other and to the larger COVID-19 epidemic. 2/10
This technology is rapidly becoming a standard course of action for COVID-19 clusters of public health interest. This seems obvious, but we can use science to understand and track the spread of COVID-19. 3/10
We enrolled two individuals with exposures linked to the White House COVID-19 outbreak into an IRB-approved research study, collected nasal swabs and sequenced the SARS-CoV-2 virus in these swabs. 2/16
Importantly, these two individuals attested that they had no direct contact with each other in the days preceding their diagnoses and are independently linked to the White House COVID-19 outbreak. 3/16