Thread by @NAChristakis

Omicron BA5 is the dominant variant of SARS2 in USA at the moment (although new COVID19 variants will surely soon appear and take its place). These variant waves are nicely visualized in UK data. We should prepare as a nation for this evolving landscape. Let's talk about this. 1/

The reasons for BA5's success (and for omicron's more generally) relate both to its intrinsically greater infectivity and its ability to re-infect previously infected or even vaccinated people. (See, eg, this article from Feb 2022 via @sigallab ): nature.com/articles/s4157… 2/

Nice and informative epidemiological data from the UK SIREN study help shed light on BA5's ability to reinfect people. 3/

SARS-CoV-2 Immunity and Reinfection EvaluatioN (SIREN) is a cohort >44,000 UK NHS healthcare workers. Participants undergo asymptomatic SARS-CoV-2 PCR testing every 2 weeks! They are now highly vaccinated (>95%). The incidence of new infections and reinfections is monitored. 4/

COVID19 PCR positivity has increased in this carefully monitored high-risk-of-exposure cohort of healthcare workers in the UK since mid-May 2022, in keeping with rise of BA5. assets.publishing.service.gov.uk/government/upl… 5/

The rate of primary infections and reinfections with SARS2 in the SIREN monitoring cohort have both increased since mid-May (and throughout 2022). Omicron is clearly able to manifest immune evasion and re-infect people. 6/

Thankfully, while Omicron (especially BA5) is causing more infections, it is apparently not causing more severe illnesses on a per-case basis, and population rates of death have not kept pace with rates of infection, though deaths HAVE gone up (since population size is high). 7/

We are not done with the COVID19 pandemic yet. While we are in the 'intermediate phase' of the pandemic, described in #ApollosArrow (and also here: wsj.com/articles/the-l…), the virus is not yet endemic and it's causing more clinical havoc, still, than I had expected early on. 8/

The USA should continue to attack COVID19, similar to Operation Warp Speed (where government de-risked drug development), in things like a pan-coronavirus vaccine or nasal vaccines (which reduce infection AND transmission science.org/doi/10.1126/sc…) | @EricTopol @VirusesImmunity 9/

This coming winter will not be easy. At the moment, we have about 400 deaths per day from COVID19 in the USA (which is bad -- about 3-10 times worse than typical flu), but this will only rise in coming months. 10/

And there's a risk of even worse trajectories. While unlikely, I think risk is 1-10% of one of two bad things possibly happening: 1) emergence of new fully-vaccine-evading strains, or 2) emergence of much deadlier strains of SARS2 (with fatality >>1%). Unlikely, but possible. 11/

We therefore should invest, as well, in ongoing monitoring of variants (especially among hospitalized COVID19 patients). The USA has gone from >60,000 sequencings per week in January 2022 to ~10,000 nowadays, which is a foolish, shortsighted economy. science.org/content/articl… 12/