Now that people in the US are concerned about poliovirus again (just 2-3 years ago @alvalesano was asked "polio, is that still a 'thing'")...here are a few references (and some twitter handles) for your paper pile.... Great review from Cara Burns, Olen Kew and others about vaccine derived polioviruses (VDPV).
pubmed.ncbi.nlm.nih.gov/25316847/

Just out in @bmj_latest, the latest on COVID VE from the 21 hospital IVY network. @CDCgov @UMIntMed @VUMChealth. Short thread. bmj.com/content/376/bm… IVY is a test negative case control study of vaccine effectiveness of hospitalized patients. It includes individual level chart abstraction. In this VE analysis there were 5582 COVID-19 cases and 5962 test-negative and syndrome-negative controls. (2/x)

The 70x figure has definitely stuck and driven a lot of conversation and recommendations. Encourage folks to look at the preprint. IMHO the AUC analysis (panel f) is more relevant than titer difference at a single time point (70x wt v. omicron at 24h, panel b). See for yourself.

https://twitter.com/LauringLab/status/1471463737722912770

Also attaching figure from another preprint by Yuen et al. Looking at genome copies and viral titers in nasal turbinates vs. lung. At this point, the upper vs. lower tract replication of omicron and relationship to transmission seems less clear?

I'm probably going to regret this, but have some thoughts about this. Have largely kept them to myself. But been getting these sorts of questions from my clinical colleagues. So, easier to share this way. (1/x)

https://twitter.com/CT_Bergstrom/status/1467611446053851145

First. Tremendous respect for @CT_Bergstrom and this is really an excellent thread. Before I go further, some COI disclosure (important to look for these when discussing drugs/vaccines and their use). I have consulted for Sanofi and Roche re: influenza drugs. (2/x)

New preprint out from the lab today, led by @alvalesano. A little thread. 1/x

SARS-CoV-2 Genomic Surveillance Reveals Little Spread Between a Large University Campus and the Surrounding Community medrxiv.org/content/10.110… You may remember way back in Fall 2020, there was a lot of talk about college towns and how outbreaks on campuses related to case counts in the surrounding communities. For example, article below. 2/x
nytimes.com/2020/09/06/us/…

Teaching virus evolution to grad students tomorrow. Just reread the assigned paper. I think it's relevant to the discussion on immunocompromised hosts and VOC. Like most things COVID, we forget lessons from other viruses 1/x
journals.plos.org/plospathogens/… Those who know me know that I love geeking out on within-host evolution and I love geeking out on poliovirus. So I will try to hold myself in check. Briefly, oral poliovirus OPV is live attenuated virus vaccine, so it replicates in gut and shed in stool. Thus, it evolves. 2/x

Seeing lots of analyses scraping GISAID data and looking at variant sequences / total sequences. I've heard chatter in my corner of the world that "Wow, Michigan really has a variant problem." Do we? Short thread about putting the epidemiology back in genomic epidemiology 1/x In Michigan, who uploads sequence data? Vast majority comes from our awesome State Lab and then my lab. Since 1/1, my lab has uploaded 1146 to GISAID. Don't know State Lab numbers but at least 2x that. There are 600+ B.1.1.7 from Michigan, according to CDC 2/x

Happy to share out latest preprint on SARS-CoV-2 within host diversity. Brief thread.
biorxiv.org/content/10.110… We've been interested in within-host diversity for some time. It's important for understanding how mutations accumulate over time (relevant for how variants arise). Important for understanding how likely it is for variants to transmit and potentially for inferring trx chains 2/x

Unfortunately very few - any? - studies that I’ve seen relating viral load to outcome stratify by day post infection or symptom onset. This is big issue (viral load varies by day and people vary in when they get tested in disease course for many reasons). nytimes.com/live/2020/12/2… For example, here’s data from my lab showing viral load by day for outpatients (purple) vs hospitalized patients (green). All tests were on presentation. If you just look at viral load on presentation, outpatients were higher - they were just tested earlier.

Been thinking more about this piece from @kakape this morning and have some thoughts to share. So thought I'd do a Xmas eve thread about SARS-CoV-2/COVID19 and immunocompromised hosts. (1/x)
sciencemag.org/news/2020/12/u… I emphasize that I respect the stated opinions out there and don't have doubts about data or what they may show. Just feel there's a perspective missing from the conversation. What can I bring to conversation? I am an infectious disease physician and study virus evolution. (2/x)

With the news of this new variant and discussions of what it means for vaccines, keep thinking about this article from @SCOTTeHENSLEY and Yewdell (who very much needs a Twitter account). Short thread.

science.sciencemag.org/content/326/59… First question from ID docs and many virologists I know is “OMG, what does this mean for vaccines.” We grow up in this pathogen vs. immune system paradigm that is sometimes distracting from issues at play. (2)