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/…
If you live in a college town like me, this has been an ongoing topic of conversation. We decided to take a look at this. Thanks to @dho@tcfriedrich who got us interested in this question. 3/x
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
See recent work from @alvalesano@mt2fus@famulare_mike and others on this. It's long been recognized that individuals with primary immunodeficiencies related to antibody generation can have prolonged "infections" with OPV. 3/x cell.com/cell-host-micr…
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
Why is that important? Well you need to know how sequencing is done. My lab is sequencing broadly in our area - we do every positive that we can get our hands on. We've been getting sequences uploaded on > 25% of cases since September. We've done better since January. 3/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
We looked at inpatients and outpatients. First we measured viral load. Why? Cause we're interested. But it's also a big factor in looking at diversity within hosts (spoiler alert). Another important (unique?) thing in our study is we analyzed data by day from symptom onset 3/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.
H/t to @Kalee_Rumfelt in my lab who did the chart review. Most studies don’t have day post symptom onset because it’s hard to retrieve. You typically don’t get it in data pulls from EMR. You have to go into chart notes one by one.
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)
I have taken care of patients with COVID19 who have a range of immunocompromising conditions. I have also published on within host evolutionary dynamics of viruses. We published a preprint in Sept and subsequent JID paper on long term evolution in lymphoma patient. (3/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.
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)
Many variants have been reported to escape this serum or that monoclonal. But large scale selection of a variant at this point is probably not driven by immune system (just not that much immunity around). (3)
