1/n Very excited to share my lab's latest manuscript, nearly 3 years after I started my independent group! This was a fantastic collaboration with Bryan Johnson and @TheMenacheryLab, led by joint 1st authors @hannah_kubinski and Hannah Despres in my lab biorxiv.org/content/10.110… @TheMenacheryLab @hannah_kubinski 2/n As Delta was emerging, we saw that most of the viral sequencing surveillance showed that a cysteine had been introduced into the nucleocapsid protein, at residue 215 (great work from the Schuck group showed this was advantageous in the absence of other mutations in N or S)

1/n Very excited to share @mmschmidt_1 's first first-author manuscript (and the second from my lab), looking at viral infectivity directly in pediatric clinical samples from children of different ages infected with SARS-CoV-2. medrxiv.org/content/10.110… 2/n Given that children typically experience milder disease symptoms than adults (and there were early questions about whether kids could transmit), we wondered if there was something different about the virus produced by children.

1/n Very excited to share the first manuscript from my lab, looking at viral load (FFU) directly in clinical samples from SARS-CoV-2 Alpha, Delta and Epsilon variants. Our data indicates that Delta is more infectious than Alpha, for the same amount of RNA medrxiv.org/content/10.110… 2/n While this point may seem pedantic, viral RNA (ie, Ct of an RT-PCR reaction, which is currently used as the sole clinical measurement of SARS-CoV-2 viral load) is not the same thing as infectious virus (as anyone who's worked on flu packaging can attest)

1/n Excited to share another great collaborative project with @MargaretGMills- this time looking at whether we can predict the presence of infectious SARS-CoV-2 in clinical samples. medrxiv.org/content/10.110… @MargaretGMills 2/n While the gold standard for detecting infectious virus is culture at BSL-3, this is time- and resource-intensive. We and others have speculated that there are RT-PCR based approaches that could be used instead, in a high-throughput fashion at BSL-2.

1/n A year after our initial observation that RNA extraction is not required for SARS-CoV-2 RT-PCR diagnostic tests, excited to post a follow-up study conducted at 10 global sites. Great collaborative project w/ @UWVirology @HESI_Global and all partners medrxiv.org/content/10.110… 2/n We used aliquots of pooled, identical samples shipped to each site, along with master-mix and primers/probes to show that the direct RT-PCR method worked in real life settings (and a range of machines), with relatively little variation among sites.

1/n An update to this work is now live on bioRxiv, including additional patient samples and further optimization, please retweet! biorxiv.org/content/10.110…

https://twitter.com/poisondartfrog7/status/1241521332979929088

2/n In addition to the original team (lead by Jason Botten’s lab) we teamed up with Keith Jerome’s group at the University of Washington, and have extended these findings to 155 clinical samples, over a range of viral loads.

1/n Our work describing the adaptation of the CDC RT-qPCR assay for use with alternative Qiagen RNA extraction kits, as well as skipping the RNA extraction step entirely is live on bioRxiv. Pls retweet. #coronavirus #COVID19 #StayAtHome biorxiv.org/content/10.110… 2/n The current shortage of approved RNA extraction kits during the COVID-19 pandemic has resulted in a severe bottleneck in testing capacity.