Our new @biorxivpreprint is up! "Host, Viral, and Environmental Transcriptome Profiles of SARS-CoV-2." COVID-19 patients (n=338) examined w/ qRT-PCR, RT-LAMP, & total RNA-seq, host responses (e.g. ACE2) & new diagnostic methods. biorxiv.org/content/10.110… Some highlights: /1
Viral evolution maps can be built directly from the total RNA-seq data, with likely origin of NYC viruses from Europe, and less commonly from Asia, plus we think an NYC-specific clade and some novel mutations, also now posted in @nextstrain and @GISAID of course. /2
Host microbiome data shows why COVID-negative patients likely came in when they were sick. We see other coronaviruses (229E, HKU1, NL63, OC43, some rhinoviruses, and various bacterial infections), as well as NP swab microbiome profiles that show immune perturbations /3
Validation of a new, 30-min RT-LAMP (Loop-mediated isothermal amplification) molecular assay for SARS-CoV-2, and which also works on oral collection extracts! - thx @Daniela_Bezdan and lots of collaborative help from @NEBiolabs. So far 99% specificity and 95% sensitivity. /4
RNA-seq of 84 samples in the NYC subway, with so far negative CoV-2 results (somewhat reassuring), but only as the outbreak started. Sequencing is ongoing here and also across the world with the @metasub Consortium to look at RNA viruses in hospitals and city centers. /5
We see increased expression of ACE2 for highly infected individuals at the site of infection, especially interesting since clinical metadata shows that ACE inhibitors are a potential infection risk factor for the millions of people taking them, even accounting for age & sex /6
HUGE team effort. Thanks to the teams at @nyphospital & @WeillCornell, our patients, @danjbuts @cemmeydan @skimomiks @nicktatonetti @genomicslab @nygenome @jfoox @alon_shaiber @jrosiene @hajirasouliha @dcdanko @WCMCPathology @sedlazeck @Daniela_Bezdan @asierra93 @nikolaya_ivanov
