This page shows preliminary results related to 13 new SARS-CoV-2 genomes (from CT[10] and NY[3]) from clinical samples collected between March 18-19, 2020. These samples were sequenced by Joseph Fauver and Tara Alpert, using a MinION platform. Phylogenetic analysis and results interpretation were done by Anderson Brito. The results reported here were obtained using a nextstrain pipeline, and can be also visualized here.
Data
The directories consensus_genomes and metadata in the main page in this repository contain all of our current SARS-COV-2 genomes and metadata.
See these results on Nextstrain
Interpretation
WARNING: These results should be considered as preliminary data
We added the new 13 SARS-COV-2 genomes with other 27 genomes we presented in the previous update, and collected other 267 genomes available on GISAID, from around the world, to uncover recent patterns of viral spread within and from Northeastern USA in the past weeks.
A growing cluster of viruses between Connecticut and New York State
Nine of the newly sequenced genomes in this update are found within a growing cluster of viruses sampled in NY and CT between March 12th and 25th, 2020. They add extra evidence for sustained local or regional transmission of the virus causing COVID-19 within and between both states.
Uncertain sources and fates
The newly sequenced virus Yale-020 is genetically related to viruses collected in Connecticut over the past weeks. These samples, all sequenced by our lab, were obtained from patients residents of the New Haven County and surrounding areas, but it is still uncertain if these five viruses are causing sustained local transmission chains. Given the current data, and the genetic similarity of these genomes with those found in viruses from Europe, an international origin of these viruses, followed by continued circulation in Clinton and Beacon Falls in a plausible scenario (see map).
A growing cluster of viruses between Connecticut and New York State
Nine of the newly sequenced genomes in this update are found within a growing cluster of viruses sampled in NY and CT between March 12th and 25th, 2020. They add extra evidence for sustained local or regional transmission of the virus causing COVID-19 within and between both states.
Domestic introductions: potential seeds of viral spread
Finally, one of the genomes (Yale-012) groups together with other 12 sequenced by our team, which were found to group with genomes of viruses most likely introduced in a coast-to-coast SARS-CoV-2 transmission from the Washington state. These CT samples were collected from patients residents of several distinct locations in Connecticut, such as the southern towns/cities of New Haven, West Haven, Greenwich, Woodbridge, and Stratford, as well as Bethlehem, Litchfield, and Berlin, in the northern part.
The Bottom Line
Altogether, the patterns we observed using genomic data and phylogenetic analysis highlight that the virus causing COVID-19 is probably widely spread in Connecticut, especially in the coastline area between Hartford and New York City (zoom in the map). Staying home is an advisable action to avoid exposure to the virus SARS-CoV-2. This applies to young and adult populations (silent, asymptomatic viral spreaders), and especially to the elderly and people with underlying health conditions, those suffering severe burdens of COVID-19.
CovidTracker 