Update 1 | 2020.04.03

Yale SARS-CoV-2 Genomic Surveillance Initiative

This report shows preliminary results related to 18 new SARS-CoV-2 genomes from clinical samples collected in Connecticut between March 13-25, 2020. These samples were sequenced by Joseph Fauver and Tara Alpert, using a MinION platform and an ARTIC protocol. Phylogenetic analysis were performed and results were interpreted by Anderson Brito. The results reported in this update were obtained using a `nextstrain` pipeline, and can be also visualized here.


The directories `consensus_genomes` and `metadata` in the main page in this repository contain all of our current SARS-COV-2 genomes and metadata.


⚠️ WARNING: These results should be considered as preliminary data: they may change in light of new evidence.


We added our 27 SARS-COV-2 genomes to 321 available from around the world to understand the timing and origins of the COVID-19 outbreak in Connecticut.


By focusing on just our genomes (CT = light blue; NY = blue-green), we can see that the COVID-19 outbreak in Connecticut was sparked by multiple introductions (see picture below).

Yale genomes

10 of our 27 genomes cluster with those from elsewhere in the United States, primarily with those from Washington state (red, below). This demonstrates that coast-to-coast SARS-CoV-2 transmission has already occurred in the United States.

Cluster 1

7 of our genomes cluster with those sequenced from New York (red) and Europe (faded), indicating that the nearby explosive outbreak in New York is starting to spill over into Connecticut. We did not see this connection with our first 9 genomes, and it is something to watch closely

Cluster 2

4 of our genomes cluster together in what may have been an introduction from Europe in early March followed by sustained local or regional transmission (see below).

Cluster 3

The remaining genomes suggest multiple, separate introductions of viruses from European countries such as Belgium and the United Kingdom.

See these results on Nextstrain →

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