This page is will be updated with a summary for the sequencing efforts at Gundersen Medical Foundation's viral genome sequencing efforts for SARS-CoV-2.
We use the Ion AmpliSeq SARS-CoV-2 Panel to sequence 237 viral specific targets encompassing the complete viral genome from SARS-COV-2-positive clinical specimens.
Current Status (updated 4/24/2020)
Viral genomes sequenced: 54
Viral genomes deposited at GISAID: 43
Viral genomes selected for sharing by public NextStrain: 39
Viral genomes available on Gundersen Nextstrain build: 33 [Contact firstname.lastname@example.org for access if you are involved in COVID19 management in our region].
[Note- different quality thresholds on GISAID/NextStrain results in the number of public genomes on these platforms being lower than the total specimen number we have analyzed. Also NextStrain began downsampling strains around 4/13/20 so we anticipate that fewer of our strains will be listed there in future. We have an in-house NextStrain implementation which allows us to view and interpret the relationships between all of our sequenced specimens.]
The easiest way to begin interacting with our data is at:
Gundersen Expert Lecture Series: "Real time epidemiological SARS-CoV-2/COVID19 sequencing in the La Crosse Region" [4/15/20]:
Contact: Paraic Kenny, PhD
Updates from this research study will be posted below. They represent preliminary analyses of rapidly emerging data so are subject to future revision/correction.
Update 4/24/2020: First look at our local build of NextStrain in which we can analyze data from the La Crosse region at greater levels of detail than are possible on the public NextStrain implementation. This view documents multiple incidences of community spread in our region - most of which are relatively small, with the exception of a large cluster in Postville, IA. Data includes 25 genomes from Gundersen, with a background set of sequences from elsewhere in MN, IA, WI, IL to provide some addiotnal phylogenetic context.
Update 4/6/2020: Use of nextstrain to map the global transmission pathways (at country-to-country resolution) taken by the viruses which caused the earliest cases in the La Crosse region.
Update 4/3/2020: Phylogenetic tree including 8 early specimens from La Crosse, compared to 2894 from around the world. These data provide genetic evidence for seven independent SARS-CoV-2 introductions to La Crosse County.
Update: 3/30/20: Phylogenetic tree including 5 early viral specimens from the La Crosse region: