Enabling high-throughput SARS-CoV-2 sequencing and surveillance

Joe Pickrell
Jan 9 · 2 min read

At Gencove, our mission is to make genome sequencing accessible and interpretable. Over the past several weeks, it has become clear that a key missing piece of the response to the coronavirus crisis in the United States involves sequencing to monitor virus strains as they arise and spread. This was driven home by the identification of an apparently more contagious virus lineage in the UK and a potentially similar report from South Africa.

It seems certain that virus lineages with worrying properties (e.g. increased transmission or vaccine escape) are arising elsewhere in the world; these variants were only identified in the countries in question because they have systems for systematic viral surveillance by genome sequencing.

To assist in addressing this gap, we have now implemented sequencing protocols and a cloud-based analytics pipeline for the sequencing of SARS-CoV-2. These are available as end-to-end sequencing services (from swab to report) or as a software integration with existing sequencers. Our goal is that sequencing will enable 1) the tracking of known SARS-CoV-2 variants of concern, and 2) surveillance for new mutations [1].

We are looking forward to rolling this out at scale in collaboration with commercial and government entities — reach out to info@gencove.com if you are interested in monitoring SARS-CoV-2 strains.

Example report for a B.1.1.7 (UK variant) sample

[1] In setting up, we have relied heavily on the publicly available data from the COG-UK consortium and are extremely grateful for the openness of this effort.

The Gencove Blog

Behind the scenes at Gencove