SARS-CoV-2 lineage/clade typing using Exatype – a single, streamlined analysis workflow

SARS-CoV-2 lineage/clade typing using Exatype – a single, streamlined analysis workflow

Dr. Natasha Wood 01/04/2021

With new SARS-CoV-2 variants of concern emerging around the world, global surveillance has become more important than ever. Large-scale sequencing allows for the identification of any new dominance of specific variants, clusters of outbreaks, and the monitoring of viral variants that impact the efficacy of vaccines

The variants of concern first identified in South Africa, the UK and Japan (from travellers from Brazil) have dominated news headlines since December 2020, with certain variants linked to increased viral transmission and a reduction in neutralising antibody efficacy. As the pandemic continues to spread, it is likely that more variants of concern will emerge over time.

To support the sequencing and surveillance efforts, we are continuously updating the features of our SARS-CoV-2 genotyping platform, Exatype, to make the analysis as simple and streamlined as possible.

One of the key additions to our platform in January 2021, was the inclusion of lineage (Pangolin) and clade (Nextstrain) typing.

With this, users can now retrieve their consensus sequences and alignments together with the lineage and clade information, without worrying about using separate online tools or continuously updating downloaded software applications. Indeed, we are constantly monitoring any changes made to the publicly available Pangolin and Nextstrain software, and automatically updating Exatype so that our implementations of the tools match the latest public versions. In short, your results will always be up-to-date.

Table of Lineage/Clade Typing data

A full set of features is listed on our SARS-CoV-2 flyer, and we welcome suggestions or comments. Please sign-up to run some demo samples – or your own data – starting today!