Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences.

ABSTRACT:

Background

More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. It is therefore important to understand how much information about Pango lineage status is contained in spike-only nucleotide sequences. Here we explore how Pango lineages might be reliably designate

SUBMITTER: O'Toole A 

PROVIDER: S-EPMC8832810 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature