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

O’Toole, Á; Pybus, OG; Abram, ME; Kelly, EJ; Rambaut, A

COVID-19 Collection

Journal article

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 designated and assigned to spike-only nucleotide sequences. We survey the genetic diversity of such sequences, and investigate the information they contain about Pango lineage status. RESULTS: Although many lineages, including the main variants of concern, can be identified clearly using spike-only sequences, some spike-only sequences are shared among tens or hundreds of Pango lineages. To facilitate the classification of SARS-CoV-2 lineages using subgenomic sequences we introduce the notion of designating such sequences to a “lineage set”, which represents the range of Pango lineages that are consistent with the observed mutations in a given spike sequence. CONCLUSIONS: We find that many lineages, including the main variants-of-concern, can be reliably identified by spike alone and we define lineage-sets to represent the lineage precision that can be achieved using spike-only nucleotide sequences. These data provide a foundation for the development of software tools that can assign newly-generated spike nucleotide sequences to Pango lineage sets. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08358-2

Publication status:: Published

Peer review status:: Peer reviewed

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APA Style

O’Toole, Á., Pybus, O. G., Abram, M. E., Kelly, E. J., & Rambaut, A. (2022). Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences. BMC Genomics, 23(1), 121–121.

MLA Style

O’Toole, Á, et al. “Pango Lineage Designation and Assignment Using SARS-CoV-2 Spike Gene Nucleotide Sequences.” BMC Genomics, vol. 23, no. 1, 2022, pp. 121–21.

Chicago Style

O’Toole, Á, OG Pybus, ME Abram, EJ Kelly, and A Rambaut. 2022. “Pango Lineage Designation and Assignment Using SARS-CoV-2 Spike Gene Nucleotide Sequences.” BMC Genomics 23 (1): 121–21.
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