Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived

Abstract

Understanding the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the outset of the coronavirus disease 2019 pandemic can provide insight into the circumstances leading to its emergence. Early SARS-CoV-2 genomic diversity has been classified into two distinct viral lineages, denoted “A” and “B,” which we hypothesized were separately introduced into humans. Recently published data contain two genomes with a haplotype suggested to be an evolutionary intermediate to these two lineages, known as “T/T.” We used a phylodynamic approach to analyze SARS-CoV-2 genomes from early 2020 to determine whether these two T/T genomes represent an evolutionarily intermediate haplotype between lineages A and B, or if they are a later descendent of either of these two lineages. We find that these two recently published T/T genomes do not represent an evolutionarily intermediate haplotype and were, instead, derived from either lineage A or lineage B. However, we cannot conclusively determine from which lineage they were derived. After including additional data from the start of the pandemic, including these two T/T genomes, we again find a discrepancy in the molecular clock when inferring the ancestral haplotype of SARS-CoV-2, corroborating existing evidence for the separate introductions of SARS-CoV-2 lineages A and B into the human population in late 2019.

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This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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DOI

https://doi.org/10.1093/ve/veaf008

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https://www.research.ed.ac.uk/en/publications/ddcf7deb-50a7-47a4-ad3e-5ecfc708d4ed