TY - JOUR
AU - Pekar, Jonathan E.
AU - Moshiri, Niema
AU - Lemey, Philippe
AU - Crits-Christoph, Alexander
AU - Débarre, Florence
AU - Goldstein, Stephen A.
AU - Hensel, Zach
AU - Rambaut, Andrew
AU - Worobey, Michael
AU - Holmes, Edward C.
AU - Wertheim, Joel O.
PY - 2025
DA - February
TI - Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived
JO - Virus Evolution
VL - 11
IS - 1
DO - https://doi.org/10.1093/ve/veaf008
AB - 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.
PB - Oxford University Press
UR - https://www.research.ed.ac.uk/en/publications/ddcf7deb-50a7-47a4-ad3e-5ecfc708d4ed
KW - Coronavirus (COVID-19)
ER