@article{Pekar_J-2025_216860,
title = {Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived},
author = {Pekar, J. and Moshiri, N. and Lemey, P. and Crits-Christoph, A. and Débarre, F. and Goldstein, S. and Hensel, Z. and Rambaut, A. and Worobey, M. and Holmes, E. and Wertheim, J.},
month = {feb},
year = {2025},
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.},
volume = {11},
issue = {1},
journal = {Virus Evolution},
publisher = {Oxford University Press},
url = {https://doi.org/10.1093/ve/veaf008},
}
