tetano
Editor, Senior Moderator
Virus Evol
. 2025 Feb 22;11(1):veaf008.
doi: 10.1093/ve/veaf008. eCollection 2025. Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived
Jonathan E Pekar[SUP] 1 2 [/SUP], Niema Moshiri[SUP] 3 [/SUP], Philippe Lemey[SUP] 4 [/SUP], Alexander Crits-Christoph[SUP] 5 [/SUP], Florence Débarre[SUP] 6 [/SUP], Stephen A Goldstein[SUP] 7 8 [/SUP], Zach Hensel[SUP] 9 [/SUP], Andrew Rambaut[SUP] 1 [/SUP], Michael Worobey[SUP] 10 [/SUP], Edward C Holmes[SUP] 11 [/SUP], Joel O Wertheim[SUP] 2 [/SUP]
Affiliations
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.
Keywords: SARS-CoV-2; molecular clock; virus evolution.
. 2025 Feb 22;11(1):veaf008.
doi: 10.1093/ve/veaf008. eCollection 2025. Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived
Jonathan E Pekar[SUP] 1 2 [/SUP], Niema Moshiri[SUP] 3 [/SUP], Philippe Lemey[SUP] 4 [/SUP], Alexander Crits-Christoph[SUP] 5 [/SUP], Florence Débarre[SUP] 6 [/SUP], Stephen A Goldstein[SUP] 7 8 [/SUP], Zach Hensel[SUP] 9 [/SUP], Andrew Rambaut[SUP] 1 [/SUP], Michael Worobey[SUP] 10 [/SUP], Edward C Holmes[SUP] 11 [/SUP], Joel O Wertheim[SUP] 2 [/SUP]
Affiliations
- PMID: 40040925
- PMCID: PMC11878783
- DOI: 10.1093/ve/veaf008
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.
Keywords: SARS-CoV-2; molecular clock; virus evolution.