Steven E Massey | Searcharxiv

arXiv2026

Emergence of the SARS-CoV-2 furin cleavage site in humans is constrained to late 2019: implications for COVID-19 origins

SARS-CoV-2 possesses a furin cleavage site (FCS) insertion in its spike protein, that is not found in other sarbecoviruses, and is responsible for its transmissibility in humans. The origin of the FCS insertion is unclear, and has been a point of debate regarding whether it arose naturally, or represents an artificial insertion. The FCS is destabilizing to spike protein, and as a consequence a compensatory mutation, D614G, rapidly emerged during the early pandemic and swept to fixation. Using a range of empirically determined parameters, a waiting time calculation can be used to determine the time interval between the appearance of the FCS and generation of the compensating D614G mutation. The waiting time is estimated to range from 37 to 65 days. Given the earliest detection of D614G on 1 January 2020, the latest dates for the appearance of the FCS range from October 28 to November 25 2019. This timeline is consistent with dates generated from phylogenetic considerations for the emergence of SARS-CoV-2 in late 2019, indicating that FCS appearance and virus emergence correspond. The waiting time approach enables discrimination between various scenarios of SARS-CoV-2 emergence, in particular cryptic circulation of a FCS-containing progenitor in the human population prior to late 2019 is unlikely, while prolonged circulation of a FCS-containing progenitor in bats appears inconsistent with absence of the compensatory mutation.

q-bio.PE↗

arXiv2021

SARS-CoV-2's closest relative, RaTG13, was generated from a bat transcriptome not a fecal swab: implications for the origin of COVID-19

RaTG13 is the closest related coronavirus genome phylogenetically to SARS-CoV-2, consequently understanding its provenance is of key importance to understanding the origin of the COVID-19 pandemic. The RaTG13 NGS dataset is attributed to a fecal swab from the intermediate horseshoe bat Rhinolophus affinis. However, sequence analysis reveals that this is unlikely. Metagenomic analysis using Metaxa2 shows that only 10.3 % of small subunit (SSU) rRNA sequences in the dataset are bacterial, inconsistent with a fecal sample, which are typically dominated by bacterial sequences. In addition, the bacterial taxa present in the sample are inconsistent with fecal material. Assembly of mitochondrial SSU rRNA sequences in the dataset produces a contig 98.7 % identical to R.affinis mitochondrial SSU rRNA, indicating that the sample was generated from this or a closely related species. 87.5 % of the NGS reads map to the Rhinolophus ferrumequinum genome, the closest bat genome to R.affinis available. In the annotated genome assembly, 62.2 % of mapped reads map to protein coding genes. These results clearly demonstrate that the dataset represents a Rhinolophus sp. transcriptome, and not a fecal swab sample. Overall, the data show that the RaTG13 dataset was generated by the Wuhan Institute of Virology (WIV) from a transcriptome derived from Rhinolophus sp. tissue or cell line, indicating that RaTG13 was in live culture. This raises the question of whether the WIV was culturing additional unreported coronaviruses closely related to SARS-CoV-2 prior to the pandemic. The implications for the origin of the COVID-19 pandemic are discussed.

q-bio.GN↗