Identification of the host reservoir of SARS-CoV-2 and determining when it spilled over into humans
Pamjula, V.; Strachan, N. J. C.; Perez-Reche, F. J.
Show abstract
1Since the emergence of SARS-CoV-2 in Wuhan in 2019 its host reservoir has not been established. Phylogenetic analysis was performed on whole genome sequences (WGS) of 71 coronaviruses and a Breda virus. A subset comprising two SARS-CoV-2 Wuhan viruses and 8 of the most closely related coronavirus sequences were used for host reservoir analysis using Bayesian Evolutionary Analysis Sampling Trees (BEAST). Within these genomes, 20 core genome fragments were combined into 2 groups each with similar clock rates (5.9x10-3 and 1.1x10-3 subs/site/year). Pooling the results from these fragment groups yielded a most recent common ancestor (MRCA) shared between SARS-COV-2 and the bat isolate RaTG13 around 2007 (95% HPD: 2003, 2011). Further, the host of the MRCA was most likely a bat (probability 0.64 - 0.87). Hence, the spillover into humans must have occurred at some point between 2007 and 2019 and bats may have been the most likely host reservoir.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases during the Pandemic 95%
- Discovery of two novel Torque Teno viruses in Callithrix penicillata provides insights on Anelloviridae diversification dynamics 94%
- Positive selection of ORF3a and ORF8 genes drives the evolution of SARS-CoV-2 during the 2020 COVID-19 pandemic 92%
Similar papers in this journal
- Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 variant of concern Gamma and lineage P.2 in Brazil 93%
- Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes 92%
- Virus-host protein co-expression networks reveal temporal organization and strategies of viral infection 92%
Similar papers in this journal
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.