tetano
Editor, Senior Moderator
Sci Rep
. 2021 Aug 30;11(1):17365.
doi: 10.1038/s41598-021-96626-8.
A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic
Simon Pollett[SUP] 1 2 3 [/SUP], Matthew A Conte[SUP] 1 [/SUP], Mark Sanborn[SUP] 1 [/SUP], Richard G Jarman[SUP] 1 [/SUP], Grace M Lidl[SUP] 1 [/SUP], Kayvon Modjarrad[SUP] 4 [/SUP], Irina Maljkovic Berry[SUP] 5 [/SUP]
Affiliations
Abstract
The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in the non-ORF1 region of the genome containing structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.
. 2021 Aug 30;11(1):17365.
doi: 10.1038/s41598-021-96626-8.
A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic
Simon Pollett[SUP] 1 2 3 [/SUP], Matthew A Conte[SUP] 1 [/SUP], Mark Sanborn[SUP] 1 [/SUP], Richard G Jarman[SUP] 1 [/SUP], Grace M Lidl[SUP] 1 [/SUP], Kayvon Modjarrad[SUP] 4 [/SUP], Irina Maljkovic Berry[SUP] 5 [/SUP]
Affiliations
- PMID: 34462471
- DOI: 10.1038/s41598-021-96626-8
Abstract
The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in the non-ORF1 region of the genome containing structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.