OmniVira

Literature detail

Origin and evolutionary analysis of the SARS-CoV-2 Omicron variant.

Yamin Sun1,2 Wenchao Lin2 Wei Dong2 Jianguo Xu1,3
Affiliations 3 institutions
  1. Research Institute of Public Health, Nankai University, Tianjin, PR China.
  2. Engineering and Research Center for Microbial Functional Genomics and Detection Technology, Ministry of Education, Nankai University.
  3. State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.
PMID 35005525 2022 J Biosaf Biosecur eng ppublish
PubMed DOI Browse context

Article

Publication summary

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved rapidly into new variants throughout the pandemic. The Omicron variant has more than 50 mutations when compared with the original wild-type strain and has been identified globally in numerous countries. In this report, we analyzed the mutational profiles of several variants, including the per-site mutation rate, to determine evolutionary relationships. The Omicron variant was found to have a unique mutation profile when compared with that of other SARS-CoV-2 variants, containing mutations that are rare in clinical samples. Moreover, the presence of five mouse-adapted mutation sites suggests that Omicron may have evolved in a mouse host. Mutations in the Omicron receptor-binding domain (RBD) region, in particular, have potential implications for the ongoing pandemic.

Mouse-adapted mutation Omicron variant Reverse zoonosis SARS-CoV-2

Structured evidence records

Evidence records

2 total
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.95
Key finding

Phylogenetic and mutational analysis of SARS-CoV-2 sequences revealed that the Omicron variant possesses a distinct mutation profile, including mouse-adapted sites indicative of possible evolution in a mouse host.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

In this report, we analyzed the mutational profiles of several variants, including the per-site mutation rate, to determine evolutionary relationships. The Omicron variant was found to have a unique mutation profile when compared with that of other SARS-CoV-2 variants, containing mutations that are rare in clinical samples. Moreover, the presence of five mouse-adapted mutation sites suggests that Omicron may have evolved in a mouse host.

Genes or proteins
receptor-binding domain (RBD)
Analysis methods
mutational profile analysis; evolutionary analysis
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.95
Key finding

Omicron harbors five mouse-adapted mutation sites and receptor-binding domain mutations indicating molecular adaptation possibly linked to evolution in a mouse host.

Virus
SARS-CoV-2
Host
Not specified
Location
Not specified
Supporting text

The Omicron variant was found to have a unique mutation profile when compared with other SARS-CoV-2 variants, containing mutations that are rare in clinical samples. Moreover, the presence of five mouse-adapted mutation sites suggests that Omicron may have evolved in a mouse host. Mutations in the Omicron receptor-binding domain (RBD) region, in particular, have potential implications for the ongoing pandemic.

Genes or proteins
receptor-binding domain; RBD
Mechanism types
host_adaptation; receptor_binding