ArticleJournal of virology2020
Computational Inference of Selection Underlying the Evolution of the Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2.
Article in Journal of virology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed, 152 citations in OpenAlex.
- Dynamic Allostery: Evolution's Double-Edged Sword in Protein Function and Disease.Journal of molecular biology · 2025Review
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- Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2.International journal of molecular sciences · 2024Review
- Bioinformatics Insights on Viral Gene Expression Transactivation: From HIV-1 to SARS-CoV-2.International journal of molecular sciences · 2024Article
- Genetic diversity and evolution of porcine hemagglutinating encephalomyelitis virus in Guangxi province of China during 2021-2024.Frontiers in microbiology · 2024Article
- Impact of COVID-19 pandemic on mother and child health in Sub-Saharan Africa - a review.Pediatric research · 2023Review
- Divergent mutations of Delta and Omicron variants: key players behind differential viral attributes across the COVID-19 waves.Virusdisease · 2023Article
- Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective.Journal of medicinal chemistry · 2023Review
- Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes.Genomics, proteomics & bioinformatics · 2022Article
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- Transmission dynamics and susceptibility patterns of SARS-CoV-2 in domestic, farmed and wild animals: Sustainable One Health surveillance for conservation and public health to prevent future epidemics and pandemics.Transboundary and emerging diseases · 2022Review
- Omicron - The new SARS-CoV-2 challenge?Reviews in medical virology · 2022Review
- An Overview of SARS-CoV-2 Molecular Diagnostics in Europe.Clinics in laboratory medicine · 2022Review
- Discovery of Natural Lead Compound fromPharmaceuticals (Basel, Switzerland) · 2022Article
- Statistical modeling of SARS-CoV-2 substitution processes: predicting the next variant.Communications biology · 2022Article
- SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights.International journal of molecular sciences · 2022Article
- Reviewing findings on the polypeptide sequence of the SARS-CoV-2 S-protein to discuss the origins of the virus.Future virology · 2022Review
- Screening of Botanical Drugs against SARS-CoV-2 Entry Reveals Novel Therapeutic Agents to Treat COVID-19.Viruses · 2022Article
- Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes.Medical review (2021) · 2022Review
- Impact of computational approaches in the fight against COVID-19: an AI guided review of 17 000 studies.Briefings in bioinformatics · 2022Review
25 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that recently emerged in China is thought to have a bat origin, as its closest known relative (BatCoV RaTG13) was described previously in horseshoe bats. We analyzed the selective events that accompanied the divergence of SARS-CoV-2 from BatCoV RaTG13. To this end, we applied a population genetics-phylogenetics approach, which leverages within-population variation and divergence from an outgroup. Results indicated that most sites in the viral open reading frames (ORFs) evolved under conditions of strong to moderate purifying selection. The most highly constrained sequences corresponded to some nonstructural proteins (nsps) and to the M protein. Conversely, nsp1 and accessory ORFs, particularly ORF8, had a nonnegligible proportion of codons evolving under conditions of very weak purifying selection or close to selective neutrality. Overall, limited evidence of positive selection was detected. The 6 bona fide positively selected sites were located in the N protein, in ORF8, and in nsp1. A signal of positive selection was also detected in the receptor-binding motif (RBM) of the spike protein but most likely resulted from a recombination event that involved the BatCoV RaTG13 sequence. In line with previous data, we suggest that the common ancestor of SARS-CoV-2 and BatCoV RaTG13 encoded/encodes an RBM similar to that observed in SARS-CoV-2 itself and in some pangolin viruses. It is presently unknown whether the common ancestor still exists and, if so, which animals it infects. Our data, however, indicate that divergence of SARS-CoV-2 from BatCoV RaTG13 was accompanied by limited episodes of positive selection, suggesting that the common ancestor of the two viruses was poised for human infection.
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