ArticleVirus research2021
Positive selection as a key player for SARS-CoV-2 pathogenicity: Insights into ORF1ab, S and E genes.
Article in Virus research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 42 citations in OpenAlex.
- Article
- Over time analysis of the codon usage of SARS-CoV-2 and its variants.Computational and structural biotechnology journal · 2025Article
- Evolution of SARS-CoV-2 in white-tailed deer in Pennsylvania 2021-2024.PLoS pathogens · 2025Article
- Analysis of SARS-CoV-2 genome evolutionary patterns.Microbiology spectrum · 2024Article
- Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations.Virology journal · 2023Article
- Article
- Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States.Nature communications · 2023Article
- Divergent mutations of Delta and Omicron variants: key players behind differential viral attributes across the COVID-19 waves.Virusdisease · 2023Article
- Mutational Patterns Observed in SARS-CoV-2 Genomes Sampled From Successive Epochs Delimited by Major Public Health Events in Ontario, Canada: Genomic Surveillance Study.JMIR bioinformatics and biotechnology · 2022Article
- Genomic epidemiology and emergence of SARS-CoV-2 variants of concern in the United Arab Emirates.Scientific reports · 2022Article
- Evolution of SARS-CoV-2 in Spain during the First Two Years of the Pandemic: Circulating Variants, Amino Acid Conservation, and Genetic Variability in Structural, Non-Structural, and Accessory Proteins.International journal of molecular sciences · 2022Article
- Statistical modeling of SARS-CoV-2 substitution processes: predicting the next variant.Communications biology · 2022Article
- Mutations and Evolution of the SARS-CoV-2 Spike Protein.Viruses · 2022Review
- Susceptibility of Pets to SARS-CoV-2 Infection: Lessons from a Seroepidemiologic Survey of Cats and Dogs in Portugal.Microorganisms · 2022Article
- Computational anti-COVID-19 drug design: progress and challenges.Briefings in bioinformatics · 2022Review
- Article
- Conserved recombination patterns across coronavirus subgenera.Virus evolution · 2022Article
- Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm.Genetics and molecular biology · 2022Article
- Evolutionary dissection of monkeypox virus: Positive Darwinian selection drives the adaptation of virus-host interaction proteins.Frontiers in cellular and infection microbiology · 2022Article
- A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia.Current research in microbial sciences · 2021Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human β-coronavirus SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China. It causes Covid-19 disease which has become pandemic. Each of the five-known human β-coronaviruses has four major structural proteins (E, M, N and S) and 16 non-structural proteins encoded by ORF1a and ORF1b together (ORF1ab) that are involved in virus pathogenicity and infectivity. Here, we performed detailed positive selection analyses for those six genes among the four previously known human β-coronaviruses and within 38 SARS-CoV-2 genomes to assess signatures of adaptive evolution using maximum likelihood approaches. Our results suggest that three genes (E, S and ORF1ab genes) are under strong signatures of positive selection among human β-coronavirus, influencing codons that are located in functional important protein domains. The E protein-coding gene showed signatures of positive selection in two sites, Asp 66 and Ser 68, located inside a putative transmembrane α-helical domain C-terminal part, which is preferentially composed by hydrophilic residues. Such Asp and Ser sites substitutions (hydrophilic residues) increase the stability of the transmembrane domain in SARS-CoV-2. Moreover, substitutions in the spike (S) protein S1 N-terminal domain have been found, all of them were located on the S protein surface, suggesting their importance in viral transmissibility and survival. Furthermore, evidence of strong positive selection was detected in three of the SARS-CoV-2 nonstructural proteins (NSP1, NSP3, NSP16), which are encoded by ORF1ab and play vital roles in suppressing host translation machinery, viral replication and transcription and inhibiting the host immune response. These results are insightful to assess the role of positive selection in the SARS-CoV-2 encoded proteins, which will allow to better understand the virulent pathogenicity of the virus and potentially identifying targets for drug or vaccine strategy design.
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