ArticleScientific reports2020
The global population of SARS-CoV-2 is composed of six major subtypes.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 60 citations in OpenAlex.
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- A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing.Microbiology spectrum · 2023Article
- Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study.Viruses · 2023Article
- Tracking of Mutational Signature of SARS-CoV-2 Omicron on Distinct Continents and Little Difference was Found.Viruses · 2023Article
- Clinical and temporal characterization of COVID-19 subgroups using patient vector embeddings of electronic health records.Journal of the American Medical Informatics Association : JAMIA · 2023Article
- Biology of the SARS-CoV-2 Coronavirus.Biochemistry. Biokhimiia · 2022Review
- A survey on the correlation between PMChemosphere · 2022Observational
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- Genomic Surveillance of SARS-CoV-2 in a University Community: Insights Into Tracking Variants, Transmission, and Spread of Gamma (P.1) Variant.Open forum infectious diseases · 2022Article
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- An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2022Article
- Analysis of SARS-COV2 spike protein variants among Iraqi isolates.Gene reports · 2022Article
- Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates.Virus research · 2022Article
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- A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion.Scientific reports · 2021Article
- Unsupervised clustering analysis of SARS-Cov-2 population structure reveals six major subtypes at early stage across the world.bioRxiv : the preprint server for biology · 2021Article
- Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.Microbial genomics · 2021Article
- Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components.Microorganisms · 2021Review
- Evolution and spread of SARS-CoV-2 likely to be affected by climate.Climate change ecology · 2021Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
The World Health Organization characterized COVID-19 as a pandemic in March 2020, the second pandemic of the twenty-first century. Expanding virus populations, such as that of SARS-CoV-2, accumulate a number of narrowly shared polymorphisms, imposing a confounding effect on traditional clustering methods. In this context, approaches that reduce the complexity of the sequence space occupied by the SARS-CoV-2 population are necessary for robust clustering. Here, we propose subdividing the global SARS-CoV-2 population into six well-defined subtypes and 10 poorly represented genotypes named tentative subtypes by focusing on the widely shared polymorphisms in nonstructural (nsp3, nsp4, nsp6, nsp12, nsp13 and nsp14) cistrons and structural (spike and nucleocapsid) and accessory (ORF8) genes. The six subtypes and the additional genotypes showed amino acid replacements that might have phenotypic implications. Notably, three mutations (one of them in the Spike protein) were responsible for the geographical segregation of subtypes. We hypothesize that the virus subtypes detected in this study are records of the early stages of SARS-CoV-2 diversification that were randomly sampled to compose the virus populations around the world. The genetic structure determined for the SARS-CoV-2 population provides substantial guidelines for maximizing the effectiveness of trials for testing candidate vaccines or drugs.
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