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In depth analysis of Cyprus-specific mutations of SARS-CoV-2 strains using computational approaches.
Oulas, Anastasis; Richter, Jan; Zanti, Maria; Tomazou, Marios; Michailidou, Kyriaki; Christodoulou, Kyproula; Christodoulou, Christina; Spyrou, George M.
  • Oulas A; Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus. anastasioso@cing.ac.cy.
  • Richter J; The Cyprus School of Molecular Medicine, Nicosia, Cyprus. anastasioso@cing.ac.cy.
  • Zanti M; Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
  • Tomazou M; Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
  • Michailidou K; The Cyprus School of Molecular Medicine, Nicosia, Cyprus.
  • Christodoulou K; Biostatistics Unit, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
  • Christodoulou C; Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
  • Spyrou GM; The Cyprus School of Molecular Medicine, Nicosia, Cyprus.
BMC Genom Data ; 22(1): 48, 2021 11 13.
Article in English | MEDLINE | ID: covidwho-1515435
Preprint
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ABSTRACT

BACKGROUND:

This study aims to characterize SARS-CoV-2 mutations which are primarily prevalent in the Cypriot population. Moreover, using computational approaches, we assess whether these mutations are associated with changes in viral virulence.

METHODS:

We utilize genetic data from 144 sequences of SARS-CoV-2 strains from the Cypriot population obtained between March 2020 and January 2021, as well as all data available from GISAID. We combine this with countries' regional information, such as deaths and cases per million, as well as COVID-19-related public health austerity measure response times. Initial indications of selective advantage of Cyprus-specific mutations are obtained by mutation tracking analysis. This entails calculating specific mutation frequencies within the Cypriot population and comparing these with their prevalence world-wide throughout the course of the pandemic. We further make use of linear regression models to extrapolate additional information that may be missed through standard statistical analysis.

RESULTS:

We report a single mutation found in the ORF1ab gene (nucleotide position 18,440) that appears to be significantly enriched within the Cypriot population. The amino acid change is denoted as S6059F, which maps to the SARS-CoV-2 NSP14 protein. We further analyse this mutation using regression models to investigate possible associations with increased deaths and cases per million. Moreover, protein structure prediction tools show that the mutation infers a conformational change to the protein that significantly alters its structure when compared to the reference protein.

CONCLUSIONS:

Investigating Cyprus-specific mutations for SARS-CoV-2 can lead to a better understanding of viral pathogenicity. Researching these mutations can generate potential links between viral-specific mutations and the unique genomics of the Cypriot population. This can not only lead to important findings from which to battle the pandemic on a national level, but also provide insights into viral virulence worldwide.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Limits: Humans Country/Region as subject: Europa Language: English Journal: BMC Genom Data Year: 2021 Document Type: Article Affiliation country: S12863-021-01007-9

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Limits: Humans Country/Region as subject: Europa Language: English Journal: BMC Genom Data Year: 2021 Document Type: Article Affiliation country: S12863-021-01007-9