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Genomic Sequences and Analysis of Five SARS-CoV-2 Variants Obtained from Patients in Lambayeque, Peru.

ABSTRACT: Here, we report the genomic sequences of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains obtained from nasopharyngeal samples from five tested coronavirus disease 2019 (COVID-19)-infected patients from the Lambayeque region in Peru during early April 2020.

SUBMITTER: Aguilar-Gamboa FR

PROVIDER: S-EPMC8407726 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Genomic Sequences and Analysis of Five SARS-CoV-2 Variants Obtained from Patients in Lambayeque, Peru.

Aguilar-Gamboa Franklin Rómulo FR Salcedo-Mejía Luis Alberto LA Serquén-López Luis Miguel LM Mechan-Llontop Marco Enrique ME Tullume-Vergara Percy Omar PO Bonifacio-Briceño Juan José JJ Salas-Asencios Ramsés R Silva Díaz Heber H Cárdenas Juan P JP

Microbiology resource announcements 20210107 1

Here, we report the genomic sequences of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains obtained from nasopharyngeal samples from five tested coronavirus disease 2019 (COVID-19)-infected patients from the Lambayeque region in Peru during early April 2020. ...[more]

PMID: 33414350

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Project description:The genome of severe acute respiratory coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has undergone a rapid evolution, resulting in the emergence of multiple SARS-CoV-2 variants with amino acid changes. This study aimed to sequence the whole genome of SARS-CoV-2 and detect the variants present in specimens from Saudi Arabia. Furthermore, we sought to analyze and characterize the amino acid changes in the various proteins of the identified SARS-CoV-2 variants. A total of 1161 samples from patients diagnosed with COVID-19 in Saudi Arabia, between 1 April 2021 and 31 July 2023, were analyzed. Whole genome sequencing was employed for variant identification and mutation analysis. The statistical analysis was performed using the Statistical Analytical Software SAS, version 9.4, and GraphPad, version 9.0. This study identified twenty-three variants and subvariants of SARS-CoV-2 within the population, with the Omicron BA.1 (21K) variant (37.0%) and the Delta (21J) variant (12%) being the most frequently detected. Notably, the Omicron subvariants exhibited a higher mean mutation rate. Amino acid mutations were observed in twelve proteins. Among these, the spike (S), ORF1a, nucleocapsid (N), and ORF1b proteins showed a higher frequency of amino acid mutations compared to other the viral proteins. The S protein exhibited the highest incidence of amino acid mutations (47.6%). Conversely, the ORF3a, ORF8, ORF7a, ORF6, and ORF7b proteins appeared more conserved, demonstrating the lowest percentage and frequency of amino acid mutations. The investigation of structural protein regions revealed the N-terminal S1 subunit of the S protein to frequently harbor mutations, while the N-terminal domain of the envelope (E) protein displayed the lowest mutation frequency. This study provides insights into the variants and genetic diversity of SARS-CoV-2, underscoring the need for further research to comprehend its genome evolution and the occurrence of mutations. These findings are pertinent to the development of testing approaches, therapeutics, and vaccine strategies.

Dataset Information

Genomic Sequences and Analysis of Five SARS-CoV-2 Variants Obtained from Patients in Lambayeque, Peru.

Publications

Genomic Sequences and Analysis of Five SARS-CoV-2 Variants Obtained from Patients in Lambayeque, Peru.

Similar Datasets

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