Genomic characteristics of SARS-COV-2 infection in the COVID-19 patients treated at the National Hospital for Tropical Diseases in the period of 2021-2022

https://doi.org/10.52322/jocmbmh.11.en.07

ABSTRACT

Objectives: To describe some genomic characteristics, variations and genetic relationships of SARS-CoV-2 in COVID-19 patients treated at the Central Tropical Diseases Hospital in the period of 2021-2022.

Participants and Methods: 300 patients diagnosed with SARS-CoV-2 infection by realtime RT-PCR testing at the Central Hospital of Tropical Diseases from January 2021 to April 2022. Samples are positive for the SARS-CoV-2 which are collected and stored for genomic sequencing testing. Cross-sectional descriptive study with 300 SARS-CoV-2 positive samples sequenced with the entire genome using the MiSeq system (Illumina). Genome sequences of SARS-CoV-2 strains were analyzed using Bioedit 7.1 and Mega 10.1 software. Variants of SARS-CoV-2 strains were identified based on the Pango database (https://cov-lineages.org/).

Results: The findings showed that the 300 SARS-CoV-2 strains in the study were classified into three variant groups including Alpha (54 strains), Delta (121 strains) and Omicron (121 strains). In the Alpha group, we only see the B.1.1.7 lineage of 20I branch (Alpha, V1), Delta variant strains belonging to 3 branches: 21A, 21I and 21J and 2 lineages including B.1.617.2 and AY.57, Omicron variant strains all belong to 21L branch but there are four lineages including BA.2, BA.2.3, BA.2.3.2, BA.2.17. Genome sequence analysis of SARS-CoV-2 variants shows that the groups recording the number of mutations are Alpha with 32 mutations throughout the entire genome, Delta with 29 mutations, Omicron with 59 mutations. They are mainly substitution mutations, followed by deletion mutations, and the gene with the highest rate of mutation is the S gene.

Conclusions: SARS-CoV-2 strains in Vietnam have a variety of variations (Alpha, Delta, Omicron) as well as many mutations, of which the highest mutation rate is in the S gene. Mutations have some differences with SARS-CoV-2 strains causing disease in other regions of the world.

Keywords: COVID-19; SARS-CoV-2; Genome sequencing; Genomic characteristics; Central Tropical Diseases Hospital

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