Sequencing and phylogenetic analysis of the ORF3a gene variant B.1.1.7 SARS-CoV-2 virus

Abstract

The problem of "new" infectious diseases has now acquired particular relevance for national and international health systems. One of these infections is the SARS-CoV-2 coronavirus. Due to the rapid spread of a new type of coronavirus in the world, molecular genetic studies of this virus are of great importance. This will help to understand the nature of the virus and develop antiviral drugs to prevent the disease. The aim is to identify a missense mutation in the ORF3 gene of the studied coronavirus strain SARS-CoV-2/human/KAZ/Britain. This paper presents the results of the development and sequencing of the ORF3 gene of the coronavirus strain SARS-Cov-2/human/KAZ/Britain. For the development and sequencing by the Sanger method of the ORF3 gene, 4 pairs of primers were developed, with an overlap of 100-150 bp. The changes in the ORF3 gene compared to other strains whose data were obtained from the GISAID database were analyzed.  As a result, the obtained amino acid sequences of the ORF3a gene of variant B.1.1.7 were compared with the reference strain HCoV-19/Wuhan/Hu-1/2019, where one mutation was determined at position 149: W (tryptophan) → L (leucine). The phylogenetic affiliation of the studied virus strain was also determined, where the genetic distance between the studied strains of the SARS-CoV-2 virus was determined. Thus, the greatest similarity with the studied strain were: HCoV-19/Wuhan/Hu-1/2019, HCoV-19/England/MILK-9E05B3/2020, HCoV-19/Japan/IC-0446/2020, HCoV-19/Germany/NI-IOV-MHH15/2020, and the strain HCoV-19/Argentina/PAIS-F0418/2021 significantly distanced itself from the SARS-CoV-2/human/KAZ/Britain strain.