Variant Analysis and Strategic Clustering to Sub-Lineage of Double Mutant Strain B.1.617 of SARS-CoV-2

Abstract

SARS-CoV-2 is an RNA coronavirus responsible for Acute Respiratory Syndrome (COVID-19). In January 2021, the re-occurrence of COVID-19 infection was at its peak, considered the second wave of epidemics. In the initial stage, it was considered a double mutant strain due to two significant mutations observed in their Spike protein (E484Q and L452R). Although it was first detected in India later on, it was spread to several countries worldwide, causing high fatality due to this strain. In the present study, we investigated the spreading of B.1.617 strain worldwide through 822 genome sequences submitted in GISAID on 21 April 2021. All genome sequences were analyzed for variations in genome sequences based on their effects due to changes in nucleotides. At Allele frequency 0.05, there were a total of 47 variations in ORF1ab, 22 in Spike protein gene, 6 variations in N gene, 5 in ORF8 and M gene, four mutations in Orf7a, and one nucleotide substitution observed for ORF3a, ORF6 and ORF7b gene. The clustering for similar mutations mentioned B.1.617 sub-lineages. The outcome of this study established relative occurrence and spread worldwide. The study’s finding represented that “double mutant” strain is not only spread through traveling but it is also observed to evolve naturally with different mutations observed in B.1.617 lineage. The information extracted from the study helps to understand viral evolution and genome variations of B.1.617 lineage. The results support the need of separating B.1.617 into sub-lineages.

SARS‐CoV‐2 variants circulating in the Fars province, southern Iran, December 2020–March 2021: A cross‐sectional study

“…COVID‐19 decreased mortality rates in February and March 2021 despite the emergence of Alpha, Beta, and Gamma variants, compared to December 2020 and January 2021, which may be attributed to the national lockdown implemented by the government in late December 2020, vaccination of the healthcare worker and a few elderly people and probably the herd immunity developed in a relative proportion of the individuals exposed to the infection. Since it has been demonstrated that SARS‐CoV‐2 variants may be capable of escaping from neutralizing antibodies and decreasing the antibody efficacy, 24 identifying the mutants would help quick implementation of control measures to reduce the consequence of the disease 25 . Although the sensitivity of the RT‐PCR test is not 100% and could be affected by the type of sampling and the items and equipment used, it has remained the mainstay of COVID‐19 diagnosis since the beginning of the outbreak 26 .…”

“…Since it has been demonstrated that SARS‐CoV‐2 variants may be capable of escaping from neutralizing antibodies and decreasing the antibody efficacy, 24 identifying the mutants would help quick implementation of control measures to reduce the consequence of the disease. 25 Although the sensitivity of the RT‐PCR test is not 100% and could be affected by the type of sampling and the items and equipment used, it has remained the mainstay of COVID‐19 diagnosis since the beginning of the outbreak. 26 In comparison to genome sequencing, the multiplexed RT‐qPCR method is a very suitable, affordable, and straightforward method to identify the variants and, as a result, to determine their origin, the time of their entry to a particular region, and places with high infection rates, thereby taking control measures to prevent the spread of infection.…”