Gene Sequencing: Key for Analyzing Mutation in SARS-CoV-2

Genomic sequencing is a sole platform that recognizes and characterizes novel mutants of microorganisms existing in various clinical samples. The main objective of this article is to summarize and provide relevant information regarding genomic sequencing platforms that are widely applied for analyzing mutations in SARS-CoV-2. Various data and literature were reviewed from scientific database like PubMed, Scopus, Google scholars and internet in order to provide collective and reliable information on genomic sequencing. Various Variants of Concern (VOC) and Variants of Interest (VOI) with higher transmissibility and infectivity are detected around the globe among which Nepal is also at high risk stage. According to the Ministry of Health and Population (MOHP) delta variants (B.1.617.2), alpha variants (B.1. 1.7), kappa variants(B.1.617.1) and newly emerged sub lineage of delta variants (A.Y.1) are the predominant one that are circulating in the country. Therefore, severe acute respiratory syndrome coronavirus 2 whole genome sequencing, Next generation sequencing (Illumina MiSeq. and Oxford Nanopore Minion) or Sanger method based on amplicon sequencing are the best optional platforms for the detection of VOC and VOI and to continue monitoring of widespread SARS-CoV-2 for proper therapy and prevention of COVID-19. Besides, variations occurring in the fragment of virus genome may produce gene dropout obstructing with laboratory molecular assays and epidemiological surveys, therefore it is very crucial to detect those markers with the aid of gene sequencing methods in order to establish higher molecular testing strategies.