SARS-CoV-2 whole-genome sequencing
Severe acute respiratory syndrome coronavirus 2 is the etiological agent of COVID 19 continues to undergo genetic diversification necessitating sustained genomic surveillance to monitor viral evolution and the emergence of novel variants. Whole genome sequencing of SARS CoV2 provides critical insights into viral genetic diversity transmission dynamics and molecular epidemiology. In this study SARS CoV2 positive clinical specimens were collected in the period of 2020 to 2021 from COVID 19 infected individuals. Virus RNA extraction from human viral transport medium specimens was carried by column method. Whole genome Illumina sequencing was carried out using next generation sequencing platforms. Sequencing libraries were prepared using an amplicon based tiled primer approach following the ARTIC protocol to cover the entire viral genome followed by high throughput sequencing. Raw sequencing reads were processed using standard bioinformatics pipelines including quality control reference based genome assembly and generation of high confidence consensus genome sequences.