High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing

The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance, determining genetic epidemiology SARS-CoV-2. In present study, we used COVIDSeq protocol, which involves multiplex-PCR, barcoding, sequencing samples detection deciphering We approach on 752 clinical in duplicates, amounting to total 1536 could be sequenced single S4 flow cell NovaSeq 6000. Our analysis suggests high concordance between technical duplicates SARS-CoV-2 well RT-PCR approaches. An in-depth revealed six detected confidence were negative RT-PCR. Additionally, assay detect 21 16 classified inconclusive pan-sarbeco positive respectively suggesting that confirmatory test. also enabled insights into evolution samples. 3 clades. This study reports two lineages B.1.112 B.1.99 first time India. 1,143 unique nucleotide variants added 73 novel identified time. To best our knowledge, this is report potential sensitivity SARS-CoV-2, with an additional advantage enabling