Retrospective Sequence Data Analysis of SARS - CoV-2 in Goa using Oxford Nanopore Technologies: A District Hospital Experience

Background: Over the past decade, with the development and refinement of third -generation sequencing technologies such as Nanopore Sequencing, Whole genome Sequencing (WGS) has become accessible to smaller institutes worldwide. The recent COVID -19 Pandemic caused by the SARS -CoV -2 virus has demonstrated the importance of Genome sequencing in observing the acquisition of new viral mutations, proving vital in monitoring the evolution of new variants of concerns and their spread within the population. Method: The study retrospectively analyzed the sequenced data of 508 samples obtained after nanopore sequencing from January 2023 to July 2023 of samples with cycle threshold <30. Results: It had shown that there was a surge of COVID -19 cases observed during March, April and May, which correlated with recombinant variants of SARS -CoV 2 in positive samples for the state of Goa belonging to the XBB 1.16 lineage. Conclusion: This study highlighted the challenges of performing such an analysis in a resource -limited environment and artefacts associated with using Midnight Primers.