A STUDY OF DETECTION AND GENOME SEQUENCING OF SARS-COV-2 FROM CLINICAL SAMPLES IN A TERTIARY CARE HOSPITAL

Abstract

Background: The continuous evolution of SARS-CoV-2 necessitates ongoing genomic surveillance to understand its transmission dynamics, mutation patterns, and impacts on public health measures and clinical outcomes.

Objectives: To analyse the distribution of SARS-CoV-2 variants and mutations within a tertiary care setting and assess their association with clinical outcomes to inform public health responses and treatment strategies.

Methods: This study conducted comprehensive genomic sequencing of SARS-CoV-2 from 400 clinical samples collected in a tertiary care hospital, employing RT-PCR for initial detection and Oxford-Nanopore Sequencing for whole-genome sequencing. Molecular analyses, including phylogenetic analysis and identification of unique genetic variants, were performed to elucidate the virus's evolution and transmission dynamics. Statistical analyses were conducted to explore the correlation between genomic variants and clinical outcomes, including disease severity and viral shedding.

Results: The study identified a high RT-PCR positivity rate (87.5%) with significant genomic diversity among the sequenced viruses. The Delta variant showed the highest mutation frequency in the Spike protein, suggesting increased transmissibility and potential vaccine escape. Unique genetic variants were identified in 28.1% of sequences, providing crucial insights into the virus's evolution. Statistical analysis revealed significant associations between specific genomic variants and clinical outcomes, particularly the increased risk of severe disease.

Conclusion: The findings highlight the complexity of SARS-CoV-2's evolution and its implications for disease transmission, diagnostic sensitivity, and vaccine efficacy. The study underscores the importance of genomic surveillance in detecting emergent mutations and informing targeted public health interventions and vaccine strategies. Continuous global collaboration and genomic analysis are essential to adapt to the evolving pandemic and mitigate the impact of COVID-19.