Blueprint of a pandemic: Insights from SARS-CoV-2 genomics surveillance in Meghalaya, India

Phibangipan Warjri; Olisha Sumer; Leader Langbang; Aesukwanmi Kynta; Daminot Pyngrope

doi:10.1016/j.diagmicrobio.2024.116670

Blueprint of a pandemic: Insights from SARS-CoV-2 genomics surveillance in Meghalaya, India

Diagn Microbiol Infect Dis. 2024 Dec 26;111(3):116670. doi: 10.1016/j.diagmicrobio.2024.116670. Online ahead of print.

Authors

Phibangipan Warjri¹, Olisha Sumer², Leader Langbang², Aesukwanmi Kynta², Daminot Pyngrope²

Affiliations

¹ Pasteur Institute, Directorate of Health Services (Research etc.), Lawmali, Shillong 793001, Meghalaya, India. Electronic address: warjri.p@gmail.com.
² Pasteur Institute, Directorate of Health Services (Research etc.), Lawmali, Shillong 793001, Meghalaya, India.

PMID: 39742706
DOI: 10.1016/j.diagmicrobio.2024.116670

Abstract

The Covid-19 pandemic uncovered several lacunae in healthcare systems exposing global unpreparedness and triggering unprecedented challenges worldwide- necessitating a shift towards mitigation and robust surveillance strategies. Here, we report the use of Whole Genome Sequencing (WGS) to detect SARS-CoV-2 variants in clinical samples of Meghalaya, India, using Oxford Nanopore Technology. SARS-CoV-2 positive samples collected from various districts of Meghalaya from August 2021 to May 2023 were subjected to WGS. Out of a total of 965 samples, Alpha (0.1 %), Delta (47.2 %) and Omicron (52.7 %) variants were detected. The Delta variant affected 53 % of individuals under the age of 18 years, while the Omicron sub variant BA.2 affected all age groups in a similar manner. The study underscores the efficacy of using a user-friendly sequencing device coupled with simplified bioinformatics, enabling remote regions to effectively combat Covid-19. This approach, characterized by rapidity, simplicity and accuracy, holds promise in confronting future health crises.

Keywords: Covid-19; Meghalaya; Nanopore sequencing; SARS-CoV-2; Whole genome sequencing.