Molecular epidemiology of Kyasanur forest disease employing ONT-NGS a field forward sequencing

Abstract

The future of infectious agent detection and molecular characterization lies in field-forward, on-site strategies. The lack of genomic information for recently circulating Kyasanur Forest Disease virus strains is critical. Kyasanur Forest Virus Disease virus PCR-positive samples from 2018 to 2020 were selected for sequencing. Detailed molecular phylogenetic analyses were performed. In this study, we deciphered KFDV whole genomes using the ONT-NGS technique to analyze targeted KFD surveillance from 2018-2020. This study is the first to report recently circulating KFDV strains employing a simple on-site field-forward approach for viral surveillance. Altogether, 19 KFDV genomes were sequenced, and 28 non-synonymous variants were detected in the viral strains circulating from 2018-2020 in the Shivamogga district of Karnataka state in India. The prevailing Variant was detected in more than 10 changes in 80 % of the samples in the viral envelope protein. Recently, circulating KFDV has been the predominant lineage over the past years. India reports seasonal outbreaks almost every year from the Karnataka state of the KFD. The genomic sequences deciphered here belong to the period (2018-2020) that covers the KFDV sequences as the first information. This will contribute to the development and revisiting of diagnostic and vaccine strategies.

Keywords: KFD; Nanopore; ONT; Sequencing.