To identify infectious agents in the future, it is essential to focus on surveillance and outbreak responses through field-based solutions [1]. Pathogen detection is required directly from clinical and environmental field-based strategies for genomic characterization.

The recent development of next-generation sequencing strategies has made it possible to use "pocket laboratories. " This will cater to a growing urgent requirement of on-site detection as well as characterization, i.e., on-site strain identification in a limited amount of samples.

Kyasanur Forest Disease (KFD) is a zoonotic disease caused by a flavivirus maintained in the sylvatic cycle through monkeys, rodents, shrews, ticks, and ground birds. The virus was transmitted through a Haemaphysalis tick bite. The leading cause of accidental infection in humans is the presence of monkeys and ticks during forest activities [2], [3]. The disease was first reported in 1957 and was confined to the Shimoga district until 1973. Furthermore, more spread to the Uttar Kannada district was reported until 1979. In 2012, cases were reported from other districts of Karnataka. 2016–2017 cases reported outside endemic zones and from other adjacent states (Kerala, TamilNadu, Goa, and Maharashtra)[4], [5], [6], [7], [8], [9]. However, details of the genomic information over the periods and the current status of recently circulating strains are still missing.

Recent advances in next-generation sequencing (NGS) technologies have revolutionized viral diagnostics to molecular-level characterization for variant detection. Next-generation sequence-based genomic characterization of viruses is the gold standard technology, even for uncultivable samples up to the strain and variant levels. Nanopore-based NGS technology requires less time, approximately 24–48hrs time, on portable machines. Consequently, this paves the way towards field-forward molecular surveillance of infectious pathogens, and recent developments in nanopore technology, pioneered by Oxford Nanopore Technologies, Inc. (ONT) with their MinION sequencing device, has opened the possibility of bringing the power of metagenomics to virtually any environment in the world. MinION is a pocket-sized, USB-powered nanopore sequencing platform weighing less than 100 g yet capable of up to 20 GB of ultra-long read (>100 kb) sequence data. The ultra-portability of the device has been leveraged to perform in-field metagenomic characterization of environments ranging from the deep subsurface to the Antarctic Dry Valleys [10], [11]. However, the most compelling application of the MinION platform is the improvement of pathogen surveillance and diagnostics and, subsequently, health outcomes for the world's most disadvantaged population. The small footprint of MinION and other hand-held molecular biology hardware is significant for austere settings with limited access to the critical infrastructure often required for traditional diagnostics and biosurveillance assays. Routine, point-of-sampling detection, phylogeny, and genomic characterization of microbial and viral pathogens from clinical and environmental samples represent a fundamental change in public health practices ([12], [13]. The clinical samples were found to be positive for KFDV by TaqMan qPCR and were used for genomic characterization by whole-genome sequencing employing nanopore technology. In this study, we performed whole-genome molecular characterization of recently circulating KFD viral strains from 2018–2020. As the strategies followed for genomic surveillance of SARS-CoV-2, the International and national surveillance plan included whole genome sequencing (WGS) of at least 10 % of PCR-positive samples [14]. Guidelines from the European Center for Disease Prevention and Control(ECDC) as for SARS-CoV-2 implemented globally, the approach may be adapted for emerging infectious threat sequencing samples positive for KFDV variants in clinical and environmental samples, followed by molecular characterization, which will be very useful to keep track of changes in mutating viruses.