The current pandemic caused by the SARS CoV-2, tracing back its origin possibly to a coronavirus associated with bats, has ignited renewed interest in understanding zoonotic spillovers across the globe. While research is more directed towards solving the problem at hand by finding therapeutic strategies and novel vaccine techniques, it is important to address the environmental drivers of pathogen spillover and the complex biotic and abiotic drivers of zoonoses. The availability of cutting-edge genomic technologies has contributed enormously to preempt viral emergence from wildlife. However, there is still a dearth of studies from species-rich South Asian countries, especially from India. In this review, we outline the importance of studying disease dynamics through environmental sampling from wildlife in India and how ecological parameters of both the virus and the host community may play a role in mediating cross-species spillovers. Non-invasive sampling using feces, urine, shed hair, saliva, shed skin, and feathers has been instrumental in providing genetic information for both the host and their associated pathogens. Here, we discuss the advances made in environmental sampling protocols and strategies to generate genetic data from such samples towards the surveillance and characterization of potentially zoonotic pathogens. We primarily focus on bat-borne or small mammal-borne zoonoses and propose a conceptual framework for non-invasive strategies to tackle the threat of emerging zoonotic infections.

The advent of next generation sequencing technologies (NGS) has greatly accelerated our understanding of critical aspects of organismal biology from non-model organisms. Bats form a particularly interesting group in this regard, as genomic data have helped unearth a vast spectrum of idiosyncrasies in bat genomes associated with bat biology, physiology, and evolution. Bats are important bioindicators and are keystone species to many eco-systems. They often live in proximity to humans and are frequently associated with emerging infectious diseases, including the COVID-19 pandemic. Nearly four dozen bat genomes have been published to date, ranging from drafts to chromosomal level assemblies. Genomic investigations in bats have also become critical towards our understanding of disease biology and host–pathogen coevolution. In addition to whole genome sequencing, low coverage genomic data like reduced representation libraries, resequencing data, etc. have contributed significantly towards our understanding of the evolution of natural populations, and their responses to climatic and anthropogenic perturbations. In this review, we discuss how genomic data have enhanced our understanding of physiological adaptations in bats (particularly related to ageing, immunity, diet, etc.), pathogen discovery, and host pathogen co-evolution. In comparison, the application of NGS towards population genomics, conservation, biodiversity assessment, and functional genomics has been appreciably slower. We reviewed the current areas of focus, identifying emerging topical research directions and providing a roadmap for future genomic studies in bats.