Hybrid genome assembly of the widespread bat Rhinolophus lepidus provides insights into susceptibility to SARS-CoV-2 infection and climate change threat.

Bats are known reservoirs for many viruses of zoonotic potential and can tolerate or clear infections efficiently. They are important hosts for multiple coronaviruses and harbour ancestral lineages of coronaviruses known to cause diseases in both humans and animals. In this study, we describe a high-quality hybrid genome assembly of the Blyth's horseshoe bat Rhinolophus lepidus. It is a widespread species and an important cell-line model system for studying virus entry and replication. We used a combination of short Illumina reads and long reads from Oxford Nanopore to assemble the genome, with N50 of 5.3 Mb and Benchmarking Universial Single-Copy Orthologs (BUSCO) score of ~94%. The Angiotensin-converting enzyme 2 receptor responsible for the entry of severe acute respiratory syndrome coronaviruses (SARS and SARS-CoV-2) was highly conserved within bats, especially the region responsible for virus entry into the cell. In total, 50% of the amino acids necessary for virus entry were conserved between humans and R. lepidus. We observed an effect of past climatic conditions on the effective population size with drastic population size reduction in the past 50,000 years. This study adds to the growing list of bat genomes which are important resources to understand the co-evolution of bats and viruses and the mechanism by which bats can tolerate and clear infections effectively.