Bat genomes illuminate adaptations to viral tolerance and disease resistance

Abstract

Zoonoses are infectious diseases transmitted from animals to humans. Compared to other mammalian orders, bats are suggested to harbor more zoonotic viruses(Olival et al. 2017). Infections in bats are largely asymptomatic(Schlottau et al. 2020; Guito et al. 2021), suggesting limited tissue-damaging inflammation and immunopathology. To investigate the genomic basis of disease resistance, the Bat1K project generated reference-quality genomes of ten bat species, including potential viral reservoirs. A systematic analysis covering 115 mammalian genomes revealed that signatures of selection in immune genes are more prevalent in bats compared with other mammalian orders. We found an excess of immune gene adaptations in the ancestral chiropteran branch and in many descending bat lineages, highlighting viral entry and detection factors, and regulators of antiviral and inflammatory responses. ISG15, an antiviral gene contributing to hyperinflammation during COVID-19(Perng and Lenschow 2018; Munnur et al. 2021), exhibits key residue changes in rhinolophid and hipposiderid bats. Cellular infection experiments show species-specific antiviral differences and an essential role offor protein conjugation in antiviral function of bat ISG15, separate from its role in secretion and inflammation in humans. Furthermore, in contrast to human ISG15, ISG15 of most rhinolophid and hipposiderid bats has strong anti-SARS-CoV-2 activity. Our work reveals molecular mechanisms contributing to viral tolerance and disease resistance in bats.