Nearly 18 months into the Covid-19 pandemic with more than 4.5 million deaths and new cases spiking again at more than 500,000 per day worldwide, the origin of the disease-causing pathogen, the SARS-CoV-2 virus, remains elusive.
Massive scientific efforts have gone into sequencing viral genomes while sampling potential wildlife in order to determine hosts and/or reservoir species, as most human viral pathogens have zoonotic origins. So far, SARS-CoV-2 relatives have been identified in several species of Asian horseshoe bat (genus Rhinolophus) as well as the Malayan pangolin (Manis javanica).
In this study, researchers reviewed swabs and samples collected from bats in Yunnan province, China, between May 2019 and November 2020 and identified 24 novel coronavirus genomes from different bat species, among them four SARS-CoV-2-like viruses present in nine samples. One of the novel bat coronaviruses, RpYN06 (short for "Rhinolophus pusillus, Yunnan, sample no. 6"), exhibited 94.5 per cent overall sequence identity to SARS-CoV-2, making it the closest relative identified to date in certain genomic regions.
Strikingly, the new viruses described in the study as well as previously identified species with high genetic similarity to SARS-CoV-2 were all discovered within a relatively small area (11 km²) of Yunnan province.
In parallel, the authors also sought to narrow the geographic search for SARS-CoV-2's origins by modelling ecological niches of 49 horseshoe bat species using GBIF-mediated occurrences. Their investigations showed suitable habitats for Rhinolophus in the tropical forests of Southeast Asia, with as many as 23 species co-occuring in hotspots extending from South Vietnam into Southern China.
While the virus's immediate progenitor remains unknown, these lines of evidence clearly show the enormous phylogenetic and genomic diversity of coronaviruses in Southeast Asia. Increased surveillance of the region's bats and other wild mammals may help track spillovers of pathogenic viruses from animals to humans.