Researchers in China and Australia have reported the discovery of novel bat coronaviruses with a similarity of up to 94.5% to SARS-CoV-2.
This finding further illuminates the diversity and complex evolutionary history of these viruses. A pre-print version of the research paper is available on the bioRxiv server.
Now, Weifeng Shi from Shandong First Medical University & Shandong Academy of Medical Sciences in Taian, China and colleagues have conducted a meta-transcriptomic analysis of samples collected from 23 bat species in Yunnan province in China during 2019 and 2020.
Using a combination of genome sequencing and sampling studies, researchers identified a number of SARS-CoV-2-related coronaviruses in wildlife species that together pointed to underestimation of the phylogenetic and genomic diversity of coronaviruses.
“Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China,” said the team.
Bats are hosts to a broad range of viruses that can infect humans, and four of the seven known human coronaviruses have zoonotic origins. They are also host to many coronaviruses, but sometimes “intermediate” hosts such as dromedary camels (MERS-CoV) are involved in the jump to humans.
Retrospective genome sequencing and sampling studies identified a number of SARS-CoV-2-related coronaviruses in wildlife species. These included the RaTG13 virus, which is the closest known relative of SARS-CoV-2, found in the Rhinolophus affinis bat. SARS-CoV-2-related viruses have also been identified in various other Rhinolophid bats across Asia.
“Collectively, these studies indicate that bats across a broad swathe of Asia harbour coronaviruses that are closely related to SARS-CoV-2 and that the phylogenetic and genomic diversity of these viruses has likely been underestimated,” said Shi and colleagues.
Notably, one of these novel bat coronaviruses – RpYN06 – exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome, with key similarities in certain genes. Low genopmic sequence identity in the spike gene made RpYN06 the second closest relative of SARS-CoV-2, next to RaTG13. This is far more similar than seen in other SARS-CoV-2-like viruses identified in wildlife species.
Indeed, while the other three SARS-CoV-2-related viruses identified here were almost identical in sequence, the spike protein sequences formed an independent lineage that was separated from known sarbecoviruses (a viral subgenus or the coronaviruses that includesSARS-CoV-2) by a relatively long branch.
“Collectively, these results highlight the extremely high, and likely underestimated, genetic diversity of the sarbecovirus spike proteins, which likely reflects their adaptive flexibility,” wrote Shi and colleagues.
The researchers say studies have previously shown that host switching of coronaviruses among bats is a frequent occurrence.
Source: News-Medical.Net
Journal information: Shi W, et al. Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. bioRxiv. 2021. doi: https://doi.org/10.1101/2021.03.08.434390
