A comprehensive survey of bat sarbecoviruses across China in relation to the origins of SARS-CoV and SARS-CoV-2

Abstract

SARS-CoV and SARS-CoV-2 have been thought to originate from bats. In this study, we screened pharyngeal and anal swabs from 13,064 bats collected between 2016 and 2021 at 703 locations across China for sarbecoviruses, covering almost all known southern hotspots, and found 146 new bat sarbecoviruses. Phylogenetic analyses of all available sarbecoviruses show that there are three different lineages, L1 as SARS-CoV related CoVs (SARSr-CoVs), L2 as SARS-CoV-2 related CoVs (SC2r-CoVs), and novel L-R (recombinants of L1 and L2) present in R. pusillus bats, in the mainland of China. Among the 146 sequences, only 4 are L-Rs. Importantly, none belongs in the L2 lineage, indicating that circulation of SC2r-CoVs in China might be very limited. All remaining 142 sequences belong in the L1 lineage, of which YN2020B-G shares the highest overall sequence identity with SARS-CoV (95.8%). The observation suggests endemic circulations of SARSr-CoVs, but not SC2r-CoVs, in bats in China. Geographic analysis of the collection sites in this study, together with all published reports, indicates that SC2r-CoVs may be mainly present in bats of Southeast Asia including the southern border of Yunnan province but absent in all other regions within China. In contrast, SARSr-CoVs appear to have broader geographic distribution, with the highest genetic diversity and sequence identity to human sarbecoviruses along the southwest border of China. Our data provide the rationale for further extensive surveys in broader geographical regions within, and beyond, Southeast Asia in order to find the most recent ancestors of human sarbecoviruses.

Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology

“…The sites sampled reflected the distribution of horseshoe bats in Great Britain, and infection was clearly common within and between populations of lesser horseshoe bats in this study, with no clear sex or age differences in likelihood of shedding. This high frequency of shedding and widespread distribution geographically and demographically, likely indicates either persistent infection and excretion, or frequent reinfection, of the gastrointestinal tract as has been reported for many other coronaviruses, such as those of cats, chickens and pigs (Quinteros, Noormohammadi et al 2022, Thayer, Gogolski et al 2022, Zhang, Chen et al 2022).…”

“…Partial RDRP (Rnase dependent RNA polymerase) sequences have been described from Chinese, Italian and Bulgarian greater horseshoe bats (Drexler, Gloza-Rausch et al 2010, Balboni, Palladini et al 2011, Balboni, Gallina et al 2012, Hu, Zeng et al 2017, Muth, Corman et al 2018) at a prevalence of 26-42% in European samples. Full sequences are also available for a number of Chinese, one Korean and one Russian greater horseshoe bat sarbecoviruses; the Asian sequences are phylogenetically very distinct from the European isolates (Lin, Wang et al 2017, Alkhovsky, Lenshin et al 2022, Sander, Moreira-Soto et al 2022, Wu, Han et al 2022.…”

Immunogenicity and protective efficacy of a rhesus adenoviral vaccine targeting conserved COVID-19 replication transcription complex

“…The SARS-CoV-2 alignments are available through the Los Alamos National Laboratory download page at GISAID. An additional 162 sarbecovirus sequences were added based on literature [34][35][36][37][38][39][40] and GenBank searches, selected to be representative of diversity, and an additional 44 alpha-and betacoronavirus sequences were added based on BLAST searches of coronavirus from human infections that were down selected to have complete sequences spanning CoV.Consv, S, M and N proteins and were representative of sampled diversity among similar sequences. This alignment is available, and the tree shown in Fig.…”

Reference-quality bat genomes illuminate adaptations to viral tolerance and disease resistance

“…These species represent divergent clades within these families. Several of these species are known to harbor coronaviruses [34][35][36] and SouthEast Asian Rhinolophidae are considered as natural reservoirs to the ancestors of SARS-CoV and SARS-CoV-2 10 . To include representatives from the sister families Rhinopomatidae and Megadermatidae, we sequenced Rhinopoma microphyllum and Megaderma spasma.…”