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Cross-species transmission of viruses from wildlife animal reservoirs poses a marked threat to human and animal health 1 . Bats have been recognized as one of the most important reservoirs for emerging viruses and the transmission of a coronavirus that originated in bats to humans via intermediate hosts was responsible for the high-impact emerging zoonosis, severe acute respiratory syndrome (SARS) 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 – 10 . Here we provide virological, epidemiological, evolutionary and experimental evidence that a novel HKU2-related bat coronavirus, swine acute diarrhoea syndrome coronavirus (SADS-CoV), is the aetiological agent that was responsible for a large-scale outbreak of fatal disease in pigs in China that has caused the death of 24,693 piglets across four farms. Notably, the outbreak began in Guangdong province in the vicinity of the origin of the SARS pandemic. Furthermore, we identified SADS-related CoVs with 96–98% sequence identity in 9.8% (58 out of 591) of anal swabs collected from bats in Guangdong province during 2013–2016, predominantly in horseshoe bats ( Rhinolophus spp.) that are known reservoirs of SARS-related CoVs. We found that there were striking similarities between the SADS and SARS outbreaks in geographical, temporal, ecological and aetiological settings. This study highlights the importance of identifying coronavirus diversity and distribution in bats to mitigate future outbreaks that could threaten livestock, public health and economic growth. Analysis of viral samples from deceased piglets shows that a bat coronavirus was responsible for an outbreak of fatal disease in China and highlights the importance of the identification of coronavirus diversity and distribution in bats in order to mitigate future outbreaks of disease.

Wild mammalian species, including bats, constitute the natural reservoir of betacoronavirus (including SARS, MERS, and the deadly SARS-CoV-2). Different hosts or host tissues provide different cellular environments, especially different antiviral and RNA modification activities that can alter RNA modification signatures observed in the viral RNA genome. The zinc finger antiviral protein (ZAP) binds specifically to CpG dinucleotides and recruits other proteins to degrade a variety of viral RNA genomes. Many mammalian RNA viruses have evolved CpG deficiency. Increasing CpG dinucleotides in these low-CpG viral genomes in the presence of ZAP consistently leads to decreased viral replication and virulence. Because ZAP exhibits tissue-specific expression, viruses infecting different tissues are expected to have different CpG signatures, suggesting a means to identify viral tissue-switching events. The author shows that SARS-CoV-2 has the most extreme CpG deficiency in all known betacoronavirus genomes. This suggests that SARS-CoV-2 may have evolved in a new host (or new host tissue) with high ZAP expression. A survey of CpG deficiency in viral genomes identified a virulent canine coronavirus (alphacoronavirus) as possessing the most extreme CpG deficiency, comparable with that observed in SARS-CoV-2. This suggests that the canine tissue infected by the canine coronavirus may provide a cellular environment strongly selecting against CpG. Thus, viral surveys focused on decreasing CpG in viral RNA genomes may provide important clues about the selective environments and viral defenses in the original hosts.

The Coronavirus Disease 2019 (COVID-19) is a new viral infection caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2). Genomic analyses have revealed that SARS-CoV-2 is related to Pangolin and Bat coronaviruses. In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. The analyses here reported show the high structural similarity of Envelope and Membrane proteins to the counterparts from Pangolin and Bat coronavirus isolates. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. Structural modelling has been applied to map the variant sites onto the predicted three-dimensional structure of the Envelope and Membrane proteins.

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 589 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus . Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats. Bats are a likely reservoir of zoonotic coronaviruses (CoVs). Here, analyzing bat CoV sequences in China, the authors find that alpha-CoVs have switched hosts more frequently than betaCoVs, identify a bat family and genus that are highly involved in host-switching, and define hotspots of CoV evolutionary diversity.

Recent studies suggest that coronaviruses circulate widely in Southeast Asian bat species and that the progenitors of the SARS-Cov-2 virus could have originated in rhinolophid bats in the region. Our objective was to assess the diversity and circulation patterns of coronavirus in several bat species in Southeast Asia. We undertook monthly live-capture sessions and sampling in Cambodia over 17 months to cover all phases of the annual reproduction cycle of bats and test specifically the association between their age and CoV infection status. We additionally examined current information on the reproductive phenology of Rhinolophus and other bat species presently known to occur in mainland southeast China, Vietnam, Laos and Cambodia. Results from our longitudinal monitoring (573 bats belonging to 8 species) showed an overall proportion of positive PCR tests for CoV of 4.2% (24/573) in cave-dwelling bats from Kampot and 4.75% (22/463) in flying-foxes from Kandal. Phylogenetic analysis showed that the PCR amplicon sequences of CoVs (n = 46) obtained clustered in Alphacoronavirus and Betacoronavirus . Interestingly, Hipposideros larvatus sensu lato harbored viruses from both genera. Our results suggest an association between positive detections of coronaviruses and juvenile and immature bats in Cambodia (OR = 3.24 [1.46–7.76], p = 0.005). Since the limited data presently available from literature review indicates that reproduction is largely synchronized among rhinolophid and hipposiderid bats in our study region, particularly in its more seasonal portions (above 16° N), this may lead to seasonal patterns in CoV circulation. Overall, our study suggests that surveillance of CoV in insectivorous bat species in Southeast Asia, including SARS-CoV-related coronaviruses in rhinolophid bats, could be targeted from June to October for species exhibiting high proportions of juveniles and immatures during these months. It also highlights the need to develop long-term longitudinal surveys of bats and improve our understanding of their ecology in the region, for both biodiversity conservation and public health reasons.

The emergence of MERS-CoV, SARS-CoV-1, and SARS-CoV-2 highlights the significant public health and economic threats posed by coronaviruses. In Lao PDR, SARS-CoV-2-related bat coronaviruses capable of binding to human ACE2 receptors have been found in northern regions, but little is known about coronavirus diversity in anthropized environments like temples. This study investigated coronavirus circulation, diversity, and prevalence in bats from caves and temples in Vientiane Province, Lao PDR. A total of 648 guano samples (505 Chaerephon plicatus , 100 Hipposideros spp., 43 Taphozous spp.) were collected between December 2022 and June 2023 and screened using pan-coronavirus RT-PCR approach. The overall positivity rate was 17.28%, significantly higher in caves (18.8%) than temples (4.41%) (p = 0.003). C. plicatus showed the highest positivity rate (21.38%), followed by Hipposideros spp. 4%, while Taphozous spp. were negative. Phylogenetic analysis revealed diverse coronavirus lineages within Alphacoronavirus (80.4%) and Betacoronavirus (19.6%) genera. Although none were closely related to known human pathogens, coronaviruses of Decacovirus genus related to Chinese bat viruses and Pedacovirus genus similar to porcine epidemic diarrhea virus (PEDV) were detected. Unclassified betacoronaviruses identified were also related to viruses from C. plicatus in Thailand. This study provides valuable insights into coronavirus circulation in both natural and anthropized environments. The detection of PEDV-like viruses underlines the need for continued surveillance at the human-bat interface, where activities like guano harvesting and temple visits increase contacts. Further genomic and functional studies would enhance our understanding of their evolutionary relationships and potential for further cross-species transmission.

Bats are associated with some of the most significant and virulent emerging zoonoses globally, yet research and surveillance of bat pathogens remains limited across parts of the world. We surveyed the prevalence and genetic diversity of coronaviruses from bats in Taita Hills, southeastern Kenya, as part of ongoing surveillance efforts in this remote part of eastern Africa. We collected fecal and intestinal samples in May 2018 and March 2019 from 16 bat species. We detected one genus of coronavirus (alphacoronavirus), with an overall RNA prevalence of 6.5% (30/463). The prevalence of coronavirus RNA was 3.8% (9/235) and 11.6% (21/181) for the two most captured free-tailed bat species, Mops condylurus and M. pumilus respectively, with no detections from other bat species (0/90). Phylogenetic analyses based on the partial RNA-dependent RNA polymerase gene and whole genome sequences revealed that the sequences clustered together and were closely related to alphacoronavirus detected in free tailed bats in Eswatini, Nigeria and Rhinolophus simulator bats in South Africa. The sequences were more distantly related to alphacoronavirus isolated from Chaerophon plicatus bat species in Yunnan province, China and Ozimops species from southwestern Australia. These findings highlight coronavirus transmission among bats that share habitats with humans and livestock, posing a potential risk of exposure. Future research should investigate whether coronaviruses detected in these bats have the potential to spillover to other hosts.

The zoonotic transmission of bat coronaviruses poses a threat to human health. However, the diversity of bat-borne coronaviruses remains poorly characterized in many geographical areas. Here, we recovered eight coronavirus genomes by performing a metagenomic analysis of fecal samples from hundreds of individual bats captured in Spain, a country with high bat diversity. Three of these genomes corresponded to potentially novel coronavirus species belonging to the alphacoronavirus genus. Phylogenetic analyses revealed that some of these viruses are closely related to coronaviruses previously described in bats from other countries, suggesting a shared viral reservoir worldwide. Using viral pseudotypes, we investigated the receptor usage of the identified viruses and found that one of them can use human ACE2, albeit with lower affinity than SARS-CoV-2. However, the receptor usage of the other viruses remains unknown. This study broadens our understanding of coronavirus diversity and identifies research priorities for the prevention of zoonotic viral outbreaks.

Bats are flying mammals distributed worldwide known to host several types of Coronavirus (CoV). Since they were reported as the probable source of spillover of highly pathogenic CoV into the human population, investigating the circulation of this virus in bats around the world became of great importance. We analyzed samples from 103 bats from two distinct regions in Brazil. Coronavirus from the Alphacoronavirus genus was detected in 12 animals, 11 from São José do Rio Preto—SP region and 1 from Barreiras—BA region, resulting in a prevalence of 17.18% and 2.56% respectively. The virus was detected not only in intestines but also in lungs and liver. Phylogenetic analysis based on nsP12 genomic region suggests that the sequences group according to host family and sampling location. Studies on the circulation of these viruses in bats remain important to understand the ecology and evolutionary relationship of these pathogens.

Bats are the reservoir or ancestral hosts of important emerging coronaviruses affecting people (e.g., SARS-CoV and SARS-CoV-2) and livestock (e.g., PEDV, SADS-CoV). Here, we analyzed 523 genetic sequences of SADS-CoV that caused large-scale die-offs of pigs in China, which is known to be able to infect human cells and related HKU2-CoVs. We used this information to identify the horseshoe bat Rhinolophus affinis as the likely spillover host for the outbreak in pigs, and identified the bat species within which these viruses evolved. We then modeled the distribution of these host species and their overlap with dense human and pig populations to identify the regions where surveillance programs can help identify spillover events and prevent future outbreaks.