Heart-nosed #bat #alphacoronaviruses use #human CEACAM6 to enter #cells

 

Abstract

Identifying viruses with zoonotic potential on the basis of their ability to enter human cells is a critical component of pandemic prediction, prevention and preparedness. Here using a computational approach that retains maximum phylogenetic diversity, we selected an optimal subset of alphacoronavirus spike proteins to screen against broad coronavirus receptor libraries. Most of the selected spike proteins did not use any of the established coronavirus receptors. However, the pseudotyped spike protein of Cardioderma cor (heart-nosed bat) coronavirus KY43 (CcCoV-KY43) could enter human cells. Using a recombinant CcCoV receptor-binding domain (RBD) and a human receptor screening platform, we identified direct interactions with the human CEACAM proteins CEACAM3, CEACAM5 and CEACAM6. Overexpression of human CEACAM6—a protein widely expressed in the human lung—conferred permissivity to otherwise refractory human cells. A crystal structure showed that the RBD binds the amino-terminal IgV-like domain of human CEACAM6. Immune surveillance studies using sera of individuals from the Taveta region of Kenya, where CcCoV-KY43 was identified, did not show significant evidence of recent spillover. Wider characterization of alphacoronaviruses related to CcCoV-KY43 showed that human CEACAM6 is used by two other CcCoVs collected in Kenya. Moreover, there was more restricted nonhuman CEACAM6 tropism for viruses isolated from Rhinolophus bats from Russia and China. Thus, alphacoronaviruses that use CEACAM6 are probably geographically widespread, and viruses from East Africa show potential for transmission to humans.

Source: 

Link: https://www.nature.com/articles/s41586-026-10394-x

____

Genetic diversity of alpha and #betacoronaviruses in cave and temple-roosting #bats in #Vientiane Province, #Lao PDR

 

Abstract

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.

Source: 

Link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0341737

____

Detection and genetic characterization of #alphacoronaviruses in co-roosting #bat species, southeastern #Kenya

 

Abstract

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.

Author summary

Bats are known to carry several zoonotic pathogens with potential to cause serious illnesses and death in humans. Yet, surveillance on the pathogens they carry remains limited in much of the world. We studied the prevalence and diversity of coronaviruses from bats in Taita Hills, southeastern Kenya to better understand the circulation of these viruses and inform disease preparedness. We detected alphacoronaviruses in urban Mops condylurus and M. pumilus bat species. The bat alpha coronaviruses we detected were closely related to alphacoronaviruses that have been previously detected in bats elsewhere in Africa and distantly related to alphacoronavirus detected from Chaerophon plicatus bat species in Yunnan province, China and Ozimops species from southwestern Australia. This work demonstrates coronavirus circulation among bats that share habitats with people and livestock providing conditions that can lead to spillover. Identifying whether coronaviruses detected in these bats have the potential to infect other hosts is critical for developing countermeasures and mitigating potential outbreaks.

Source: PLoS Neglected Tropical Diseases, https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0012805

____

Diversity and #spillover #risk of swine acute diarrhea syndrome and related #coronaviruses in #China and Southeast #Asia

 

ABSTRACT

Bats are the reservoir hosts of emerging coronaviruses (CoVs) affecting human and livestock health. We assessed the diversity, evolution, and geographic distribution of two alphacoronaviruses (subgenus Rhinacovirus) with considerable potential for emergence: swine acute diarrhea syndrome coronavirus (SADS-CoV), which has caused large outbreaks in pigs in China and can infect primary human airway epithelial cells in vitro; and the related Rhinolophus bat coronavirus HKU2 (HKU2-CoV). Phylogenetic analyses of 523 rhinacovirus sequences from bats in China and Southeast Asia suggest these viruses should be reclassified into at least two distinct CoV species representing two well-supported monophyletic clades. Stronger phylogenetic clustering by sampling location than by host species suggests infrequent long-distance transmission of rhinacoviruses in southern China. Ancestral state reconstruction analysis indicates that R. sinicus/thomasi and R. affinis have played an important role in rhinacovirus evolution in southern China and that R. affinis is the likely reservoir host of SADS-CoV that spilled over into pigs. We used species distribution modeling of Rhinolophus spp. bat hosts of rhinacoviruses, combined with pig and human density data, to identify potential geographic rhinacovirus spillover risk in Southeast Asia. Areas of high pig density within suitable bat habitat exist primarily in southern China and northern Vietnam, and hotspots of the highest human density within suitable bat habitat are primarily along the southern coast of China, Java, and central Thailand. Targeted surveillance of pigs and people in these regions may facilitate the timely detection of bat CoV spillover events and mitigate the risk of future outbreaks.

IMPORTANCE

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.

Source: mBio, https://journals.asm.org/doi/full/10.1128/mbio.01197-24?af=R

____

Analysis of the metagenomic assembled #genome of #MERS-CoV and Alpha-CoV from #Camelus dromedarius in #Saudi Arabia

Abstract

Background

Dromedary camels are known carriers of Middle East respiratory syndrome coronavirus (MERS-CoV). This study aimed to identify respiratory RNA viruses circulating in the nasal cavities of camels that could potentially cause disease in humans.

Methods

Shotgun metagenomic paired-end sequencing was performed on four pools of nasal swabs collected from 40 camels originating from Sudan and Djibouti, using the MiSeq platform.

Results

Alphacoronavirus 229E was commonly detected in the camel pools. MERS-CoV was found in both pools from Sudan and one from Djibouti. Camel parainfluenza virus 3 (PIV3) was detected in the male camel pool from Sudan. Furthermore, near-complete (99.9 %) metagenomic assembled genomes (MAGs) of alphacoronavirus 229E (SIAU MAG01) and MERS-CoV (SIAU MAG02) were retrieved from the female camel pool from Sudan. Another MAG of alphacoronavirus 229E (SIAU MAG03) was recovered from a male camel pool imported from Sudan. In the phylogenetic analysis, SIAU MAG02 clustered with MERS-CoV genome sequences retrieved from humans and camels in the Middle East. The alphacoronavirus 229E MAGs from camels formed a distinct clade separate from the human alphacoronavirus 229E lineage. SIAU MAG04 clustered with PIV3 sequences recovered from Camelus dromedarius in the United Arab Emirates.

Conclusions

Overall, respiratory viruses belonging to alpha and beta coronaviruses, notably MERS-CoV, recognized by the World Health Organization as an emerging infectious disease of critical concern, were observed in dromedary camels from African origins, potentially posing a risk of transmission to humans.

Source: Journal of Infection and Public Health, https://www.sciencedirect.com/science/article/pii/S1876034125002576?via%3Dihub

____

Identification and characterization of novel #bat #coronaviruses in #Spain

Abstract

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.

Author summary

Bats carry many different viruses, some of which can infect humans. Among these, bat coronaviruses are of particular concern. To be better prepared for future pandemics, it is important to understand how many of these viruses exist and their ability to infect different hosts. However, research in this area has often focused on certain parts of the world, while other regions remain underexplored. Spain has a rich diversity of bats, but very few studies have looked for coronaviruses in bats from the Iberian Peninsula. Here, we used viral metagenomics to test for the presence of coronaviruses in more than 200 bat samples collected across Spain. We identified eight coronavirus genomes, three of which may constitute new species. We also examined how closely related they are to previously known viruses, and whether they can use the same cellular receptors as known coronaviruses. Notably, we found that one of the viruses could use human ACE2, the SARS-CoV-2 receptor. Our findings reveal that bats in Spain host a diverse range of coronaviruses, including some that could potentially infect humans. This highlights the importance of studying coronavirus diversity more broadly worldwide.

Source: PLoS Pathogens, https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1013371

____

Novel #human #coronavirus in an #infant #patient with #pneumonia, Republic of #Korea

ABSTRACT

Coronaviruses (CoVs) pose a significant threat to public health, causing a wide spectrum of clinical manifestations and outcomes. Beyond precipitating global outbreaks, Human CoVs (HCoVs) are frequently found among patients with respiratory infections. To date, limited attention has been directed towards alphacoronaviruses due to their low prevalence and fatality rates. Nasal swab and serum samples were collected from a paediatric patient, and an epidemiological survey was conducted. Retrospective surveillance investigated the molecular prevalence of CoV in 880 rodents collected in the Republic of Korea (ROK) from 2018 to 2022. Next-generation sequencing (NGS) and phylogenetic analyses characterized the novel HCoV and closely related CoVs harboured by Apodemus spp. On 15 December 2022, a 103-day-old infant was admitted with fever, cough, sputum production, and rhinorrhea, diagnosed with human parainfluenza virus 1 (HPIV-1) and rhinovirus co-infection. Elevated AST/ALT levels indicated transient liver dysfunction on the fourth day of hospitalization. Metagenomic NGS (mNGS) identified a novel HCoV in nasal swab and serum samples. Retrospective rodent surveillance and phylogenetic analyses showed the novel HCoV was closely related to alphacoronaviruses carried by Apodemus spp. in the ROK and China. This case highlights the potential of mNGS to identify emerging pathogens and raises awareness of possible extra-respiratory manifestations, such as transient liver dysfunction, associated with novel HCoVs. While the liver injury in this case may be attributable to the novel HCoV, further research is necessary to elucidate its clinical significance, epidemiological prevalence, and zoonotic origins.

Source: Emerging Microbes and Infections, https://www.tandfonline.com/doi/full/10.1080/22221751.2025.2466705

____