Considering that bat ecology alterations may be linked with pathogen spillover, research on bat coronaviruses, particularly on the infection and transmission pattern among bats in relation with their ecology, is essential. We captured bats distributed in Korea from 2021 to 2022, examined coronaviruses in oral swabs, feces, urine, and ectoparasites, and were able to detect alphacoronavirus. We investigated coronaviruses, but noted no substantial differences in the body condition index in the coronavirus-positive bats. Binary logistic regression analysis revealed that bat ecological factors that were significantly associated with coronavirus-positive were roost type, sample type, and bat species. Coronavirus-positive ectoparasite cases suggested additional study on the potential role of them as the viral transmission vectors or fomites. Reinfection of a different coronavirus in recaptured bats was evident, suggesting the possibility that coronavirus circulation can evade the potential protective immunity acquired from previous coronavirus infections. The present findings provide comprehensive information on the coronaviruses transmission dynamics within bat populations linked with bat ecology.

Coronavirus has garnered more attention recently, particularly in the aftermath of the 2019 pandemic. The β genus of the coronavirus family has demonstrated a significant threat to humanity. Current mitigation strategies involve the development of vaccines and repurposing drugs for symptomatic management of coronavirus infection, specifically SARS-Cov 2. Fusion inhibitors that are available as antiviral drugs for coronavirus have targeted the heptad repeat (HR) 1 and 2 in the S2 domain of the spike protein. The current study identified a fusion peptide (FP) upstream of HR1 as a potential target for developing membrane fusion inhibitors, and mimetic peptides analogous to the FP segment were tested for antiviral activity. Four mimetic fusion peptides (MFPs) (RSA59PP (MFP633), RSA59P (MFP634), RSMHV2P (MFP635), and RSMHV2PP (MFP636)) that are analogous to the FP of murine β coronavirus mouse hepatitis virus (MHV), MHV-A59/RSA59 (PP) and MHV-2/RSMHV2 (P) with central proline mutations, were tested. Results show the ability of MFPs to reduce cell-to-cell fusion and viral replication in vitro. MFP633, which contains a central double proline, exhibited the most potent inhibitory effect in spike protein-mediated membrane fusion assays. Biophysical experiments also demonstrated the strongest interactions between double-proline containing MFPs (MFP633 and MFP636) with biomimetic liposomes. In vivo studies using a liposome-mediated delivery system in mice confirmed the antiviral activity of MFP633. These findings suggest that targeting FPs could develop effective fusion inhibitors against coronaviruses. MFPs act on the host cell membrane by competing with the viral FP during the early stage of host-viral membrane fusion events. MFP633 is a promising peptide drug candidate that warrants future examination to assess whether this and other dual-proline containing peptides may exert similar anti-viral effects in other coronaviruses with conserved FP structures.

Despite the diminishing global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus continues to circulate and undergo mutations, posing ongoing challenges for public health. A comprehensive understanding of virus entry mechanisms is crucial for managing new epidemic strains. However, the cellular processes post-endocytosis remain largely unexplored. This study employs proximity labeling to examine proteins near ACE2 post-viral infection and identified syntaxin-6 (STX6) as a factor that inhibits SARS-CoV-2 infection by impeding the endocytic release of the virus. SARS-CoV-2 infection enhances early endosome recruitment of STX6. STX6 appears to hinder the maturation of viral particles-laden early endosomes into late endosomes, from which the virus could escape. Instead, it promotes the trafficking of the virus toward the autophagy-lysosomal degradation pathway. STX6 exhibits a broad-spectrum effect against various SARS-CoV-2 variants and several other viruses that enter via endocytosis. We report for the first time the function of STX6 as a restrictive factor in viral infection.IMPORTANCEVirus entry is the first step of the virus life cycle, and the exploitation of the endo-lysosome pathway for cellular entry by viruses has been well documented. Meanwhile, the intrinsic defense present within cells interferes with virus entry. We identified STX6 as a host restriction factor for viral entry by facilitating the virus trafficking to the autophagy-lysosomal degradation pathway. Notably, STX6 exhibits broad-spectrum antiviral activity against diverse severe acute respiratory syndrome coronavirus 2 variants and other viruses employing endocytosis for entry.

Vertebrate lungs contain diverse microbial communities, but little is known about the drivers of community composition or consequences for health. Microbiome assembly by processes such as dispersal, coevolution, and host-switching can be probed with comparative surveys; however, few studies exist for lung microbiomes, particularly for the fungal component, the mycobiome. Distinguishing among fungal taxa that are generalist or specialist symbionts, potential pathogens, or incidentally inhaled spores is urgent because of potential for emerging diseases. Here, we characterize the avian lung mycobiome and test the relative influences of environment, phylogeny, and functional traits. We used metabarcoding and culturing from 195 lung samples representing 32 bird species across 20 families. We identified 526 fungal taxa as estimated by distinct sequence types (zOTUs) including many opportunistic pathogens. These were predominantly from the phylum Ascomycota (79%) followed by Basidiomycota (16%) and Mucoromycota (5%). Yeast and yeast-like taxa (Malassezia, Filobasidium, Saccharomyces, Meyerozyma, and Aureobasidium) and filamentous fungi (Cladosporium, Alternaria, Neurospora, Fusarium, and Aspergillus) were abundant. Lung mycobiomes were strongly shaped by environmental exposure, and further modulated by host identity, traits, and phylogenetic affinities. Our results implicate migratory bird species as potential vectors for long-distance dispersal of opportunistically pathogenic fungi.

Most human emerging infectious diseases are zoonotic, originating in animal hosts prior to spillover to humans. Prioritizing the surveillance of wildlife that overlaps with humans and human activities can increase the likelihood of detecting viruses with a high potential for human infection. Here, we obtained fecal swabs from two fruit bat species-Eidolon helvum (n = 6) and Epomophorus wahlbergi (n = 43) (family Pteropodidae)-in peridomestic habitats in Nairobi, Kenya, and used metagenome sequencing to detect microorganisms. A near-complete genome of a novel virus assigned taxonomically to the Coronaviridae family Betacoronavirus genus and Nobecovirus subclade was characterized from E. wahlbergi. Phylogenetic analysis indicates this unique Nobecovirus clade shares a common ancestor with Eidolon/Rousettus Nobecovirus subclades isolated from Madagascar, Kenya, and Cameroon. Recombination was detected across open reading frames, except the spike protein, in all BOOTSCAN analyses, indicating intra-host coinfection and genetic exchange between genome regions. Although Nobecoviruses are currently bat-specific and are not known to be zoonotic, the propensity of coronaviruses to undergo frequent recombination events and the location of the virus alongside high human and livestock densities in one of East Africa's most rapidly developing cities justifies continued surveillance of animal viruses in high-risk urban landscapes.

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During the COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SC2) infection was confirmed in various animal species demonstrating a wide host range of the virus. Prior studies have shown that the ACE2 protein is the primary receptor used by the virus to gain cellular entry and begin the replication cycle. In previous studies, we demonstrated that human and various bat ACE2 proteins can be utilized by SC2 viruses for entry. Bats are a suspected natural host of SC2 because of genetic homology with other bat coronaviruses. In this work, we demonstrate that expression of ACE2 genes from the common vampire bat (CVB) (Desmodus rotundus) and the pallid bat (PB) (Antrozous pallidus), supports infection and replication of some SC2 viruses in cell culture. Two cell lines were produced, CVB-ACE2 and PB-ACE2, expressing ACE2 from these bat species along with human TMPRSS2, in a model previously established using a non-permissive chicken DF-1 cell line. Results demonstrate that the original Wuhan lineage (WA1) virus and the Delta variant were able to infect and replicate in either of the bat ACE2 cell lines. In contrast, the Lambda and Omicron variant viruses infected both cell lines, but viral titers did not increase following infection. Viral detection using immunofluorescence demonstrated abundant spike (S) protein staining for the WA1 and Delta variants but little signal for the Lambda and Omicron variants. These studies demonstrate that while ACE2 from CVB and PB can be utilized by SC2 viruses to gain entry for infection, later variants (Lambda and Omicron) replicate poorly in these cell lines. These observations suggest more efficient human adaption in later SC2 variants that become less fit for replication in other animal species.

DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity of ACE2 utilization among merbecoviruses and their receptor species tropism remain unknown. Here, we reveal that HKU5 enters host cells utilizing Pipistrellus abramus (P.abr) and several non-bat mammalian ACE2s through a binding mode distinct from that of any other known ACE2-using coronaviruses. We defined the molecular determinants of receptor species tropism and identified a single amino acid mutation enabling HKU5 to utilize human ACE2, providing proof of principle for machine-learning-assisted outbreak preparedness. We show that MERS-CoV and HKU5 have markedly distinct antigenicity and identified several HKU5 inhibitors, including two clinical compounds. Our findings profoundly alter our understanding of coronavirus evolution, as several merbecovirus clades independently evolved ACE2 utilization, and pave the way for developing countermeasures against viruses poised for human emergence.

Merbecoviruses comprise four viral species with remarkable genetic diversity: MERS-related coronavirus, Tylonycteris bat coronavirus HKU4, Pipistrellus bat coronavirus HKU5, and Hedgehog coronavirus 1. However, the potential human spillover risk of animal merbecoviruses remains to be investigated. Here, we reported the discovery of HKU5-CoV lineage 2 (HKU5-CoV-2) in bats that efficiently utilize human angiotensin-converting enzyme 2 (ACE2) as a functional receptor and exhibits a broad host tropism. Cryo-EM analysis of HKU5-CoV-2 receptor-binding domain (RBD) and human ACE2 complex revealed an entirely distinct binding mode compared with other ACE2-utilizing merbecoviruses with RBD footprint largely shared with ACE2-using sarbecoviruses and NL63. Structural and functional analyses indicate that HKU5-CoV-2 has a better adaptation to human ACE2 than lineage 1 HKU5-CoV. Authentic HKU5-CoV-2 infected human ACE2-expressing cell lines and human respiratory and enteric organoids. This study reveals a distinct lineage of HKU5-CoVs in bats that efficiently use human ACE2 and underscores their potential zoonotic risk.

High-affinity and specific binding toward the human angiotensin-converting enzyme 2 (hACE2) receptor by severe acute respiratory syndrome coronavirus (SARS)-related coronaviruses (SARSr-CoVs) remains incompletely understood. We report cryo-electron microscopy structures of eight different S-proteins from SARSr-CoVs found across Asia, Europe, and Africa. These S-proteins all adopt tightly packed, locked, prefusion conformations. These structures enable the classification of SARSr-CoV S-proteins into three types, based on their receptor-binding motif (RBM) structures and ACE2 binding characteristics. Type-2 S-proteins often preferentially bind bat ACE2 (bACE2) over hACE2. We report a structure of a type-2 BtKY72-RBD in complex with bACE2 to understand ACE2 specificity. Structure-guided mutagenesis of BtKY72-RBD reveals that multiple synergistic mutations in four different regions of RBM are required to achieve high-affinity hACE2 binding. Similar RBM changes can also confer hACE2 binding to another type-2 BM48-31 S-protein, which is primarily non-ACE2 binding. These results provide an understanding of how high-affinity hACE2 binding may be acquired by SARSr-CoV S-proteins.

Globally, over 768 million confirmed cases and 6.9 million deaths had been documented as of July 17, 2023. Coronaviruses have a relatively large RNA genome. As with other viruses, SARS-CoV-2 does have an envelope film produced from host cells that are assisted by virally encoded glycoproteins that are required for infectivity, immunological assault, and viral particle production. Although the intermediate source of origin and transmission to humans is unexplained, rapid transmission from human to human has been established. This review focuses on the mechanistic framework for understanding the SARS-CoV-2 viral infection. Additionally, it discusses the origins and implications of COVID-19 using direct quotations from the published scientific literature to avoid misinterpretation of this catastrophic event that resulted in a massive loss of human life and impact on the global economy. The current available information unfolds large number of topics related with COVID-19 and/or the coronavirus (SARS-CoV-2) responsible of the disease. This review article also delves into the multifaceted aspects of COVID-19 and SARS-CoV-2, with a specific focus on a controversial yet essential issue: the possible association between SARS-CoV-2's origin and aldose reductase, an enzyme known for its role in diabetic retinopathy. Exploring this connection holds utmost significance, offering valuable insights into COVID-19's pathogenesis and unlocking new avenues for therapeutic interventions. It is important to trace back the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19).

COVID-19 caused a public health emergency, which instituted a global effort to develop vaccines using different platforms, such as basic types and new-generation vaccines. Considering the importance of vaccination in preventing the severity of infectious diseases and the success in developing and approving vaccines against COVID-19 in record time, it is essential to learn about the characteristics of these vaccines. This study aimed to conduct a structured, systematic review following the PRISMA guideline, to analyze the general characteristics of vaccines approved globally for use against COVID-19. We used the list of approved vaccines available by the WHO as guidance to search for studies in the literature. We searched the terms "SARS-CoV-2 and vaccine and safety and efficacy" in the MEDLINE via PUBMED and Web of Science databases. We conducted the research on both bases, including complete articles published from January 2020 to June 2023. The selection of files occurred between May/2021 and June/2023. Therefore, the paper did not consider articles published after this period or vaccines approved after this moment. This study only included approved vaccines; phase three studies published in English. We found 11 published articles from phase three that met the established criteria. The vaccines included in this study were: Cominarty, mRNA-1273 or Spikevax, Vaxzevria or AZD1222 or Covishield, CoronaVac or PicoVacc, and Ad26.COV2.S, SputnikV or Gam-Covid-Vac, Covaxin, NVX-CoV2373 or Covovax or Nuvaxovid, WIV04 and HB02, CoVLP or Covifenz and Convidecia or Ad5-nCoV. We summarized the main findings of each vaccine, considering the vaccine composition, number of doses, efficacy analyses, and main adverse effects. In general, the vaccines had high efficacy rates and few adverse effects. Efficacy values are important for vaccine approval, but they will not necessarily reflect the real-world impact of vaccination. It was seen that the effectiveness of COV2.S, CoronaVac/PicoVacc, Cominarty, and Covaxin vaccines was lower than the efficacy, whereas, for AZD1222/Vaxzevria/Covishield, the two parameters remained at similar rates. All vaccines evaluated have different compositions, dosages, populations, and study designs. All are effective in at least preventing symptomatic COVID-19, causing mild or moderate adverse effects when present.

Bats have adapted to pathogens through diverse mechanisms, including increased resistance-rapid pathogen elimination, and tolerance-limiting tissue damage following infection. In the Egyptian fruit bat (an important model in comparative immunology), several mechanisms conferring disease tolerance were discovered, but mechanisms underpinning resistance remain poorly understood. Previous studies on other species suggested that the elevated basal expression of innate immune genes may lead to increased resistance to infection. Here, we test whether such transcriptional patterns occur in Egyptian fruit bat tissues through single-cell and spatial transcriptomics of gut, lung, and blood cells, comparing gene expression between bat, mouse, and human. Despite numerous recent loss and expansion events of interferons in the bat genome, interferon expression and induction are remarkably similar to that of mouse. In contrast, central complement system genes are highly and uniquely expressed in key regions in bat lung and gut epithelium, unlike in human and mouse. Interestingly, the unique expression of these genes in the bat gut is strongest in the crypt, where developmental expression programs are highly conserved. The complement system genes also evolve rapidly in their coding sequences across the bat lineage. Finally, the bat complement system displays strong hemolytic activity. Together, these results indicate a distinctive transcriptional divergence of the complement system, which may be linked to bat resistance, and highlight the intricate evolutionary landscape of bat immunity.

Pandemics originating from zoonotic viruses have posed significant threats to human health and agriculture. Recent discoveries have revealed that wild-rice plants also harbour viral pathogens capable of severely impacting rice production, a cornerstone food crop. In this study, we conducted virome analysis on ~1000 wild-rice individual colonies and discovered a novel single-strand positive-sense RNA virus prevalent in these plants. Through comprehensive genomic characterization and comparative sequence analysis, this virus was classified as a new species in the genus Polerovirus, designated Rice less tiller virus (RLTV). Our investigations elucidated that RLTV could be transmitted from wild rice to cultivated rice via a specific insect vector, the aphid Rhopalosiphum padi, causing less tiller disease symptoms in rice plants. We generated an infectious cDNA clone for RLTV and demonstrated systemic infection of rice cultivars and induction of severe disease symptoms following mechanical inoculation or stable genetic transformation. We further illustrated transmission of RLTV from stable transgenic lines to healthy rice plants by the aphid vector, leading to the development of disease symptoms. Notably, our database searches showed that RLTV and another polerovirus isolated from a wild plant species are widely circulating not only in wild rice but also cultivated rice around the world. Our findings provide strong evidence for a wild plant origin for rice viruses and underscore the imminent threat posed by aphid-transmitted rice Polerovirus to rice cultivar.

Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.

The emergence of zoonotic viral diseases, notably exemplified by the recent coronavirus disease pandemic in 2019 (COVID-19), underscores the critical need to understand the dynamics of viruses circulating in wildlife populations. This study aimed to investigate the diversity of coronaviruses in bat populations from northeastern Brazil, particularly in the state of Ceará, where little research on bat pathogens has been conducted previously. Bat sampling was performed between March 2021 and March 2022 across three municipalities, resulting in the collection of oral and rectal swabs from 298 captured individuals. Molecular analyses revealed alphacoronaviruses in multiple bat species. Additionally, a novel Betacoronavirus was identified in Artibeus planirostris, which did not fall within an established subgenus. Phylogenetic placement of these new coronavirus sequences suggests that closely related coronavirus lineages can infect a wide range of bat species sampled in distantly related Brazilian states and biomes. No SARS-CoV-2 and influenza A viruses were found in the sampled bats. These findings expand our understanding of coronavirus diversity in Brazilian bats. The detection of coronaviruses in various bat species underscores the importance of bats as reservoirs for these viruses. The absence of SARS-CoV-2 in the sampled bats indicates a lack of spillback events from human or environmental sources. However, the potential for future transmission events underscores the importance of ongoing surveillance and transmission mitigation protocols in wildlife management practices.

Among pathogens associated with mammals, numerous viruses with a direct transmission route impact human, domestic and wild species health. Host and landscape factors affect viral infection and transmission dynamics of these viruses, along with barriers to host dispersal and gene exchange. However, studies show biases toward certain locations, hosts and detected pathogens, with regional variations in similar host-virus associations.

Using a systematic review, in two electronic repositories for articles published until December 2022, we analysed the available information on host- and landscape-associated factors influencing the infection and transmission of directly transmitted viruses in mammals.

In the analysis, about 50% of papers examined either host traits, landscape composition or configuration measures, while approximately 24% combined host and landscape-associated factors. Additionally, approximately 17% of the articles included climatic data and 30% integrated factors related to anthropogenic impact, as these variables have a role in host density, distribution and virus persistence. The most significant and frequent host traits used as predictor variables were sex, age, body weight, host density and species identity. Land cover was the most evaluated landscape attribute, while some explored configuration variables like edge density and fragmentation indexes. Finally, temperature, precipitation and features such as human population density and human footprint index were also typically measured and found impactful.

Given the many contributions host- and landscape-related factors have in pathogen dynamics, this systematic study contributes to a better knowledge of host-virus dynamics and the identification of variables and gaps that can be used for disease prevention.

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.

Accumulating data suggest that some bat species host emerging viruses that are highly pathogenic in humans and agricultural animals. Laboratory-based studies have highlighted important adaptations in bat immune systems that allow them to better tolerate viral infections compared to humans. Simultaneously, ecological studies have discovered critical extrinsic factors, such as nutritional stress, that correlate with virus shedding in wild-caught bats. Despite some progress in independently understanding the role of bats as reservoirs of emerging viruses, there remains a significant gap in the molecular understanding of factors that drive virus spillover from bats. Driven by a collective goal of bridging the gap between the fields of bat virology, immunology, and disease ecology, we hosted a satellite symposium at the 2024 American Society for Virology meeting. Bringing together virologists, immunologists, and disease ecologists, we discussed the intrinsic and extrinsic factors such as virus receptor engagement, adaptive immunity, and virus ecology that influence spillover from bat hosts. This article summarizes the topics discussed during the symposium and emphasizes the need for interdisciplinary collaborations and resource sharing.

Bats are recognized as primary natural reservoirs for alpha- and betacoronaviruses. The interspecies transmission of bat coronaviruses to other mammalian hosts, including livestock and humans, can lead to epidemics, epizootics, and global pandemics.

This study aims to describe coronaviruses associated with horseshoe bats (Rhinolophus spp.) in the southern regions of the European part of Russia.

Fecal samples were collected from bats inhabiting caves on the southern macroslope of the Greater Caucasus (Sochi-Adler region) during 2020, 2021, and 2024. Viral genomes were detected and analyzed using high-throughput sequencing (NGS) and RT-PCR.

A novel alphacoronavirus, designated Kudep virus (GenBank acc. # PQ649435), was identified in R. ferrumequinum. Presumably the Kudep virus represents a novel species within the subgenus Decacovirus of the genus Alphacoronavirus. The virus Showed 72% nucleotide identity to a Cardioderma bat coronavirus from Kenya and up to 67% nucleotide identity to the YN2012 virus group found in horseshoe bats in China. RT-PCR screening revealed active circulation of both Kudep virus and the previously described SARS-like betacoronavirus Khosta-1 in the study area. Infection rates in a single R. ferrumequinum colony during autumn 2021 reached 59.2% and 70.5% for Kudep and Khosta-1, respectively. Frequent co-infections with both viruses were observed in individual bats.

Our findings expand the understanding of the distribution of bat alphacoronaviruses and their genetic diversity. We demonstrate the presence of a persistent natural foci of two potentially zoonotic bat coronaviruses, ecologically associated with R. ferrumequinum in the southern European part of Russia.

The continued emergence of SARS-CoV-2 variants and the threat of future Sarbecovirus zoonoses have spurred the design of vaccines that can induce broad immunity against multiple coronaviruses. Here, we use computational methods to infer ancestral phylogenetic reconstructions of receptor binding domain (RBD) sequences across multiple Sarbecovirus clades and incorporate them into a multivalent adenoviral-vectored vaccine. Mice immunized with this pan-Sarbecovirus vaccine are protected in the upper and lower respiratory tracts against infection by historical and contemporary SARS-CoV-2 variants, SARS-CoV, and pre-emergent SHC014 and Pangolin/GD coronavirus strains. Using genetic and immunological approaches, we demonstrate that vaccine-induced protection unexpectedly is conferred principally by CD4+ and CD8+ T cell-mediated anamnestic responses. Importantly, prior mRNA vaccination or SARS-CoV-2 respiratory infection does not alter the efficacy of the mucosally delivered pan-Sarbecovirus vaccine. These data highlight the promise of a phylogenetic approach for antigen and vaccine design against existing and pre-emergent Sarbecoviruses with pandemic potential.

The coronavirus-induced disease 19 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections, has had a devastating impact on millions of lives globally, with severe mortality rates and catastrophic social implications. Developing tools for effective vaccine strategies and platforms is essential for controlling and preventing the recurrence of such pandemics. Moreover, molecular virology tools that facilitate the study of viral pathogens, impact of viral mutations, and interactions with various host proteins are essential. Viral replicon- and virus-like particle (VLP)-based systems are excellent examples of such tools. This review outlines the importance, advantages, and disadvantages of both the replicon- and VLP-based systems that have been developed for SARS-CoV-2 and have helped the scientific community in dimming the intensity of the COVID-19 pandemic.

Bats possess a range of distinctive characteristics, including flight, echolocation, impressive longevity, and the ability to harbor various zoonotic pathogens. Additionally, they account for the second-highest species diversity among mammalian orders, yet their phylogenetic relationships and demographic history remain underexplored. Here, we generated de novo assembled genomes for 17 bat species and 2 of their mammalian relatives (the Amur hedgehog and Chinese mole shrew), with 12 genomes reaching chromosome-level assembly. Comparative genomics and ChIP-seq assays identified newly gained genomic regions in bats potentially linked to the regulation of gene activity and expression. Notably, some antiviral infection-related gene under positive selection exhibited the activity of suppressing cancer, evidencing the linkage between virus tolerance and cancer resistance in bats. By integrating published bat genome assemblies, phylogenetic reconstruction established the proximity of noctilionoid bats to vesper bats. Interestingly, we found 2 distinct patterns of ancient population dynamics in bats and population changes since the last glacial maximum does not reflect species phylogenetic relationships. These findings enriched our understanding of adaptive mechanisms and demographic history of bats.

The COVID-19 pandemic presents a major threat to global public health. Several lines of evidence have shown that the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), along with two other highly pathogenic coronaviruses, SARS-CoV and Middle East Respiratory Syndrome (MERS-CoV) originated from bats. To prevent and control future coronavirus outbreaks, it is necessary to investigate the interspecies infection and pathogenicity risks of animal-related coronaviruses. Currently used infection models, including in vitro cell lines and in vivo animal models, fail to fully mimic the primary infection in human tissues. Here, we employed organoid technology as a promising new model for studying emerging pathogens and their pathogenic mechanisms. We investigated the key host-virus interaction patterns of five human coronaviruses (SARS-CoV-2 original strain, Omicron BA.1, MERS-CoV, HCoV-229E, and HCoV-OC43) in different human respiratory organoids. Five indicators, including cell tropism, invasion preference, replication activity, host response and virus-induced cell death, were developed to establish a comprehensive evaluation system to predict coronavirus interspecies infection and pathogenicity risks. Using this system, we further examined the pathogenicity and interspecies infection risks of three SARS-related coronaviruses (SARSr-CoV), including WIV1 and rRsSHC014S from bats, and MpCoV-GX from pangolins. Moreover, we found that cannabidiol, a non-psychoactive plant extract, exhibits significant inhibitory effects on various coronaviruses in human lung organoid. Cannabidiol significantly enhanced interferon-stimulated gene expression but reduced levels of inflammatory cytokines. In summary, our study established a reliable comprehensive evaluation system to analyse infection and pathogenicity patterns of zoonotic coronaviruses, which could aid in prevention and control of potentially emerging coronavirus diseases.

Coronaviruses (CoVs) pose a threat to human health globally, as highlighted by severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and the COVID-19 pandemic. Bats from the Greater Mekong Subregion (GMS) are an important natural reservoir for CoVs. Here we report the differential prevalence of CoVs in bats within Yunnan Province across biological and ecological variables. We also show the coexistence of CoVs in individual bats and identify an additional putative host for SARS-related CoV, with higher dispersal capacity than other known hosts. Notably, 11 SARS-related coronaviruses (SARSr-CoVs) were discovered in horseshoe bats (family Rhinolophidae) and a Chinese water myotis bat (Myotis laniger) by pan-CoV detection and Illumina sequencing. Our findings facilitate an understanding of the fundamental features of the distribution and circulation of CoVs in nature as well as zoonotic spillover risk in the One health framework.

In the 21st century, three betacoronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have emerged in humans worldwide as a result of animal spillover, causing severe respiratory infections and resulting in more than seven million deaths. In 2013, a novel Betacoronavirus closely related to MERS-CoV (Betacoronavirus cameli) was discovered in European hedgehogs (Erinaceus europaeus), raising questions on the possibility of hedgehog-to-human transmission. Hence, the present study aimed to investigate and characterize the presence and genetic diversity of coronaviruses in hedgehogs from Portugal, as well as their potential for cross-species transmission. To achieve this, fecal samples from 110 hedgehogs at two recovery centers and one environmental non-governmental organization were tested for coronaviruses using a broad-spectrum nested RT-PCR assay targeting the RdRp gene. Of these samples, 24.5 % tested positive, most belonging to the Betacoronavirus genus. However, the present study also reports, for the first time, Alphacoronaviruses in hedgehogs, showing 100 % identity with a Bat coronavirus (a variant of Alphacoronavirus miniopteri). The genome sequencing of one betacoronavirus-positive sample yielded 65 % of a full-length genome, with the closest homology (93.5 %) to Betacoronavirus erinacei from the United Kingdom. Computational protein-protein docking studies predicted the binding affinity between the spike protein of hedgehog coronavirus and cell receptors of mammal species that interact with hedgehogs. The results obtained raise the question of whether hedgehog CoV uses the same receptor as MERS-CoV or a different receptor to enter host cells. Thus, this study enhances our understanding of the epidemiology of coronaviruses, emphasizing the need for further investigation into cross-species transmission risks.

Respiratory infections caused by coronaviruses have posed serious and unpredictably public health threats; reliable animal models continue to be essential for advancing our understanding of the virus's transmission, pathophysiology, and immunological mechanisms. In response to the critical need for centralized resources in coronavirus research, the COVID-AMD database (Coronavirus Disease Animal Model Database, https://www.uc-med.net/CoV-AMD ) has been developed as an integrated platform. Data was gathered from public literature databases, refined and integrated using ETL (Extract, Transform, Load) methodology. After data conversion and cleaning, COVID-AMD was implemented using MySQL relational database with jQuery and JBoss. COVID-AMD database consolidates comprehensive data on animal models infected with various CoVs, including MERS-CoV, SARS-CoV, and SARS-CoV-2, featuring methodologies for establishing infection models, clinical features, and phenotypic data. It catalogs 869 animal models across 29 species and 312 virus strains, covering five diseases and ten infection routes. With global and advanced search capabilities, it facilitated data preprocessing, integration, analysis, and visualization, and provided tools for comparative analysis, model recommendation and omics analysis based on model and phenotype data. The open access to this rich repository aims to enable rapid identification of animal models for CoVs, thereby accelerating the development and clinical trial progression of prospective therapeutics and vaccines.

RNA virus-induced excessive inflammation and impaired antiviral interferon (IFN-I) responses are associated with severe disease. This innate immune response, also referred to as "dysregulated immunity" is caused by viral single-stranded RNA (ssRNA)- and double-stranded-RNA (dsRNA)-mediated exuberant inflammation and viral protein-induced IFN antagonism. However, key host factors and the underlying mechanism driving viral RNA-mediated dysregulated immunity are poorly defined. Here, using viral ssRNA and dsRNA mimics, which activate toll-like receptor 7 (TLR7) and TLR3, respectively, we evaluated the role of viral RNAs in causing dysregulated immunity. We observed that murine bone marrow-derived macrophages (BMDMs), when stimulated with TLR3 and TLR7 agonists, induced differential inflammatory and antiviral cytokine response. TLR7 activation triggered a robust inflammatory cytokine/chemokine induction compared to TLR3 activation, whereas TLR3 stimulation induced significantly increased IFN/IFN stimulated gene (ISG) response relative to TLR7 activation. To define the mechanistic basis for dysregulated immunity, we examined cell-surface and endosomal TLR levels and downstream mitogen-activated protein kinase (MAPK) and nuclear factor kappa B (NF-kB) activation. We identified significantly higher cell-surface and endosomal TLR7 levels compared to TLR3, which were associated with early and robust MAPK (p-ERK1/2, p-P38, and p-JNK) and NF-kB activation in TLR7-stimulated macrophages. Furthermore, blocking EKR1/2 and NF-kB activity reduced TLR3/7-induced inflammatory cytokine/chemokine levels, whereas only ERK1/2 inhibition enhanced viral RNA mimic-induced IFN/ISG responses. Collectively, our results illustrate that high cell-surface and endosomal TLR7 expression and robust ERK1/2 activation drive viral ssRNA mimic-induced excessive inflammatory and reduced IFN/ISG response and blocking ERK1/2 activity would likely mitigate viral-RNA/TLR-induced dysregulated immunity.

Bats (Order Chiroptera) are an important reservoir of emerging zoonotic microbes, including viruses of public health concern such as henipaviruses, lyssaviruses, and SARS-related coronaviruses. Despite the continued discovery of new viruses in bat populations, a significant proportion of these viral agents remain uncharacterized, highlighting the imperative for additional research aimed at elucidating their evolutionary relationship and taxonomic classification.

In order to delve deeper into the viral reservoir hosted by bats, the present study employed Next Generation Sequencing (NGS) technology to analyze 13,105 swab samples obtained from various locations in China. Analysis of 378 sample pools revealed the presence of 846 vertebrate-associated viruses. Subsequent thorough examination, adhering to the International Committee on Taxonomy of Viruses (ICTV) criteria for virus classification, identified a total of 120 putative viral species with the potential to emerge as novel viruses, comprising a total of 294 viral strains. Phylogenetic analysis of conserved genomic regions indicated the novel virus exhibited a diverse array of viral lineages and branches, some of which displayed close genetic relationships to known human and livestock pathogens, such as poxviruses and pestiviruses.

This study investigates the breadth of DNA and RNA viruses harbored by bats, delineating several novel evolutionary lineages and offering significant contributions to virus taxonomy. Furthermore, the identification of hitherto unknown viruses with relevance to human and livestock health underscores the importance of this study in encouraging infectious disease monitoring and management efforts in both public health and veterinary contexts. Video Abstract.