Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History

Phylogenetic relationships and species composition of host community influence the transmission of coronaviruses in sympatric bats

Since the emergence of Severe Acute Respiratory Syndrome (SARS) in 2002, bats have been recognized as important reservoirs of diverse coronaviruses (CoVs). Despite extensive research on the broad geographic transmission of bat CoVs, there is a notable gap in understanding the transmission dynamics within sympatric bat communities. Using a phylogeographic Bayesian statistical framework, we examined CoV transmission patterns and their determinants in a region where four bat roosting caves coexist and CoVs circulate persistently. Our findings reveal that two subgenera of CoVs, α-CoVs and β-CoVs dominate different bat caves at varying times. Notably, β-CoVs show more frequent cross-species transmission events among the dominant reservoir hosts, bats of Rhinolophidae. Phylogenetic distance between host species emerges as the key influence factor of viral cross-species transmission, whereas cohabitation duration and the number of hosts sharing caves do not significantly influence viral transmission. In addition, we emphasize that the compositional similarity of species in the roosting caves is critical for the inter-cave transmission of bat-CoVs, rather than the distance between cave. These results provide novel insights into the complex transmission dynamics of bat CoVs within sympatric bat communities.

Processing of genomic RNAs by Dicer in bat cells limits SARS-CoV-2 replication

Bats are reservoirs for numerous viruses that cause serious diseases in other animals and humans. Several mechanisms are proposed to contribute to the tolerance of bats to these pathogens. This study investigates the response of bat cells to double-stranded RNA generated by SARS-CoV-2 replication. Here, we found the involvement of Dicer in the processing of viral genomic RNAs during SARS-CoV-2 infection. Examining RNA sequencing of infected cells, small-interfering RNA (siRNA)-like fragments were found derived from viral RNAs. Depletion of Dicer showed a reduction in these RNAs and an increase in viral loads suggesting unlike other mammals, bats may use Dicer to limit viral replication. This prompted the exploration of key dsRNA sensors in bat cells. Our analysis showed significant upregulation of OAS1 and MX1 in response to dsRNA, while PKR levels remained low, suggesting alternative dsRNA-response mechanisms are present that eschew the common PKR-based system. These results further show how bats employ distinct strategies for antiviral defense that may contribute to tolerating viral infections. They suggest the involvement of Dicer in antiviral mechanisms in bats, a function not observed in other mammals. This highlights a mechanism for bat originating viruses to evolve features that in other animals could cause extreme antiviral responses such as is seen with SARS-CoV-2.

Discovery of a novel Betacoronavirus 1, cpCoV, in goats in China: The new risk of cross-species transmission

Betacoronavirus is a causative agent of respiratory and enteric diseases in humans and animals. Several ruminants are recognized to be intermediate hosts in the transmission of emerging coronaviruses from reservoir hosts to humans. Here, we first report a novel Betacoronavirus isolated from goats suffering from diarrhea in China, putatively named caprine coronavirus (cpCoV). Full-genome characterization and nuclear acid comparisons demonstrated that this virus is an evolutionarily distinct Betacoronavirus belonging to the subgenus Embecovirus and is a Betacoronavirus 1 species. Notably, on phylogenetic trees based on complete genomes and RdRp, S, and N genes, the cpCoVs were grouped into a clade distinct from other Betacoronavirus strains and were closely related to the HKU23- and HKU23-associated coronaviruses. CpCoV possessed a unique genome organization with a truncated NS4a protein and an elongated NS4b protein that showed no significant matches in the GenBank database. The homology of the S and NS4a-4b genes between cpCoV and Embecovirus was less than 95%. Analysis revealed possible recombination events occurred during the evolution of cpCoV and HKU23, and there are striking similarities between the two viruses in evolutionary terms. In addition, cpCoV showed a narrow cell tropism, replicating in human- and bovine-origin cells in vitro, and caused diarrhea and enteric pathologic changes in goats and calves in vivo. We have provided epidemiological, virological, evolutionary, and experimental evidence that cpCoV is a novel etiological agent for enteric disease in goats. Evidently, a spilling-over event might have occurred between ruminants, including goats, camels, cattle, and wild animals. This study highlights the importance of identifying coronavirus diversity and inter-species transmission in ruminants worldwide, broadens our understanding of the ecology of coronaviruses, and aids in the prevention of animal-to-human transmission and outbreaks.

Genome-Wide Genomic Analysis and Evolutionary Insights into Bovine Coronavirus Strains in Southwest China

The global epidemic of bovine coronavirus (BCoV) has caused enormous economic losses. The characterisation and genetic composition of endemic strains in Southwest China remain elusive. This study aimed to fill this gap by isolating three BCoV strains from this region and sequencing their whole genomes. To elucidate the genetic evolution and characterisation of the prevalent strains, the results of BCoV sequences were compared in GenBank, with a focus on genetic evolution, mutation, and recombination patterns. The results showed close homology between strains NN190313 and NN230328, while strain NN221214 showed less similarity to these two strains but clustered with the French strain of the European branch. Intriguingly, NN190313 and NN230328 were grouped with goat-derived BCoV strains from Jiangsu Province in Eastern China in the Asian-American branch. In addition, recombination analyses revealed significant signals between NN230328 and either a Chinese goat-derived strain (XJCJ2301G) or a Shandong strain (ShX310). This study highlights the importance of monitoring cross-species transmission between cattle and goats, especially in the mountainous areas of Southwest China where mixed farming occurs, and thus, the monitoring of cross-species transmission between cattle and goats is important for preventing new public health challenges, providing important insights for research on cross-species transmission, early prevention, and control measures, with potential applications in vaccine development.

Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63

Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In this study, we developed a two-pool, long-amplicon (900-1100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. Over a period of six epidemiological seasons from 2017 to 2023, we retrospectively analyzed 14,704 nasopharyngeal swabs collected from patients hospitalized in St. Petersburg clinics. Of these samples, 5010 (34.07%) tested positive for respiratory viruses, with 424 (2.88% of all samples) identified as seasonal human coronaviruses. The assessment of species diversity showed that predominant hCoV species alternate between seasons. Whole-genome sequences for 85 seasonal human coronaviruses (hCoVs) with >70% genome coverage were obtained, including 23 hCoV-OC43, 6 hCoV-HKU1, 39 hCoV-229E, and 17 hCoV-NL63. These represent the first near-complete genomes of seasonal hCoVs from the Russian Federation, addressing a significant gap in the genomic epidemiology of these viruses. A detailed phylogenetic analysis of the sequenced genomes was conducted, highlighting the emergence of hCoV-229E subclades 7b.1 and 7b.2, which carry numerous substitutions in the Spike protein. Additionally, we sequenced a historical hCoV-229E isolate collected in the USSR in 1979, the oldest sequenced 229E virus from Eurasia, and demonstrated that it belongs to Genotype 2. The newly developed PCR-based sequencing protocol for seasonal hCoVs is straightforward and well-suited for genomic surveillance, providing a valuable tool to enhance our understanding of the genetic diversity of human seasonal coronaviruses.

Origin and cross-species transmission of bat coronaviruses in China

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.

Novel coronaviruses and mammarenaviruses of hedgehogs from Russia including the comparison of viral communities of hibernating and active specimens

Introduction

Small mammals, especially rodents and bats, are known reservoirs of zoonotic viruses, but little is known about the viromes of insectivorous species including hedgehogs (order Eulipotyphla), which often live near human settlements and come into contact with humans.

Methods

We used high-throughput sequencing and metaviromic analysis to describe the viromes of 21 hedgehogs (Erinaceus sp.) sampled from summer 2022 to spring 2023. We captured 14 active animals from the wild (seven in European Russia and the other seven in Central Siberia). The remaining 7 animals were hibernating in captivity (captured in European Russia before the experiment).

Results and discussion

The diversity of identified viral taxa as well as the total number of reads classified as viral was high in all active animals (up to eight different viral families per animal), but significantly lower in hibernating animals (zero or no more than three different viral families per animal). The present study reports, for the first time, betacoronaviruses and mammasrenaviruses in hedgehogs from Russia. Erinaceus coronaviruses (EriCoVs) were found in 4 of 7 active animals captured in the wild, in European Russia, making it is the easiest finding of EriCoVs in Europe. One animal was found to carry of two different EriCoVs. Both strains belong to the same phylogenetic clade as other coronaviruses from European hedgehogs. Pairwise comparative analysis suggested that one of these two strains arose by recombination with an unknown coronavirus, since all of identified SNPs (n = 288) were found only in the local genome region (the part of ORF1b and S gene). The novel mammarenaviruses (EriAreVs) were detected in 2 out of 7 active and in 2 out of 7 hibernating animals from the European Russia. Several complete L and S segments of EriAreVs were assembled. All identified EriAreVs belonged to the same clade as the recently described MEMV virus from Hungarian hedgehogs. As the hibernating hedgehogs were positive for EriAreVs when kept in controlled conditions without contact with each other, we suggest the possibility of persistent arenavirus infection in hedgehogs, but further experiments are needed to prove this.

Pathogenesis and virulence of coronavirus disease: Comparative pathology of animal models for COVID-19

Animal models that can replicate clinical and pathologic features of severe human coronavirus infections have been instrumental in the development of novel vaccines and therapeutics. The goal of this review is to summarize our current understanding of the pathogenesis of coronavirus disease 2019 (COVID-19) and the pathologic features that can be observed in several currently available animal models. Knowledge gained from studying these animal models of SARS-CoV-2 infection can help inform appropriate model selection for disease modelling as well as for vaccine and therapeutic developments.

Discordant phylodynamic and spatiotemporal transmission patterns driving the long-term persistence and evolution of human coronaviruses

Four distinct species of human coronaviruses (HCoVs) circulate in humans. Despite the recent attention due to SARS-CoV-2, a comprehensive understanding of the molecular epidemiology and genomic evolution of HCoVs remains unclear. Here, we employed primary differentiated human nasal epithelial cells for the successful isolation and genome sequencing of HCoVs derived from two retrospective cohorts in Singapore and Tanzania. Phylodynamic inference shows that HCoV-229E and HCoV-OC43 were subject to stronger genetic drift and reduced purifying selection from the early 2000s onwards, primarily targeting spike Domain A and B. This resulted in increased lineage diversification, coinciding with a higher effective reproductive number (Re>1.0). However, HCoV-NL63 and HCoV-HKU1 experienced weaker genetic drift and selective pressure with prolonged regional persistence. Our findings suggest that HCoV-229E and HCoV-OC43 viruses are adept at generating new variants and achieving widespread intercontinental dissemination driven by continuous genetic drift, recombination, and complex migration patterns.

Seasonal human coronavirus NL63 epidemics in children in Guilin, China, reveal the emergence of a new subgenotype of HCoV-NL63

Introduction

Seasonal human coronavirus NL63 (HCoV-NL63) is a frequently encountered virus linked to mild upper respiratory infections. However, its potential to cause more severe or widespread disease remains an area of concern. This study aimed to investigate a rare localized epidemic of HCoV-NL63-induced respiratory infections among pediatric patients in Guilin, China, and to understand the viral subtype distribution and genetic characteristics.

Methods

In this study, 83 pediatric patients hospitalized with acute respiratory infections and positive for HCoV-NL63 were enrolled. Molecular analysis was conducted to identify the viral subgenotypes and to assess genetic variations in the receptor-binding domain of the spiking protein.

Results

Among the 83 HCoV-NL63-positive children, three subgenotypes were identified: C4, C3, and B. Notably, 21 cases exhibited a previously unreported subtype, C4. Analysis of the C4 subtype revealed a unique amino acid mutation (I507L) in the receptor-binding domain of the spiking protein, which was also observed in the previously reported C3 genotype. This mutation may suggest potential increases in viral transmissibility and pathogenicity.

Discussion

The findings of this study highlight the rapid mutation dynamics of HCoV-NL63 and its potential for increased virulence and epidemic transmission. The presence of a unique mutation in the C4 subtype, shared with the C3 genotype, raises concerns about the virus's evolving nature and its potential public health implications. This research contributes valuable insights into the understanding of HCoV-NL63's epidemiology and pathogenesis, which is crucial for effective disease prevention and control strategies. Future studies are needed to further investigate the biological significance of the observed mutation and its potential impact on the virus's transmissibility and pathogenicity.

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation

BACKGROUND

Zoonotic viruses cause substantial public health and socioeconomic problems worldwide. Understanding how viruses evolve and spread within and among wildlife species is a critical step when aiming for proactive identification of viral threats to prevent future pandemics. Despite the many proposed factors influencing viral diversity, the genomic diversity and structure of viral communities in East Africa are largely unknown.

RESULTS

Using 38.3 Tb of metatranscriptomic data obtained via ultradeep sequencing, we screened vertebrate-associated viromes from 844 bats and 250 rodents from Kenya and Uganda collected from the wild. The 251 vertebrate-associated viral genomes of bats (212) and rodents (39) revealed the vast diversity, host-related variability, and high geographic specificity of viruses in East Africa. Among the surveyed viral families, Coronaviridae and Circoviridae showed low host specificity, high conservation of replication-associated proteins, high divergence among viral entry proteins, and frequent recombination. Despite major dispersal limitations, recurrent mutations, cocirculation, and occasional gene flow contribute to the high local diversity of viral genomes.

CONCLUSIONS

The present study not only shows the landscape of bat and rodent viromes in this zoonotic hotspot but also reveals genomic signatures driven by the evolution and dispersal of the viral community, laying solid groundwork for future proactive surveillance of emerging zoonotic pathogens in wildlife. Video Abstract.

Bat species assemblage predicts coronavirus prevalence

Anthropogenic disturbances and the subsequent loss of biodiversity are altering species abundances and communities. Since species vary in their pathogen competence, spatio-temporal changes in host assemblages may lead to changes in disease dynamics. We explore how longitudinal changes in bat species assemblages affect the disease dynamics of coronaviruses (CoVs) in more than 2300 cave-dwelling bats captured over two years from five caves in Ghana. This reveals uneven CoV infection patterns between closely related species, with the alpha-CoV 229E-like and SARS-related beta-CoV 2b emerging as multi-host pathogens. Prevalence and infection likelihood for both phylogenetically distinct CoVs is influenced by the abundance of competent species and naïve subadults. Broadly, bat species vary in CoV competence, and highly competent species are more common in less diverse communities, leading to increased CoV prevalence in less diverse bat assemblages. In line with the One Health framework, our work supports the notion that biodiversity conservation may be the most proactive measure to prevent the spread of pathogens with zoonotic potential.

The antiviral potential of the antiandrogen enzalutamide and the viral-androgen signaling interplay in seasonal coronaviruses

The sex disparity in COVID-19 outcomes with males generally faring worse than females has been associated with the androgen-regulated expression of the protease TMPRSS2 and the cell receptor ACE2 in the lung and fueled interest in antiandrogens as potential antivirals. In this study, we explored enzalutamide, an antiandrogen used commonly to treat prostate cancer, as a potential antiviral against the human coronaviruses which cause seasonal respiratory infections (HCoV-NL63, -229E, and -OC43). Using lentivirus-pseudotyped and authentic HCoV, we report that enzalutamide reduced 229E and NL63 entry and infection in both TMPRSS2- and nonexpressing immortalized cells, suggesting a TMPRSS2-independent mechanism. However, no effect was observed against OC43. To decipher this distinction, we performed RNA-sequencing analysis on 229E- and OC43-infected primary human airway cells. Our results show a significant induction of androgen-responsive genes by 229E compared to OC43 at 24 and 72 h postinfection. The virus-mediated effect on AR-signaling was further confirmed with a consensus androgen response element-driven luciferase assay in androgen-depleted MRC-5 cells. Specifically, 229E induced luciferase-reporter activity in the presence and absence of the synthetic androgen mibolerone, while OC43 inhibited induction. These findings highlight a complex interplay between viral infections and androgen-signaling, offering insights for disparities in viral outcomes and antiviral interventions.

Development of Rapid Isothermal Detection Methods Real-Time Fluorescence and Lateral Flow Reverse Transcription Recombinase-Aided Amplification Assay for Bovine Coronavirus

Bovine coronavirus (BCoV) is a notable pathogen affecting newly born calves and adult cattle, increasing mortality rates among calves and reducing productivity in meat and dairy industries, thereby causing substantial economic losses. Current primary laboratory methods for detecting BCoV include RT-PCR assay, real-time RT-PCR assay, and ELISA. However, these methods are time-consuming, require specialized technicians, and necessitate a laboratory environment. Consequently, there is an urgent need for a rapid, sensitive, and easy to use diagnostic method to detect BCoV. This study introduces two innovative protocols: the real-time fluorescent reverse transcription recombinase-aided amplification (RT-RAA) and the test strip RT-RAA (RT-RAA-LFD). Our results indicate that real-time RT-RAA can complete the reaction in 20 min at 39°C, while RT-RAA-LFD can achieve detection in just 17.5 min at 35°C. These new approaches offer higher specificity, with no cross-reactivity to other viruses, and significantly enhanced sensitivity compared to existing methods (1.46 × 101 and 1.46 × 102 copies/μL, respectively). We evaluated the performance of our methods using 242 clinical samples, and compared with RT-PCR and RT-qPCR. Both real-time RT-RAA and RT-qPCR yielded similar detection rates, the detection rate of RT-RAA-LFD was better than RT-PCR. The RT-RAA methods developed in this study effectively overcome the limitations associated with both RT-PCR and RT-qPCR by offering advantages including a single, low reaction temperature that allows for room temperature operation. Both methods boast shorter reaction times, simpler and more portable instrumentation, as well as reduced technical and environmental demands. Generally, both RT-RAA methods established in this study offer new avenues for the rapid detection of BCoV, contributing significantly to the monitoring, prevention, and control of the disease in global bovine industry.

The role of receptors in the cross-species spread of coronaviruses infecting humans and pigs

The pandemic caused by SARS-CoV-2, which has proven capable of infecting over 30 animal species, highlights the critical need for understanding the mechanisms of cross-species transmission and the emergence of novel coronavirus strains. The recent discovery of CCoV-HuPn-2018, a recombinant alphacoronavirus from canines and felines that can infect humans, along with evidence of SARS-CoV-2 infection in pig cells, underscores the potential for coronaviruses to overcome species barriers. This review investigates the origins and cross-species transmission of both human and porcine coronaviruses, with a specific emphasis on the instrumental role receptors play in this process.

Corona- and Paramyxoviruses in Bats from Brazil: A Matter of Concern?

Chiroptera are one of the most diverse mammal orders. They are considered reservoirs of main human pathogens, where coronaviruses (CoVs) and paramyxoviruses (PMVs) may be highlighted. Moreover, the growing number of publications on CoVs and PMVs in wildlife reinforces the scientific community's interest in eco-vigilance, especially because of the emergence of important human pathogens such as the SARS-CoV-2 and Nipha viruses. Considering that Brazil presents continental dimensions, is biologically rich containing one of the most diverse continental biotas and presents a rich biodiversity of animals classified in the order Chiroptera, the mapping of CoV and PMV genetics related to human pathogens is important and the aim of the present work. CoVs can be classified into four genera: Alphacoronavirus, Betacoronavirus, Deltacoronavirus and Gammacoronavirus. Delta- and gammacoronaviruses infect mainly birds, while alpha- and betacoronaviruses contain important animal and human pathogens. Almost 60% of alpha- and betacoronaviruses are related to bats, which are considered natural hosts of these viral genera members. The studies on CoV presence in bats from Brazil have mainly assayed phyllostomid, molossid and vespertilionid bats in the South, Southeast and North territories. Despite Brazil not hosting rhinophilid or pteropodid bats, which are natural reservoirs of SARS-related CoVs and henipaviruses, respectively, CoVs and PMVs reported in Brazilian bats are genetically closely related to some human pathogens. Most works performed with Brazilian bats reported alpha-CoVs that were closely related to other bat-CoVs, despite a few reports of beta-CoVs grouped in the Merbecovirus and Embecovirus subgenera. The family Paramyxoviridae includes four subfamilies (Avulavirinae, Metaparamyxovirinae, Orthoparamyxovirinae and Rubulavirinae), and bats are significant drivers of PMV cross-species viral transmission. Additionally, the studies that have evaluated PMV presence in Brazilian bats have mainly found sequences classified in the Jeilongvirus and Morbillivirus genera that belong to the Orthoparamyxovirinae subfamily. Despite the increasing amount of research on Brazilian bats, studies analyzing these samples are still scarce. When surveying the representativeness of the CoVs and PMVs found and the available genomic sequences, it can be perceived that there may be gaps in the knowledge. The continuous monitoring of viral sequences that are closely related to human pathogens may be helpful in mapping and predicting future hotspots in the emergence of zoonotic agents.

Unraveling the evolutionary patterns and phylogenomics of coronaviruses: A consensus network approach

The COVID-19 pandemic emphasizes the significance of studying coronaviruses (CoVs). This study investigates the evolutionary patterns of 350 CoVs using four structural proteins (S, E, M, and N) and introduces a consensus methodology to construct a comprehensive phylogenomic network. Our clustering of CoVs into 4 genera is consistent with the current CoV classification. Additionally, we calculate network centrality measures to identify CoV strains with significant average weighted degree and betweenness centrality values, with a specific focus on RaTG13 in the beta genus and NGA/A116E7/2006 in the gamma genus. We compare the phylogenetics of CoVs using our distance-based approach and the character-based model with IQ-TREE. Both methods yield largely consistent outcomes, indicating the reliability of our consensus approach. However, it is worth mentioning that our consensus method achieves an approximate 5000-fold increase in speed compared to IQ-TREE when analyzing the data set of 350 CoVs. This improved efficiency enhances the feasibility of conducting large-scale phylogenomic studies on CoVs.

Robust evidence for bats as reservoir hosts is lacking in most African virus studies: a review and call to optimize sampling and conserve bats

Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus-bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoir and/or bridging hosts for viruses that cause human disease. We present data from 162 papers (of 1322) with original findings on (1) numbers and species of bats sampled across bat families and the continent, (2) how bats were selected for study inclusion, (3) if bats were terminally sampled, (4) what types of ecological data, if any, were recorded and (5) which viruses were detected and with what methodology. We propose a scheme for evaluating presumed virus-host relationships by evidence type and quality, using the contrasting available evidence for Orthoebolavirus versus Orthomarburgvirus as an example. We review the wording in abstracts and discussions of all 162 papers, identifying key framing terms, how these refer to findings, and how they might contribute to people's beliefs about bats. We discuss the impact of scientific research communication on public perception and emphasize the need for strategies that minimize human-bat conflict and support bat conservation. Finally, we make recommendations for best practices that will improve virological study metadata.

Viral maintenance and excretion dynamics of coronaviruses within an Egyptian rousette fruit bat maternal colony: considerations for spillover

Novel coronavirus species of public health and veterinary importance have emerged in the first two decades of the twenty-first century, with bats identified as natural hosts for progenitors of many coronaviruses. Targeted wildlife surveillance is needed to identify the factors involved in viral perpetuation within natural host populations, and drivers of interspecies transmission. We monitored a natural colony of Egyptian rousette bats at monthly intervals across two years to identify circulating coronaviruses, and to investigate shedding dynamics and viral maintenance within the colony. Three distinct lineages were detected, with different seasonal temporal excretion dynamics. For two lineages, the highest periods of coronavirus shedding were at the start of the year, when large numbers of bats were found in the colony. Highest peaks for a third lineage were observed towards the middle of the year. Among individual bat-level factors (age, sex, reproductive status, and forearm mass index), only reproductive status showed significant effects on excretion probability, with reproductive adults having lower rates of detection, though factors were highly interdependent. Analysis of recaptured bats suggests that viral clearance may occur within one month. These findings may be implemented in the development of risk reduction strategies for potential zoonotic coronavirus transmission.

Co-Circulation of Multiple Coronavirus Genera and Subgenera during an Epizootic of Lethal Respiratory Disease in Newborn Alpacas (Vicugna pacos) in Peru: First Report of Bat-like Coronaviruses in Alpacas

Coronaviruses (CoVs) infect a wide range of hosts, including humans, domestic animals, and wildlife, typically causing mild-to-severe respiratory or enteric disease. The main objective of this study was to identify CoV genera and subgenera detected in Peruvian alpacas. Lung lavage specimens were collected from 32 animals aged 1 to 6 weeks. CoVs were identified by using RT-PCR to amplify a pan-CoV conserved region of the RNA-dependent RNA polymerase-encoding gene. A nested PCR was performed to identify β-CoVs. Then, β-CoV-positive samples were subjected to RT-PCR using specific primers to identify the Embecovirus subgenus. Out of 32 analyzed samples, 30 (93.8%) tested positive for at least one CoV genus. β-, α-, or unclassified CoVs were identified in 24 (80%), 1 (3.3%), and 1 (3.3%) of the positive samples, respectively. A CoV genus could not be identified in two (6.7%) samples. A mixture of different CoV genera was detected in two (6.7%) samples: one was co-infected with β- and α-CoVs, and the other contained a β- and an unclassified CoV. A sequence analysis of the amplicons generated by the PCR identified 17 β-CoV strains belonging to the subgenus Embecovirus and two α-CoV strains belonging to Decacovirus. A phylogenetic analysis of two strains revealed a relationship with an unclassified Megaderma BatCoV strain. A subgenus could not be identified in nine β-CoV samples. Our data show a high prevalence and a high genetic diversity of CoV genera and subgenera that infect alpacas, in which the β-CoV subgenus Embecovirus predominated. Our data also suggest a new role for bats in the dissemination and transmission of uncommon CoVs to alpacas raised in rural Peru.

Roost selection by synanthropic bats in rural Kenya: implications for human-wildlife conflict and zoonotic pathogen spillover

Many wildlife species are synanthropic and use structures built by humans, creating a high-risk interface for human-wildlife conflict and zoonotic pathogen spillover. However, studies that investigate features of urbanizing areas that attract or repel wildlife are currently lacking. We surveyed 85 buildings used by bats and 172 neighbouring buildings unused by bats (controls) in southeastern Kenya during 2021 and 2022 and evaluated the role of microclimate and structural attributes in building selection. We identified eight bat species using buildings, with over 25% of building roosts used concurrently by multiple species. Bats selected taller cement-walled buildings with higher water vapour pressure and lower presence of permanent human occupants. However, roost selection criteria differed across the most common bat species: molossids selected structures like those identified by our main dataset whereas Cardioderma cor selected buildings with lower presence of permanent human occupants. Our results show that roost selection of synanthropic bat species is based on specific buildings attributes. Further, selection criteria that facilitate bat use of buildings are not homogeneous across species. These results provide information on the general mechanisms of bat-human contact in rural settings, as well as specific information on roost selection for synanthropic bats in urbanizing Africa.

Epidemiology of porcine deltacoronavirus among Chinese pig populations in China: systematic review and meta-analysis

Porcine deltacoronavirus (PDCoV) is a newly emerging and important porcine enteropathogenic coronavirus that seriously threatens the swine industry in China and worldwide. We conducted a systematic review and meta-analysis to access the prevalence of PDCoV infection in pig population from mainland China. Electronic databases were reviewed for PDCoV infection in pig population, and meta-analysis was performed to calculate the overall estimated prevalence using random-effect models. Thirty-nine studies were included (including data from 31,015 pigs). The overall estimated prevalence of PDCoV infection in pigs in China was 12.2% [95% confidence interval (CI), 10.2-14.2%], and that in Central China was 24.5% (95%CI, 16.1-32.9%), which was higher than those in other regions. During 2014-2021, the estimated prevalence of PDCoV infection was the highest in 2015 at 20.5% (95%CI, 10.1-31.0%) and the lowest in 2021 at 4.8% (95%CI, 2.3-7.3%). The prevalence of PDCoV infection in sows was 23.6% (95%CI, 15.8-31.4%), which was higher than those in suckling piglets, nursery piglets, and finishing pigs. The prevalence of PDCoV infection was significantly associated with sampling region, sampling year, pig stage, and clinical signs (diarrhea). This study systematically evaluated the epidemiology of PDCoV infection in Chinese pig population. The findings provide us with a comprehensive understanding of PDCoV infection and are beneficial for establishing new controlling strategies worldwide.

Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine complete genomes, including two novel coronavirus species, across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk warrants closer surveillance.

The coronavirus recombination pathway

Recombination is thought to be a mechanism that facilitates cross-species transmission in coronaviruses, thus acting as a driver of coronavirus spillover and emergence. Despite its significance, the mechanism of recombination is poorly understood, limiting our potential to estimate the risk of novel recombinant coronaviruses emerging in the future. As a tool for understanding recombination, here, we outline a framework of the recombination pathway for coronaviruses. We review existing literature on coronavirus recombination, including comparisons of naturally observed recombinant genomes as well as in vitro experiments, and place the findings into the recombination pathway framework. We highlight gaps in our understanding of coronavirus recombination illustrated by the framework and outline how further experimental research is critical for disentangling the molecular mechanism of recombination from external environmental pressures. Finally, we describe how an increased understanding of the mechanism of recombination can inform pandemic predictive intelligence, with a retrospective emphasis on SARS-CoV-2.

Coronavirus sampling and surveillance in bats from 1996-2019: a systematic review and meta-analysis

The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses. We performed a systematic review of coronavirus sampling (testing for RNA positivity) in bats globally. We identified 110 studies published between 2005 and 2020 that collectively reported positivity from 89,752 bat samples. We compiled 2,274 records of infection prevalence at the finest methodological, spatiotemporal and phylogenetic level of detail possible from public records into an open, static database named datacov, together with metadata on sampling and diagnostic methods. We found substantial heterogeneity in viral prevalence across studies, reflecting spatiotemporal variation in viral dynamics and methodological differences. Meta-analysis identified sample type and sampling design as the best predictors of prevalence, with virus detection maximized in rectal and faecal samples and by repeat sampling of the same site. Fewer than one in five studies collected and reported longitudinal data, and euthanasia did not improve virus detection. We show that bat sampling before the SARS-CoV-2 pandemic was concentrated in China, with research gaps in South Asia, the Americas and sub-Saharan Africa, and in subfamilies of phyllostomid bats. We propose that surveillance strategies should address these gaps to improve global health security and enable the origins of zoonotic coronaviruses to be identified.

Unravelling Antigenic Cross-Reactions toward the World of Coronaviruses: Extent of the Stability of Shared Epitopes and SARS-CoV-2 Anti-Spike Cross-Neutralizing Antibodies

The human immune repertoire retains the molecular memory of a very great diversity of target antigens (epitopes) and can recall this upon a second encounter with epitopes against which it has previously been primed. Although genetically diverse, proteins of coronaviruses exhibit sufficient conservation to lead to antigenic cross-reactions. In this review, our goal is to question whether pre-existing immunity against seasonal human coronaviruses (HCoVs) or exposure to animal CoVs has influenced the susceptibility of human populations to SARS-CoV-2 and/or had an impact upon the physiopathological outcome of COVID-19. With the hindsight that we now have regarding COVID-19, we conclude that although antigenic cross-reactions between different coronaviruses exist, cross-reactive antibody levels (titers) do not necessarily reflect on memory B cell frequencies and are not always directed against epitopes which confer cross-protection against SARS-CoV-2. Moreover, the immunological memory of these infections is short-term and occurs in only a small percentage of the population. Thus, in contrast to what might be observed in terms of cross-protection at the level of a single individual recently exposed to circulating coronaviruses, a pre-existing immunity against HCoVs or other CoVs can only have a very minor impact on SARS-CoV-2 circulation at the level of human populations.

Molecular mechanisms of human coronavirus NL63 infection and replication

Human coronavirus NL63 (HCoV-NL63) is spread globally, causing upper and lower respiratory tract infections mainly in young children. HCoV-NL63 shares a host receptor (ACE2) with severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 but, unlike them, HCoV-NL63 primarily develops into self-limiting mild to moderate respiratory disease. Although with different efficiency, both HCoV-NL63 and SARS-like CoVs infect ciliated respiratory cells using ACE2 as receptor for binding and cell entry. Working with SARS-like CoVs require access to BSL-3 facilities, while HCoV-NL63 research can be performed at BSL-2 laboratories. Thus, HCoV-NL63 could be used as a safer surrogate for comparative studies on receptor dynamics, infectivity and virus replication, disease mechanism, and potential therapeutic interventions against SARS-like CoVs. This prompted us to review the current knowledge on the infection mechanism and replication of HCoV-NL63. Specifically, after a brief overview on the taxonomy, genomic organization and virus structure, this review compiles the current HCoV-NL63-related research in virus entry and replication mechanism, including virus attachment, endocytosis, genome translation, and replication and transcription. Furthermore, we reviewed cumulative knowledge on the susceptibility of different cells to HCoV-NL63 infection in vitro, which is essential for successful virus isolation and propagation, and contribute to address different scientific questions from basic science to the development and assessment of diagnostic tools, and antiviral therapies. Finally, we discussed different antiviral strategies that have been explored to suppress replication of HCoV-NL63, and other related human coronaviruses, by either targeting the virus or enhancing host antiviral mechanisms.

Evolution of increased positive charge on the SARS-CoV-2 spike protein may be adaptation to human transmission

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve and infect individuals. The exterior surface of the SARS-CoV-2 virion is dominated by the spike protein, and the current work examined spike protein biochemical features that have changed during the 3 years in which SARS-CoV-2 has infected humans. Our analysis identified a striking change in spike protein charge, from -8.3 in the original Lineage A and B viruses to -1.26 in most of the current Omicron viruses. We conclude that in addition to immune selection pressure, the evolution of SARS-CoV-2 has also altered viral spike protein biochemical properties, which may influence virion survival and promote transmission. Future vaccine and therapeutic development should also exploit and target these biochemical properties.

Evaluating the Virology and Evolution of Seasonal Human Coronaviruses Associated with the Common Cold in the COVID-19 Era

Approximately 15-30% of all cases of the common cold are due to human coronavirus infections. More recently, the emergence of the more severe respiratory coronaviruses, SARS-CoV and MERS-CoV, have highlighted the increased pathogenic potential of emergent coronaviruses. Lastly, the current emergence of SARS-CoV-2 has demonstrated not only the potential for significant disease caused by emerging coronaviruses, but also the capacity of novel coronaviruses to promote pandemic spread. Largely driven by the global response to the COVID-19 pandemic, significant research in coronavirus biology has led to advances in our understanding of these viruses. In this review, we evaluate the virology, emergence, and evolution of the four endemic coronaviruses associated with the common cold, their relationship to pandemic SARS-CoV-2, and discuss the potential for future emergent human coronaviruses.

Coronaviruses: Troubling Crown of the Animal Kingdom

The existence of coronaviruses has been known for many years. These viruses cause significant disease that primarily seems to affect agricultural species. Human coronavirus disease due to the 2002 outbreak of Severe Acute Respiratory Syndrome and the 2012 outbreak of Middle East Respiratory Syndrome made headlines; however, these outbreaks were controlled, and public concern quickly faded. This complacency ended in late 2019 when alarms were raised about a mysterious virus responsible for numerous illnesses and deaths in China. As we now know, this novel disease called Coronavirus Disease 2019 (COVID-19) was caused by Severe acute respiratory syndrome-related-coronavirus-2 (SARS-CoV-2) and rapidly became a worldwide pandemic. Luckily, decades of research into animal coronaviruses hastened our understanding of the genetics, structure, transmission, and pathogenesis of these viruses. Coronaviruses infect a wide range of wild and domestic animals, with significant economic impact in several agricultural species. Their large genome, low dependency on host cellular proteins, and frequent recombination allow coronaviruses to successfully cross species barriers and adapt to different hosts including humans. The study of the animal diseases provides an understanding of the virus biology and pathogenesis and has assisted in the rapid development of the SARS-CoV-2 vaccines. Here, we briefly review the classification, origin, etiology, transmission mechanisms, pathogenesis, clinical signs, diagnosis, treatment, and prevention strategies, including available vaccines, for coronaviruses that affect domestic, farm, laboratory, and wild animal species. We also briefly describe the coronaviruses that affect humans. Expanding our knowledge of this complex group of viruses will better prepare us to design strategies to prevent and/or minimize the impact of future coronavirus outbreaks.

Tilapia Lake Virus Vaccine Development: A Review on the Recent Advances

Tilapia tilapinevirus (or tilapia lake virus, TiLV) is a recently emerging virus associated with a novel disease affecting and decimating tilapia populations around the world. Since its initial identification, TiLV has been reported in 17 countries, often causing mortalities as high as 90% in the affected populations. To date, no therapeutics or commercial vaccines exist for TiLV disease control. Tilapia exposed to TiLV can develop protective immunity, suggesting that vaccination is achievable. Given the important role of vaccination in fish farming, several vaccine strategies are currently being explored and put forward against TiLV but, a comprehensive overview on the efficacy of these platforms is lacking. We here present these approaches in relation with previously developed fish vaccines and discuss their efficacy, vaccine administration routes, and the various factors that can impact vaccine efficacy. The overall recent advances in TiLV vaccine development show different but promising levels of protection. The field is however hampered by the lack of knowledge of the biology of TiLV, notably the function of its genes. Further research and the incorporation of several approaches including prime-boost vaccine regimens, codon optimization, or reverse vaccinology would be beneficial to increase the effectiveness of vaccines targeting TiLV and are further discussed in this review.

Breaking barriers: Scientific contributions in virology from women in low- and middle-income countries

The advancement of science has been a collective effort and benefits from a diversity of views and gender representation. However, support for and recognition of women in science is often insufficient. Despite historically being marginalized by the scientific community, research by women has advanced the field of virology, from the discovery of rotavirus and isolation of human immunodeficiency virus (HIV) to a vaccine for polio and the initial description of a virus’ ability to cause cancer. Although women in science, technology, engineering, and mathematics (STEM) fields are continuing to share their diverse wealth of knowledge and innovation, even today many are under-recognized and under-supported in low- and middle-income countries (LMICs). This review will highlight women in virology from LMICs in Africa, Asia, and Latin America where the barriers to scientific education and achievement for women can be far greater than in high income countries. Despite these barriers, the women we profile below have made important contributions to translational virology. We hope this review will contribute to the global expansion of efforts to provide improved access to and retention in scientific careers for women.

Evolutionary Origin, Genetic Recombination, and Phylogeography of Porcine Kobuvirus

The newly identified porcine Kobuvirus (PKV) has raised concerns owing to its association with diarrheal symptom in pigs worldwide. The process involving the emergence and global spread of PKV remains largely unknown. Here, the origin, genetic diversity, and geographic distribution of PKV were determined based on the available PKV sequence information. PKV might be derived from the rabbit Kobuvirus and sheep were an important intermediate host. The most recent ancestor of PKV could be traced back to 1975. Two major clades are identified, PKVa and PKVb, and recombination events increase PKV genetic diversity. Cross-species transmission of PKV might be linked to interspecies conserved amino acids at 13-17 and 25-40 residue motifs of Kobuvirus VP1 proteins. Phylogeographic analysis showed that Spain was the most likely location of PKV origin, which then spread to pig-rearing countries in Asia, Africa, and Europe. Within China, the Hubei province was identified as a primary hub of PKV, transmitting to the east, southwest, and northeast regions of the country. Taken together, our findings have important implications for understanding the evolutionary origin, genetic recombination, and geographic distribution of PKV thereby facilitating the design of preventive and containment measures to combat PKV infection.

Human Coronavirus Cell Receptors Provide Challenging Therapeutic Targets

Coronaviruses interact with protein or carbohydrate receptors through their spike proteins to infect cells. Even if the known protein receptors for these viruses have no evolutionary relationships, they do share ontological commonalities that the virus might leverage to exacerbate the pathophysiology. ANPEP/CD13, DPP IV/CD26, and ACE2 are the three protein receptors that are known to be exploited by several human coronaviruses. These receptors are moonlighting enzymes involved in several physiological processes such as digestion, metabolism, and blood pressure regulation; moreover, the three proteins are expressed in kidney, intestine, endothelium, and other tissues/cell types. Here, we spot the commonalities between the three enzymes, the physiological functions of the enzymes are outlined, and how blocking either enzyme results in systemic deregulations and multi-organ failures via viral infection or therapeutic interventions is addressed. It can be difficult to pinpoint any coronavirus as the target when creating a medication to fight them, due to the multiple processes that receptors are linked to and their extensive expression.

Evolving ribonucleocapsid assembly/packaging signals in the genomes of the human and animal coronaviruses: targeting, transmission and evolution

A world-wide COVID-19 pandemic intensified strongly the studies of molecular mechanisms related to the coronaviruses. The origin of coronaviruses and the risks of human-to-human, animal-to-human and human-to-animal transmission of coronaviral infections can be understood only on a broader evolutionary level by detailed comparative studies. In this paper, we studied ribonucleocapsid assembly-packaging signals (RNAPS) in the genomes of all seven known pathogenic human coronaviruses, SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-HKU1, HCoV-229E and HCoV-NL63 and compared them with RNAPS in the genomes of the related animal coronaviruses including SARS-Bat-CoV, MERS-Camel-CoV, MHV, Bat-CoV MOP1, TGEV and one of camel alphacoronaviruses. RNAPS in the genomes of coronaviruses were evolved due to weakly specific interactions between genomic RNA and N proteins in helical nucleocapsids. Combining transitional genome mapping and Jaccard correlation coefficients allows us to perform the analysis directly in terms of underlying motifs distributed over the genome. In all coronaviruses, RNAPS were distributed quasi-periodically over the genome with the period about 54 nt biased to 57 nt and to 51 nt for the genomes longer and shorter than that of SARS-CoV, respectively. The comparison with the experimentally verified packaging signals for MERS-CoV, MHV and TGEV proved that the distribution of particular motifs is strongly correlated with the packaging signals. We also found that many motifs were highly conserved in both characters and positioning on the genomes throughout the lineages that make them promising therapeutic targets. The mechanisms of encapsidation can affect the recombination and co-infection as well.Communicated by Ramaswamy H. Sarma.

A Glimpse on the Evolution of RNA Viruses: Implications and Lessons from SARS-CoV-2

RNA viruses are characterised by extremely high genetic variability due to fast replication, large population size, low fidelity, and (usually) a lack of proofreading mechanisms of RNA polymerases leading to high mutation rates. Furthermore, viral recombination and reassortment may act as a significant evolutionary force among viruses contributing to greater genetic diversity than obtainable by mutation alone. The above-mentioned properties allow for the rapid evolution of RNA viruses, which may result in difficulties in viral eradication, changes in virulence and pathogenicity, and lead to events such as cross-species transmissions, which are matters of great interest in the light of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemics. In this review, we aim to explore the molecular mechanisms of the variability of viral RNA genomes, emphasising the evolutionary trajectory of SARS-CoV-2 and its variants. Furthermore, the causes and consequences of coronavirus variation are explored, along with theories on the origin of human coronaviruses and features of emergent RNA viruses in general. Finally, we summarise the current knowledge on the circulating variants of concern and highlight the many unknowns regarding SARS-CoV-2 pathogenesis.

Comparative sequence analysis of SARS nCoV and SARS CoV genomes for variation in structural proteins

SARS-nCoV was identified as corona virus had spread worldwide very quickly and affected more than million people worldwide. To halt this acceleration and for efficient control the knowledge on genomic information is of utmost importance. We attempted to determine the nature of variation i.e., insertion, deletion, substitution, among structural sequences required to code for membrane, spike, nucleocapsid, envelope protein and glycosylation variation between SARS CoV and SARS nCoV spike glycoproteins, respectively. Comparative sequence analysis was performed by using retrieved sequences from the NCBI database. The analyzed sequences revealed, that the sequences coding for envelope protein show minor substituting amino acids. SARS CoV showed 94.74 percent amino acid identities with SARS nCoV amino acid sequences coding for envelope protein. In comparison to SARS nCoV, distinct amino acid residues vary in SARS CoV sequences coding for membrane, nucleocapsid, and spike proteins, respectively. S protein coding sequences of SARS CoV exhibited one deletion, six insertion and six hundred three substitutions in SARS nCoV sequence. Insertion of valine was found in receptor binding domain of SARS nCoV at position 487, and NSPR amino acid residues at position 683–686. Deletions and substitutions were also found in nucleotide sequences of strain B.1.617.2 of SARS nCoV. Additionally, binding interaction pattern of ACE2 receptor protein with original wild-type SARS-CoV-2 strain with the recently evolved Omicron variant was also evaluated. The docking results substantiated that the specific variation in binding residues is likely to impact virulence pattern of both variants.

Tracing the origin of Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): A systematic review and narrative synthesis

The aim of the study was to trace and understand the origin of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through various available literatures and accessible databases. Although the world enters the third year of the coronavirus disease 2019 pandemic, health and socioeconomic impacts continue to mount, the origin and mechanisms of spill-over of the SARS-CoV-2 into humans remain elusive. Therefore, a systematic review of the literature was performed that showcased the integrated information obtained through manual searches, digital databases (PubMed, CINAHL, and MEDLINE) searches, and searches from legitimate publications (1966-2022), followed by meta-analysis. Our systematic analysis data proposed three postulated hypotheses concerning the origin of the SARS-CoV-2, which include zoonotic origin (Z), laboratory origin (L), and obscure origin (O). Despite the fact that the zoonotic origin for SARS-CoV-2 has not been conclusively identified to date, our data suggest a zoonotic origin, in contrast to some alternative concepts, including the probability of a laboratory incident or leak. Our data exhibit that zoonotic origin (Z) has higher evidence-based support as compared to laboratory origin (L). Importantly, based on all the studies included, we generated the forest plot with 95% confidence intervals (CIs) of the risk ratio estimates. Our meta-analysis further supports the zoonotic origin of SARS/SARS-CoV-2 in the included studies.

Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats

Public health emergencies like SARS, MERS, and COVID-19 have prioritized surveillance of zoonotic coronaviruses, resulting in extensive genomic characterization of coronavirus diversity in bats. Sequencing viral genomes directly from animal specimens remains a laboratory challenge, however, and most bat coronaviruses have been characterized solely by PCR amplification of small regions from the best-conserved gene. This has resulted in limited phylogenetic resolution and left viral genetic factors relevant to threat assessment undescribed. In this study, we evaluated whether a technique called hybridization probe capture can achieve more extensive genome recovery from surveillance specimens. Using a custom panel of 20,000 probes, we captured and sequenced coronavirus genomic material in 21 swab specimens collected from bats in the Democratic Republic of the Congo. For 15 of these specimens, probe capture recovered more genome sequence than had been previously generated with standard amplicon sequencing protocols, providing a median 6.1-fold improvement (ranging up to 69.1-fold). Probe capture data also identified five novel alpha- and betacoronaviruses in these specimens, and their full genomes were recovered with additional deep sequencing. Based on these experiences, we discuss how probe capture could be effectively operationalized alongside other sequencing technologies for high-throughput, genomics-based discovery and surveillance of bat coronaviruses.

Extensive Recombination-driven Coronavirus Diversification Expands the Pool of Potential Pandemic Pathogens

The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last 20 years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare the dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) that bundles nucleotide identity, recombination, and phylogenetic analysis into a single pipeline. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from undersampled or unsampled lineages, including in typically highly conserved regions of the genome. In several cases, no parental origin of recombinant regions could be found in genetic databases, demonstrating our shallow characterization of coronavirus diversity and expanding the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.

Molecular evolution of human coronavirus-NL63, -229E, -HKU1 and -OC43 in hospitalized children in China

Human coronaviruses (HCoVs) HCoV-NL63, HCoV-229E, HCoV-HKU1 and HCoV-OC43 have been circulated in the human population worldwide, and they are associated with a broad range of respiratory diseases with varying severity. However, there are neither effective therapeutic drugs nor licensed vaccines available for the treatment and prevention of infections by the four HCoVs. In this study, we collected nasopharyngeal aspirates of children hospitalized for respiratory tract infection in China during 2014-2018 and conducted next-generation sequencing. Sequences of four HCoVs were then selected for an in-depth analysis. Genome sequences of 2 HCoV-NL63, 8 HCoV-229E, 2 HCoV-HKU1, and 6 HCoV-OC43 were obtained. Based on the full-length S gene, a strong temporal signal was found in HCoV-229E and the molecular evolutionary rate was 6 × 10^-4 substitutions/site/year. Based on the maximum-likelihood (ML) phylogenetic tree of complete S gene, we designated H78 as a new sub-genotype C2 of HCoV-HKU1, and the obtained P43 sequence was grouped into the reported novel genotype K of HCoV-OC43 circulating in Guangzhou, China. Based on the complete genome, potential recombination events were found to occur as two phenomena, namely intraspecies and interspecies. Moreover, we observed two amino acid substitutions in the S1 subunit of obtained HCoV-NL63 (G534V) and HCoV-HKU1 (H512R), while residues 534 and 512 are important for the binding of angiotensin-converting enzyme 2 and neutralizing antibodies, respectively. Our findings might provide a clue for the molecular evolution of the four HCoVs and help in the early diagnosis, treatment and prevention of broad-spectrum HCoV infection.

Distinct Molecular Mechanisms Characterizing Pathogenesis of SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has continued for over 2 years, following the outbreak of coronavirus-19 (COVID-19) in 2019. It has resulted in enormous casualties and severe economic crises. The rapid development of vaccines and therapeutics against SARS-CoV-2 has helped slow the spread. In the meantime, various mutations in the SARS-CoV-2 have emerged to evade current vaccines and therapeutics. A better understanding of SARS-CoV-2 pathogenesis is a prerequisite for developing efficient, advanced vaccines and therapeutics. Since the outbreak of COVID-19, a tremendous amount of research has been conducted to unveil SARSCoV-2 pathogenesis, from clinical observations to biochemical analysis at the molecular level upon viral infection. In this review, we discuss the molecular mechanisms of SARS-CoV-2 propagation and pathogenesis, with an update on recent advances.

Detection of coronavirus in vampire bats (Desmodus rotundus) in southern Brazil

The vampire bat (Desmodus rotundus) is a haematophagous animal that feeds exclusively on the blood of domestic mammals. Vampire bat feeding habits enable their contact with mammalian hosts and may enhance zoonotic spillover. Moreover, they may carry several pathogenic organisms, including coronaviruses (CoVs), for which they are important hosts. The human pathogens that cause severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV) and possibly coronavirus disease 2019 (SARS-CoV-2) all originated in bats but required bridge hosts to spread into human populations. To monitor the presence of potential zoonotic viruses in bats, the present work evaluated the presence of CoVs in vampire bats from southern Brazil. A total of 101 vampire bats were captured and euthanized between 2017 and 2019 in Rio Grande do Sul state, southern Brazil. The brain, heart, liver, lungs, kidneys and intestines were collected and macerated individually. The samples were pooled and submitted to high-throughput sequencing (HTS) using the Illumina MiSeq platform and subsequently individually screened using a pancoronavirus RT-PCR protocol. We detected CoV-related sequences in HTS, but only two (2/101; 1.98%) animals had CoV detected in the intestines by RT-PCR. Partial sequences of RdRp and spike genes were obtained in the same sample and the RdRp region in the other sample. The sequences were classified as belonging to Alphacoronavirus. The sequences were closely related to alphacoronaviruses detected in vampire bats from Peru. The continuous monitoring of bat CoVs may help to map and predict putative future zoonotic agents with great impacts on human health.

Detection of coronavirus in vampire bats (Desmodus rotundus) in southern Brazil

The vampire bat (Desmodus rotundus) is a haematophagous animal that feeds exclusively on the blood of domestic mammals. Vampire bat feeding habits enable their contact with mammalian hosts and may enhance zoonotic spillover. Moreover, they may carry several pathogenic organisms, including coronaviruses (CoVs), for which they are important hosts. The human pathogens that cause severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV) and possibly coronavirus disease 2019 (SARS-CoV-2) all originated in bats but required bridge hosts to spread into human populations. To monitor the presence of potential zoonotic viruses in bats, the present work evaluated the presence of CoVs in vampire bats from southern Brazil. A total of 101 vampire bats were captured and euthanized between 2017 and 2019 in Rio Grande do Sul state, southern Brazil. The brain, heart, liver, lungs, kidneys and intestines were collected and macerated individually. The samples were pooled and submitted to high-throughput sequencing (HTS) using the Illumina MiSeq platform and subsequently individually screened using a pancoronavirus RT-PCR protocol. We detected CoV-related sequences in HTS, but only two (2/101; 1.98%) animals had CoV detected in the intestines by RT-PCR. Partial sequences of RdRp and spike genes were obtained in the same sample and the RdRp region in the other sample. The sequences were classified as belonging to Alphacoronavirus. The sequences were closely related to alphacoronaviruses detected in vampire bats from Peru. The continuous monitoring of bat CoVs may help to map and predict putative future zoonotic agents with great impacts on human health.

Emerging viruses: Cross-species transmission of coronaviruses, filoviruses, henipaviruses, and rotaviruses from bats

Emerging infectious diseases, especially if caused by bat-borne viruses, significantly affect public health and the global economy. There is an urgent need to understand the mechanism of interspecies transmission, particularly to humans. Viral genetics; host factors, including polymorphisms in the receptors; and ecological, environmental, and population dynamics are major parameters to consider. Here, we describe the taxonomy, geographic distribution, and unique traits of bats associated with their importance as virus reservoirs. Then, we summarize the origin, intermediate hosts, and the current understanding of interspecies transmission of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Nipah, Hendra, Ebola, Marburg virus, and rotaviruses. Finally, the molecular interactions of viral surface proteins with host cell receptors are examined, and a comparison of these interactions in humans, intermediate hosts, and bats is conducted. This uncovers adaptive mutations in virus spike protein that facilitate cross-species transmission and risk factors associated with the emergence of novel viruses from bats.

The spike glycoprotein of SARS-CoV-2: A review of how mutations of spike glycoproteins have driven the emergence of variants with high transmissibility and immune escape

Late in 2019, SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) emerged, causing an unknown type of pneumonia today called coronaviruses disease 2019 (COVID-19). COVID-19 is still an ongoing global outbreak that has claimed and threatened many lives worldwide. Along with the fastest vaccine developed in history to fight SARS-CoV-2 came a critical problem, SARS-CoV-2. These new variants are a result of the accumulation of mutations in the sequence and structure of spike (S) glycoprotein, which is by far the most critical protein for SARS-CoV-2 to recognize cells and escape the immune system, in addition to playing a role in SARS-CoV-2 infection, pathogenicity, transmission, and evolution. In this review, we discuss mutation of S protein and how these mutations have led to new variants that are usually more transmissible and can thus mitigate the immunity produced by vaccination. Here, analysis of S protein sequences and structures from variants point out the mutations among them, how they emerge, and the behavior of S protein from each variant. This review brings details in an understandable way about how the variants of SARS-CoV-2 are a result of mutations in S protein, making them more transmissible and even more aggressive than their relatives.

Characterization of Deltacoronavirus in Black-Headed Gulls (Chroicocephalus ridibundus) in South China Indicating Frequent Interspecies Transmission of the Virus in Birds

Deltacoronavirus (DCoV) is a genus of coronavirus (CoV) commonly found in avian and swine, but some DCoVs are capable of infecting humans, which causes the concern about interspecies transmission of DCoVs. Thus, monitoring the existence of DCoVs in animals near communities is of great importance for epidemic prevention. Black-headed gulls (Chroicocephalus ridibundus) are common migratory birds inhabiting in most urban and rural wetlands of Yunnan Province, China, which is a typical habitat for black-headed gulls to overwinter. Whether Yunnan black-headed gulls carry CoV has never been determined. In this study, we identified three strains of DCoVs in fecal samples of Yunnan black-headed gulls by reverse-transcriptional PCR and sequenced their whole genomes. Genomic analysis revealed that these three strains shared genomic identity of more than 99%, thus named DCoV HNU4-1, HNU4-2, and HNU4-3; their NSP12 showed high similarity of amino acid sequence to the homologs of falcon coronavirus UAE-HKU27 (HKU27), houbara coronavirus UAE-HKU28 (HKU28), and pigeon coronavirus UAE-HKU29 (HKU29). Since both HKU28 and HKU29 were found in Dubai, there might be cross-border transmission of these avian DCoVs through specific routes. Further coevolutionary analysis supported this speculation that HNU4 (or its ancestors) in black-headed gulls originated from HKU28 (or its homologous strain) in houbara, which was interspecies transmission between two different avian orders. In addition, interspecies transmission of DCoV, from houbara to falcon, pigeon and white-eye, from sparrow to common-magpie, and quail and mammal including porcine and Asian leopard cat, from munia to magpie-robin, was predicted. This is the first report of black-headed gull DCoV in Asia which was highly homolog to other avian DCoVs, and the very “active” host-switching events in DCoV were predicted, which provides important reference for the study of spread and transmission of DCoVs.

Ecology, evolution and spillover of coronaviruses from bats

In the past two decades, three coronaviruses with ancestral origins in bats have emerged and caused widespread outbreaks in humans, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the first SARS epidemic in 2002-2003, the appreciation of bats as key hosts of zoonotic coronaviruses has advanced rapidly. More than 4,000 coronavirus sequences from 14 bat families have been identified, yet the true diversity of bat coronaviruses is probably much greater. Given that bats are the likely evolutionary source for several human coronaviruses, including strains that cause mild upper respiratory tract disease, their role in historic and future pandemics requires ongoing investigation. We review and integrate information on bat-coronavirus interactions at the molecular, tissue, host and population levels. We identify critical gaps in knowledge of bat coronaviruses, which relate to spillover and pandemic risk, including the pathways to zoonotic spillover, the infection dynamics within bat reservoir hosts, the role of prior adaptation in intermediate hosts for zoonotic transmission and the viral genotypes or traits that predict zoonotic capacity and pandemic potential. Filling these knowledge gaps may help prevent the next pandemic.

Human Alphacoronavirus Universal Primers for Genome Amplification and Sequencing

Rapid and accurate sequencing covering the entire genome is essential to identify genetic variations of viral pathogens. However, due to the low viral titers in clinical samples, certain amplification steps are required for viral genome sequencing. At present, there are no universal primers available for alphacoronaviruses and that, since these viruses have diverse strains, new primers specific to the target strain must be continuously developed for sequencing. Thus, in this study, we aimed to develop a universal primer set valid for all human alphacoronaviruses and applicable to samples containing trace amounts of the virus. To this aim, we designed overlapping primer pairs capable of amplifying the entire genome of all known human alphacoronaviruses. The selected primers, named the AC primer set, were composed of 10 primer pairs stretching over the entire genome of alphacoronaviruses, and produced PCR products of the expected size (3-5 kb) from both the HCoV-229E and HCoV-NL63 strains. After genome amplification, an evaluation using various sequencing platforms was carried out. The amplicon library sequencing data were assembled into complete genome sequences in all sequencing strategies examined in this study. The sequencing accuracy varied depending on the sequencing technology, but all sequencing methods showed a sequencing error of less than 0.01%. In the mock clinical specimen, the detection limit was 10^-3 PFU/ml (10² copies/ml). The AC primer set and experimental procedure optimized in this study may enable the fast diagnosis of mutant alphacoronaviruses in future epidemics.