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A novel jeilongvirus was identified through next-generation sequencing in cell cultures inoculated with spleen and kidney extracts. The spleen and kidney were obtained from a Peromyscus gossypinus rodent (cotton mouse) found dead in the city of Gainesville, in North-Central Florida, USA. Jeilongviruses are paramyxoviruses of the subfamily Orthoparamyxovirinae that have been found in bats, cats, and rodents. We designated the virus we discovered as Gainesville rodent jeilong virus 1 (GRJV1). Preliminary results indicate that GRJV1 can complete its life cycle in various human, non-human primate, and rodent cell lines, suggesting that the virus has a generalist nature with the potential for a spillover event. The early detection of endemic viruses circulating within hosts in North-Central Florida can significantly enhance surveillance efforts, thereby bolstering our ability to monitor and respond to potential outbreaks effectively. [ABSTRACT FROM AUTHOR]

ABSTRACT Bats are natural hosts of multiple viruses, many of which have clear zoonotic potential. The search for emerging viruses has been aided by the implementation of metagenomic tools, which have also enabled the detection of unprecedented viral diversity. Currently, this search is mainly focused on RNA viruses, which are largely over-represented in databases. To compensate for this research bias, we analyzed fecal samples from 189 Spanish bats belonging to 22 different species using viral metagenomics. This allowed us to identify 52 complete or near-complete viral genomes belonging to the families Adenoviridae, Circoviridae, Genomoviridae, Papillomaviridae, Parvoviridae, Polyomaviridae and Smacoviridae. Of these, 30 could constitute new species, doubling the number of viruses currently described in Europe. These findings open the door to a more thorough analysis of bat DNA viruses and their zoonotic potential.IMPORTANCEMetagenomics has become a fundamental tool to characterize the global virosphere, allowing us not only to understand the existing viral diversity and its ecological implications but also to identify new and emerging viruses. RNA viruses have a higher zoonotic potential, but this risk is also present for some DNA virus families. In our study, we analyzed the DNA fraction of fecal samples from 22 Spanish bat species, identifying 52 complete or near-complete genomes of different viral families with zoonotic potential. This doubles the number of genomes currently described in Europe. Metagenomic data often produce partial genomes that can be difficult to analyze. Our work, however, has characterized a large number of complete genomes, thus facilitating their taxonomic classification and enabling different analyses to be carried out to evaluate their zoonotic potential. For example, recombination studies are relevant since this phenomenon could play a major role in cross-species transmission.

Introduction: SARS-CoV-2 isolates of a given clade may contain low frequency genomes that encode amino acids or deletions which are typical of a different clade. Methods: Here we use high resolution ultra-deep sequencing to analyze SARSCoV-2 mutant spectra. Results: In 6 out of 11 SARS-CoV-2 isolates from COVID-19 patients, the mutant spectrum of the spike (S)-coding region included two or more amino acids or deletions, that correspond to discordant viral clades. A similar observation is reported for laboratory populations of SARS-CoV-2 USA-WA1/2020, following a cell culture infection in the presence of remdesivir, ribavirin or their combinations. Moreover, some of the clade-discordant genome residues are found in the same haplotype within an amplicon. Discussion: We evaluate possible interpretations of these findings, and reviewed precedents for rapid selection of genomes with multiple mutations in RNA viruses. These considerations suggest that intra-host evolution may be sufficient to generate minority sequences which are closely related to sequences typical of other clades. The results provide a model for the origin of variants of concern during epidemic spread-in particular Omicron lineages-that does not require prolonged infection, involvement of immunocompromised individuals, or participation of intermediate, non-human hosts. [ABSTRACT FROM AUTHOR]

A novel jeilongvirus was identified through next-generation sequencing in cell cultures inoculated with spleen and kidney extracts. The spleen and kidney were obtained from a Peromyscus gossypinus rodent (cotton mouse) found dead in the city of Gainesville, in North-Central Florida, USA. Jeilongviruses are paramyxoviruses of the subfamily Orthoparamyxovirinae that have been found in bats, cats, and rodents. We designated the virus we discovered as Gainesville rodent jeilong virus 1 (GRJV1). Preliminary results indicate that GRJV1 can complete its life cycle in various human, non-human primate, and rodent cell lines, suggesting that the virus has a generalist nature with the potential for a spillover event. The early detection of endemic viruses circulating within hosts in North-Central Florida can significantly enhance surveillance efforts, thereby bolstering our ability to monitor and respond to potential outbreaks effectively.

IntroductionSARS-CoV-2 isolates of a given clade may contain low frequency genomes that encode amino acids or deletions which are typical of a different clade.MethodsHere we use high resolution ultra-deep sequencing to analyze SARS-CoV-2 mutant spectra.ResultsIn 6 out of 11 SARS-CoV-2 isolates from COVID-19 patients, the mutant spectrum of the spike (S)-coding region included two or more amino acids or deletions, that correspond to discordant viral clades. A similar observation is reported for laboratory populations of SARS-CoV-2 USA-WA1/2020, following a cell culture infection in the presence of remdesivir, ribavirin or their combinations. Moreover, some of the clade-discordant genome residues are found in the same haplotype within an amplicon.DiscussionWe evaluate possible interpretations of these findings, and reviewed precedents for rapid selection of genomes with multiple mutations in RNA viruses. These considerations suggest that intra-host evolution may be sufficient to generate minority sequences which are closely related to sequences typical of other clades. The results provide a model for the origin of variants of concern during epidemic spread─in particular Omicron lineages─that does not require prolonged infection, involvement of immunocompromised individuals, or participation of intermediate, non-human hosts.

The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling. [Display omitted] • Common ancestor of SARS-CoV-2 linked to Huanan market matches the global common ancestor • Wildlife mitochondrial DNA identified in samples from stalls positive for SARS-CoV-2 • DNA from raccoon dogs, civets, and other wildlife species detected in market samples • Genotypes of potential hosts were reconstructed for retracing animal geographic origins DNA of mammalian wildlife species susceptible to SARS-CoV-2 was detected along with SARS-CoV-2 and other viruses in environmental samples from animal stalls located at the market epicenter of the emergence of COVID-19. [ABSTRACT FROM AUTHOR]

Bats are natural hosts of multiple viruses, many of which have clear zoonotic potential. The search for emerging viruses has been aided by the implementation of metagenomic tools, which have also enabled the detection of unprecedented viral diversity. Currently, this search is mainly focused on RNA viruses, which are largely over-represented in databases. To compensate for this research bias, we analyzed fecal samples from 189 Spanish bats belonging to 22 different species using viral metagenomics. This allowed us to identify 52 complete or near-complete viral genomes belonging to the families Adenoviridae , Circoviridae , Genomoviridae , Papillomaviridae , Parvoviridae, Polyomaviridae and Smacoviridae . Of these, 30 could constitute new species, doubling the number of viruses currently described in Europe. These findings open the door to a more thorough analysis of bat DNA viruses and their zoonotic potential., Importance: Metagenomics has become a fundamental tool to characterize the global virosphere, allowing us not only to understand the existing viral diversity and its ecological implications but also to identify new and emerging viruses. RNA viruses have a higher zoonotic potential, but this risk is also present for some DNA virus families. In our study, we analyzed the DNA fraction of fecal samples from 22 Spanish bat species, identifying 52 complete or near-complete genomes of different viral families with zoonotic potential. This doubles the number of genomes currently described in Europe. Metagenomic data often produce partial genomes that can be difficult to analyze. Our work, however, has characterized a large number of complete genomes, thus facilitating their taxonomic classification and enabling different analyses to be carried out to evaluate their zoonotic potential. For example, recombination studies are relevant since this phenomenon could play a major role in cross-species transmission., Competing Interests: The authors declare no conflict of interest.

Keywords: Congenital Zika Syndrome; epidemic; teratogenesis; animal models; viral emergence; birth defects EN Congenital Zika Syndrome epidemic teratogenesis animal models viral emergence birth defects 1 5 5 07/27/21 20210723 NES 210723 Introduction In 2015, an outbreak of Zika virus (ZIKV) infection caused a disproportionate increase in the number of cases of microcephaly in Brazil ([9]). Although two major ZIKV lineages referred to as African lineage (ZIKV SP AF sp ) and Asian lineage (ZIKV SP AS sp ) have been identified, phylogenetic and genomic analyses pointed to those cases as caused by a ZIKV SP AS sp ([11]). In 2016, the Northeast, Southeast, and Central-West regions were severely hit by the ZIKV epidemic accounting for 93.5% of the nationwide reported cases (16.11, 42.98 and 15.8%, respectively), whereas in Southern Brazil, only few cases of ZIKV infection (< 0.5%) had been reported ([30]; [5]; [24]) (Figure 1). In Brazil, ZIKV disease displayed uneven epidemiological outcomes across the regions B ( b [30]; [5]) (Figure 1), thus the epidemic potential of ZIKV to cause disease in humans and new outbreaks cannot be discarded. [Extracted from the article]

Porcine reproductive and respiratory syndrome (PRRS) is an economically devastating disease of swine in many parts of the world. Porcine reproductive and respiratory syndrome virus (PRRSV) type 1 is endemic in Europe, and prevalence of the subtypes differ spatially. In this study, we investigated a severe PRRS outbreak reported in 30 farms located in eastern Russia that belong to a large swine production company in the region that was also experiencing a pseudorabies outbreak in the system. Data included 28 ORF5 sequences from samples across 18 of the 25 infected sites, reverse transcriptase real-time polymerase chain reaction (RT-qPCR) results from diagnostic testing, reports of clinical signs, and animal movement records. We observed that the outbreak was due to two distinct variants of wildtype PRRSV type 1 subtype 1 with an average genetic distance of 15%. Results suggest that the wildtype PRRSV variants were introduced into the region around 2019, before affecting this production system (i.e., sow farms, nurseries, and finisher farms). Clinical signs did not differ between the variants, but they did differ by stage of pig production. Biosecurity lapses, including movement of animals from infected farms contributed to disease spread.

From the first detection in the Eastern oysters (Crassostrea virginica) in 1972, herpes‐like viruses/herpesviruses have been identified in at least 20 bivalve species and have caused massive mortalities in six cultured species of bivalves. Among them, the Pacific oyster (Crassostrea gigas) is most threatened by massive mortalities associated with detection of Ostreid herpesvirus 1 (OsHV‐1) and its variants. These mortality events have been reported in more than 12 countries, and OsHV‐1 itself has been reported in 15 countries worldwide. Traditionally, the genotype OsHV‐1 (or OsHV‐1 Var) is the main contributor to bivalve mortalities, but the emergence of variants (e.g. OsHV‐1 μVar and related ones, acute viral necrosis virus—AVNV, OsHV‐1‐SB) is now responsible for new mortality outbreaks in Pacific oysters and other bivalve species. In addition to OsHV‐1, Vibrio bacteria and other abiotic and host factors also significantly contribute to mortality outbreaks. To this end, the current contribution aims to synthesize the body of literature on our current knowledge of these mass mortality events to provide insights into the role of each risk factor and complex interactions in the disease process. Specifically, this review encompasses our current knowledge and critical gaps. Important suggestions for future investigation are also presented. [ABSTRACT FROM AUTHOR]

Viral hemorrhagic septicemia virus (VHSV), a rhabdovirus infecting teleost fish, has repeatedly crossed the boundary from marine fish species to freshwater cultured rainbow trout. These naturally replicated cross-species transmission events permit the study of general and repeatable evolutionary events occurring in connection with viral emergence in a novel host species. The purpose of the present study was to investigate the adaptive molecular evolution of the VHSV glycoprotein, one of the key virus proteins involved in viral emergence, following emergence from marine species into freshwater cultured rainbow trout. A comprehensive phylogenetic reconstruction of the complete coding region of the VHSV glycoprotein was conducted, and adaptive molecular evolution was investigated using a maximum likelihood approach to compare different codon substitution models allowing for heterogeneous substitution rate ratios among amino acid sites. Evidence of positive selection was detected at six amino acid sites of the VHSV glycoprotein, within the signal peptide, the confirmation-dependent major neutralizing epitope, and the intracellular tail. Evidence of positive selection was found exclusively in rainbow trout-adapted virus isolates, and amino acid combinations found at the six sites under positive selection pressure differentiated rainbow trout- from non-rainbow trout-adapted isolates. Furthermore, four adaptive sites revealed signs of recurring identical changes across phylogenetic groups of rainbow trout-adapted isolates, suggesting that repeated VHSV emergence in freshwater cultured rainbow trout was established through convergent routes of evolution that are associated with immune escape. IMPORTANCE This study is the first to demonstrate that VHSV emergence from marine species into freshwater cultured rainbow trout has been accompanied by bursts of adaptive evolution in the VHSV glycoprotein. Furthermore, repeated detection of the same adaptive amino acid sites across phylogenetic groups of rainbow troutadapted isolates indicates that adaptation to rainbow trout was established through parallel evolution. In addition, signals of convergent evolution toward the maintenance of genetic variation were detected in the conformation-dependent neutralizing epitope or in close proximity to disulfide bonds involved in the structural conformation of the neutralizing epitope, indicating adaptation to immune response-related genetic variation across freshwater cultured rainbow trout. [ABSTRACT FROM AUTHOR]

Bats are recognized reservoirs for many emerging zoonotic viruses of public health importance. Identifying and cataloguing the viruses of bats is a logical approach to evaluate the range of potential zoonoses of bat origin. We characterized the fecal pathogen microbiome of both insectivorous and frugivorous bats, incorporating 281 individual bats comprising 20 common species, which were sampled in three locations of Yunnan province, by combining reverse transcription polymerase chain reaction (RT-PCR) assays and next-generation sequencing. Seven individual bats were paramyxovirus-positive by RT-PCR using degenerate primers, and these paramyxoviruses were mainly classified into three genera (Rubulavirus, Henipavirus and Jeilongvirus). Various additional novel pathogens were detected in the paramyxovirus-positive bats using Illumina sequencing. A total of 7066 assembled contigs (≥200 bp) were constructed, and 105 contigs matched eukaryotic viruses (of them 103 belong to 2 vertebrate virus families, 1 insect virus, and 1 mycovirus), 17 were parasites, and 4913 were homologous to prokaryotic microorganisms. Among the 103 vertebrate viral contigs, 79 displayed low identity (

Zika virus (ZIKV) is currently one of the most important emerging viruses in the world. Recently, it has caused outbreaks and epidemics, and has been associated with severe clinical manifestations and congenital malformations. However to date, little is known about the pathogenicity of the virus and the consequences of ZIKV infection. In this paper, we provide an overview of the current knowledge on ZIKV. [ABSTRACT FROM AUTHOR]

The mechanisms of viral RNA genome segmentation are unknown. On extensive passage of foot-and-mouth disease virus in baby hamster kidney-21 cells, the virus accumulated multiple point mutations and underwent a transition akin to genome segmentation. The standard single RNA genome molecule was replaced by genomes harboring internal in-frame deletions affecting the L- or capsid-coding region. These genomes were infectious and killed cells by complementation. Here we show that the point mutations in the nonstructural protein-coding region (P2, P3) that accumulated in the standard genome before segmentation increased the relative fitness of the segmented version relative to the standard genome. Fitness increase was documented by intracellular expression of virus-coded proteins and infectious progeny production by RNAs with the internal deletions placed in the sequence context of the parental and evolved genome. The complementation activity involved several viral proteins, one of them being the leader proteinase L. Thus, a history of genetic drift with accumulation of point mutations was needed to allow a major variation in the structure of a viral genome. Thus, exploration of sequence space by a viral genome (in this case an unsegmented RNA) can reach a point of the space in which a totally different genome structure (in this case, a segmented RNA) is favored over the form that performed the exploration. [ABSTRACT FROM AUTHOR]

The transmission of viruses between different host species is a major source of emerging diseases and is of particular concern in the case of zoonotic transmission from mammals to humans. Several zoonosis risk factors have been identified, but it is currently unclear which viral traits primarily determine this process as previous work has focused on a few hundred viruses that are not representative of actual viral diversity. Here, we investigate fundamental virological traits that influence cross-species transmissibility and zoonotic propensity by interrogating a database of over 12,000 mammalian virus-host associations. Our analysis reveals that enveloped viruses tend to infect more host species and are more likely to be zoonotic than nonenveloped viruses, while other viral traits such as genome composition, structure, size, or the viral replication compartment play a less obvious role. This contrasts with the previous notion that viral envelopes did not significantly impact or even reduce zoonotic risk and should help better prioritize outbreak prevention efforts. We suggest several mechanisms by which viral envelopes could promote cross-species transmissibility, including structural flexibility of receptor-binding proteins and evasion of viral entry barriers.

Abstract: Viral emergence as a result of zoonotic transmission constitutes a continuous public health threat. Emerging viruses such as SARS coronavirus, hantaviruses and henipaviruses have wildlife reservoirs. Characterising the viruses of candidate reservoir species in geographical hot spots for viral emergence is a sensible approach to develop tools to predict, prevent, or contain emergence events. Here, we explore the viruses of Eidolon helvum, an Old World fruit bat species widely distributed in Africa that lives in close proximity to humans. We identified a great abundance and diversity of novel herpes and papillomaviruses, described the isolation of a novel adenovirus, and detected, for the first time, sequences of a chiropteran poxvirus closely related with Molluscum contagiosum. In sum, E. helvum display a wide variety of mammalian viruses, some of them genetically similar to known human pathogens, highlighting the possibility of zoonotic transmission. [Copyright &y& Elsevier]

Porcine reproductive and respiratory syndrome (PRRS) is an economically devastating disease of swine in many parts of the world. Porcine reproductive and respiratory syndrome virus (PRRSV) type 1 is endemic in Europe, and prevalence of the subtypes differ spatially. In this study, we investigated a severe PRRS outbreak reported in 30 farms located in eastern Russia that belong to a large swine production company in the region that was also experiencing a pseudorabies outbreak in the system. Data included 28 ORF5 sequences from samples across 18 of the 25 infected sites, reverse transcriptase real-time polymerase chain reaction (RT-qPCR) results from diagnostic testing, reports of clinical signs, and animal movement records. We observed that the outbreak was due to two distinct variants of wildtype PRRSV type 1 subtype 1 with an average genetic distance of 15%. Results suggest that the wildtype PRRSV variants were introduced into the region around 2019, before affecting this production system (i.e., sow farms, nurseries, and finisher farms). Clinical signs did not differ between the variants, but they did differ by stage of pig production. Biosecurity lapses, including movement of animals from infected farms contributed to disease spread. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant's respective emergence period, finding that Delta emerged 1.37-2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%-167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1-10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta's enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability., Competing Interests: N.D.G. is a paid consultant for Tempus Labs and the National Basketball Association and has received speaking fees from Goldman Sachs. P.C.S. is a co-founder of, shareholder in, and scientific advisor to Sherlock Biosciences, Inc., as well as a board member of and shareholder in Danaher Corporation. The remaining authors declare no competing interests., (© 2022 The Authors.)

Rift Valley fever virus (RVFV) is a zoonotic phlebovirus of the Phenuiviridae family with great opportunity for emergence in previously unaffected regions, despite its current geographical limits. Outbreaks of RVFV often infect humans or domesticated animals, such as livestock, concurrently and occur sporadically, ranging from localized outbreaks in villages to multi-country events that spread rapidly. The true burden of Rift Valley fever (RVF) is not well defined due to underreporting, misdiagnosis caused by the broad spectrum of disease presentation, and minimal access for rapid and accurate laboratory confirmation. Severe symptoms may include hemorrhagic fever, loss of vision, psychological impairment or disturbances, and organ failure. Those living in endemic areas and travelers should be aware of the potential for exposure to ongoing outbreaks or interepidemic transmission, and engage in behaviors to minimize exposure risks, as vaccinations in humans are currently unavailable and animal vaccinations are not used routinely or ubiquitously. The lack of vaccines approved for use in humans is concerning, as RVFV has proven to be highly pathogenic in naïve populations, causing severe disease in a large percent of confirmed cases, which could have considerable impact on human health.

Swine are a key reservoir host for influenza A viruses (IAVs), with the potential to cause global pandemics in humans. Gaps in surveillance in many of the world's largest swine populations impede our understanding of how novel viruses emerge and expand their spatial range in pigs. Although US swine are intensively sampled, little is known about IAV diversity in Canada's population of ~12 million pigs. By sequencing 168 viruses from multiple regions of Canada, our study reveals that IAV diversity has been underestimated in Canadian pigs for many years. Critically, a new H1 clade has emerged in Canada (H1α-3), with a two-amino acid deletion at H1 positions 146-147, that experienced rapid growth in Manitoba's swine herds during 2014-2015. H1α-3 viruses also exhibit a higher capacity to invade US swine herds, resulting in multiple recent introductions of the virus into the US Heartland following large-scale movements of pigs in this direction. From the Heartland, H1α-3 viruses have disseminated onward to both the east and west coasts of the United States, and may become established in Appalachia. These findings demonstrate how long-distance trading of live pigs facilitates the spread of IAVs, increasing viral genetic diversity and complicating pathogen control. The proliferation of novel H1α-3 viruses also highlights the need for expanded surveillance in a Canadian swine population that has long been overlooked, and may have implications for vaccine design.

Several picornaviruses (Picornaviridae) are currently attracting interest without the need of being "emergent". The Parechovirus genus, validated 40 years after the discovery of the first two members ("echoviruses 22 and 23") includes neurotropic viruses whose molecular diagnosis demonstrated the involvement in infant meningitis and newborn sepsis, in particular type 3. Improvements in multiplex molecular diagnosis of respiratory infections - thanks to the Influenza AH1N1pdm2009 pandemy - showed that rhinoviruses may be involved in severe forms. The risk of the re-emergence of poliomyelitis in Europe, after an 11-year period of elimination, is a serious threat, owing to the circulation of the wild-type poliovirus in the Middle East and Africa because of conflicts, population displacements and poverty. The current widespread epidemics of hand-foot-mouth disease and/or meningitis infections due to enterovirus 71, with fatal encephalitis and cardio-pulmonary failure, are clear evidence of its emergence in South-East Asia. Although uncommon in Europe and less frequently incriminated than coxsackieviruses A6 and A10 in hand-foot-mouth disease, EV71 represents a real risk for the future. Extensive genotyping of the enteroviruses by the Enterovirus Surveillance Network should ward off these two potential risks of emergence/reemergence.