ICTV Virus Taxonomy Profile: Caliciviridae

Novel viruses discovered in metatranscriptomic analysis of farmed barramundi in Asia and Australia

Barramundi aquaculture is at risk of severe disease outbreaks and massive production losses. Here we used bioinformatics to screen 84 farmed barramundi transcriptomes to identify novel viruses that could threaten barramundi aquaculture and to establish a barramundi aquaculture virome. We discovered five novel viruses: latid herpesvirus 1 (LatHV-1) from the Alloherpesviridae family, barramundi parvovirus 1 (BParV1) from the Parvoviridae family, barramundi calicivirus 1 (BCaV1) from the Caliciviridae family, and barramundi associated picorna-like virus 1 and 2 (BPicV1 and BPicV2) from the Picornaviridae family. LatHV-1, BCaV1, and BParV1 are closely related to pathogenic viruses found in other fish species that can cause mass mortality in farms. To aid in future viral surveillance, we also designed and successfully tested an RT-PCR assay for the detection of BCaV1. Overall, we discovered a range of pathogenic viruses in barramundi aquaculture, paving the way for developing effective detection methods to assist early outbreak management.

Sequencing of historic samples provides complete coding sequences of chicken calicivirus from the United States

Here, we report the coding-complete genomic sequences of two chicken caliciviruses from US poultry flocks in 2003 and 2004. They show the same genomic organization as that of other members of the Bavovirus genus and have the highest nucleotide identity (~88%) with strains from clinically normal chickens from Germany in 2004 and Netherlands in 2019.

The Feline calicivirus capsid protein VP1 is a client of the molecular chaperone Hsp90

Feline calicivirus (FCV) icosahedral viral capsids are composed of dozens of structural subunits that rely on cellular chaperones to self-assemble in an orderly fashion. Here, we report that the heat shock protein 90 (Hsp90) inhibition significantly reduced FCV particle production, suggesting a role in the replicative cycle. We found that Hsp90 inhibition was not related to the synthesis or stability of the early proteins that translate from the gRNA nor to the minor capsid protein VP2 but with a reduction in the major capsid protein VP1 levels, both translated late in infection from the subgenomic RNAs. Reduction in VP1 levels was observed despite an augment of the leader of the capsid (LC)-VP1 precursor levels, from which the LC and VP1 proteins are produced after proteolytic processing by NS6/7. The direct interaction of VP1 with Hsp90 was observed in infected cells. These results suggest that upon release from the polyprotein precursor, VP1 becomes a client of Hsp90 and that this interaction is required for an efficient FCV replicative cycle.

Extensive Diversity of Viruses in Millipedes Collected in the Dong Nai Biosphere Reserve (Vietnam)

Advances in sequencing technologies and bioinformatics have led to breakthroughs in the study of virus biodiversity. Millipedes (Diplopoda, Myriapoda, Arthropoda) include more than 12,000 extant species, yet data on virus diversity in Diplopoda are scarce. This study aimed to explore the virome of the millipedes collected in the Dong Nai Biosphere Reserve in Vietnam. We studied 14 species of millipedes and managed to assemble and annotate the complete coding genomes of 16 novel viruses, the partial coding genomes of 10 more viruses, and several fragmented viral sequences, which may indicate the presence of about 54 more viruses in the studied samples. Among the complete and partial genomes, 27% were putative members of the order Picornavirales. Most of the discovered viruses were very distant from the viruses currently present in the relevant databases. At least eight viruses meet the criteria to be recognized as a new species by the International Committee on Taxonomy of Viruses, and, for two of them, a higher taxonomic status (genus and even family) can be suggested.

Viruses Identified in Shrews (Soricidae) and Their Biomedical Significance

Shrews (Soricidae) are common small wild mammals. Some species of shrews, such as Asian house shrews (Suncus murinus), have a significant overlap in their habitats with humans and domestic animals. Currently, over 190 species of viruses in 32 families, including Adenoviridae, Arenaviridae, Arteriviridae, Astroviridae, Anelloviridae, Bornaviridae, Caliciviridae, Chuviridae, Coronaviridae, Filoviridae, Flaviviridae, Hantaviridae, Hepadnaviridae, Hepeviridae, Nairoviridae, Nodaviridae, Orthoherpesviridae, Orthomyxoviridae, Paramyxoviridae, Parvoviridae, Phenuiviridae, Picobirnaviridae, Picornaviridae, Polyomaviridae, Poxviridae, Rhabdoviridae, Sedoreoviridae, Spinareoviridae, and three unclassified families, have been identified in shrews. Diverse shrew viruses, such as Borna disease virus 1, Langya virus, and severe fever with thrombocytopenia syndrome virus, cause diseases in humans and/or domestic animals, posing significant threats to public health and animal health. This review compiled fundamental information about shrews and provided a comprehensive summary of the viruses that have been detected in shrews, with the aim of facilitating a deep understanding of shrews and the diversity, epidemiology, and risks of their viruses.

Translation of Overlapping Open Reading Frames Promoted by Type 2 IRESs in Avian Calicivirus Genomes

Caliciviruses have positive-sense RNA genomes, typically with short 5'-untranslated regions (5'UTRs) that precede the long open reading frame 1 (ORF1). Exceptionally, some avian caliciviruses have long 5'UTRs containing a picornavirus-like internal ribosomal entry site (IRES), which was likely acquired by horizontal gene transfer. Here, we identified numerous additional avian calicivirus genomes with IRESs, predominantly type 2, and determined that many of these genomes contain a ~200-300 codon-long ORF (designated ORF1*) that overlaps the 5'-terminal region of ORF1. The activity of representative type 2 IRESs from grey teal calicivirus (GTCV) and Caliciviridae sp. isolate yc-13 (RaCV1) was confirmed by in vitro translation. Toeprinting showed that in cell-free extracts and in vitro reconstituted reactions, ribosomal initiation complexes assembled on the ORF1* initiation codon and at one or two AUG codons in ORF1 at the 3'-border and/or downstream of the IRES. Initiation at all three sites required eIF4A and eIF4G, which bound to a conserved region of the IRES; initiation on the ORF1* and principal ORF1 initiation codons involved eIF1/eIF1A-dependent scanning from the IRES's 3'-border. Initiation on these IRESs was enhanced by the IRES trans-acting factors (ITAFs) Ebp1/ITAF45, which bound to the apical subdomain Id of the IRES, and PTB (GTCV) or PCBP2 (RaCV1).

Rabbit hemorrhagic disease virus 2, 2010-2023: a review of global detections and affected species

Rabbit hemorrhagic disease virus 2/genotype GI.2 (RHDV2/GI.2; Caliciviridae, Lagovirus) causes a highly contagious disease with hepatic necrosis and disseminated intravascular coagulation in several Leporidae species. RHDV2 was first detected in European rabbits (Oryctolagus cuniculus) in France in 2010 and has since spread widely. We gather here data on viral detections reported in various countries and affected species, and discuss pathology, genetic differences, and novel diagnostic aspects. RHDV2 has been detected almost globally, with cases reported in Europe, Africa, Oceania, Asia, and North America as of 2023. Since 2020, large scale outbreaks have occurred in the United States and Mexico and, at the same time, cases have been reported for the first time in previously unaffected countries, such as China, Japan, Singapore, and South Africa, among others. Detections have been notified in domestic and wild European rabbits, hares and jackrabbits (Lepus spp.), several species of cottontail and brush rabbits (Sylvilagus spp.), pygmy rabbits (Brachylagus idahoensis), and red rock rabbits (Pronolagus spp.). RHDV2 has also been detected in a few non-lagomorph species. Detection of RHDV2 causing RHD in Sylvilagus spp. and Leporidae species other than those in the genera Oryctolagus and Lepus is very novel. The global spread of this fast-evolving RNA virus into previously unexploited geographic areas increases the likelihood of host range expansion as new species are exposed; animals may also be infected by nonpathogenic caliciviruses that are disseminated by almost all species, and with which genetic recombination may occur.

The Disorderly Nature of Caliciviruses

An intrinsically disordered protein (IDP) or region (IDR) lacks or has little protein structure but still maintains function. This lack of structure creates flexibility and fluidity, allowing multiple protein conformations and potentially transient interactions with more than one partner. Caliciviruses are positive-sense ssRNA viruses, containing a relatively small genome of 7.6-8.6 kb and have a broad host range. Many viral proteins are known to contain IDRs, which benefit smaller viral genomes by expanding the functional proteome through the multifunctional nature of the IDR. The percentage of intrinsically disordered residues within the total proteome for each calicivirus type species can range between 8 and 23%, and IDRs have been experimentally identified in NS1-2, VPg and RdRP proteins. The IDRs within a protein are not well conserved across the genera, and whether this correlates to different activities or increased tolerance to mutations, driving virus adaptation to new selection pressures, is unknown. The function of norovirus NS1-2 has not yet been fully elucidated but includes involvement in host cell tropism, the promotion of viral spread and the suppression of host interferon-λ responses. These functions and the presence of host cell-like linear motifs that interact with host cell caspases and VAPA/B are all found or affected by the disordered region of norovirus NS1-2. The IDRs of calicivirus VPg are involved in viral transcription and translation, RNA binding, nucleotidylylation and cell cycle arrest, and the N-terminal IDR within the human norovirus RdRP could potentially drive liquid-liquid phase separation. This review identifies and summarises the IDRs of proteins within the Caliciviridae family and their importance during viral replication and subsequent host interactions.

Wastewater surveillance together with metaviromic data revealed the unusual resurgence of infectious diseases after the first wave of the COVID-19 outbreak

How to address public health priorities after COVID-19 is becoming a critical task. To this end, we conducted wastewater surveillance for six leading pathogens, namely, SARS-CoV-2, norovirus, rotavirus, influenza A virus (IAV), enteroviruses and respiratory syncytial virus (RSV), in Nanchang city from January to April 2023. Metaviromic sequencing was conducted at the 1st, 4th, 7th, 9th, 12th and 14th weeks to reveal the dynamics of viral pathogens that were not covered by qPCR. Amplicon sequencing of the conserved region of norovirus GI and GII and the rotavirus and region encoding nonstructural protein of RSV was also conducted weekly. The results showed that after a rapid decrease in SARS-CoV-2 sewage concentrations occurred in January 2023, surges of norovirus, rotavirus, IAV and RSV started at the 6th, 7th, 8th and 11th weeks, respectively. The dynamics of the sewage concentrations of norovirus, rotavirus, IAV and RSV were consistent with the off-season resurgence of the above infectious diseases. Notably, peak sewage concentrations of norovirus GI, GII, rotavirus, IAV and RSV were found at the 6th, 3rd, 7th, 7th and 8th weeks, respectively. Astroviruses also resurge after the 7th week, as revealed by metaviromic data, suggesting that wastewater surveillance together with metaviromic data provides an essential early warning tool for revealing patterns of infectious disease resurgence.

Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom

The Caliciviridae family, comprising positive-sense RNA viruses, is characterised by its non-enveloped, small virions, broad host range, and notable tendency for host switching. These viruses are primarily associated with gastroenteric disease, though they can lead to haemorrhagic or respiratory infections. Our study employed a metagenomics analysis of faecal samples from stoats (Mustela erminea), identifying two novel calicivirus species, named stoat vesivirus and stoat valovirus. Stoat vesivirus was identified in three samples (ST008, ST006, ST004), exhibiting a genome wide nucleotide identity of approximately 92 %. The complete coding sequences of these samples were 8471 (ST004) and 8322 (ST006) nucleotides in length, respectively. Each comprised three open reading frames (ORF), closely resembling the Vesivirus mink calicivirus (China/2/2016), with 70-72 % similarity in ORF1, 61-62 % in ORF2 and 71 % in ORF3. Phylogenetic analysis robustly supported stoat vesivirus as belonging within the Vesivirus genus. The second calivicirus (stoat valovirus), detected solely in sample ST008, was 6527 nucleotides in length and with complete coding sequences present. It shared highest similarity with St-Valérien swine virus and marmot norovirus HT16, showing 39.5 and 38.8 % protein identity with ORF1 and 43.3 and 42.9 % for VP1. Stoat valovirus is borderline for meeting the ICTV criteria for a new genus, demonstrating 60 % divergence in ORF1 compared to the other valovirus', however it clusters basally within the Valovirus genus, supporting leaving it included in this genus.

Molecular epidemiology and strain diversity of circulating feline Calicivirus in Thai cats

Feline calicivirus (FCV) is a significant viral pathogen causing upper respiratory tract and oral diseases in cats. The emergence of the virulent systemic FCV variant (VS-FCV) has raised global concern in the past decade. This study aims to explore the epidemiology, genetic characterization, and diversity of FCV strains circulating among Thai cats. Various sample types, including nasal, oral, and oropharyngeal swabs and fresh tissues, were collected from 184 cats across different regions of Thailand from 2016 to 2021. Using reverse transcription real-time polymerase chain reaction (RT-qPCR), FCV infection was investigated, with additional screening for feline herpesvirus-1 (FHV-1) by qPCR. The detection rates for FCV, FHV-1, and co-infection were 46.7, 65.8, and 31.5%, respectively. Significantly, the odds ratio (OR) revealed a strong association between the detection of a single FCV and the presence of gingivostomatitis lesions (OR: 7.15, 95% CI: 1.89-26.99, p = 0.004). In addition, FCV detection is notably less likely in vaccinated cats (OR: 0.22, 95% CI: 0.07-0.75, p = 0.015). Amino acid sequence analysis based on the VP1 major capsid protein gene of the 14 FCV-Thai (FCV-TH) strains revealed genetic diversity compared to the other 43 global strains (0 to 86.6%). Intriguingly, a vaccine-like FCV variant was detected in one cat. In summary, this study provides insights into the epidemiology and molecular characteristics of FCV diversity within the Thai cat population for the first time. The identification of unique physicochemical characteristics in the capsid hypervariable region of some FCV-TH strains challenges previous hypotheses. Therefore, further exploration of vaccine-like FCV variants is crucial for a comprehensive understanding and to improve viral prevention and control strategies.

Noroviruses: Evolutionary Dynamics, Epidemiology, Pathogenesis, and Vaccine Advances-A Comprehensive Review

Noroviruses constitute a significant aetiology of sporadic and epidemic gastroenteritis in human hosts worldwide, especially among young children, the elderly, and immunocompromised patients. The low infectious dose of the virus, protracted shedding in faeces, and the ability to persist in the environment promote viral transmission in different socioeconomic settings. Considering the substantial disease burden across healthcare and community settings and the difficulty in controlling the disease, we review aspects related to current knowledge about norovirus biology, mechanisms driving the evolutionary trends, epidemiology and molecular diversity, pathogenic mechanism, and immunity to viral infection. Additionally, we discuss the reservoir hosts, intra-inter host dynamics, and potential eco-evolutionary significance. Finally, we review norovirus vaccines in the development pipeline and further discuss the various host and pathogen factors that may complicate vaccine development.

Highs and Lows in Calicivirus Reverse Genetics

In virology, the term reverse genetics refers to a set of methodologies in which changes are introduced into the viral genome and their effects on the generation of infectious viral progeny and their phenotypic features are assessed. Reverse genetics emerged thanks to advances in recombinant DNA technology, which made the isolation, cloning, and modification of genes through mutagenesis possible. Most virus reverse genetics studies depend on our capacity to rescue an infectious wild-type virus progeny from cell cultures transfected with an "infectious clone". This infectious clone generally consists of a circular DNA plasmid containing a functional copy of the full-length viral genome, under the control of an appropriate polymerase promoter. For most DNA viruses, reverse genetics systems are very straightforward since DNA virus genomes are relatively easy to handle and modify and are also (with few notable exceptions) infectious per se. This is not true for RNA viruses, whose genomes need to be reverse-transcribed into cDNA before any modification can be performed. Establishing reverse genetics systems for members of the Caliciviridae has proven exceptionally challenging due to the low number of members of this family that propagate in cell culture. Despite the early successful rescue of calicivirus from a genome-length cDNA more than two decades ago, reverse genetics methods are not routine procedures that can be easily extrapolated to other members of the family. Reports of calicivirus reverse genetics systems have been few and far between. In this review, we discuss the main pitfalls, failures, and delays behind the generation of several successful calicivirus infectious clones.

Tailored wastewater surveillance framework uncovered the epidemics of key pathogens in a Northwestern city of China

Wastewater surveillance enables rapid pathogen monitoring and community prevalence estimation. However, how to design an integrated and tailored wastewater surveillance framework to monitor major health threats in metropolises remains a major challenge. In this study, we first analyzed the historical clinical data of Xi'an city and designed a wastewater surveillance framework covering five key endemic viruses, namely, SARS-CoV-2, norovirus, influenza A virus (IAV), influenza B virus (IBV), respiratory syncytial virus (RSV), and hantavirus. Amplicon sequencing of SARS-CoV-2, norovirus and hantavirus was conducted biweekly to determine the prevalent community genotypes circulating in this region. The results showed that from April 2023 to August 2023, Xi'an experienced two waves of SARS-CoV-2 infection, which peaked in the middle of May-2023 and late August-2023. The sewage concentrations of IAV and RSV peaked in early March and early May 2023, respectively, while the sewage concentrations of norovirus fluctuated throughout the study period and peaked in late August. The dynamics of the sewage concentrations of SARS-CoV-2, norovirus, IAV, RSV, and hantavirus were in line with the trends in the sentinel hospital percent positivity data, indicating the role of wastewater surveillance in enhancing the understanding of epidemic trends. Amplicon sequencing of SARS-CoV-2 revealed a transition in the predominant genotype, which changed from DY.1 and FR.1.4 to the XBB and EG.5 subvariants. Amplicon sequencing also revealed that there was only one predominant hantavirus genotype in the local population, while highly diverse genotypes of norovirus GI and GII were found in the wastewater. In conclusion, this study provided valuable insights into the dynamics of infection trends and predominant genotypes of key pathogens in a city without sufficient clinical surveillance, highlighting the role of a tailored wastewater surveillance framework in addressing public health priorities. More importantly, our study provides the first evidence demonstrating the applicability of wastewater surveillance for hantavirus, which is a major health threat locally.

Update on feline calicivirus: viral evolution, pathogenesis, epidemiology, prevention and control

Feline calicivirus (FCV) is a prevalent and impactful viral pathogen affecting domestic cats. As an RNA virus, FCV exhibits high mutability and genetic plasticity, enabling its persistence within cat populations. Viral genetic diversity is associated with a broad spectrum of clinical manifestations, ranging from asymptomatic infections and mild oral and upper respiratory tract diseases to the potential development of virulent systemic, and even fatal conditions. This diversity poses distinctive challenges in diagnosis, treatment, and prevention of diseases caused by FCV. Over the past four decades, research has significantly deepened understanding of this pathogen, with an emphasis on molecular biology, evolutionary dynamics, vaccine development, and disease management strategies. This review discusses various facets of FCV, including its genomic structure, evolution, innate immunity, pathogenesis, epidemiology, and approaches to disease management. FCV remains a complex and evolving concern in feline health, requiring continuous research to enhance understanding of its genetic diversity, to improve vaccine efficacy, and to explore novel treatment options.

A highly divergent enteric calicivirus in a bovine calf in India

A highly divergent bovine calicivirus was identified in an Indian calf with enteritis. The whole genome of this virus was sequenced, revealing distinct amino acid motifs in the polyprotein encoded by open reading frame 1 (ORF1) that are unique to caliciviruses. Phylogenetic analysis showed that it was related to members of the genus Nebovirus of the family Caliciviridae. Although it showed only 33.7-34.2% sequence identity in the VP1 protein to the nebovirus prototype strains, it showed 90.6% identity in VP1 to Kirklareli virus, a nebovirus detected in calves with enteritis in Turkey in 2012. An in-house-designed and optimized reverse transcription polymerase chain reaction (RT-PCR) assay was used to screen 120 archived bovine diarrhoeic fecal samples, 40 each from the Indian states of Uttar Pradesh, Haryana, and Himachal Pradesh, revealing frequent circulation of these divergent caliciviruses in the bovine population, with an overall positivity rate of 64.17% (77/120). This underscores the importance of conducting a comprehensive investigation of the prevalence of these divergent caliciviruses and assessing their associations with other pathogens responsible for enteritis in India.

Detection and complete genome characterization of a genogroup X (GX) sapovirus (family Caliciviridae) from a golden jackal (Canis aureus) in Hungary

In this study, a novel genotype of genogroup X (GX) sapovirus (family Caliciviridae) was detected in the small intestinal contents of a golden jackal (Canis aureus) in Hungary and characterised by viral metagenomics and next-generation sequencing techniques. The complete genome of the detected strain, GX/Dömsöd/DOCA-11/2020/HUN (PP105600), is 7,128 nt in length. The ORF1- and ORF2-encoded viral proteins (NSP, VP1, and VP2) have 98%, 95%, and 88% amino acid sequence identity to the corresponding proteins of genogroup GX sapoviruses from domestic pigs, but the nucleic acid sequence identity values for their genes are significantly lower (83%, 77%, and 68%). During an RT-PCR-based epidemiological investigation of additional jackal and swine samples, no other GX strains were detected, but a GXI sapovirus strain, GXI/Tótfalu/WBTF-10/2012/HUN (PP105601), was identified in a faecal sample from a wild boar (Sus scrofa). We report the detection of members of two likely underdiagnosed groups of sapoviruses (GX and GXI) in a golden jackal and, serendipitously, in a wild boar in Europe.

Human norovirus cultivation systems and their use in antiviral research

Human norovirus (HuNoV) is a major cause of acute gastroenteritis and foodborne diseases, affecting all age groups. Despite its clinical needs, no approved antiviral therapies are available. Since the discovery of HuNoV in 1972, studies on anti-norovirals, mechanism of HuNoV infection, viral inactivation, etc., have been hampered by the lack of a robust laboratory-based cultivation system for HuNoV. A recent breakthrough in the development of HuNoV cultivation systems has opened opportunities for researchers to investigate HuNoV biology in the context of de novo HuNoV infections. A tissue stem cell-derived human intestinal organoid/enteroid (HIO) culture system is one of those that supports HuNoV replication reproducibly and, to our knowledge, is most widely distributed to laboratories worldwide to study HuNoV and develop therapeutic strategies. This review summarizes recently developed HuNoV cultivation systems, including HIO, and their use in antiviral studies.

Viral gastroenteritis

Since the discovery of norovirus in 1972 as a cause of what was contemporarily known as acute infectious non-bacterial gastroenteritis, scientific understanding of the viral gastroenteritides has continued to evolve. It is now recognised that a small number of viruses are the predominant cause of acute gastroenteritis worldwide, in both high-income and low-income settings. Although treatment is still largely restricted to the replacement of fluid and electrolytes, improved diagnostics have allowed attribution of illness, enabling both targeted treatment of individual patients and prioritisation of interventions for populations worldwide. Questions remain regarding specific genetic and immunological factors underlying host susceptibility, and the optimal clinical management of patients who are susceptible to severe or prolonged manifestations of disease. Meanwhile, the worldwide implementation of rotavirus vaccines has led to substantial reductions in morbidity and mortality, and spurred interest in vaccine development to diminish the impact of the most prevalent viruses that are implicated in this syndrome.

Serological characterisation of Lagovirus virus-like particles originating from native and mutated VP60 of rabbit haemorrhagic disease virus 2 and European brown hare syndrome virus

Introduction

Since lagoviruses cannot be cultivated in vitro, using expression systems is an alternative and promising way of producing diagnostic viral antigens. It opens up their use as active immunogens for vaccine production.

Material and Methods

Virus-like particles (VLPs) were produced in a baculovirus expression system in Spodoptera frugiperda 9 (Sf9) insect cells based on wild-type and mutated variants of the virus capsid VP60 protein from a Polish strain of European brown hare syndrome virus (EBHSV) and wild-type and mutated versions of this protein from a Polish strain of rabbit haemorrhagic disease virus 2 (RHDV2). The mutations were the substitution of an arginylglycylaspartic acid (Arg-Gly-Asp/RGD) motif in the P2 subdomain and, in the S or P2 domain, the substitution of three lysines. The VLPs were purified with sucrose gradient ultracentrifugation.

Results

Protein production was confirmed by Western blot analysis using rabbit or hare sera and ELISA tests with different types of monoclonal antibody. The haemagglutination properties of some VLPs were also evaluated. Electron microscopy of wild-type EBHSV, wild-type RHDV2 and the four VP60 variants produced in this experiment revealed the formation of characteristic VLP structures.

Conclusion

For the first time, mutated VLPs of RHDV2 with an RGD motif in the VP60 sequence were obtained, which could potentially be used to deliver cargo to eukaryotic cells. Virus-like particles based on the VP60 proteins of EBHSV and RHDV with a three-lysine substitution in the S or P2 domains were also obtained. Potential exists for VLPs of EBHSV and RHDV2 as vaccine candidates.

Application of the zebrafish model in human viral research

Viruses are a leading cause of infectious diseases. Well-developed animal models are valuable for understanding the immune responses to viral infections and the pathogenesis of viral diseases. Zebrafish is a commonly used small vertebrate model organism with strong reproductive ability, a short life cycle, and rapid embryonic development. Moreover, zebrafish and human genomes are highly similar; they have approximately 70 % homology in protein-coding genes, and 84 % of genes associated with human diseases have zebrafish counterparts. Recent years, different groups have developed zebrafish models for human viral infections and diseases, offering new insights into the molecular mechanisms of human viral pathogenesis as well as the development of antiviral strategies. The zebrafish model has become a simple and effective model system for understanding host-virus interaction. This review provides a comprehensive summary of the use of zebrafish models in human viral research, particularly in SARS-CoV-2.

Assessment of Gastroenteric Viruses in Marketed Bivalve Mollusks in the Tourist Cities of Rio de Janeiro, Brazil, 2022

This study investigated the prevalence and genetic diversity of gastroenteric viruses in mussels and oysters in Rio de Janeiro, Brazil. One hundred and thirty-four marketed bivalve samples were obtained between January and December 2022. The viral analysis was performed according to ISO/TS 15216, and the screening revealed the detection of norovirus GII/GI (40.3%), sapovirus (SaV; 12.7%), human mastadenovirus (7.5%), and rotavirus A (RVA; 5.9%). In total, 44.8% (60) of shellfish samples tested positive for one or more viruses, 46.7% (28/60) of the positive samples tested positive for a single viral agent, 26.7% (16) tested positive for two viral agents, 8.3% (5) for three viral agents, and 13.3% (8) for four viral agents. Additionally, three mussel samples were contaminated with the five investigated viruses (5%, 3/60). Norovirus GII showed the highest mean viral load (3.4 × 105 GC/g), followed by SaV (1.4 × 104 GC/g), RVA (1.1 × 104 GC/g), human mastadenovirus (3.9 × 103 GC/g), and norovirus GI (6.7 × 102 GC/g). Molecular characterization revealed that the recovered norovirus strains belonged to genotypes GII.2, GII.6, GII.9, GII.17, and GII.27; SaV belonged to genotypes GI.1 and GIV.1; RVA to genotypes G6, G8, P[8]-III, and human mastadenovirus to types F40 and F41. The GII.27 norovirus characterized in this study is the only strain of this genotype reported in Brazil. This study highlights the dissemination and diversity of gastroenteric viruses present in commercialized bivalves in a touristic area, indicating the potential risk to human health and the contribution of bivalves in the propagation of emerging pathogens.

Apoptosis activation during Lagovirus europaeus/GI.2 infection in rabbits

Rabbit Haemorrhagic Disease (RHD) is a severe disease caused by Lagovirus europaeus/GI.1 and GI.2. Immunological processes such as apoptosis are important factors involved in the pathogenesis of Rabbit Haemorrhagic Disease (RHD). The process of programmed cell death has been quite well characterized in infection with GI.1 strains, but apoptosis in infection with GI.2 strains has not been widely studied. This is particularly important as several studies have shown that significant differences in the host immune response are observed during infection with different strains of Lagovirus europaeus. In this study, we analyzed the gene expression, protein levels and activity of key apoptotic cell death factors in the spleen, kidney, lung, and heart of rabbits. As a result, we showed that there is a significant increase in caspase-3, Bax, Bcl2 and Bax/Bcl2 mRNA gene expression ratio in organs of infected animals. Our results show also increased levels of cleaved caspase-3, caspase-6 and PARP. Moreover, significant activity of caspase-3 was also detected. Our results indicate that caspase-3, caspase-6 and genes coding Bcl2 family proteins play a key role in the apoptotic response in Lagovirus europaeus/GI.2 infection in organs that are not the target of virus replication.

The 2.6 Å Structure of a Tulane Virus Variant with Minor Mutations Leading to Receptor Change

Human noroviruses (HuNoVs) are a major cause of acute gastroenteritis, contributing significantly to annual foodborne illness cases. However, studying these viruses has been challenging due to limitations in tissue culture techniques for over four decades. Tulane virus (TV) has emerged as a crucial surrogate for HuNoVs due to its close resemblance in amino acid composition and the availability of a robust cell culture system. Initially isolated from rhesus macaques in 2008, TV represents a novel Calicivirus belonging to the Recovirus genus. Its significance lies in sharing the same host cell receptor, histo-blood group antigen (HBGA), as HuNoVs. In this study, we introduce, through cryo-electron microscopy (cryo-EM), the structure of a specific TV variant (the 9-6-17 TV) that has notably lost its ability to bind to its receptor, B-type HBGA-a finding confirmed using an enzyme-linked immunosorbent assay (ELISA). These results offer a profound insight into the genetic modifications occurring in TV that are necessary for adaptation to cell culture environments. This research significantly contributes to advancing our understanding of the genetic changes that are pivotal to successful adaptation, shedding light on fundamental aspects of Calicivirus evolution.

Recombination between non-structural and structural genes as a mechanism of selection in lagoviruses: The evolutionary dead-end of an RHDV2 isolated from European hare

The genus Lagovirus, belonging to the family Caliciviridae, emerged around the 1980s. It includes highly pathogenic species, rabbit hemorrhagic disease virus (RHDV/GI.1) and European brown hare syndrome virus (EBHSV/GII.1), which cause fatal hepatitis, and nonpathogenic viruses with enteric tropism, rabbit calicivirus (RCV/GI.3,4) and hare calicivirus (HaCV/GII.2). Lagoviruses have evolved along two independent genetic lineages: GI (RHDV and RCV) in rabbits and GII (EBHSV and HaCV) in hares. To be emphasized is that genomes of lagoviruses, like other caliciviruses, are highly conserved at RdRp-VP60 junctions, favoring intergenotypic recombination events at this point. The recombination between an RCV (genotype GI.3), donor of non-structural (NS) genes, and an unknown virus, donor of structural (S) genes, likely led to the emergence of a new lagovirus in the European rabbit, called RHDV type 2 (GI.2), identified in Europe in 2010. New RHDV2 intergenotypic recombinants isolated in rabbits in Europe and Australia originated from similar events between RHDV2 (GI.2) and RHDV (GI.1) or RCV (GI.3,4). RHDV2 (GI.2) rapidly spread worldwide, replacing RHDV and showing several lagomorph species as secondary hosts. The recombination events in RHDV2 viruses have led to a number of viruses with very different combinations of NS and S genes. Recombinant RHDV2 with NS genes from hare lineage (GII) was recently identified in the European hare. This study investigated the first RHDV2 (GI.2) identified in Italy in European hare (RHDV2_Bg12), demonstrating that it was a new virus that originated from the recombination between RHDV2, as an S-gene donor and a hare lagovirus, not yet identified but presumably nonpathogenic, as an NS gene donor. When rabbits were inoculated with RHDV2_Bg12, neither deaths nor seroconversions were recorded, demonstrating that RHDV2_Bg12 cannot infect the rabbit. Furthermore, despite intensive and continuous field surveillance, RHDV2_Bg12 has never again been identified in either hares or rabbits in Italy or elsewhere. This result showed that the host specificity of lagoviruses can depend not only on S genes, as expected until today, but potentially also on some species-specific NS gene sequences. Therefore, because RHDV2 (GI.2) infects several lagomorphs, which in turn probably harbor several specific nonpathogenic lagoviruses, the possibility of new speciation, especially in those other than rabbits, is real. RHDV2 Bg_12 demonstrated this, although the attempt apparently failed.

Murine norovirus infection of macrophages induces intrinsic apoptosis as the major form of programmed cell death

Human norovirus is the leading cause of acute gastroenteritis worldwide, however despite the significance of this pathogen, we have a limited understanding of how noroviruses cause disease, and modulate the innate immune response. Programmed cell death (PCD) is an important part of the innate response to invading pathogens, but little is known about how specific PCD pathways contribute to norovirus replication. Here, we reveal that murine norovirus (MNV) virus-induced PCD in macrophages correlates with the release of infectious virus. We subsequently show, genetically and chemically, that MNV-induced cell death and viral replication occurs independent of the activity of inflammatory mediators. Further analysis revealed that MNV infection promotes the cleavage of apoptotic caspase-3 and PARP. Correspondingly, pan-caspase inhibition, or BAX and BAK deficiency, perturbed viral replication rates and delayed virus release and cell death. These results provide new insights into how MNV harnesses cell death to increase viral burden.

High-resolution melting analysis for simultaneous detection and discrimination between wild-type and vaccine strains of feline calicivirus

High-resolution melting (HRM) analysis, a post-polymerase chain reaction (PCR) application in a single closed tube, is the straightforward method for simultaneous detection, genotyping, and mutation scanning, enabling more significant dynamic detection and sequencing-free turnaround time. This study aimed to establish a combined reverse-transcription quantitative PCR and HRM (RT-qPCR-HRM) assay for diagnosing and genotyping feline calicivirus (FCV). This developed method was validated with constructed FCV plasmids, clinical swab samples from living cats, fresh-frozen lung tissues from necropsied cats, and four available FCV vaccines. We performed RT-qPCR to amplify a 99-base pair sequence, targeting a segment between open reading frame (ORF) 1 and ORF2. Subsequently, the HRM assay was promptly applied using Rotor-Gene Q® Software. The results significantly revealed simultaneous detection and genetic discrimination between commercially available FCV vaccine strains, wild-type Thai FCV strains, and VS-FCV strains within a single PCR reaction. There was no cross-reactivity with other feline common viruses, including feline herpesvirus-1, feline coronavirus, feline leukemia virus, feline immunodeficiency virus, and feline morbillivirus. The detection limit of the assay was 6.18 × 101 copies/µl. This study, therefore, is the first demonstration of the uses and benefits of the RT-qPCR-HRM assay for FCV detection and strain differentiation in naturally infected cats.

Analysing the interplay of environmental virology, public health, and sanitation: a comprehensive review from a Kenyan perspective

This comprehensive review examines the interplay between environmental virology, public health, and sanitation in the unique context of Kenya. The review sheds light on the specific viral threats faced by the country, including waterborne viruses, zoonotic infections, and emerging viral diseases, and their implications for public health. It explores the prevailing public health challenges in Kenya associated with environmental viromics, such as infectious viral diseases, and the rising burden of other infectious particles. The role of sanitation in mitigating viral infections is highlighted, emphasising the importance of clean water supply, proper waste management, and hygienic practises. The review also presents strategies for strengthening environmental virology research in Kenya, including enhancing laboratory capacities and leveraging technological advancements. Furthermore, the policy implications and recommendations derived from the review emphasise the need for multi-sectoral collaboration, evidence-based decision-making, and long-term investments in infrastructure and behaviour change interventions. Implementing these strategies can enhance the understanding of environmental virology, improve public health outcomes, and ensure sustainable sanitation practises in Kenya, ultimately contributing to the well-being of the population and sustainable development.

First detection and molecular characterization of rabbit hemorrhagic disease virus (RHDV) in Algeria

Since the first detection of rabbit hemorrhagic disease (RHD), the rabbit hemorrhagic disease virus (RHDV) has been responsible for high morbidity and mortality worldwide, both in domestic and in wild rabbits. Despite the apparent control of RHD in rabbitries through vaccination, several studies highlighted the rapid evolution of RHDV by recombination, which may facilitate the emergence of new pathogenic strains. The aim of this study was to confirm the presence and characterize RHDV in Algeria. For this, rabbit samples were collected in the north of Algeria, between 2018 and 2021, from small farms where the virus was suspected after the sudden death of a high number of rabbits, and from healthy hunted wild rabbits. The domestic rabbits revealed clinical signs and lesions that were suggestive of RHD. RT-PCR showed that 79.31% of the domestic rabbit samples were positive for RHDV, while in 20.69%, including the hunted rabbits, the virus was not detected. Phylogenetic analysis of the Algerian strains allowed the confirmation and identification as GI.2 (RHDV2), and showed a close relation to GI.3P-GI.2 recombinant strains, suggesting a potential introduction from other countries, with an older strain potentially originated from neighboring Tunisia, while more recent isolates grouped with strains from North America. Our study reports for the first time the presence of GI.2 (RHDV2) in Algeria with multiple routes of introduction. Consequently, we propose that RHDV control in Algeria should be based on epidemiological surveys in association with an adequate prophylactic program.

Viral Diversity and Epidemiology in Critically Endangered Yangtze Finless Porpoises (Neophocaena asiaeorientalis asiaeorientalis)

The Yangtze finless porpoise (YFP) (Neophocaena asiaeorientalis asiaeorientalis) is a critically endangered freshwater cetacean, with about 1,249 individuals thought to be left in the wild. However, viral entities and viral diseases of YFPs remain obscure. In this study, anal swabs for virome analysis were collected during the physical examination of YFPs in the Tian-E-Zhou Oxbow (TEO) ex situ reserve. A total of 19 eukaryotic viral species belonging to 9 families, including Papillomaviridae, Herpesviridae, Picornaviridae, Picobirnaviridae, Caliciviridae, Retroviridae, Parvoviridae, Virgaviridae, and Narnaviridae, and other unclassified viruses were identified based on metasequencing. Among these detected viruses, a novel herpesvirus (NaHV), two different kobuviruses (NaKV1-2), and six different papillomaviruses (NaPV1 to -6) were considered potential risks to YFPs and confirmed by PCR or reverse transcription-PCR (RT-PCR). Most YFPs sampled were found to harbor one or more kinds of detected viral genomes (52/58 [89.7%]). Surveillance results demonstrated that kobuvirus and herpesvirus displayed obvious age distribution and PVs showed significant gender difference in YFPs. According to species demarcation criteria in individual genera in Papillomaviridae, two novel species (referred to as Omikronpapillomavirus 2 and 3) and four novel isolates of PV were identified in YFPs. Further evolutionary analysis suggested that NaPVs would occupy the mucosal niche and that virus-host codivergence mixed with duplications and host-switching events drives the evolution of cetacean PVs. Divergence times of PVs in YFP and other cetacean reflect the incipient speciation of YFPs. In summary, our findings revealed the potential viral entities, their prevalence, and their evolutionary history in YFPs, which raises an important issue regarding effects of viral infection on the fitness of YFPs. IMPORTANCE The Yangtze finless porpoise (YFP) is the only cetacean species in freshwater following the functional extinction of the baiji (Lipotes vexillifer). Health management, disease treatment, and other special measures are important for maintaining the existing YFP populations, especially in in situ and ex situ reserves. The discovery of potential viral entities and their prevalence in YFPs raises an important issue regarding the effects of viral infection on the fitness of YFPs and may contribute to the conservation of YFPs. The evolutionary history of papillomaviruses in YFP and other cetaceans reflects the phylogeny of their hosts and supports the status of incipient species, opening a window to investigate the evolutionary adaptation of cetaceans to freshwater as well as their phylogeny to remedy the deficiency of fossil evidence.

Predicting Dominant Genotypes in Norovirus Seasons in Japan

Human noroviruses are an etiological agent of acute gastroenteritis. Since multiple genotypes co-circulate every season changing their proportions, it may be desirable to develop multivalent vaccines by formulating genotype composition of seed strains to match that of dominant strains. Here, performances of the models for predicting dominant genotypes, defined as the two most prevalent genotypes, were evaluated using observed genotype frequencies in Japan and genomic sequences for GI and GII strains. In the null model, genotype proportions in the target season were predicted to be the same as those in the immediately preceding season. In the fitness model, genotype proportions were predicted taking into account the acquisition of novel P-types through recombination and genotype-specific proliferation efficiency, as well as herd immunity to VP1 assuming the duration (d) of 0-10 years. The null model performed better in GII than in GI, apparently because dominant genotypes were more stable in the former than in the latter. Performance of the fitness model was similar to that of the null model irrespective of the assumed value of d. However, performance was improved when dominant genotypes were predicted as the union of those predicted with d = 0-10, suggesting that d may vary among individuals.

Prevalence of Reversed Genome Organizations for Viruses in the Family Iflaviridae, Order Picornavirales

Viruses in the order Picornavirales possess a positive-strand RNA genome that encodes structural proteins (SPs) and nonstructural proteins (NSPs). According to the recent report of the International Committee on Taxonomy of Viruses (ICTV), there are 8 families in Picornavirales, and monopartite picornaviruses in each family exhibit distinct types of genome organizations with rearranged genes coding for SPs and NSPs, namely, TypeI (5'-SPs-NSPs-3') and TypeII (5'-NSPs-SPs-3'). In the present study, 2 iflaviruses with the 2 genome types were unexpectedly identified in a damselfly host species, suggesting that these 2 genome types coexisted in the same host species, and the families of order Picornavirales might be more complex than previously thought. The consequent systematic homologous screening with all the publicly available picornaviruses successfully revealed a considerable number of candidates rearranged genome types of picornaviruses in various families of Picornavirales. Subsequently, phylogenetic trees were reconstructed based on RNA dependent RNA polymerase and coat protein, which evidently confirmed the prevalence of the 10 typeII iflaviruses in the Iflaviridae family. This suggests that genome types may not be relevant to viral taxonomy in this family. However, candidate picornaviruses with reversed genome types in the Secoviridae and Dicistroviridae families require further investigation. All in all, as the number of newly discovered viruses increases, more viruses with non-canonical genome arrangements will be uncovered, which can expand our current knowledge on the genome complexity and evolution of picornaviruses. IMPORTANCE Monopartite viruses in the order Picornavirales exhibit distinct genome arrangement of nonstructural proteins and structural proteins for each of the 8 families. Recent studies indicated that at least 4 ifla-like viruses possessed reversed genome organization in the family Iflaviridae, raising the possibility that this phenomenon may commonly present in different families of picornaviruses. Since we discovered 2 iflaviruses with exchanged structural and nonstructural proteins simultaneously in the damselfly, a systematic screening was subsequently performed for all of the current available picornaviruses (1,543 candidates). The results revealed 10 picornaviruses with reversed genome organization in the family Iflaviridae, implying that this phenomenon might prevalence in the order Picornavirales. These results will contribute to a better understanding for the future study on the genome complexity and taxonomy of picornaviruses.

Investigation of removal and inactivation efficiencies of human sapovirus in drinking water treatment processes by applying an in vitro cell-culture system

Here, we examined the efficiencies of drinking water treatment processes for the removal and inactivation of human sapovirus (HuSaV). We applied a recently developed in vitro cell-culture system to produce purified solutions of HuSaV containing virus concentrations high enough to conduct virus-spiking experiments, to develop an integrated cell culture-polymerase chain reaction (ICC-PCR) assay to quantify the infectivity of HuSaV, and to conduct virus-spiking experiments. In virus-spiking coagulation-sedimentation-rapid sand filtration (CS-RSF) and coagulation-microfiltration (C-MF) experiments, HuSaV removals of 1.6-3.7-log₁₀ and 1.2->4.3-log₁₀, respectively, were observed. The removal ratios observed with CS-RSF were comparable and correlated with those of murine norovirus (MNV, a widely used surrogate for human noroviruses) and pepper mild mottle virus (PMMoV, a potential surrogate for human enteric viruses in physical and physicochemical drinking water treatment processes), and those observed with C-MF were higher than but still correlated with those of MNV and PMMoV, indicating that MNV and PMMoV are both potential surrogates for HuSaV in CS-RSF and C-MF. For astrovirus (AstV, a representative human enteric virus), removal ratios of 1.8-3.3-log₁₀ and 1.1->4.0-log₁₀ were observed with CS-RSF and C-MF, respectively. The removal ratios of AstV observed with CS-RSF were comparable and correlated with those of PMMoV, and those observed with C-MF were higher than but still correlated with those of PMMoV, indicating that PMMoV is a potential surrogate for AstV in CS-RSF and C-MF. When the efficacy of chlorine treatment was examined by using the developed ICC-PCR assay, 3.8-4.0-log₁₀ inactivation of HuSaV was observed at a CT value (free-chlorine concentration [C] multiplied by contact time [T]) of 0.02 mg-Cl₂·min/L. The infectivity reduction ratios of HuSaV were comparable with those of MNV. For AstV, 1.3-1.7-log₁₀ and >3.4-log₁₀ inactivation, as evaluated by ICC-PCR, was observed at CT values of 0.02 and 0.09 mg-Cl₂·min/L, respectively. These results indicate that HuSaV and AstV are both highly sensitive to chlorine treatment and more sensitive than a chlorine-resistant virus, coxsackievirus B5 (1.3-log₁₀ inactivation at a CT value of 0.4 mg-Cl₂·min/L, as evaluated by the ICC-PCR assay).

An Outbreak of Limping Syndrome Associated with Feline Calicivirus

Feline calicivirus (FCV) is a common viral pathogen found in domestic cats. FCV is highly contagious and demonstrates a high genetic variability. Upper respiratory tract disease, oral ulcerations, salivation, and gingivitis-stomatitis have been regarded as typical clinical signs of FCV infection. Ulcerative dermatitis, abortion, severe pneumonia, enteritis, chronic stomatitis, and virulent systemic disease have been reported more sporadically. Limping syndrome has been also described either in naturally or experimentally FCV-infected cats. In this study, we monitored a small outbreak of FCV infection in two household cats, in which limping disease was monitored with a 12-day lag time. The complete genome sequence was determined for the viruses isolated from the oropharyngeal and rectal swabs of the two animals, mapping up to 39 synonymous nucleotide mutations. The four isolates were sensitive to low pH conditions and trypsin treatment, a pattern usually associated with viruses isolated from the upper respiratory tract. Overall, the asynchronous pattern of infections and the results of genome sequencing suggest that a virus of respiratory origin was transmitted between the animals and that the FCV strain was able to retain the limping disease pathotype during the transmission chain, as previously observed in experimental studies with FCV strains associated with lameness.

Chemokine CCL6 Plays Key Role in the Inhibitory Effect of Vitamin A on Norovirus Infection

Norovirus (NoV) is the most common viral cause of acute gastroenteritis worldwide. Vitamin A has demonstrated the potential to protect against gastrointestinal infections. However, the effects of vitamin A on human norovirus (HuNoV) infections remain poorly understood. This study aimed to investigate how vitamin A administration affects NoV replication. We demonstrated that treatment with retinol or retinoic acid (RA) inhibited NoV replication in vitro based on their effects on HuNoV replicon-bearing cells and murine norovirus-1 (MNV-1) replication in murine cells. MNV replication in vitro showed significant transcriptomic changes, which were partially reversed by retinol treatment. RNAi knockdown of CCL6, a chemokine gene that was downregulated by MNV infection but upregulated by retinol administration, resulted in increased MNV replication in vitro. This suggested a role of CCL6 in the host response to MNV infections. Similar gene expression patterns were observed in the murine intestine after oral administration of RA and/or MNV-1.CW1. CCL6 directly decreased HuNoV replication in HG23 cells, and might indirectly regulate the immune response against NoV infection. Finally, relative replication levels of MNV-1.CW1 and MNV-1.CR6 were significantly increased in CCL6 knockout RAW 264.7 cells. This study is the first to comprehensively profile transcriptomes in response to NoV infection and vitamin A treatment in vitro, and thus may provide new insights into dietary prophylaxis and NoV infections.

Norovirus MLKL-like protein initiates cell death to induce viral egress

Non-enveloped viruses require cell lysis to release new virions from infected cells, suggesting that these viruses require mechanisms to induce cell death. Noroviruses are one such group of viruses, but there is no known mechanism that causes norovirus infection-triggered cell death and lysis1-3. Here we identify a molecular mechanism of norovirus-induced cell death. We found that the norovirus-encoded NTPase NS3 contains an N-terminal four-helix bundle domain homologous to the membrane-disruption domain of the pseudokinase mixed lineage kinase domain-like (MLKL). NS3 has a mitochondrial localization signal and thus induces cell death by targeting mitochondria. Full-length NS3 and an N-terminal fragment of the protein bound the mitochondrial membrane lipid cardiolipin, permeabilized the mitochondrial membrane and induced mitochondrial dysfunction. Both the N-terminal region and the mitochondrial localization motif of NS3 were essential for cell death, viral egress from cells and viral replication in mice. These findings suggest that noroviruses have acquired a host MLKL-like pore-forming domain to facilitate viral egress by inducing mitochondrial dysfunction.

Norovirus MLKL-like pore forming protein initiates programed cell death for viral egress

Non-enveloped viruses require cell lysis to release new virions from infected cells, suggesting that these viruses require mechanisms to induce cell death. Noroviruses are one such group of viruses, but a mechanism of norovirus-infection triggered cell death and lysis are unknown. Here we have identified a molecular mechanism of norovirus-induced cell death. We found that the norovirus-encoded NTPase contains a N-terminal four helix bundle domain homologous to the pore forming domain of the pseudokinase Mixed Lineage Kinase Domain-Like (MLKL). Norovirus NTPase acquired a mitochondrial localization signal, thereby inducing cell death by targeting mitochondria. NTPase full length (NTPase-FL) and N-terminal fragment (NTPase-NT) bound mitochondrial membrane lipid cardiolipin, permeabilized mitochondrial membrane and induced mitochondrial dysfunction. Both the N-terminal region and the mitochondrial localization motif of NTPase were essential for cell death, virus egress from cells and virus replication in mice. These findings suggest that noroviruses stole a MLKL-like pore forming domain and co-opted it to facilitate viral egress by inducing mitochondrial dysfunction.

Rapid, simple, and cost-effective plaque assay for murine norovirus using microcrystalline cellulose

Murine norovirus (MNV) is used widely as a practical alternative to human norovirus (HuNoV). Plaque-forming assays for MNV are important for developing therapeutic agents against HuNoV infections. Although agarose-overlay MNV assays have been reported, recent improvements in cellulose derivatives suggest that they could be optimized further, particularly with respect to improving the overlay material. To determine which overlay material is optimal for the MNV plaque assay, we compared four typical cellulose derivatives [microcrystalline cellulose (MCC), hydroxyethyl cellulose (HEC), hydroxypropyl methylcellulose (HPMC), and carboxymethyl cellulose (CMC)] with conventional agarose. We found that 3.5% (w/v) MCC-containing medium provided clear round-shaped plaques on RAW 264.7 cells 1 day after inoculation; the visibility of plaques was comparable with that of the original agarose-overlay assay. Removing residual MCC powder from the MCC-overlay assay before fixing was important for obtaining distinct plaques that are clearly countable. Finally, after calculating the plaque diameter as a percentage of well diameter, we found that 12- and 24-well plates were better than other plates for accurate plaque counting. The MCC-based MNV plaque assay is cost-effective and rapid, and produces plaques that are easy to count. Accurate virus quantification using this optimized plaque assay will enable reliable estimation of norovirus titers.

A novel vesivirus (family Caliciviridae) in European badgers (Meles meles) in Hungary, 2020/2021

In this study, a novel vesivirus (family Caliciviridae) was detected and characterized in faecal and tissue (blood and spleen) specimens collected from three (23.1%) out of 13 European badgers (Meles meles) in Hungary that were tested using RT-PCR and sequencing methods. The complete genome of the vesivirus strain European badger/B40/2021/HUN (OQ161773) is 8,375 nucleotides in length. The ORF1, ORF2, and ORF3 proteins have 81.1%, 70.5%, and 64.2% amino acid sequence identity, respectively, to the corresponding proteins of Asian badger vesivirus, which was first reported in badgers in China in 2022. These results indicate that more than one lineage/species of vesiviruses circulates in mustelid badgers in geographically different regions.

Genetic Evolution and Biological Characteristics of Feline Caliciviruses Isolated from Dogs

Feline calicivirus (FCV) is a highly contagious pathogen associated with oral and upper respiratory tract diseases (URTD), and it is also possibly considered as an enteric pathogen. Some studies found FCV-like viruses in the enteric tract of dogs, but there was a lack of understanding regarding the epidemiology and biological properties of FCVs in dogs. In this study, 252 fecal/feces samples were collected from dogs, with or without diarrhea, from 2020 to 2021. There were 6 FCV-positive samples (2.41%, 6/252), from which only two FCVs were successfully isolated and the complete genome sequences obtained. Phylogenetic analysis showed that the two canine-origin FCV isolates belonged to genogroup I and formed a monophyletic cluster with previous FCV strains, sharing a common ancestor. However, there was genetic diversity when the nt identity of the VP1 proteins between the two canine-origin FCV isolates (77.4% nt identity) was compared. In particular, the genomic sequence of the canine/GXHC01-21 isolate showed evidence of recombination at the 3ʹ end of the ORF1 gene with sequence identity very similar to the FCV strain, GX2019, previously isolated from cats in Guangxi in 2019. A comparison of their replication properties indicated that the two isolates could not replicate efficiently in MDCK cells. This was also seen in the enteric FCV isolate, GXNN04-20. However, both displayed similar plaque phenotypes to the respiratory FCV isolate, GX01-13. In addition, it was found that sera from vaccinated cats had low cross-reactivity in a neutralizing antibody test against the two canine-origin FCV isolates. Moreover, high neutralizing antibody titers (≥1 : 128) against canine-origin FCV viruses were observed in the two canine serum samples. This confirmed that interspecies transmission had occurred between cats and dogs. Our results provided an in-depth understanding of the genetic evolution and characteristics of FCVs circulating in dogs.

Porcine sapovirus-induced RIPK1-dependent necroptosis is proviral in LLC-PK cells

Sapoviruses belonging to the genus Sapovirus within the family Caliciviridae are commonly responsible for severe acute gastroenteritis in both humans and animals. Caliciviruses are known to induce intrinsic apoptosis in vitro and in vivo, however, calicivirus-induced necroptosis remains to be fully elucidated. Here, we demonstrate that infection of porcine kidney LLC-PK cells with porcine sapovirus (PSaV) Cowden strain as a representative of caliciviruses induces receptor-interacting protein kinase 1 (RIPK1)-dependent necroptosis and acts as proviral compared to the antiviral function of PSaV-induced apoptosis. Infection of LLC-PK cells with PSaV Cowden strain showed that the interaction of phosphorylated RIPK1 (pRIPK1) with RIPK3 (pRIPK3), mixed lineage kinase domain-like protein (pMLKL) increased in a time-dependent manner, indicating induction of PSaV-induced RIPK1-dependent necroptosis. Interfering of PSaV-infected cells with each necroptotic molecule (RIPK1, RIPK3, or MLKL) by treatment with each specific chemical inhibitor or knockdown with each specific siRNA significantly reduced replication of PSaV but increased apoptosis and cell viability, implying proviral action of PSaV-induced necroptosis. In contrast, treatment of PSaV-infected cells with pan-caspase inhibitor Z-VAD-FMK increased PSaV replication and necroptosis, indicating an antiviral action of PSaV-induced apoptosis. These results suggest that PSaV-induced RIPK1-dependent necroptosis and apoptosis‒which have proviral and antiviral effects, respectively‒counterbalanced each other in virus-infected cells. Our study contributes to understanding the nature of PSaV-induced necroptosis and apoptosis and will aid in developing efficient and affordable therapies against PSaV and other calicivirus infections.

Benchmarking Bioinformatic Tools for Amplicon-Based Sequencing of Norovirus

In order to survey noroviruses in our environment, it is essential that both wet-lab and computational methods are fit for purpose. Using a simulated sequencing data set, denoising-based (DADA2, Deblur and USEARCH-UNOISE3) and clustering-based pipelines (VSEARCH and FROGS) were compared with respect to their ability to represent composition and sequence information. Open source classifiers (Ribosomal Database Project [RDP], BLASTn, IDTAXA, QIIME2 naive Bayes, and SINTAX) were trained using three different databases: a custom database, the NoroNet database, and the Human calicivirus database. Each classifier and database combination was compared from the perspective of their classification accuracy. VSEARCH provides a robust option for analyzing viral amplicons based on composition analysis; however, all pipelines could return OTUs with high similarity to the expected sequences. Importantly, pipeline choice could lead to more false positives (DADA2) or underclassification (FROGS), a key aspect when considering pipeline application for source attribution. Classification was more strongly impacted by the classifier than the database, although disagreement increased with norovirus GII.4 capsid variant designation. We recommend the use of the RDP classifier in conjunction with VSEARCH; however, maintenance of the underlying database is essential for optimal use. IMPORTANCE In benchmarking bioinformatic pipelines for analyzing high-throughput sequencing (HTS) data sets, we provide method standardization for bioinformatics broadly and specifically for norovirus in situations for which no officially endorsed methods exist at present. This study provides recommendations for the appropriate analysis and classification of norovirus amplicon HTS data and will be widely applicable during outbreak investigations.

Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing

The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.

Highly diverse ribonucleic acid viruses in the viromes of eukaryotic host species in Yunnan province, China

Background

The diversity in currently documented viruses and their morphological characteristics indicates the need for understanding the evolutionary characteristics of viruses. Notably, further studies are needed to obtain a comprehensive landscape of virome, the virome of host species in Yunnan province, China.

Materials and methods

We implemented the metagenomic next-generation sequencing strategy to investigate the viral diversity, which involved in 465 specimens collected from bats, pangolins, monkeys, and other species. The diverse RNA viruses were analyzed, especially focusing on the genome organization, genetic divergence and phylogenetic relationships.

Results

In this study, we investigated the viral composition of eight libraries from bats, pangolins, monkeys, and other species, and found several diverse RNA viruses, including the Alphacoronavirus from bat specimens. By characterizing the genome organization, genetic divergence, and phylogenetic relationships, we identified five Alphacoronavirus strains, which shared phylogenetic association with Bat-CoV-HKU8-related strains. The pestivirus-like virus related to recently identified Dongyang pangolin virus (DYPV) strains from dead pangolin specimens, suggesting that these viruses are evolving. Some genomes showed higher divergence from known species (e.g., calicivirus CS9-Cali-YN-CHN-2020), and many showed evidence of recombination events with unknown or known strains (e.g., mamastroviruses BF2-astro-YN-CHN-2020 and EV-A122 AKM5-YN-CHN-2020). The newly identified viruses showed extensive changes and could be assigned as new species, or even genus (e.g., calicivirus CS9-Cali-YN-CHN-2020 and iflavirus Ifla-YN-CHN-2020). Moreover, we identified several highly divergent RNA viruses and estimated their evolutionary characteristics among different hosts, providing data for further examination of their evolutionary dynamics.

Conclusion

Overall, our study emphasizes the close association between emerging viruses and infectious diseases, and the need for more comprehensive surveys.

Identification of a Novel Solinvivirus with Nuclear Localization Associated with Mass Mortalities in Cultured Whiteleg Shrimp (Penaeus vannamei)

The emergence and spread of disease-causing viruses in shrimp aquaculture is not uncommon. Since 2016, unusual mortalities have been affecting the Brazilian shrimp industry and we have associated these unusual mortalities with a novel variant of infectious myonecrosis virus (IMNV). The transcriptome analysis of these diseased shrimp showed an additional divergent viral sequence that we have assigned to the family Solinviviridae. The novel virus has been tentatively termed Penaeus vannamei solinvivirus (PvSV) (GenBank accession: OP265432). The full-length genome of the PvSV is 10.44 kb (excluding the poly A tail) and codes for a polyprotein of 3326 aa. Five conserved domains coding for a helicase, RdRp, calicivirus coat protein, G-patch and tegument protein were identified. The genome organization of the PvSV is similar to other (Nylan deria fulva virus 1) solinvivirus. A unique feature of this virus that differs from other members of the Solinviviridae is the presence of putative nuclear localization signals. The tissue tropism of this virus is wide, infecting cells of the hepatopancreas, gastrointestinal tract, lymphoid organ and muscle tissue. Another unique feature is that it is the only RNA virus of penaeid shrimp that shows a nuclear localization by in situ hybridization. The PvSV has a wide distribution in Brazil and has been found in the states of Maranhão State (Perizes de Baixo), Piaui State (Mexeriqueira), Ceará State (Camocim, Jaguaruana, Aracati and Alto Santo) and Pará State where it has been detected in coinfections with IMNV. The diagnostic methods developed here (real-time RT-PCR and in situ hybridization) are effective for the detection of the pathogen and should be employed to limit its spread. Furthermore, the identification of the PvSV shows the increasing host range of the relatively new family Solinviviridae.

Detection of a new emerging strain of rabbit haemorrhagic disease virus 2 (GI.2) in China

Introduction

In May 2020, an outbreak of rabbit haemorrhagic disease 2 (RHD2) caused by the rabbit haemorrhagic disease virus 2 (RHDV2, GI.2) occurred in Sichuan, China. The acute onset and short disease course resulted in rabbit mortality as high as 42.86%. Currently, basic research on the aetiology and genetic characteristics of GI.2 is lacking in China.

Material and Methods

Pathological changes in various tissues from infected rabbits were investigated and the viral genome was characterised. This study used RT-PCR, histopathology and scanning electron microscopy to identify the pathogen in samples from infected rabbits that had died. Phylogenetic trees were constructed based on whole genome sequence analysis, and recombination events were analysed.

Results

RT-PCR identified the presence of GI.2. Histopathology revealed liver cell necrosis and haemorrhaging into lung alveoli. Electron microscopy demonstrated spherical GI.2 particles that were 40 nm in size. The gene sequence length of the isolate was 7,445 bp (GenBank accession number MW178244). A phylogenetic analysis based on the genome of the isolated strain and 60 reference strains showed that the isolate was grouped together with GI.2 strain MT586027.1 in a relatively independent sub-branch. The results of the recombination analysis showed that the strain was recombined from the MT586027.1 (major parent) and MN90145.1 (minor parent) strains, and recombination breakpoints were at locations in the 2858–5137 nt range.

Conclusion

The results of this study extend our understanding of the molecular epidemiology of GI.2.

Genetic and phylogenetic analysis of capsid gene of feline calicivirus in Nanjing, China

Feline calicivirus (FCV) is a common and important pathogen in cats, typically resulting in upper respiratory tract disease or ulcerative oral lesions. Although there are large number of researches on FCV and vaccines against FCV have been widely used for years, the explanation for vaccination failure and further studies on the prevalence of FCV are still necessary in China. In this study, 86 nasopharyngeal swabs from pet cats with upper respiratory symptoms from several Nanjing animal hospitals were collected in 2020. Among them, 36 (41.86%) were positive for FCV. In addition, 13 FCV capsid genes were sequenced. The comparative analysis of linear B-cell epitopes of VP1 gene indicated that there were many amino acid variations existed among FCV vaccine strains and these strains currently circulating in Nanjing, which may relate to the failure of vaccination and maybe aid for future vaccine design. Besides, phylogenetic analysis of capsid gene revealed two genotypes. Except for the F86 strain, most of the strains were clustered with FCV I genotype, which indicated that FCV I genotype was the most prevalent genotype currently circulating in Nanjing. In conclusion, this study provided useful information as to the evolution and genetic variants of FCV in Nanjing, which is urgent for the future instructions of effective disease prevention and control strategies.

Characterization of a Novel RNA Virus Causing Massive Mortality in Yellow Catfish, Pelteobagrus fulvidraco, as an Emerging Genus in Caliciviridae (Picornavirales)

An emerging disease in farmed yellow catfish (Pelteobagrus fulvidraco) causing massive mortality broke out in 2020 in Hubei, China. Histopathological examination indicated significant changes in kidneys and spleens of diseased fish. Electron microscopy revealed large numbers of viral particles in the kidneys and spleens. These particles were spherical with a diameter of approximately 35 nm. By using RNA sequencing and rapid identification of cDNA ends, the full nucleotide sequence of the virus was identified. The viral genome comprises 7,432 bp and contains three open reading frames sharing no nucleotide sequence similarity with other viruses; however, the amino acid sequence partially matched that of the nonstructural (NS) proteins from viruses in the order Picornavirales. Combined with the phylogenetic analysis, the conserved amino acid motifs and the domains of the viral genome predict a genome order typical of a calicivirus. Therefore, this virus was tentatively named yellow catfish calicivirus (YcCV). Cell culture showed that YcCV could cause a cytopathic effect in the channel catfish kidney cell line (CCK) at early passages. In artificial infection, this virus could infect healthy yellow catfish and led to clinical symptoms similar to those that occurred naturally. In situ hybridization analysis detected positive signals of the virus in kidney, spleen, liver, heart, and gill tissues of diseased fish. This study represents the first report of calicivirus infection in yellow catfish and provides a solid basis for future studies on the control of this viral disease.

IMPORTANCE Caliciviruses are rapidly evolving viruses that cause pandemic outbreaks associated with significant morbidity and mortality globally. A novel calicivirus identified from yellow catfish also causes substantial mortality. Using an RNA sequencing (RNA-seq) and rapid amplification of cDNA ends (RACE) method, the full nucleotide sequence was identified and characterized, and this virus was tentatively named yellow catfish calicivirus (YcCV). A nucleotide sequence similarity search found no match with other viruses, and an amino acid sequence comparison indicated approximately 23.3% amino acid homology with the viruses in the order Picornavirales. These findings may represent a new avenue to explain virus evolution and suggest a need to further study the pathogenesis of calicivirus and characterize possible interactions among interspecific viruses in the aquaculture environment.

Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck's Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family

Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular genetics and bioinformatics methods can shed light on their genetic architecture and evolutionary relationships. Here, we present and characterize the complete genome sequence of calicivirus isolated from a sandpiper-Temminck's stint (Calidris temminckii), preliminarily named Temminck's stint calicivirus (TsCV). Its genome is a linear, non-segmented, single-stranded (+sense) RNA with genome organization typical of avian caliciviruses. Comparative studies have shown significant divergence of the nucleotide sequence of the TsCV genome, as well as the amino acid sequence of the major capsid protein from all publicly available genomic and protein sequences, with the highest genome sequence similarity to unclassified Ruddy turnstone calicivirus A (43.68%) and the lowest pairwise divergence of the major capsid protein with unclassified goose calicivirus (57.44%). Phylogenetic analysis, as well as a comparative analysis of the homologous proteins, showed evidence of another separate genus within the Caliciviridae family-previously proposed, but not yet accepted by International Committee on Taxonomy of Viruses (ICTV)-the Sanovirus genus, which combines seven previously unclassified genomic sequences of avian caliciviruses, including the newly discovered TsCV, which we propose to consider as a separate species.