SARS-CoV-2 3CL protease (3CL) plays crucial role in the viral life cycle by releasing different non-structural proteins from viral polyproteins. It also interacts with several host factors and orchestrates different host...SARS-CoV-2 3CL protease (3CL) plays crucial role in the viral life cycle by releasing different non-structural proteins from viral polyproteins. It also interacts with several host factors and orchestrates different host cell pathways by cleaving key cellular factors involved in immune modulation, cellular metabolism and cell death. Several host factors have been identified as high confidence substrates of 3CL which regulates host cellular environment both in an enzyme-dependent and enzyme-independent manner. Degradation of RIG-I, TRIM25 and NLRP12 by 3CL downregulates the innate immune response while enzyme-independent interaction with host factors like MAVS promote both its degradation and upregulation. Cellular transcription and translation are altered by interaction of 3CL with host proteins. It affects cell-death by interacting with factors like Gal-8, NDP52 and GSDMD. Post-COVID neurodegenerative disorders have been observed due to the downregulation of neuronal factors like NEMO and UBE3A. The spectrum of 3CL interaction with the key host factors indicates the alternate role of viral protease that modulates host response during infection. Several 3CL targets and their cleavage sites on the target proteins have been identified. This review highlights the crosstalk between 3CL and different host factors as possible alternate therapeutic targets to inhibit the viral propagation as well as address the post COVID clinical issues.
Theiler's murine encephalomyelitis virus (TMEV) is a natural enteric pathogen of mice that, when injected intracranially, induces a demyelinating disease resembling multiple sclerosis. However, data on viral shedding fol...Theiler's murine encephalomyelitis virus (TMEV) is a natural enteric pathogen of mice that, when injected intracranially, induces a demyelinating disease resembling multiple sclerosis. However, data on viral shedding following intracranial infection are sparse for some strains and entirely absent for others, such as the Daniels strain, making it difficult to accurately assess the biological risks associated with infected animals. In our study, we used a combination of RT-qPCR and immunoassays to evaluate viral shedding and the associated infectious risk. We show that viral RNA is detectable in the feces of some mice and that the proportion of shedding animals varies by mouse line. Nevertheless, none of the sentinel mice exposed to soiled bedding from infected animals exhibited seroconversion, indicating that the viral particles are either present at levels below the minimum infectious dose or represent residual, non-infectious material rather than active, transmission-competent virus.
Spiraea plants showing symptoms of virus infection were investigated using high-throughput sequencing which resulted in the identification of two novel viruses: an emaravirus named Spiraea chlorotic leaf spot distortion...Spiraea plants showing symptoms of virus infection were investigated using high-throughput sequencing which resulted in the identification of two novel viruses: an emaravirus named Spiraea chlorotic leaf spot distortion virus (SCLSDV), and an alphacytorhabdovirus named Spiraea alphacytorhabdovirus 1 (SpCRV-1). The complete genome of SCLSDV comprises four RNA segments, each encoding a distinct protein: RNA-dependent RNA polymerase, glycoprotein precursor, nucleocapsid protein, and movement protein, respectively. SCLSDV shares 33.99-71.78% amino acid identity with pear chlorotic leaf spot-associated virus. Virus purification and electron microscopy confirmed pleomorphic, enveloped particles (80-100 nm) matching the morphology of members of the genus Emaravirus. The alphacytorhabdovirus shares 70% of nucleotide identity with Actinidia virus D and encodes eight putative proteins. Both novel viruses were detected in a mixed infection with Spiraea yellow leaf spot virus. Additionally, SCLSDV was consistently detected in a single infection in 50 out of 77 plant samples exhibiting yellow spot disease, characterized by chlorotic lesions, leaf distortion, and necrosis. These findings suggest that strong yellow spot symptoms and leaf distortion are likely associated with SCLSDV infection. Furthermore, eriophyid mites were collected from symptomatic plants and identified morphologically as Calepitrimerus sp. Given the known role of eriophyid mites in emaravirus transmission, their presence suggests it could be a potential vector for SCLSDV.
Imakado S, Pham NTK, Khamrin P
… +15 more, Shimizu-Onda Y, Hoque SA, Trinh QD, Hussain M, Yodmeeklin A, Kumthip K, Nishimura S, Kobayashi M, Sugita K, Okitsu S, Maneekarn N, Hayakawa S, Komine-Aizawa S, Yoshimune K, Ushijima H
Noroviruses (NoVs) are a leading cause of acute gastroenteritis (AGE) worldwide, with genetic diversity driven by recombination and genotype replacement. This study investigated the prevalence and molecular characteristi...Noroviruses (NoVs) are a leading cause of acute gastroenteritis (AGE) worldwide, with genetic diversity driven by recombination and genotype replacement. This study investigated the prevalence and molecular characteristics of NoVs among Japanese children with AGE from July 2021 to June 2024. A total of 1,095 stool samples were collected from three prefectures (Kyoto, Osaka, and Shizuoka), and NoV RNA was detected in 456 cases (41.6%). Genogroup GII predominated (96.9%), while GI infections were rare. Genotyping identified eight genotypes, including two GI (GI.1, GI.6) and six GII (GII.2, GII.3, GII.4, GII.6, GII.7, GII.17). GII.4 remained the predominant genotype (71.7%) throughout the study period. Notably, GII.7 emerged in 2023-2024 and became the second most prevalent genotype. Analysis of the ORF1/ORF2 junction identified multiple RdRp-capsid combinations, with recombinant strains accounting for 92.5% of detections. The predominant recombinant lineages were GII.4[P16] and GII.4[P31], followed by GII.2[P16]. Phylogenetic analysis indicated close relatedness to strains circulating internationally. These findings demonstrate the sustained predominance of GII.4, the emergence of GII.7, and the high prevalence of recombinant strains among Japanese children, highlighting the importance of continuous molecular surveillance.
BACKGROUND: Selective pressure drives SARS-CoV-2 evolution, with spike RBD substitutions shaping ACE2 binding and antibody escape. N481K RBD mutation emerged early in Qatar (2020) and later re-emerged globally, reaching...BACKGROUND: Selective pressure drives SARS-CoV-2 evolution, with spike RBD substitutions shaping ACE2 binding and antibody escape. N481K RBD mutation emerged early in Qatar (2020) and later re-emerged globally, reaching near-fixation by 2024-2025, yet its functional significance remained unexplored. METHODS: We analyzed the temporal and geographic circulation of N481K across > 17 million SARS-CoV-2 genomes (2020-2025). Structural effects were assessed using modeling, docking, and molecular dynamics. Functional impact was evaluated using VSV pseudovirus neutralization tests with sera from infected individuals (n = 48) and vaccinated cohorts: mRNA (n = 16), Sinopharm (n = 45), and AstraZeneca (n = 28). RESULTS: N481K was detected in 4.14% (703,777/17,016,111) of global genomes and reached near-fixation (> 90%) in dominant Omicron lineages by 2024, with prevalence rising from 71.5% in early 2024 to 94.4% by week 36 of 2025. Structural analyses showed a 0.706 Å RMSD deviation and higher ACE2 docking affinity (-313 vs. - 308 kcal/mol) compared to the wild-type (WT) RBD. Molecular dynamics confirmed increased stability and lower binding free energy for N481K versus WT (-77.07 ± 0.90 vs. - 43.09 ± 0.98 kcal/mol). Among samples with detectable WT neutralization (n = 89), mean neutralization declined from 69.76% (WT) to 42.47% (N481K) (p < 0.0001), with the largest reductions in AstraZeneca, Sinopharm, and infected cohorts. mRNA recipients retained the highest neutralization [77.5% (WT) vs. 56.0% (N481K)]. CONCLUSION: N481K enhances ACE2 binding while partially evading antibody neutralization, suggesting viral fitness and persistence.
Anelloviruses are circular single stranded DNA viruses that are highly prevalent among humans and other mammal and avian hosts, with persistent infections enduring throughout the lifespan without causing disease. Investi...Anelloviruses are circular single stranded DNA viruses that are highly prevalent among humans and other mammal and avian hosts, with persistent infections enduring throughout the lifespan without causing disease. Investigating these viruses in non-human primate hosts can offer a phylogenetic perspective on anellovirus-primate evolutionary dynamics, and studying wild populations can help build a translational framework for natural host-virus interactions. Here we report six complete anellovirus genomes identified in wild geladas (Theropithecus gelada), a primate endemic to the Ethiopian Highlands. Anellovirus genomes were identified in blood samples taken from geladas in the Simien Mountains National Park, Ethiopia. The six genomes represented four new anellovirus species-level lineages, and phylogenetic analysis of the ORF1 (capsid protein) sequences revealed that these anelloviruses cluster with other viruses in the Alphatorquevirus genus. As the first report of complete anellovirus genomes in geladas, this study expands the known host range of the Alphatorquevirus genus and anelloviruses more broadly, adds to our knowledge of the gelada virome, and contributes to our understanding of the shared primate virome.
Highly replicative influenza viruses have been linked to elevated nasopharyngeal viral load in patients, while in murine model these viruses are associated with amplified cytokine responses, and greater severity. In the...Highly replicative influenza viruses have been linked to elevated nasopharyngeal viral load in patients, while in murine model these viruses are associated with amplified cytokine responses, and greater severity. In the present study, five anti-influenza agents-including four neuraminidase inhibitors (zanamivir, laninamivir, peramivir, and oseltamivir acid) and one polymerase acidic endonuclease inhibitor (baloxavir acid)-were evaluated against both a laboratory strain (PR8) and four clinical isolates lacking known resistance mutations. Madin-Darby Canine Kidney (MDCK) and A549 human lung epithelial cells were inoculated at 1x10 and 3x10 virus copies/mL, respectively, and exposed to varying concentrations of the drug for 72 hours. Subsequent analysis measured viral loads and infectious units. Both classes of antiviral drugs demonstrated substantial activity, particularly against strains that proliferate rapidly in vitro. While all tested anti-influenza drugs reduced viral particles production by approximately 50% in clinical isolates, achieving 90% suppression with neuraminidase inhibitors was limited to the PR8 laboratory strain. In A549 cell cultures, PR8 showed a 90% reduction in viral particles production with any of the compounds; however, neuraminidase inhibitors typically had diminished impact on clinical isolates. Notably, baloxavir acid consistently achieved robust suppression in both the PR8 strain and clinical isolates in MDCK and A549 cell lines. The present study finds that antiviral drugs can significantly impact highly replicative influenza viruses, but do not always suppress them to undetectable levels. Effectiveness varies by the epidemic strains, likely due to unknown genetic factors. Further research is needed to identify these traits and improve diagnosis and treatment.
Mycoviruses play diverse ecological roles ranging from conferring hypovirulence to establishing mutualistic symbioses. While these agents are vital for biocontrol, their genomic diversity within basal fungi is still poor...Mycoviruses play diverse ecological roles ranging from conferring hypovirulence to establishing mutualistic symbioses. While these agents are vital for biocontrol, their genomic diversity within basal fungi is still poorly understood. In this study, we identified and characterized two novel double-stranded RNA (dsRNA) viruses co-infecting the basal fungus Conidiobolus macrozygosporus isolate RCEF7522. Complete genome sequences of the two viruses were determined by high-throughput sequencing and rapid amplification of cDNA ends (RACE). CmzV1 contains a dsRNA genome of 5,086 bp (G + C content: 48.3%) encoding two open reading frames (ORFs): a coat protein (CP, 852 aa, 92.46 kDa) and RNA-dependent RNA polymerase (RdRp, 731 aa, 83.18 kDa). BLASTp analysis revealed highest sequence identity with Cronartium ribicola totivirus 1 (CrTV1) at 28.61% for CP and 34.65% for RdRp. CmzV2 contains a dsRNA genome of 3,179 bp (G + C: 50.9%) encoding a hypothetical protein (HP, 285 aa, 32.98 kDa) and RdRp (672 aa, 77.19 kDa). CmzV2 shares 35.74% RdRp sequence identity with Plasmopara viticola lesion-associated virus 1 and 40-41% identity with genus Zybavirus members in the RdRp region. Phylogenetic analysis based on RdRp sequences indicates that CmzV1 clusters with genus Totivirus (family Orthototiviridae) and CmzV2 groups with genus Zybavirus (family Amalgaviridae). Based on genomic characteristics and phylogenetic relationships, CmzV1 is proposed as a novel species in genus Totivirus, and CmzV2 as a novel species in genus Zybavirus. Although the ~ 6.0 kb viral genome identified in RCEF7522 could not be fully recovered, this work expands the known diversity of mycoviruses in basal fungi and contributes to our understanding of mycovirus distribution across fungal taxa.
Canine parvovirus type 2 (CPV-2) remains one of the most significant viral pathogens causing infectious disease in domestic dogs worldwide, particularly causing severe hemorrhagic gastroenteritis in puppies. In recent ye...Canine parvovirus type 2 (CPV-2) remains one of the most significant viral pathogens causing infectious disease in domestic dogs worldwide, particularly causing severe hemorrhagic gastroenteritis in puppies. In recent years, canine circovirus (CanineCV) has emerged as an additional enteric virus of concern, although its role in co-infection with CPV-2 remains poorly characterized in Southeast Asia. This study determines the prevalence, co-infection rate, and molecular characteristics of CPV-2 and CanineCV co-infections in domestic dogs across three major regions of Vietnam. A total of 254 rectal swab samples were collected from 2023 to 2024 from dogs exhibiting clinical signs consistent with CPV-2 infection. All samples were tested for CPV-2 and CanineCV by real-time PCR, and CPV-2-positive samples were genotyped using a SimpleProbe assay. CPV-2-only infection resulted in a prevalence of 77.17%, while CPV-2-CanineCV co-infection had a prevalence of 22.83%. Vaccinated canines have 11.36% co-infection, while those with unknown vaccination history has 28.79% and unvaccinated has 19.23%. Genotyping results demonstrated that CPV-2c was the dominant variant, accounting for 93.31% overall and 93.1% in co-infections at a 22.78% co-infection rate, whereas CPV-2a was infrequent, at 6.69% overall and 6.9% in co-infections at a 23.53% co-infection rate, and CPV-2b was not detected. The highest co-infection rate was recorded in the Central region of Vietnam at 50%, compared with 9.38% in the North and 4.55% in the South. Seasonal analysis showed a high co-infection rate during the fall with no significant difference. Age distribution revealed that younger puppies were most affected and vulnerable to co-infection, with 37.50% in < 2 months, 24.24% in 2-3 months, 23.20% in 3-6 months, and 18.18% in 6-12 months. These findings suggest that CanineCV co-circulates extensively with CPV-2, particularly in younger dogs. The results also highlight the continued dominance of CPV-2c in Vietnam and underscore the importance of including CanineCV in diagnostic, vaccines, and epidemiological surveillance of canine enteric diseases.
Gomes AJC, Lemes Garcia YLN, Geraldini DB
… +12 more, Domit C, de Lima FH, Araújo JP, Gularte JS, Filippi M, de Abreu Góes Pereira VM, Demoliner M, Sita A, Spilki FR, de Freitas Calmon M, Rahal P, da Costa VG
Circoviruses (CVs) infect diverse mammals, birds, and freshwater fish and are linked to diseases causing major economic losses. Despite being well studied in psittacines, their circulation in other avian groups and mamma...Circoviruses (CVs) infect diverse mammals, birds, and freshwater fish and are linked to diseases causing major economic losses. Despite being well studied in psittacines, their circulation in other avian groups and mammals is poorly understood. We conducted molecular surveillance of CVs in migratory birds and mammals along the Paraná coast, southern Brazil. Sterna hirundinacea specimen tested positive by Nested-PCR for GullCV. In the GullCV-infected bird, histopathology revealed nonspecific lesions, including marked splenic lymphoid atrophy, cachexia-related changes, acute tubular necrosis, and generalized congestion. Sanger sequencing revealed 83% nucleotide identity with CV sequences previously reported in gulls from the United States, which was consistent with results obtained by NGS and Rep-based phylogenetic analysis. These findings contribute to the understanding of CV diversity, distribution, and host range.
RNA viruses are highly abundant and diverse in marine ecosystems, yet the currently discovered viral species represent only a minute fraction of the total diversity, with viral communities in port ecosystems particularly...RNA viruses are highly abundant and diverse in marine ecosystems, yet the currently discovered viral species represent only a minute fraction of the total diversity, with viral communities in port ecosystems particularly understudied. To bridge this gap, in summer, approximately 100 L of surface water was collected from Yangshan Port. Viral particles were concentrated using tandem filtration and 50-kDa tangential-flow ultrafiltration, followed by metatranscriptomic sequencing of extracted RNA. This approach yielded 74 full-length RNA-dependent RNA polymerase (RdRp) sequences, which clustered into 72 distinct genus-level (or higher) taxonomic units-significantly expanding the known diversity of seaport RNA viruses. Phylogenetic and EFI-EST network analyses showed that 93% of these sequences belong to the two dominant phyla, Pisuviricota and Kitrinoviricota, forming a seasonally stable backbone consistent with a previously obtained winter dataset. Notably, five sequences formed a maximally supported (99% bootstrap) basal clade within Kitrinoviricota. They share only 8-24% amino-acid identity with representatives of the four ICTV-recognized classes and exhibit DALI Z-scores ≤ 20, precluding assignment to any currently established class. Three of these candidate novel-class viruses were already detectable in the winter metatranscriptome (bit-score ≥ 40, ≥ 98% amino-acid identity), indicating year-round persistence of this lineage in Yangshan Port. Their taxonomic novelty thus reflects a gap in the current ICTV framework rather than seasonal sporadicity. Two sequences represent true seasonal debutants absent from public databases. These sequences not only fill a notable gap in the summer virome but also lack a class-level taxonomic anchor within the ICTV hierarchy, jointly occupying a "season-new" and "taxon-new" niche that prioritizes them for downstream isolation and functional characterization.
Leaves of Passiflora sp. plants showing systemic chlorosis, mottling, and leaf malformation were observed in Fujian, China, in 2023. High-throughput sequencing of leaf samples from a single plant revealed the presence of...Leaves of Passiflora sp. plants showing systemic chlorosis, mottling, and leaf malformation were observed in Fujian, China, in 2023. High-throughput sequencing of leaf samples from a single plant revealed the presence of passion fruit woodiness virus (PFWV) and a previously undescribed virus. The complete genome of the novel virus is 8,316 nt in length and exhibits a typical Carlavirus genome organization with six open reading frames. Phylogenetic analyses based on replicase and coat protein sequences placed the virus within the genus Carlavirus (family Betaflexiviridae). Mechanical inoculation assays showed that the virus is transmissible to Nicotiana benthamiana, inducing characteristic symptoms. These results indicate that the virus, designated provisionally as passiflora chlorotic crinkle virus (PCCV), represents a novel species of the genus Carlavirus.
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne zoonotic pathogen. We evaluated nanopore adaptive sampling (NAS) for whole-genome assembly using two wildlife-derived SFTSV isolates (Vero cell-cu...Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne zoonotic pathogen. We evaluated nanopore adaptive sampling (NAS) for whole-genome assembly using two wildlife-derived SFTSV isolates (Vero cell-cultured) sequenced alongside tick-derived samples. Using the PromethION platform, complete L, M, and S segments were successfully assembled in a single run. NAS supported the reconstruction of previously characterized isolate, including an extended S segment, and enabled the characterization of a genotype B-2 isolate. These results suggest that NAS is an effective tool for genomic surveillance of SFTSV under complex sequencing conditions.
Lumpy skin disease (LSD) is a re-emerging transboundary viral disease of major economic importance affecting cattle worldwide. In Algeria, LSD was reported for the first time in June 2024, based on clinical observations...Lumpy skin disease (LSD) is a re-emerging transboundary viral disease of major economic importance affecting cattle worldwide. In Algeria, LSD was reported for the first time in June 2024, based on clinical observations and serological evidence. This study aimed to perform molecular detection and phylogenetic characterization of the first LSD virus (LSDV) strains circulating in Algeria. From June to August 2024, blood samples were collected from clinically affected cattle in eastern Algeria, a region characterized by active outbreaks and environmental conditions favorable to vector-borne transmission. Animals exhibited typical clinical signs of LSD, including fever, generalized skin nodules, ocular and nasal discharge, and lymphadenopathy. Blood samples were selected to detect LSDV during the viremic phase of infection and enable molecular confirmation under field conditions. Molecular detection was performed using PCR targeting the P32 gene for specific identification of Capripoxvirus. Selected samples were further analyzed using a multi-target PCR approach targeting partial P32 and F genes, as well as complete GPCR and RPO30 genes, followed by sequencing and phylogenetic analysis. LSDV was successfully detected, and sequence analysis revealed genetically homogeneous strains belonging to the pathogenic clade. The Algerian isolates showed close genetic relationships with strains circulating across Africa, the Middle East, Asia, and Europe, suggesting a shared epidemiological origin. A characteristic deletion in the GPCR gene further distinguished field strains from vaccine-related strains. This study provides the first molecular and phylogenetic characterization of LSDV associated with the initial outbreak in Algeria, highlighting transboundary spread patterns and emphasizing the need for enhanced surveillance to monitor virus circulation and evolution and evolution.
Alphacoronaviruses comprise human, livestock, and wildlife coronaviruses of importance, particularly to the livestock industry worldwide. Domestic livestock have the potential to serve as intermediate hosts of coronaviru...Alphacoronaviruses comprise human, livestock, and wildlife coronaviruses of importance, particularly to the livestock industry worldwide. Domestic livestock have the potential to serve as intermediate hosts of coronaviruses, given the contact they have with both humans and wildlife. With the aim of detection and subsequent complete genome sequencing of novel and known but previously undetected alphacoronaviruses, a screening RT-PCR assay was established. In vitro transcripts of two human alphacoronaviruses were generated to evaluate assay performance, and a collection of archived bat and livestock viral RNA samples was tested as part of assay validation. Confirmation of RT-PCR-positive outcomes was done by Sanger and high-throughput sequencing, before phylogenetic analysis. The assay can detect both human alphacoronaviruses with a detection limit of 46 copies/reaction of Alphacoronavirus amsterdamense and 504 copies/reaction of Alphacoronavirus chicagoense in vitro transcripts, as estimated by a probit regression analysis. Validation screening of domestic and peri-domestic livestock species, including cattle, sheep, goats, donkeys, pigs, rabbits, and grasscutters, did not yield any positive outcomes. Confirmed detections were made in bats (3.11%), comprising 1.84% alphacoronaviruses and 1.27% betacoronaviruses. Two complete genomes were obtained for an Alphacoronavirus chicagoense-related bat coronavirus and a putative member of the subgenus Hibecovirus. A near-complete genome was obtained for a Chaerephon spp. bat alphacoronavirus, which was found to be most closely related to a similar virus from Nigeria. This study presents a sensitive assay for coronavirus surveillance and provides additional complete genomes, thereby enhancing our understanding of coronavirus diversity.
Enterovirus D68 (EV-D68) is a re-emerging respiratory pathogen that is increasingly associated with severe respiratory disease and occasional neurological complications, yet its circulation in Portugal remains poorly doc...Enterovirus D68 (EV-D68) is a re-emerging respiratory pathogen that is increasingly associated with severe respiratory disease and occasional neurological complications, yet its circulation in Portugal remains poorly documented. In the present study, we investigated the presence of EV-D68 in respiratory samples collected in southern Portugal (Algarve region) from October 2024 to February 2025. Screening of 150 respiratory samples from patients (115 from children and 35 from adults), all previously positive for rhinovirus/enterovirus, revealed eight EV-D68-positive cases, corresponding to a detection rate of 5.44%, spanning a broad age range from infancy to the elderly. Clinical manifestations ranged from mild respiratory illness to severe conditions, including pneumonia and acute respiratory distress syndrome. Neurological manifestations, including complex febrile seizures and encephalomyelitis, were also observed in EV-D68-positive patients. Some cases involved coinfections, while others presented with EV-D68 as the sole detected respiratory pathogen. Genomic characterization from one isolate revealed a VP1 fragment belonging to clade B3, and a complete genome from another isolate clustered within clade A2. Phylogenetic analysis confirmed clustering with contemporary European isolates. These findings provide preliminary evidence of EV-D68 detection in southern Portugal and document the presence of clades A2 and B3 among the characterized samples. The results illustrate the heterogeneous clinical presentations observed in affected patients and highlight the value of continued molecular monitoring and genomic characterization of EV-D68.
Although feline astrovirus (FAstV) is recognized as a cause of feline gastroenteritis, the prevalence of asymptomatic infections in Japan remains unclear. We examined fecal samples from 124 domestic and 195 stray cats (n...Although feline astrovirus (FAstV) is recognized as a cause of feline gastroenteritis, the prevalence of asymptomatic infections in Japan remains unclear. We examined fecal samples from 124 domestic and 195 stray cats (n = 319) for FAstV and two common feline enteric viruses, feline enteric coronavirus (FECoV) and feline bocaparvovirus (FBoV). FAstV was detected only in stray cats (6/195, 3.08%). Among FAstV-positive samples, PCR-based co-detection with FECoV and/or FBoV was observed in 5/6 (83.3%). Phylogenetic analysis of two complete ORF2 sequences (TYT-100 and TYT-101) and two partial ORF2 sequences (~ 500 bp; TYT-13 and TYT-14) showed that Japanese FAstV strains clustered together and were genetically distinct from previously reported strains, based on available sequences. These findings suggest a low prevalence of FAstV with frequent co-detection of other enteric viruses in asymptomatic cats in Japan.
A novel trirhavirus, tentatively named "goji trirhavirus 1" (GqTRV1), was identified by high-throughput sequencing of a "Ningnongqi17" goji sample exhibiting severe leaf twisting symptoms, collected from a commercial pla...A novel trirhavirus, tentatively named "goji trirhavirus 1" (GqTRV1), was identified by high-throughput sequencing of a "Ningnongqi17" goji sample exhibiting severe leaf twisting symptoms, collected from a commercial plantation in Yinchuan, Ningxia, China. The complete genome sequence of GqTRV1 was determined by RT-PCR and the rapid amplification of cDNA ends (RACE) method. The genome of GqTRV1 comprises three negative-sense single-stranded RNAs (RNA1, RNA2, and RNA3), which encode eight putative proteins, including L, N, P2, P3, P4, P6, P7, and P8. Conserved 3'-AAUUCUUUUGN(N)nCUC-5' motifs were identified at the gene junction regions. The genome shows complete 11-nucleotide terminal complementarity between the 5' and 3' ends, as well as conserved 12-nucleotide terminal identity among all RNA segments. Phylogenetic analysis based on the L protein sequence placed GqTRV1 within the genus Trirhavirus, forming a well-supported subclade with chenopodium trirhavirus 1 (CheTRV1) and capsicum trirhavirus 1 (CapTRV1). Pairwise sequence comparisons demonstrated that GqTRV1 exhibits higher nucleotide identity with CheTRV1(65.0%) and CapTRV1(65.6%) than to other trirhaviruses. These findings support the classification of GqTRV1 as a distinct member of the genus Trirhavirus.
Since 2016, mass mortality events characterized primarily by severe abdominal swelling and ascites have emerged in Chinese soft-shelled turtle (Pelodiscus sinensis) farms in China, leading to substantial economic losses....Since 2016, mass mortality events characterized primarily by severe abdominal swelling and ascites have emerged in Chinese soft-shelled turtle (Pelodiscus sinensis) farms in China, leading to substantial economic losses. However, the cause of the disease has remained elusive, as no bacteria or parasites were detected in the diseased turtles. Tissue homogenate filtrate was used to infect Vero, GCO, TSK, TSL, and C6/36 cells, all of which produced cytopathic effects (CPE). Spherical, suspected viral particles with diameters approximately 30 nanometers (nm) were observed in the kidney tissue of diseased turtles using transmission electron microscopy (TEM). The complete viral genome was obtained through a combination of sequence-independent single-primer amplification (SISPA) and high-throughput sequencing, with rapid amplification of cDNA ends (RACE) employed to determine the terminal sequences. The genome is a positive-sense single-stranded RNA comprising 10,956 nucleotides (nt), exhibiting classic Orthoflavivirus characteristics and encoding a single open reading frame (ORF). Phylogenetic analysis indicated that the virus was most closely related to Trionyx sinensis flavivirus isolate YH2018, member of the Orthoflavivirus genus. Consequently, the virus has been named P. sinensis flavivirus isolate HZ2016 (PSFV-HZ2016). In an artificial challenge experiment, injection of tissue filtrate resulted in 100% mortality among healthy turtles within 16 days post-infection. Infected turtles displayed symptoms similar to those of the primary cases. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) revealed broad tissue tropism, with the highest viral load detected in the heart. Histopathological analysis confirmed multi-organ damage consistent with severe systemic infection. These findings identify PSFV-HZ2016 as a novel and highly virulent Orthoflavivirus responsible for ascites-associated mortality in P. sinensis, providing crucial insights for diagnosis, surveillance, and disease management in aquaculture.