VP1 Gene Research Articles

Identification of a Novel Porcine Teschovirus Subtype 19 within the Species Teschovirus A

Porcine teschovirus (PTV) is a member of the genus Teschovirus in the family Picornaviridae. Several novel PTVs in Teschovirus were identified in our previous study. To elucidate the taxonomic status of the species and subtypes, PTV-positive samples were inoculated into porcine kidney (PK-15) and swine testicular (ST) cells. A total of 58 PTV strains were successfully isolated and 21 different VP1 gene sequences were obtained. A phylogenetic analysis of the VP1 gene revealed that these PTV isolates comprised 11 genotypes, including 10 known genotypes (PTV 1–6, PTV 8–9, PTV 11, and Teschovirus B3), and a newly identified genotype. A nearly complete genome sequence of the novel PTV genotype isolate, PTV-SG2, was obtained. The homologies of the nucleotides and amino acids between PTV-SG2 and other PTVs were 69.7%–85.0% and 76.1%–90.4%, respectively. A phylogenetic analysis of the P1, polyprotein, and 3 CD genes revealed that PTV-SG2 belonged to a novel genotype within Teschovirus A, and a genetic divergence analysis of the novel PTV isolate further verified its taxonomic status. Based on the PTV naming convention, the novel PTV genotype identified in the present study was provisionally named PTV 19. Serum neutralization tests indicated that PTV 19 is a serotype-specific and completely different from previously reported PTV serotypes. Therefore, PTV 19 is a novel PTV serogroup. In conclusion, this study identified a PTV genotype and serotype within Teschovirus A.

Molecular typing of canine parvovirus type 2 by VP2 gene sequencing and restriction fragment length polymorphism in affected dogs from Egypt.

Canine parvovirus-2 (CPV-2) is one of the most common infectious diseases in dogs characterized by severe gastroenteritis, vomiting, and bloody diarrhea. Little information is available about this topic in Egypt, particularly in the Delta region. This study reports the prevalence and molecular analysis of CPV-2 variants collected from El-Gharbia and Kafrelsheikh governorates in the Delta of Egypt. In this study, 320 rectal swabs were collected from infected domestic dogs from two districts in delta Egypt. The samples were investigated by rapid immunochromatographic test and polymerase chain reaction for detection the prevalence of CPV-2 variants. The genetic characterization was performed using restriction fragment length polymorphism (RFLP) analysis and partial VP2 gene sequence. The viral antigen was detected in (264/320, 82.5%) of samples by IC test, while PCR was found more sensitive by detecting (272/320, 85%) positive samples. The RFLP technique using MboII restriction enzyme was successfully used for the differentiation of CPV-2c antigenic variants from CPV-2a/2b strains. Interestingly, the molecular and phylogenetic analysis revealed that both CPV-2a and CPV-2c are circulating in the study area. Deduced amino acid sequence analysis showed changes at residue (N426E) and residue (T440A).: Our results indicated that CPV-2 is prevalent among dogs in Egypt, and therefore further molecular and epidemiological studies of CPV-2 are warranted.

Reemerging of Encephalomyocarditis Virus in Pigs in Brazil: Pathological and Viral Characterization

Encephalomyocarditis virus (EMCV) is a zoonotic disease caused by a highly pathogenic virus that affects wild and domestic animal species, with rodents as its reservoir. Most recently, in South America, this virus was detected in an outbreak affecting humans in Peru. In Brazil, EMCV infection was described in some wild species, in horses, and once in farrowing pigs. The aim of this study is to report the reemergence of EMCV in commercial growing–finishing pigs from two different farms that experienced sudden pig death in midwest Brazil. This aim was achieved through gross pathology, histologic examination, RT‒PCR analysis, and genetic characterization of the virus. Clinical signs, such as trembling, dyspnea, and squealing sounds shortly before death, were only occasionally observed and were nonspecific. On gross examination, cardiomegaly was observed, along with multifocal pale tan foci in the epicardium extending to the myocardium on the cut surface. Microscopically, there was severe myocardial necrosis, dystrophic mineralization, fibrosis, and lymphoplasmacytic and histiocytic myocarditis. Gross and microscopic examinations of the rats were unremarkable. The RT‒PCR analyses of the pig and rat organs were positive for EMCV, and the phylogenetic analysis of the VP1 gene showed that the samples from pigs and rats contained similar strains that had their closest relatives identified in humans in Peru. This is the first genetic characterization of EMCV in Brazil, and the other findings confirm the reemergence of the disease that was transmitted from rats to pigs.

Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencing.

During the last decade, porcine rotavirus H was detected in the USA, Asian regions, South Africa, Brazil, and a couple of European countries. In the presented study, the virus was identified in piglets on a farrow-to-finish farm in Russia during metagenomic surveillance. Currently, it is the first identification of this species in the country. As a diagnostic method, nanopore-based metagenomic sequencing was applied. The obtained nanopore reads allowed for the assembly of 10 genome segments out of 11. The phylogenetic analysis revealed the virus belonged to the porcine cluster and had GX-P3-I3-R3-C3-M8-A7-N1-T5-E3-H3 genome constellation. Moreover, three potential new genotype groups for VP3, NSP1, and NSP3 genes were determined. Additionally, a recombination between RVH and RVC in the NSP3 gene was detected. The study provides significant information about a novel RVH strain.

Expression of VP1 protein of foot-and-mouth disease virus serotype O originated from Indonesia in mammalian cells as potential immunogen

In 2022, Indonesia experienced foot-and-mouth disease (FMD) outbreak resulting in the death of hundreds of cattle; after more than 30 years, the country maintained FMD-free status. The FMD viral polypeptides-1 (VP1) protein contains major antigenic sites, making the protein have an important role in diagnostic applications or vaccine development. In this study, a synthetic codon-optimized vp1 gene from FMD virus serotype O was integrated into pcDNA3.1 vector and transformed to Escherichia coli TOP10F’ for plasmid propagation. The pcDNA3.1-1D-VP1 FMDV plasmid was then verified using agarose gel, showing in 659 bp size of the DNA fragment. The VP1 recombinant plasmid was transfected into HEK293T cells in DMEM medium supplemented with 10% FBS. Protein profiles were determined with SDS-PAGE showing target protein at 33KDa. Protein expression was confirmed by in-cell western assay using anti-VP1 type O polyclonal antibody and IRDye® 800CW goat anti-rabbit IgG as the secondary antibody. The result revealed a high-intensity fluorescence signal, indicating a strong interaction between expressed protein and anti-VP1 antibody. Thus, the results of this study demonstrate the potential for VP1 protein to be used as an immunogen in vaccine or diagnostic development against FMD infection. Nonetheless, some additional studies should be conducted.

First identification of a novel Aichivirus D in goats with diarrhea

This study identifies a novel Aichivirus D in goats for the first time, and a case-control study suggested that the virus is associated with diarrhea in goats. The goat Aichivirus D shared the highest gnomic sequence homology with ovine Aichivirus D strain, and may origin from ovine Aichivirus D through natural VP1 gene recombination. These findings contribute to a better understanding of the host range and genetic evolution of Aichivirus D.

Cutavirus Infection in Large-Plaque Parapsoriasis, a Premalignant Condition of Mycosis Fungoides.

Cutavirus (CuV) is associated with mycosis fungoides; however, the CuV status in parapsoriasis en plaques (PP), a premalignant inflammatory condition of mycosis fungoides, has not been fully delineated. Fifty-five Japanese patients with chronic inflammatory skin diseases, including 13 patients with PP, were studied. CuV DNA was detected significantly more frequently in biopsies of the lesional skin from patients with PP (38%; 4 of 13) than in those from patients with other inflammatory skin diseases (2%; 1 of 42; P = .009). All CuV-positive PP cases were of the large-plaque parapsoriasis (LPP) subtype. The viral loads ranged from 83 450 to 2 164 170 copies/103 cells. We recovered near-full-length CuV sequences from the CuV-positive LPP biopsies, all of which were of the Japanese/Asian genotype. The CuV genome appeared to be present within lymphoid cells infiltrating the epidermis and dermis. CuV NS1 and VP1 gene transcripts were also detected in the affected tissues. The detection of high levels of CuV DNA with the expression of viral mRNA suggests a potential role for CuV in the pathogenesis of LPP, making it necessary to study further the impact of CuV, especially regarding the viral genotype, on the outcomes of patients with CuV-positive LPP.

Analysis of coxsackievirus A6 circulation in the territories of the Far Eastern Federal district of the Russian Federation in 2014–2019

Introduction. Molecular epidemiological monitoring of enterovirus infection (EVI) in the territories of the Russian Federation showed that coxsackievirus A6 (CVA-6) had been one of the most prevalent types of enteroviruses that circulated among the country population during last years and had caused majority of EVI outbreaks.
 Objective — to evaluate coxsackievirus A6 circulation in the territories of the Far Eastern Federal district (FEFD) in 2014–2019 utilizing methods of molecular genetics.
 Materials and methods. RT-PCR was employed to detect enterovirus RNA in biological material collected in 9 territories of the FEFD . In order to establish enterovirus types, amplification of positive samples was carried out to detect nucleotide sequence fragments of the VP1 and VP2 genes. Molecular genetic analysis of the Far Eastern CVA-6 strains was based on detection of nucleotide sequences of VP1 and 3Dpol gene fragments. Phylogenetic trees were constructed by the means of Bayesian phylogenetic methods.
 Results. Total 1773 nucleotide sequences of 43 types of non-polio enteroviruses were obtained in 2014-2019. Majority of the sequences belonged to coxsackievirus A6 (524; 29.5%). In the years of the highest CVA-6 detection an increase in EVI incidence as well as EVI outbreaks were observed in the territories of FEFD. The most prevalent manifestations of EVI caused by CVA-6 in FEFD were herpangina and exanthemic forms. Phylogenetic analysis showed that Far Eastern strains of CVA-6 during in the analyzed period of time belonged to D3 subgenotype that is dominant in the world. The circulation of several recombinant forms of CVA-6 (RF-A, -H, -L, -N, -R) was also registered.
 Conclusion. The genetic diversity of CVA-6 strains circulating in the territories of the FEFD in 2014–2019 revealed in this study requires further investigation in order to obtain new knowledge about the CVA-6 molecular epidemiology and improve the enterovirus surveillance system.

Continuous clinicopathological and molecular recognition of very virulent infectious bursal disease virus in commercial broiler chickens

Gumboro virus is one of the most dangerous immunosuppressant viruses that infect chickens and causes massive financial losses around the world. The purpose of the current study is to conduct a molecular survey of chicken farms for the infectious bursal disease virus (IBDV). On the basis of postmortem (PM) lesions, 125 bursal samples from 25 farms were collected from clinically diseased commercial chicken farms with increased mortality and suspected Gumboro virus infection. Pooled bursal samples from suspected IBD-vaccinated flocks were tested for IBDV by real-time polymerase chain reaction (RT-PCR). Fifteen out of 25 pooled specimens were found positive for IBDV, with a 60% detection rate, and confirmed positive for very virulent IBDV (vvIBDV). Nucleotide phylogenetic analysis of VP1 and VP2 genes was employed to compare the five chosen isolates with strains identified in various localities in 2022. The VP1 and VP2 genes are allotted into groups (I, II). The strains in our study were related to group II and it acquired a new mutation in the VP2 gene that clustered it into new subgroup B. By mutation analysis, the VP2 gene of all strains had a characteristic mutation to vvIBDV. It acquired new mutations in HVRs contrasted with HK64 in Y220F, A222T/V in all strains in our study, and Q221K that was found in IBD-EGY-AH5 and AH2 in the major hydrophilic region peak A in the loop PBC in addition to G254S in all strains in our study and Q249k that found in IBD-EGY-AH1 and AH3 in the minor hydrophilic region 1 in the loop PDE. These mutations are important in the virulency and antigenicity of the virus. The VP1 had 242E and 390L were characteristic of vvIBDV and KpnI restriction enzyme (777GGTAC/C782) in addition to a new mutation (F243Y and N383H) in tIBD-EGY-AH1 and AH4 strains. According to the current study, the strains were distinct from the vaccinal strain; they could be responsible for the most recent IBDV outbreaks observed in flocks instead of received vaccinations. The current study highlighted the importance of regular IBD monitoring to maintain up to date on the type of challenge viruses and the efficacy of commercial vaccinations.

The analysis of the genotype of Sapovirus outbreaks in Zhejiang Province

BackgroundSapovirus (SaV) infection is increasing globally. Concurrently, several SaV-outbreaks were observed in children of Zhejiang province, China, in recent years, In this study, the genotypes of Sapovirus from seven outbreaks in the Zhejiang province were analysed.MethodsA total of 105 faecal samples were collected from children aged between 4 and 17 years from the Zhejiang Provincial Center for Disease Control and Prevention between October 2021 and February 2023. Genotypes were processed using reverse transcription polymerase chain reaction and Sanger sequencing, while next-generation sequencing was used to generate a complete viral genome. Deduced amino acid sequences were analysed to detect VP1 gene mutations.ResultsIn total, 60 SaV-positive patients were detected at a 57.14% (60/105) positivity rate. Positive rates in the seven outbreaks were: 22.22% (2/9), 15.00% (3/20), 93.10% (27/29), 84.21% (16/19), 28.57% (2/7), 53.33% (8/15) and 33.33% (2/6), respectively. Four genotypes were identified in the seven outbreaks, of which, GI.1 accounted for 14.29% (1/7), GI.2 accounted for 14.29% (1/7), GI.6 and GII.5 accounted for 14.29% (1/7), and GI.6 accounted for 57.14% (4/7). All patients were children and outbreaks predominantly occurred in primary schools and during cold seasons. Additionally, the complete sequence from the GI.6 outbreak strain showed high homology (identity: 99.99%) with few common substitutions (Y300S, N302S and L8M) in VP1 protein.ConclusionsSaV genotype diversity was observed in the seven outbreaks, with GI.6 being the main SaV genotype in Zhejiang province. It demonstrated high homology and may provide a platform for SaV prevention and control measures.

Detection of Feline Cupripoxvirus and Variation Analysis of Its VP1 Gene in Chengdu from 2020 to 2023

Feline calicivirus (FCV) is an important pathogen causing infectious diseases in the oral cavity and upper respiratory tract of cats. Research on its prevalence and genetic variations contributes to the prevention and treatment of related diseases, as well as the development of new vaccines. In this study, a total of 113 samples of eye, nose, and throat secretions were collected from cats with respiratory and oral inflammation symptoms in Chengdu area from 2020 to 2023. The samples were tested using the RT-PCR method. The VP1 gene region was then cloned, sequenced, and subjected to homology analysis and phylogenetic analysis with domestic and foreign FCV reference strains. The results showed that among the 113 samples, 24 tested positive for FCV, with a positive rate of 21.24%. The nucleotide homology between the 5 FCV VP1 genes obtained in this study and the reference strains ranged from 72.6% to 84.1%, while the amino acid homology ranged from 84.0% to 95.9%. Phylogenetic analysis showed that the strains obtained in this study clustered into two gene groups (GⅠ and GⅡ) in the domestic and foreign FCV strain evolution tree. Strains SMU-M2, SMU-M7, SMU-M13, and SMU-M71 belonged to the GⅡ subtype, while strain SMU-M8 belonged to the (GⅠ subtype. The FCV vaccine strain had a distant genetic relationship with the prevalent FCV strains in Chengdu. The study revealed that FCV is prevalent in the cat population of Chengdu, and there is a low genetic homology and significant sequence differences between the prevalent strains and vaccine strains. This suggests the need to evaluate the actual protective efficiency of existing commercial FCV vaccines and promote the development of new vaccines with better cross-protection against prevalent strains.

Rapid detection of grass carp reovirus type 1 using RPA-based test strips combined with CRISPR Cas13a system.

Due to the existence of grass carp reovirus (GCRV), grass carp hemorrhagic disease occurs frequently, and its high pathogenicity and infectivity are great challenges to the aquaculture industry. As a highly pathogenic pathogen, the outbreak of hemorrhagic disease often causes tremendous economic losses. Therefore, it is important to rapidly and accurately detect GCRV on site to control timely. In this study, recombinant enzyme amplification (RPA) combined with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a system was employed to establish a method to detect the vp7 gene of grass carp reovirus type 1. This method can be adopted for judging the results by collecting fluorescence signal, ultraviolet excitation visual fluorescence and test strip. Combined with the RPA amplification experiment, the detection limit of the RPA-CRISPR method can reach 7.2 × 101 copies/μL of vp7 gene per reaction, and the detection process can be completed within 1 h. In addition, this method had no cross-reaction with the other 11 common aquatic pathogens. Then, the performance of the RPA-CRISPR/Cas13a detection method was evaluated by comparing it with the real-time fluorescence quantitative PCR detection method of clinical samples. The results of RPA-CRISPR/Cas13a detection were shown to be in consistence with the results obtained from the real-time fluorescence quantitative PCR detection. The coincidence rate of this method with 26 GCRV clinical samples was 92.31%. In summary, this method has high sensitivity, specificity and on-site practicability for detecting GCRV type 1, and has great application potential in on-site GCRV monitoring.

Molecular epidemiology and phylodynamic analysis of enterovirus 71 in Beijing, China, 2009–2019

BackgroundEnterovirus 71(EV71)-associated hand, foot and mouth disease (HFMD) decreased dramatically in Beijing from 2009 to 2019. This study was to investigate the epidemiological characteristics, evolutionary dynamics, geographic diffusion pathway, and other features of EV71 in Beijing, China.MethodsWe conducted a retrospective study of EV71-associated HFMD and its causative agent in Beijing, China, from 2009 to 2019. Phylogenetic and phylogeographic methods based on the EV71 genome were used to determine the evolution features, origin, and spatiotemporal dynamics. Positive selection sites in the VP1 gene were identified and exhibited in the tertiary structure. Bayesian birth-death skyline model was used to estimate the effective reproductive number (Re).ResultsEV71-associated HFMD decreased greatly in Beijing. From 2009 to 2019, EV71 strains prevalent in Beijing shared high homology in each gene segment and evolved with a rate of 4.99*10− 3 substitutions per site per year. The genetic diversity of EV71 first increased and peaked in 2012 and then decreased with fluctuations. The time to the most recent common ancestor (TMRCA) of EV71 in Beijing was estimated around 2003 when the EV71 strains were transmitted to Beijing from east China. Beijing played a crucial role in seeding EV71 to central China as well. Two residues (E145Q/G, A293S) under positive selection were detected from both the VP1 dataset and the P1 dataset. They were embedded within the loop of the VP1 capsid and were exposed externally. Mean Re estimate of EV71 in Beijing was about 1.007.ConclusionIn recent years, EV71 was not the primary causative agent of HFMD in Beijing. The low Re estimate of EV71 in Beijing implied that strategies for preventing and controlling HFMD were performed effectively. Beijing and east China played a crucial role in disseminating EV71 to other regions in China.

Complete viral protein coding genes NS1 and VP1 sequences and phylogenetic analysis of a novel recombinant Mink Enteritis Virus isolated in China

The primary objective of this study was to detect the presence of MEV in mink samples and investigate the genetic characteristics of the virus. In 2017, a newly identified strain of MEV, named MEV-HLJ, was isolated. The virus’s complete NS1 and VP1 gene sequences were amplified using PCR and subjected to phylogenetic analysis. The results indicated that despite moderate virulence, MEV- HLJ belonged to the attenuated group. Recombination analysis using the GARD programme identified a putative recombination breakpoint at nucleotide position 2,075 between the NS1 and VP1 genes. Separate phylogenetic trees were constructed to confirm the recombinant event. This study provides insights into the genetic diversity and evolution of MEV isolates.

Detection and Phylogenetic Analysis of Group A Rotaviruses in Faeces of Diarrhoeic Bovine, Caprine, Ovine, Porcine and Human Population from Central India

Background: Rotavirus infection is a leading cause of acute dehydrating diarrhoea in humans, primarily affecting infants and young children and causes neonatal diarrhoea in the majority of domestic animals. However, there is a dearth of literature in India on geographic or temporal comparisons of rotavirus transmission between humans and animals. Methods: Prior to analysis with one-step RT-PCR, RNA-PAGE confirmed 40 rotaviruses recovered from a total of 306 faecal and stool samples obtained from domestic animals, (245) suffering from watery diarrhoea and children (61) suffering from diarrhoea. The RT-PCR positive sample were subjected to sequence analysis followed by BLAST analysis to confirm the presence of VP7 gene specific to rotavirus. The sequences of rotavirus in study were aligned with Indian and global VP7 sequences and were further subjected for phylogenetic analysis. \Result: Only three samples of three different species (Human, cattle and buffalo) could show the positivity, while remaining 37 failed in RT-PCR. Besides, the similarity of the nucleotide sequence of one of the positive isolates recovered from cattle calf with one of the Indian human rotavirus sequences in phylogenetic analysis indicates the possibility of inter-species transmission of rota viral strains circulating in the area, indicating organism’s zoonotic significance.

Phylodynamic characteristics of reassortant DS-1-like G3P[8]-strains of rotavirus type A isolated in Nizhny Novgorod (Russia).

Since 2013, there has been an increase in reports of the spread of a double intergroup reassortant strain of rotavirus type A (RVA) with the genotype G3P[8] and other genes belonging to the second genogroup I2-R2-C2-M2-A2-N2-T2-E2-H2. In our study, we provide a molecular genetic characterization of rotaviruses with genotype G3P[8]-I2 isolated in Nizhny Novgorod. In our study, we used RT-PCR, Sanger sequencing, RNA-PAGE methods. Phylogenetic and phylodynamic analysis were performed using the Bayesian approach. According to our study, there was a significant increase in the proportion of G3P[8] from 15% during the period of 2020-2021 to 53% during the period of 2021-2022 in Nizhny Novgorod, Russia. Phylogenetic analysis based on the VP4 gene revealed that DS-1-like RVAs isolated in Nizhny Novgorod belong to different clusters of the P[8]-3.1 lineage, with a level of variation ranging from 1.1% to 1.3%. Based on the VP6 gene, the equine-like RVAs identified by us carry genetic variants belonging to three distinct clusters of the lineage I2-V, with a variation level ranging from 2.0% to 4.5%. These data indicate the genotypic diversity of circulating DS-1-like G3 RVAs. Phylogenetic analysis of the VP7 gene allowed us to assign the isolates identified in our study to the G3-1 lineage. We estimated that the circulation of the most recent common ancestor of the spreading strains dates back to 2002. Additionally, we determined the typical level of mutations in the VP7 gene, which amounted to 2.14*10-3 substitutions/per site/per year.

Genomic analysis of two rare human G3P[9] rotavirus strains in Ningxia, China

G3P (Matthijnssens et al., 2008b [9]) is a rare combination of human rotavirus VP7/VP4 genotypes with a complex evolutionary pattern but limited related studies. Detailed genomic characterisation and genetic evolutionary analyses of G3P (Matthijnssens et al., 2008b [9]) rotaviruses have helped to enhance our understanding of rotavirus diversity. For the first time, we detected two human G3P (Matthijnssens et al., 2008b [9]) Rotavirus A (RVA) strains, RVA/Human-tc/CHN/2020999/2020/G3P (Matthijnssens et al., 2008b [9]) and RVA/Human-wt/CHN/23582009/2023/G3P (Matthijnssens et al., 2008b [9]), in diarrhoea patients from the Ningxia region of China, and carried out a whole-genome analysis of these strains. 2,020,999 and 23,582,009 have identical gene constellations: G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3, and this genotypic constellation was reported first time in China. They are closely related in 11 genome segments. The genotypes of these two strains are different from the human RVA strains L621 and E2451, which are only G3P (Matthijnssens et al., 2008b [9]) strains reported so far in China, but are identical to those of the Thai feline strain Meesuk and the Korean human strain CAU12–2-51.Phylogenetic analysis showed that the VP6, VP1-VP3, and NSP2 genes of the two strains in this study clustered with human/bovine and feline/bovine rotavirus strains to form a sublineage distinct from the common DS-1-like G2 human rotavirus. In contrast, the VP7, VP4, NSP1, and NSP3-NSP5 gene segments were closely associated with human/feline rotavirus and feline rotavirus strains. These findings suggest that the evolutionary origin of the G3P (Matthijnssens et al., 2008b [9]) human rotavirus found in Ningxia, China, is consistent with the Meesuk and CAU12–2-51 strains， may have arisen through reassortment between uncommon human/bovine， feline/bovine rotavirus strains and human/feline， feline rotaviruses. However, VP1-VP2 gene segments did not have the same lineage as strains Meesuk and CAU12–2-51, suggesting that these genes might be derived from additional reassortment event.

Metatranscriptomic assessment of diarrhoeic faeces reveals diverse RNA viruses in rotavirus group A infected piglets and calves from India.

RNA viruses are a major group contributing to emerging infectious diseases and neonatal diarrhoea, causing morbidity and mortality in humans and animals. Hence, the present study investigated the metatranscriptomic-derived faecal RNA virome in rotavirus group A (RVA)-infected diarrheic piglets and calves from India. The viral genomes retrieved belonged to Astroviridae in both species, while Reoviridae and Picornaviridae were found only in piglets. The nearly complete genomes of porcine RVA (2), astrovirus (AstV) (6), enterovirus G (EVG) (2), porcine sapelovirus (PSV) (2), Aichivirus C (1), and porcine teschovirus (PTV) (1) were identified and characterised. In the piglet, AstVs of PAstV2 (MAstV-26) and PAstV4 (MAstV-31) lineages were predominant, followed by porcine RVA, EVG, PSV, Aichivirus C, teschovirus (PTV-17) in decreasing order of sequence reads. In contrast, AstV accounted for the majority of reads in bovines and belonged to MAstV-28 and a proposed MAstV-35. Both RVA G4P[6] strains exhibited prototype Gottfried strains like a genotypic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Ten out of eleven genes were of porcine origin, while the VP7 gene clustered with G4-lineage-1, consisting of human strains, suggesting a natural porcine-human reassortant. In the recombination analysis, multiple recombination events were detected in the PAstV4 and PAstV2 genomes, pointing out that these viruses were potential recombinants. Finally, the study finds diverse RNA virome in Indian piglets and calves for the first time, which may have contributed to diarrhoea. In the future, the investigation of RNA virome in animals will help in revealing pathogen diversity in multifactorial diseases, disease outbreaks, monitoring circulating viruses, viral discovery, and evaluation of their zoonotic potential.

Molecular Characterization of Gastroenteric Viruses in Wastewater from Cities in Uruguay.

Group A Rotavirus, Human Astrovirus, and Norovirus (RVA, HAstV, and NoV) are recognized as the major causative agents of acute gastroenteritis in children and adults worldwide. The aim of this study was to determine the prevalence and molecular epidemiology of RVA, HAstV, and NoV in wastewater from three cities in Uruguay. Thirty-six samples from Bella Unión, Salto, and Fray Bentos cities were analyzed using quantitative and qualitative PCR. RVA was the most frequently detected virus (50%), followed by HAstV (39%), NoV GII (36%), and NoV GI (25%). RVA strains were characterized as P[8] and G3 based on the VP4 and VP7 genes, respectively. Among NoV-positive samples, genotypes GI.2, GI.3, GI.5, GI.6, GI.7, GII.2, GII.6, and GII.4 were detected, and only one HAstV genotype (MLB1) was found. Our wastewater-based epidemiological approach provides a snapshot of the overall genetic diversity of these viruses in three cities of the Uruguay River basin during 2017-2018. These findings reinforce the importance of this environmental surveillance tool for monitoring epidemiological trends of enteric viruses circulating in the population, which can be used to guide public health intervention.

Epidemiology and molecular characterization of Feline panleukopenia virus from suspected domestic cats in selected Bangladesh regions.

Feline panleukopenia (FPL) is a highly contagious cat disease and is endemic in Bangladesh. The study aims to describe the epidemiology and molecular characterization of the Feline panleukopenia virus from the suspected domestic cats in selected Bangladesh regions. Randomly, 161 rectal swabs were collected from the pet hospitals between July 2021 and December 2022. A structured questionnaire was administered through face-to-face interviews with cat owners in order to collect data on potential risk factors for FPL, such as age, sex, sharing litter boxes and every day utensils in multicat households, vaccination history, hospital visits for other diseases, and season. The rectal swabs were tested by PCR targeting the VP2 capsid protein gene, and six PCR-positive samples were further sequenced for molecular characterizations. The risk factors for FPLV were identified using multivariable logistic regression analysis. The overall prevalence of FPL among suspects was 22.9%. The mortality and case fatality were 10.6%, and 45.9%, respectively. However, mortality in kittens was significantly higher (16.4%) than younger cats. The odds of FPL were 8.83 times (95% CI: 3.14-24.85) higher among unvaccinated cats than vaccinated cats. The winter season had almost six times (95% CI: 1.38-24.40) higher odds of FPL than rainy season. In a multicat house, the odds of FPL was about five times (95% CI: 1.93-13.45) higher for cats that shared a litter box and food utensils compared to those that did not engage in such sharing. Visiting hospitals for other reasons nearly triples the odds of FPL (OR: 2.80, 95% CI: 1.04-7.54) compared to cats that do not visit hospitals. Analysis of partial sequence of the VP2 gene revealed genetic variations among the isolates from different regions. Among these isolates, four were identical to FPLV isolates from South Korea and China, while one showed complete homology with FPLV isolates from Thailand. In contrast, the remaining one was 100% identical to Carnivore protoparvovirus-1 isolated from a feline sample in Italy. Our isolates were classified into three distinct clades alongside Feline panleukopenia virus and Carnivore protoparvovirus-1. One in every three suspected cats was infected with Feline panleukopenia. Regular vaccination of the cats, especially those that share common litter box and food utensils and visit hospitals for other purposes, will help reduce the prevalence of FPL in Bangladesh. Besides, it is worth emphasizing the existence of genetic diversity among the circulating Feline panleukopenia viruses in Bangladesh.