First detection of feline bocaparvovirus 2 and feline chaphamaparvovirus in healthy cats in Turkey

Feline bocaviruses found in Thailand have undergone genetic recombination for their evolutions

Feline bocaviruses (FBoVs) have been discovered for a decade and are often detected in feces, possibly associated with diarrhea in cats. Studies on FBoV evolution remain limited and have mainly focused on prevalence and genetic characterization. Although genetic recombination serves as a potential mechanism in bocavirus evolution, research on this process for FBoVs has been scarce. In this study, we characterized 19 complete coding sequences of FBoVs obtained from Thai cats, revealing that FBoV-1, -2, and -3 were endemic in Thailand. Genetic characterizations showed that most Thai FBoVs were closely related to previously detected strains in Thailand and China. Recombination analyses indicated intragenic, intraspecies recombination in all FBoV species, with recombination breakpoints commonly found in the NP1 and VP1/2 genes, highlighting these genes may be hotspots for FBoV recombination. However, no interspecies recombination was detected. Selective pressure analysis of various FBoV genes revealed that these viruses underwent purifying selection. Although the VP1/2 gene of all FBoV species was under the strongest negative selection pressure, positive selection sites were only found in FBoV-1 and FBoV-3. This study is the first to identify natural recombination in FBoV-2 and FBoV-3 and provides evidence that genetic recombination is a potential driver of FBoV evolutions. Additionally, this study offers up-to-date information on the genetic characteristics, evolutionary dynamics, and selective pressure status of FBoVs, which should be continuously monitored.

Epidemiology and genotypic diversity of feline bocavirus identified from cats in Harbin, China

Feline bocavirus (FBoV) is a globally distributed linear, single-stranded DNA virus infect cats, currently classified into three distinct genotypes. Although FBoV can lead to systemic infections, its complete pathogenic potential remains unclear. In this study, 289 blood samples were collected from healthy cats in Harbin, revealing an overall FBoV prevalence of 12.1%. Notably, genotypes 1 and 3 of FBoV were found co-circulating among the cat population in Harbin. Additionally, recombination events were detected, particularly in the newly discovered NG/104 and DL/102 strains. Furthermore, negative selection sites were predominantly observed across the protein coding genes of FBoV. These findings suggest a co-circulation of genetically diverse FBoV strains among cats in Harbin, indicate that purifying selection is the primary driving force shaping the genomic evolution of FBoV, and also underscore the importance of comprehensive surveillance efforts to enhance our understanding of the epidemiology and evolutionary characteristics of FBoV.

Viral metagenomic analysis reveals diverse viruses and a novel bocaparvovirus in the enteric virome of snow leopard (Panthera uncia)

The enteric virome, comprising a complex community of viruses inhabiting the gastrointestinal tract, plays a significant role in health and disease dynamics. In this study, the fecal sample of a wild snow leopard was subjected to viral metagenomic analysis using a double barcode Illumina MiSeq platform. The resulting reads were de novo assembled into contigs with SOAPdenovo2 version r240. Additional bioinformatic analysis of the assembled genome and genome annotation was done using the Geneious prime software (version 2022.0.2). Following viral metagenomic analysis and bioinformatic analysis, a total of 7 viral families and a novel specie of bocaparvovirus tentatively named Panthera uncia bocaparvovirus (PuBOV) with GenBank accession number OQ627713 were identified. The complete genome of PuBOV was predicted to contain 3 open reading frames (ORFs), contains 5433 nucleotides and has a G + C content of 47.40 %. BLASTx analysis and pairwise sequence comparison indicated the novel virus genome was a new species in the genus Bocaparvovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. This study provides valuable insights into the diversity and composition of the enteric virome in wild endangered snow leopards. The identification and characterization of viruses in wildlife is crucial for developing effective strategies to manage and mitigate potential zoonotic and other viral disease threats to human and animal health.

TaqMan-based real-time polymerase chain reaction for the detection of feline chaphamaparvovirus

Feline chaphamaparvovirus (FeChPV) is a new viral strain detected in Chinese Mainland in recent years. The symptoms mainly include diarrhea and bloody stool in young cats, which can lead to death in severe cases. In this study, a TaqMan-based real-time quantitative PCR (qPCR) with specific primers and TaqMan probes based on the VP1 gene sequence of FeChPV was performed to detect the virus. The established qPCR indicated that there is no cross-reaction of FeChPV with other common feline viruses. The minimum detection limit of the established qPCR method is 3.75 × 10 copies/µL, while conventional PCR is 3.75 × 103 copies/µL. The result that the proposed qPCR protocol was shown to be 100 times more sensitive than conventional PCR. The correlation coefficients exceeded 0.995, and the amplification efficiency was 98%. The difference within and between groups is less than 5%, indicating that the established method has good repeatability. The results of clinical sample detection shown that 16 positive samples were detected from 45 stool samples by the established qPCR method. The conventional PCR method only detected 3 positive samples. In conclusion, the established qPCR method is fast and effective in identifying FeChPV, with higher specificity and sensitivity. It could be used as a diagnostic tool to quantitatively detect the virus content, which is conducive to disease monitoring and epidemiological investigation.

Molecular identification of carnivore chaphamaparvovirus 2 (feline chaphamaparvovirus) in cats with diarrhea from China

Chaphamaparvovirus carnivoran2 (feline chaphamaparvovirus, FeChPV) is a novel feline parvovirus originally detected in Canadian cats in 2019, and it has also been identified in domestic cats in other nations. To evaluate the prevalence and genetic diversity of FeChPV in China, rectal swabs of pet cats from Henan, Guangdong, Anhui, Zhejiang, and Inner Mongolia provinces were collected. Of the 230 samples subjected to nested polymerase chain reaction, 6 (2.6%) tested positive for FeChPV. Although all positive samples were from cats with diarrhea, statistical analyses revealed no correlation between the presence of the virus and clinical symptoms (p > 0.05). Phylogenetic trees of nonstructural protein 1 (NS1) and capsid protein (VP1) demonstrated that these six new strains formed a major branch with other reference FeChPV strains and considerably differed from Chaphamaparvoviru carnivoran1. Moreover, recombination analysis revealed that the FeChPV strain CHN20201025, previously detected in a dog, was a recombinant and strains CHN200228 and CHN180917, identified in this study, were the closest relatives to the parental strains. The findings of this study and a previous study wherein FeChPV was detected in dogs suggest that FeChPV can propagate between species. Additionally, these findings indicate that the genetic diversity of FeChPV can provide an insight into the epidemiological status of FeChPV in China.

Genetic Diversity and Evolution of Viruses Infecting Felis catus: A Global Perspective

Cats harbor many important viral pathogens, and the knowledge of their diversity has been greatly expanded thanks to increasingly popular molecular sequencing techniques. While the diversity is mostly described in numerous regionally defined studies, there lacks a global overview of the diversity for the majority of cat viruses, and therefore our understanding of the evolution and epidemiology of these viruses was generally inadequate. In this study, we analyzed 12,377 genetic sequences from 25 cat virus species and conducted comprehensive phylodynamic analyses. It revealed, for the first time, the global diversity for all cat viruses known to date, taking into account highly virulent strains and vaccine strains. From there, we further characterized and compared the geographic expansion patterns, temporal dynamics and recombination frequencies of these viruses. While respiratory pathogens such as feline calicivirus showed some degree of geographical panmixes, the other viral species are more geographically defined. Furthermore, recombination rates were much higher in feline parvovirus, feline coronavirus, feline calicivirus and feline foamy virus than the other feline virus species. Collectively, our findings deepen the understanding of the evolutionary and epidemiological features of cat viruses, which in turn provide important insight into the prevention and control of cat pathogens.

Investigation of canine chaphamaparvovirus, canine bufavirus, and canine adenovirus in dogs with diarrhea: First report of novel canine bufavirus in Turkey

Viral enteritis is a significant cause of death among dogs younger than 6 months. In this study, the presence of canine chaphamaparvovirus (CaChPV), canine bufavirus (CBuV), and canine adenovirus (CAdV) was investigated in 62 diarrheal dogs previously tested for other viral pathogens (canine parvovirus type 2, canine coronavirus, and canine circovirus). CBuV was detected in two dogs (3.22%) and CaChPV in one dog (1.61%). One dog tested positive for three parvoviruses (CPV-2b, CBuV, and CaChPV). All dogs tested negative to CAdV-1/CAdV-2. A long genome fragment of one of the two identified CBuVs and of the CaChPV was obtained and analyzed. New Turkish CBuVs had high identity rates (96%-98% nt; 97%-98% aa) with some Italian CBuV strains (CaBuV/9AS/2005/ITA and CaBuV/35/2016/ITA). The phylogenetic analysis powerfully demonstrated that these viruses belonged to a novel genotype (genotype 2). A part of the genome ChPV-TR-2021-19 revealed high identity rates (> 98% nt and > 99% aa) with some Canadian CaChPV strains (NWT-W88 and NWT-W171) and the Italian CaChPV strain Te/37OVUD/2019/IT. This study is the first report on the detection of CBuV-2 and the concomitant presence of three canine parvoviruses in Turkey. The obtained data will contribute to the molecular epidemiology and the role in the etiology of enteric disease of new parvoviruses.

Novel Chaphamaparvovirus in Insectivorous Molossus molossus Bats, from the Brazilian Amazon Region

Chaphamaparvovirus (CHPV) is a recently characterized genus of the Parvoviridae family whose members can infect different hosts, including bats, which constitute the second most diverse order of mammals and are described worldwide as important transmitters of zoonotic diseases. In this study, we identified a new CHPV in bat samples from the municipality of Santarém (Pará state, North Brazil). A total of 18 Molossus molossus bats were analyzed using viral metagenomics. In five animals, we identified CHPVs. These CHPV sequences presented the genome with a size ranging from 3797 to 4284 bp. Phylogenetic analysis-based nucleotide and amino acid sequences of the VP1 and NS1 regions showed that all CHPV sequences are monophyletic. They are also closely related to CHPV sequences previously identified in bats in southern and southeast Brazil. According to the International Committee on Taxonomy of Viruses (ICTV) classification criteria for this species (the CHPV NS1 gene region must have 85% identity to be classified in the same species), our sequences are likely a new specie within the genus Chaphamaparvovirus, since they have less than 80% identity with other CHPV described earlier in bats. We also make some phylogenetic considerations about the interaction between CHPV and their host. We suggest a high level of specificity of CPHV and its hosts. Thus, the findings contribute to improving information about the viral diversity of parvoviruses and show the importance of better investigating bats, considering that they harbor a variety of viruses that may favor zoonotic events.

Detection of FeChPV in a cat shelter outbreak of upper respiratory tract disease in China

Feline parvovirus often causes a fatal infectious disease and has a serious impact on domestic cats and wild felines. Feline chaphamaparvovirus (FeChPV) is a novel type of feline parvovirus that has been successively identified in Canada, Italy, and Turkey. The prevalence and pathogenicity of FeChPV in other regions is still unknown. In this study, we recorded the detection of FeChPV in a cat shelter in China. A high prevalence (81.08%, 30/37) of FeChPV was detected in cats with symptoms of upper respiratory tract disease (URTD) in this cat shelter. Multiple pathogen testing indicated high coinfection rates of 80% (24/30) with other common viruses in FeChPV-positive cats. Analyses of the necropsy and histopathological findings revealed severe lymphadenitis, encephalitis, and viral DNA in several tissues (including brain) of the deceased cat. Finally, we obtained nearly full-length genomes of four strains with 98.4%~98.6% homology with previously reported genomes. Notably, VP1 proteins showed seven unique amino acid mutations, while NS1 proteins carried eight mutations. In the evolutionary tree based on VP1 and NS1, the sequences clustered in a large branch with Italian and Canadian FeChPV strains. Given the possible association of FeChPV with URTD, further studies are necessary to evaluate the pathogenicity and epidemiological characteristics of this novel feline pathogen.

Molecular evidence of rat bocavirus among rodents in Peninsular Malaysia

Rat bocavirus (RBoV) and rodent bocavirus (RoBoV) have previously been detected in Rattus norvegicus; however, these viruses have not been reported in rodent populations in Malaysia. We investigated the presence of RBoV and RoBoV in archived rodent specimens. DNA barcoding of the rodent cytochrome c oxidase gene identified five different species: Rattus tanezumi R3 mitotype, Rattus tiomanicus, Rattus exulans, Rattus argentiventer, and Rattus tanezumi sensu stricto. Three spleens were positive for RBoV (1.84%; 3/163), but no RoBoV was detected. Phylogenetic analyzes of the partial non-structural protein 1 gene grouped Malaysian RBoV strains with RBoV strains from China. Further studies among rats from different geographical locations are warranted for this relatively new virus.

Differential Viral Genome Diversity of Healthy and RSS-Affected Broiler Flocks

The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. To determine the difference in the virome of healthy and diseased broilers, samples from 11 healthy and 17 affected broiler flocks were collected at two time points and analyzed by Next-Generation Sequencing. Virus genomes of Parvoviridae, Astroviridae, Picornaviridae, Caliciviridae, Reoviridae, Adenoviridae, Coronaviridae, and Smacoviridae were identified at various days of poultry production. De novo sequence analysis revealed 288 full or partial avian virus genomes, of which 97 belonged to the novel genus Chaphamaparvovirus. This study expands the knowledge of the diversity of enteric viruses in healthy and RSS-affected broiler flocks and questions the association of some viruses with the diseases.

Emerging Respiratory Viruses of Cats

In recent years, advances in diagnostics and deep sequencing technologies have led to the identification and characterization of novel viruses in cats as protoparviruses and chaphamaparvoviruses, unveiling the diversity of the feline virome in the respiratory tract. Observational, epidemiological and experimental data are necessary to demonstrate firmly if some viruses are able to cause disease, as this information may be confounded by virus- or host-related factors. Also, in recent years, researchers were able to monitor multiple examples of transmission to felids of viruses with high pathogenic potential, such as the influenza virus strains H5N1, H1N1, H7N2, H5N6 and H3N2, and in the late 2019, the human hypervirulent coronavirus SARS-CoV-2. These findings suggest that the study of viral infections always requires a multi-disciplinary approach inspired by the One Health vision. By reviewing the literature, we provide herewith an update on the emerging viruses identified in cats and their potential association with respiratory disease.