Genetic Analysis of Cachavirus-Related Parvoviruses Detected in Pet Cats: The First Report From China

Molecular epidemiological investigation and recombination analysis of Cachavirus prevalent in China

Chaphamaparvovirus carnivoran1 (canine Chaphamaparvovirus, also known as Cachavirus [CachaV]) is a novel parvovirus first reported in dog feces collected from the United States in 2017 and China in 2019. To continuously track its infection and evolution status, 276 canine anal swabs were obtained from pet hospitals in central, northern, and eastern China between 2021 and 2023 and screened via polymerase chain reaction; subsequently, a systematic study was conducted. Of these samples, nine (3.3%) were positive for CachaV. Using polymerase chain reaction, whole genome sequences of the nine CachaV-positive strains were amplified. The NS1 amino acid sequence identity between CachaV strains from China and other countries was 96.23-99.85%, whereas the VP1 protein sequence identity was 95.83-100%. CHN230521 demonstrated the highest identity for NS1 amino acids (99.85%) and VP1 amino acids (100%) with NWT-W88 and CP-T015. According to the model prediction of CHN220916-VP1 protein, Met64Thr, Thr107Ala, and Phe131Ser mutations may cause tertiary structural changes in VP1 protein. Interestingly, each of the nine CachaV strains harbored the same site mutations in NS1 (Ser252Cys, Gly253Leu, and Gly254Thr). Although no explicit recombination events were predicted, the clustering and branching of the phylogenetic tree were complicated. Based on the evolution trees for VP1 and NS1, the nine CachaV strains identified from 2021 to 2023 were closely related to those identified in gray wolves and cats. This study may be beneficial for evaluating the prevalence of CachaVs in China, thereby understanding the evolution trend of CachaVs.

The prevalence, genetic diversity and evolutionary analysis of cachavirus firstly detected in northeastern China

Canine cachavirus is a novel parvovirus belonging to the genus Chaphamaparvovirus that was first detected in dogs in the United States. However, our knowledge of the prevalence and genetic characteristics of cachavirus is relatively limited. In this study, 325 canine fecal specimens collected from healthy and diarrheic dogs in northeastern China were screened with PCR. Twenty-two of the 325 (6.8%) samples were positive for cachavirus. The diarrhea samples showed high viral coinfection rates, and we detected coinfections with canine astrovirus (CaAstV) and cachavirus for the first time. A sequence analysis revealed that the Chinese cachavirus strains have point mutations in four consecutive amino acid codons relative to the original American strain. A codon usage analysis of the VP1 gene showed that most preferred codons in cachavirus were A- or T-ending codons, as in traditional canine parvovirus 2. A co-evolutionary analysis showed that cachavirus has undergone cospeciation with its hosts and has been transmitted among different host species. Our findings extend the limited cachavirus sequences available, and provide detailed molecular characterization of the strains in northeastern China. Further epidemiological surveillance is required to determine the significance and evolution of cachavirus.

Phylogenetic Analysis and Codon Usage Bias Reveal the Base of Feline and Canine Chaphamaparvovirus for Cross-Species Transmission

Chaphamaparvoviruses (ChPVs) are ancient viruses that have been detected in a variety of hosts. In this study, through a phylogenetic analysis and the adaptability of ChPV to multiple hosts, we evaluated the basis for the ability of feline (FeChPV) and canine ChPV (CaChPV) for cross-species transmission. Phylogenetic analysis showed that FeChPV and CaChPV were closely related. Notably, two strains of ChPVs isolated from domestic cats and two from dogs clustered together with CaChPVs and FeChPVs, respectively, suggesting that the stringent boundaries between canine and feline ChPV may be broken. Further analysis revealed that CaChPV and FeChPV were more adapted to dogs than to cats. Mutation analysis identified several shared mutations in cross-species-transmissible strains. Furthermore, the VP structures of FeChPV and CaChPV exhibited a high degree of similarity across both cross-species-transmissible and non-cross-species-transmissible strains. However, it is crucial to note that these results are largely computational, and limitations exist in terms of the number and diversity of samples analyzed; the capacity for cross-species transmission should be approached with caution and elucidated in further studies.

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.

Old and Novel Enteric Parvoviruses of Dogs

Parvovirus infections have been well known for around 100 years in domestic carnivores. However, the use of molecular assays and metagenomic approaches for virus discovery and characterization has led to the detection of novel parvovirus species and/or variants in dogs. Although some evidence suggests that these emerging canine parvoviruses may act as primary causative agents or as synergistic pathogens in the diseases of domestic carnivores, several aspects regarding epidemiology and virus-host interaction remain to be elucidated.

Retrospective Detection and Phylogenetic Analysis of Cachavirus-Related Parvoviruses in Dogs in China

Cachavirus (CachaV) infection was first reported in the USA in 2019. This virus has been previously detected in pet dogs and cats in China. In the present study, we retrospectively examined this virus in 413 dogs and 127 cats. Swab samples obtained from these animals were collected during 2015–2017. Notably, CachaV was detected in four samples from dogs with diarrhea but not in cats; however, the correlation between healthy dogs and those with enteritis was not statistically significant. Furthermore, we amplified early complete genomic sequences of the four strains detected in our study dogs (CHN1601, CHN1602, CHN1703, and CHN1704). Among these strains, the sequence identity of the NS1 protein and the seven previously reported strains in China were 97.44%–99.7%, whereas that of VP1 protein was 98.02%–99.6%. Interestingly, in the NS1 coding region, CHN1704 demonstrated 99.7% (highest) similarity with the CachaV strain NWT-W88 detected from a wolf and 64.5% similarity with the NS1 of a bat parvovirus (BtPV) strain. Conversely, in the VP1 coding region, CHN1703 demonstrated 99.7% (highest) similarity with the prototype CachaV strain IDEXX1 detected from dogs and 63.3% similarity with BtPV strain. For the phylogenetic analysis of NS1 and VP1, the four strains detected during 2016-2017 were merged with other Chinese and foreign CachaV strains to form the major branch. We believe that these results helped improve the understanding of how CachaV evolved and suggest that the virus has been circulating in China since at least March 2016.

Molecular Characterization of Feline Chaphamaparvovirus (Carnivore chaphamaparvovirus 2) Firstly Detected in Dogs from China

A new type of parvovirus known as feline chaphamaparvovirus (FeChPV) was discovered in the feces of shelter cats in Canada in 2019, and >50% of cats were reported to be infected with this virus. In this study, two FeChPV-positive samples were identified from the rectal swabs of 285 dogs with diarrhea but none in 50 healthy dogs. Whole genome sequences of these two FeChPV strains (OQ162042 and OQ162043) were amplified and compared with those of the two viruses originally discovered in Canada (IDEXX-1 and VRI849). The whole genome, NS1, and VP1 of the two FeChPV strains shared a high identity of 95.0%–97.8% nucleotide, 96.9%–98.6% amino acid (aa), and 97.2%–98.8% aa with the reported FeChPV strains, respectively. The phylogenetic tree of NS1 and VP1 revealed that two FeChPV strains, namely, CHN20201025 and CHN20201226, were closely clustered with the two FeChPV prototypes detected in Canada in a group. Moreover, CHN20201025 and CHN20201226 were obviously different from Carnivore chaphamaparvovirus 1 and were classified as Carnivore chaphamaparvovirus 2. This is the first study to report the identification of FeChPV in fecal samples from dogs in China, and the genetic analysis of the FeChPV, which was previously detected in Canadian cats, would improve our understanding of its host spectrum.

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.

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.

The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats

Feline panleukopenia (FPL) is a severe, often fatal disease caused by feline panleukopenia virus (FPV). How infection with FPV might impact the composition of the entire eukaryotic enteric virome in cats has not been characterized. We used meta-transcriptomic and viral particle enrichment metagenomic approaches to characterize the enteric viromes of 23 cats naturally infected with FPV (FPV-cases) and 36 age-matched healthy shelter cats (healthy controls). Sequencing reads from mammalian infecting viral families largely belonged to the Coronaviridae, Parvoviridae and Astroviridae. The most abundant viruses among the healthy control cats were feline coronavirus, Mamastrovirus 2 and Carnivore bocaparvovirus 3 (feline bocavirus), with frequent coinfections of all three. Feline chaphamaparvovirus was only detected in healthy controls (6 out of 36, 16.7%). Among the FPV-cases, in addition to FPV, the most abundant viruses were Mamastrovirus 2, feline coronavirus and C. bocaparvovirus 4 (feline bocaparvovirus 2). The latter and feline bocaparvovirus 3 were detected significantly more frequently in FPV-cases than in healthy controls. Feline calicivirus was present in a higher proportion of FPV-cases (11 out of 23, 47.8%) compared to healthy controls (5 out of 36, 13.9%, p = 0.0067). Feline kobuvirus infections were also common among FPV-cases (9 out of 23, 39.1%) and were not detected in any healthy controls (p < .0001). While abundant in both groups, astroviruses were more frequently present in FPV-cases (19 out of 23, 82.6%) than in healthy controls (18 out of 36, p = .0142). The differences in eukaryotic virome composition revealed here indicate that further investigations are warranted to determine associations between enteric viral co-infections on clinical disease severity in cats with FPL.

Distribution and diversity of dog parvoviruses in wild, free-roaming and domestic canids of Newfoundland and Labrador, Canada

Some parvoviruses of carnivorans can infect multiple host species. Since many canine parvoviruses were only discovered recently, their host-range is still unexplored. We examined the host distribution and diversity of five dog parvoviruses in four canine populations from Newfoundland and Labrador, Canada, and investigated the potential for these viruses to cross the species barriers. Canine bocavirus 2 (CBoV-2) and the minute virus of canines were detected in stool from free-roaming dogs from Labrador (5/48 [10.4%] and 3/48 [6.3%], respectively) and two different CBoV-2 variants were identified. Canine bufavirus was identified in stool from free-roaming dogs (1/48, 2.1%) and foxes (3/80, 3.8%) from Labrador, but two different variants were observed in the two host species. The variant found in foxes was highly divergent from previously identified strains. Two cachavirus 1 variants, genetically similar to those circulating in other Canadian wildlife, were found in spleens from Newfoundland coyotes (3/87, 3.5%). Canine parvovirus type 2 (CPV-2) was found in stool from free-roaming dogs from Labrador (2/48, 4.2%) and in spleens from Newfoundland coyotes (3/87, 3.5%). Comparing CPV-2 sequences from these hosts to those retrieved from local symptomatic domestic dogs revealed the presence of a highly heterogeneous viral population as detected strains belonged to five different clades. The close relationship between CPV-2a strains from a dog and a coyote suggests the occurrence of viral transfer between wild and domestic canids. The identification of highly related strains with a similar molecular signature characteristic of older CPV-2 strains in free-roaming and domestic dogs suggests a probable common ancestry and that older CPV-2 strains, which have not been identified in dogs since the 1990s, persist in this part of Canada. Follow-up studies should evaluate samples from a larger number of animals and host species to extensively investigate the possible occurrence of cross-species transmission for recently discovered parvoviruses.

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.

Small but mighty: old and new parvoviruses of veterinary significance

In line with the Latin expression "sed parva forti" meaning "small but mighty," the family Parvoviridae contains many of the smallest known viruses, some of which result in fatal or debilitating infections. In recent years, advances in metagenomic viral discovery techniques have dramatically increased the identification of novel parvoviruses in both diseased and healthy individuals. While some of these discoveries have solved etiologic mysteries of well-described diseases in animals, many of the newly discovered parvoviruses appear to cause mild or no disease, or disease associations remain to be established. With the increased use of animal parvoviruses as vectors for gene therapy and oncolytic treatments in humans, it becomes all the more important to understand the diversity, pathogenic potential, and evolution of this diverse family of viruses. In this review, we discuss parvoviruses infecting vertebrate animals, with a special focus on pathogens of veterinary significance and viruses discovered within the last four years.

Newlavirus, a Novel, Highly Prevalent, and Highly Diverse Protoparvovirus of Foxes (Vulpes spp.)

The genus Protoparvovirus (family Parvoviridae) includes several viruses of carnivores. We describe a novel fox protoparvovirus, which we named Newlavirus as it was discovered in samples from Newfoundland and Labrador, Canada. Analysis of the full non-structural protein (NS1) sequence indicates that this virus is a previously uncharacterized species. Newlavirus showed high prevalence in foxes from both the mainland (Labrador, 54/137, 39.4%) and the island of Newfoundland (22/50, 44%) but was not detected in samples from other carnivores, including coyotes (n = 92), lynx (n = 58), martens (n = 146), mink (n = 47), ermines (n = 17), dogs (n = 48), and ringed (n = 4), harp (n = 6), bearded (n = 6), and harbor (n = 2) seals. Newlavirus was found at similar rates in stool and spleen (24/80, 30% vs. 59/152, 38.8%, p = 0.2) but at lower rates in lymph nodes (2/37, 5.4%, p < 0.01). Sequencing a fragment of approximately 750 nt of the capsid protein gene from 53 samples showed a high frequency of co-infection by more than one strain (33.9%), high genetic diversity with 13 genotypes with low sequence identities (70.5-87.8%), and no geographic segregation of strains. Given the high prevalence, high diversity, and the lack of identification in other species, foxes are likely the natural reservoir of Newlavirus, and further studies should investigate its distribution.

Emerging Parvoviruses in Domestic Cats

Parvovirus infections in cats have been well known for around 100 years. Recently, the use of molecular assays and metagenomic approaches for virus discovery and characterization has led to the detection of novel parvovirus lineages and/or species infecting the feline host. However, the involvement of emerging parvoviruses in the onset of gastroenteritis or other feline diseases is still uncertain.

Feline chaphamaparvovirus in cats with enteritis and upper respiratory tract disease

Feline chaphamaparvovirus (FeChPV) is a novel parvovirus, first discovered in a multi-facility feline shelter in Canada in 2019, during an outbreak of acute gastro-enteritis (AGE) in cats, and detected at high prevalence (47.0%) in faecal samples. Whether this finding was anecdotal or similar viruses are common components of feline virome is still unclear. Also, the potential impact of this virus on feline health is uncertain. Herewith, a case-control study was performed to investigate whether this novel parvovirus may play a role as enteric pathogen, screening samples collected from cats with and without AGE signs. Furthermore, we extended the research by testing archival paired oropharyngeal and ocular samples collected from cats with or without upper respiratory tract disease (URTD). FeChPV DNA was detected at high prevalence rate (36.8%, 14/38) in clinical cases, representing the most frequently identified enteric virus, followed by feline panleukopenia parvovirus (23.7%, 9/38), feline coronavirus (5.3%, 2/38), feline kobuvirus (5.3%, 2/38) and noroviruses (5.3%, 2/38). The different prevalence rates of FeChPV between the case and control group were statistically significant, suggesting a possible association of the virus with acute gastro-enteric disease. The virus was also detected at low rate in the respiratory samples of cats with (3.3%, 6/183) or without URTD (4.3%, 6/140), although there was no significant association between FeChPV and URTD. The complete VP encoding gene was determined for five viruses and the nearly full-length genome was reconstructed for three viruses, namely 313R/2019/ITA, 284R/2019/ITA and 49E/2019/ITA. In the NS1-based tree, the Italian strains clustered tightly with the two FeChPV prototypes detected in Canada, within a monophyletic cluster related to but clearly distinct from canine chaphamaparvovirus, currently classified in the species Carnivore chaphamaparvovirus 1 (CaChPV-1).