Detection and genetic characterization of a novel parvovirus (family Parvoviridae) in barn owls (Tyto alba) in Hungary

Known and novel parvoviruses identified in domestic pigeons

BACKGROUND

Parvoviridae is a family of single-stranded linear DNA viruses whose members infect both vertebrate and invertebrate species of animals, causing diseases of various systems and often associated with pathology of the gastrointestinal tract. Additionally, parvoviruses are known to induce illnesses causing diarrhea in various avian species as well; however, data on their occurrence and pathology in pigeons is scarce.

RESULTS

In this study, we developed molecular biology methods to detect and quantify parvovirus genetic material in samples acquired from racing pigeons of different health status. Our intention was to determine a connection between the presence of the virus and the occurrence of clinical signs in sampled birds. The results of quantitative analysis indicate no direct association of parvoviruses with the manifestation of enteric disease in pigeons. High-throughput sequencing was performed on samples testing positive in quantitative PCR with TaqMan probe and in digital droplet PCR. It allowed us to assemble two coding-complete pigeon parvovirus genomes, one belonging to new species and referred to as pigeon parvovirus 2, and the second which is a member of species Aveparvovirus columbid1. Additionally, we analyze two coding-complete genomic sequences acquired from pigeon feces in USA, one representing species Aveparvovirus columbid1 and one being a member of Chaphamaparvovirus genus in Hamaparvovirinae subfamily.

CONCLUSIONS

This is the first report of parvovirus in pigeons outside Asia. The findings of our research emphasize the need to further explore the poorly understood biology and pathology of pigeon parvoviruses.

Visible and rapid detection of feline chaphamaparvovirus using multienzyme isothermal rapid amplification and lateral flow dipstick assay

Feline chaphamaparvovirus (FeChPV) is a novel parvovirus previously reported in Canadian cats and Chinese dogs with diarrhea in 2019 and 2020, respectively. Herein, we aimed to establish a simple detection method for FeChPV in field clinics. The primers and probes for the multienzyme isothermal rapid amplification and lateral flow dipstick (MIRA-LFD) assay were designed to target the conserved regions of the FeChPV genome and determine the optimal reaction temperature and time. Without relying on precision instruments, FeChPV detection using the MIRA-LFD assay was completed within 20 min at 37°C, without any cross-reaction with other reference viruses. The newly established MIRA-LFD assay had a detection limit of 32.3 copies/μL, which was 10-fold lower than that of the nested polymerase chain reaction (PCR) assay. Furthermore, the MIRA-LFD assay detected 29 FeChPV-positive samples among 417 cats with diarrhea, providing a slightly higher positivity rate than the nested PCR assay. These results indicate that the newly developed MIRA-LFD assay for FeChPV detection is an efficient, economical, reliable, and simple method that can help in the early prevention and control of FeChPV infection.

Genomic characterization of parvovirus and beak and feather disease virus in cockatiel (Nymphicus hollandicus)

This study reveals the genomes of psittaciform chaphamaparvovirus 5 (PsChPV-5) and a beak and feather disease virus (BFDV), discovered in the fecal samples of cockatiels. The genomes of PsChPV-5 and BFDV are 4,366 and 2,009 base pairs long, respectively, each exhibiting the characteristic genomic structures of their respective genera.

Detection of a parvovirus and a beak and feather disease virus genome sequence from rose-ringed parakeet (Psittacula krameri)

This study reports a genome of psittaciform chaphamaparvovirus 4 (PsChPV-4) and a beak and feather disease virus (BFDV) detected in fecal materials of rose-ringed parakeet. The genomes of PsChPV-4 and BFDV were 4,304 and 2,009 bp long, respectively, and both genomes possessed a genomic structure consistent with their respective genera.

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.

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.

Novel Virus Identification through Metagenomics: A Systematic Review

Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.

Characterization of a Novel Complete-Genome Sequence of a Galliform Chaphamaparvovirus from a Free-Range Laying Chicken Clinically Diagnosed with Spotty Liver Disease

This study reports a novel complete genome of galliform chaphamaparvovirus 4, which was detected in the bile of a free-range laying chicken diagnosed with spotty liver disease. The genome was 4,367 bp in length, enclosed by two identical inverted terminal repeats. The detection of this novel chaphamaparvovirus represents a notable concern for the poultry industry in Australia.

Identification and genomic characterization of a novel porcine parvovirus in China

Porcine parvoviruses (PPVs) are a group of small non-enveloped viruses with seven species (porcine parvovirus 1–7, PPV1-7) have been identified. In this study, a novel porcine parvovirus, provisionally named porcine parvovirus 8 (PPV8), was initially identified via high-throughput sequencing (HTS) in porcine reproductive and respiratory syndrome virus-positive samples collected from swine herds in Guangdong province, 2021. The nearly full-length genome of PPV8 strain GDJM2021 is 4,380 nucleotides in length with two overlapping open ORFs encoding NS1 and VP1 respectively. Sequence analysis indicated that PPV8 shared 16.23–44.18% sequence identity at the genomic levels to PPV1-7 with the relatively highest homology to PPV1. PPV8-GDJM2021 shared 31.86–32.68% aa sequence identity of NS1 protein with those of PPV1 and porcine bufavirus (PBuV), and formed an independent branch neighboring to those formed by members of the genus Protoparvovirus. Of the 211 clinical samples collected from 1990 to 2021, 37 samples (17.5%) distributed over 12 regions in China were positive for PPV8 with time spanning 24 years (1998–2021). To our knowledge, this is the first report on the genomic characterization of the novel PPV8 and its epidemiological situations in China.

Characterization of a Near-Complete Genome Sequence of a Chaphamaparvovirus from an Australian Boobook Owl (Ninox boobook)

This study reports a complete genome sequence of a variant of psittacine chaphamaparvovirus 2 detected in kidney tissue from an Australian boobook (Ninox boobook), compiled using next-generation sequencing. The genome was 4,312 bp long, encoding four open reading frames. The detection of this variant in boobook represents a significant host-switching event.