Phylogenetic analysis of canine distemper virus in South African wildlife

Unusual Canine Distemper Virus Infection in Captive Raccoons (Procyon lotor)

Canine morbillivirus, also known as canine distemper virus (CDV), is the causative agent of canine distemper (CD), which is a serious contagious disease of canines, large felids, and, occasionally, raccoons. This study included seven raccoons from the Timisoara Zoological Garden, Romania. CDV was detected using RT-qPCR on blood samples, but several other exams were also performed-clinical, bacteriological, immunohistochemistry (IHC) and histopathology, toxicological screening, and necropsy-which confirmed CDV infection. Severe digestive disorders (diarrhea and frequent hematemesis) were observed. The necropsy findings included pseudo membranous gastroenteritis, congestion, and pulmonary edema in two raccoons. Immunohistochemistry showed immunolabeled CDV antigenantibodies on the viral nucleocapsid. Histopathology revealed lymphocyte depletion in mesenteric lymphnodes and intranuclear and intracytoplasmic inclusions in the enterocytes of the small intestine. Based on the RT-qPCR assay, laboratory tests, and the lesions observed, it was established that the raccoons were infected with CDV, which was the cause of death in two cases. The results from the necropsy, histology, and immunohistochemistry in the raccoons are comparable with reported CDV lesions in dogs. In conclusion, several exams may be performed to establish the etiology of possible interspecific viral infection, but only very specific exams can identify aCDV infection. Laboratory analyses must be completed by RT-qPCR assay or IHC to establish infection with uncommon viruses in raccoons with high accuracy.

Biomolecular Analysis of Canine Distemper Virus Strains in Two Domestic Ferrets (Mustela putorius furo)

Canine distemper is a contagious and severe systemic viral disease that affects domestic and wild carnivores worldwide. In this study, two adult female ferrets (Mustela putorius furo) were evaluated for cutaneous lesions. Scab, fur, and swab samples from the external auditory canal, cutaneous lesions, and scrapings were analyzed. Canine distemper virus (CDV)-positive samples underwent RT-PCR/RFLP with the restriction enzyme PsiI, and the hemagglutinin gene sequence was obtained. According to the restriction enzyme and sequence analyses, the viral strains were typed as CDV field strains that are included within the Europe lineage and distinct from those including vaccinal CDV strains. The sequence analysis showed the highest nucleotide identity rates in older Europe lineage CDV strains collected from dogs and a fox in Europe. This study is the first to report on CDV infection in ferrets in southern Italy and contributes to the current knowledge about natural CDV infection in this species. In conclusion, vaccination remains crucial for preventing the disease and counteracting cross-species infection. Molecular biology techniques can enable the monitoring of susceptible wild animals by ensuring the active surveillance of CDV spread.

Phylogenetic characterization of the canine distemper virus isolated from veterinary clinics in the Mekong Delta, Vietnam

Background and Aim

Canine distemper (CD) caused by the CD virus (CDV) has a high mortality rate that severely affects dog populations and other terrestrial carnivores worldwide. However, the genetics of CDV strains circulating in various regions in Vietnam, especially the Mekong Delta, remains unclear. This study aimed to characterize the molecular status of CDV strains circulating in the Mekong Delta, Vietnam.

Materials and Methods

Ocular/nasal swabs were collected from 550 dogs with clinically suspected CDV infection from veterinary clinics in three Vietnamese provinces. A reverse transcription-polymerase chain reaction on the part of the hemagglutinin gene was performed. A phylogenetic tree was constructed to analyze the relationship between the detected CDV and GenBank sequences.

Results

The molecular study demonstrated that 4.18% (23/550) of the dogs were positive for CDV. The clinical findings revealed that the positive dogs exhibited clinical signs of distemper. The phylogenetic analysis indicated that the identified CDV sequences were clustered in the same branch with the genotype Asia-1 and distantly related to the vaccine strains. Notably, the CDV sequences detected in this study were grouped with the sequences previously found in southeast Vietnam; however, they were distant from those found in the north.

Conclusion

The present study confirmed the presence of CDV and to the best of our knowledge, highlighted for the first time that the CDV strains circulating in the Mekong Delta of Vietnam belong to the genotype Asia-1.

Detection of Selected Canine Viruses in Nigerian Free-Ranging Dogs Traded for Meat Consumption

Animal trade favors the spreading of emerging and re-emerging pathogens. Concerns have been previously expressed regarding the risks of dog trade in spreading zoonotic pathogens in Nigeria. However, the role of these dogs in disseminating highly pathogenic canine viruses has not yet been explored. The present study aimed to identify selected canine viruses in dogs traded for meat consumption in Nigeria. A total of 100 blood samples were screened for carnivore protoparvovirus-1 (CPPV-1), canine adenovirus 1/2 (CAdV-1/2), canine circovirus (CaCV), and canine distemper virus (CDV) by using real-time PCR and conventional PCR and/or sequencing. CPPV-1 DNA was identified in 83% of canine samples while CaCV DNA and CDV RNA were detected in 14% and 17% of the dog samples, respectively. None of the dogs tested positive for CAdV-1/2. The CaCVs identified in this study clustered along with other European, Asian, and American strains. Moreover, CDV strains identified in Nigeria clustered in a separate lineage with the closest genetic relatedness to the Europe-South America-1 clade. Further surveys prior to and after arrival of dogs at the slaughtering points are required to clarify the real virus burden in these animals.

An appraisal of gene targets for phylogenetic classification of canine distemper virus: Is the hemagglutinin the best candidate?

Sequence analysis of the canine distemper virus (CDV) hemagglutinin (H) gene may provide important insights on virus-host interactions and has also been frequently used for CDV phylogenetic classification. Herein, we performed an in silico analysis of CDV complete genomes (CGs) available in GenBank in order to investigate the suitability of H for CDV classification into lineages/genotypes. In addition, we analyzed the other viral genes for their potential use in CDV classification. Initially, we collected 116 CDV CGs from GenBank and compared their phylogenetic classification with that of their respective H nucleotide (nt) and amino acid (aa) sequences. Subsequently, we calculated the geodesic distance between the CG and H phylogenetic trees. These analyses were later performed with other CDV genes. All CDV CGs were also evaluated for possible recombination events. Nucleotide and aa analyses of H misclassified some Vaccine/America 1/Asia 3 lineage sequences compared to CG analysis, finding supported by both Maximum Likelihood (ML) and Bayesian Markov Chain Monte Carlo (B-MCMC) methods. Moreover, aa-based H analysis showed additional disagreements with the classification obtained by CG. The geodesic distance between the H and CG trees was 0.0680. Strong recombination signals were identified in the H gene, including Vaccine/America 1/Asia 3 lineage sequences. In contrast, C and P were the only genes that fully reproduced the CG classification (by ML and/or B-MCMC) and that did not show strong recombination signals. Furthermore, the P phylogenetic tree showed the lowest geodesic distance from the CG tree (0.0369). These findings suggest C and P as potential targets for CDV phylogenetic classification, especially when full genome sequencing is not possible. Finally, since our results were obtained considering the CDV CGs available to date, future analyses performed as more CDV sequences become available will be useful to assess probable issues of H-based phylogeny and to consolidate the suitability of the C and P genes for CDV classification.

Canine morbillivirus (CDV): a review on current status, emergence and the diagnostics

The increasing host range of canine morbillivirus (CDV) affecting important wildlife species such as Lions, Leopard, and Red Pandas has raised the concern. Canine distemper is a pathogen of dogs affecting the respiratory, gastrointestinal, and nervous systems. Seventeen lineages of CDV are reported, and the eighteenth lineage was proposed in 2019 from India. Marked genomic differences in the genome of wild-type virus and vaccine strain are also reported.The variations at the epitope level can be differentiated using specific monoclonal antibodies in neutralization tests. Keeping in mind the current status of the emergence of CDV, genetic and molecular study of circulating strains of the specific geographical region are the essential components of the disease control strategy. New target-based diagnostics and vaccines are in need to counter the effects of the emerging virus population. Control of CDV is necessary to save the endangered, vulnerable, and many other wildlife species to maintain balance in the ecological system. This review provides an overview on emergence reported in CDV, diagnostics developed till today, and a perspective on the disease control strategy, keeping wildlife in consideration.

A new canine distemper virus lineage identified from red pandas in China

Canine distemper virus (CDV) is a highly contagious virus that causes multi-systemic, sub-clinical to fatal diseases in a wide range of carnivore species. Based on the sequences of the haemagglutinin (H) gene, CDV strains have been classified into 18 major genetic lineages. In this study, we characterized the genomes of CDV isolated from the lungs of two dead red pandas in China. Histopathological and immunohistochemical analyses revealed damage due to viral infection in these lungs. The two strains showed a deep genetic distance from the other 18 recognized lineages (>4.6% at nucleotide level and >5.0% at amino acid level). The maximum clade credibility tree of the H- gene sequences showed that they belonged to an independent clade and had diverged a relatively long time ago from the Asia-4 lineage (since 1884). These results suggest that the analyzed strains belong to a new CDV lineage, which we designate as Asia-6. Our finding indicates that CDV infections in wildlife in China are complex and are a threat to endangered carnivores.

TEMPORAL AND SPATIAL PATTERNS IN CANINE DISTEMPER VIRUS CASES IN WILDLIFE DIAGNOSED AT THE SOUTHEASTERN COOPERATIVE WILDLIFE DISEASE STUDY, 1975-2019

Canine distemper is a high-impact disease of many mammal species and has caused substantial carnivore population declines. Analysis was conducted on passive surveillance data of canine distemper (CDV)-positive wild mammal cases submitted to the Southeastern Cooperative Wildlife Disease Study, Athens, Georgia, US, between January 1975 and December 2019. Overall, 964 cases from 17 states were CDV positive, including 646 raccoons (Procyon lotor), 254 gray foxes (Urocyon cinereoargenteus), 33 striped skunks (Mephitis mephitis), 18 coyotes (Canis latrans), four red foxes (Vulpes vulpes), three gray wolves (Canis lupus), three American black bears (Ursus americanus), two American mink (Mustela vison), and one long-tailed weasel (Mustela frenata). Raccoon and gray fox case data from the state of Georgia (n=441) were selected for further analysis. Autoregressive integrated moving average models were developed predicting raccoon and gray fox case numbers. The best-performing model for gray foxes used numbers of gray fox CDV cases from the previous 2 mo and of raccoon cases in the present month to predict the numbers of gray fox cases in the present month. The best-performing model for raccoon prediction used numbers of raccoon CDV cases from the previous month and of gray fox cases in the present month and previous 2 mo to predict numbers of raccoon cases in the present month. Temporal trends existed in CDV cases for both species, with cases more likely to occur during the breeding season. Spatial clustering of cases was more likely to occur in areas of medium to high human population density; fewer cases occurred in both the most densely populated and sparsely populated areas. This pattern was most prominent for raccoons, which may correspond to high transmission rates in suburban areas, where raccoon population densities are probably highest, possibly because of a combination of suitable habitat and supplemental resources.

Sylvatic Canine Morbillivirus in Captive Panthera Highlights Viral Promiscuity and the Need for Better Prevention Strategies

Canine Distemper Virus (CDV) is a multi-host morbillivirus that infects virtually all Carnivora and a few non-human primates. Here we describe a CDV outbreak in an exotic felid rescue center that led to the death of eight felids in the genus Panthera. Similar to domestic dogs and in contrast to previously described CDV cases in Panthera, severe pneumonia was the primary lesion and no viral antigens or CDV-like lesions were detected in the central nervous system. Four tigers succumbed to opportunistic infections. Viral hemagglutinin (H)-gene sequence was up to 99% similar to strains circulating contemporaneously in regional wildlife. CDV lesions in raccoons and skunk were primarily encephalitis. A few affected felids had at least one previous vaccination for CDV, while most felids at the center were vaccinated during the outbreak. Panthera sharing a fence or enclosure with infected conspecifics had significantly higher chances of getting sick or dying, suggesting tiger-tiger spread was more likely than recurrent spillover. Prior vaccination was incomplete and likely not protective. This outbreak highlights the need for further understanding of CDV epidemiology for species conservation and public health.

MODIFIED LIVE DISTEMPER VACCINES CARRY LOW MORTALITY RISK FOR CAPTIVE AFRICAN WILD DOGS, LYCAON PICTUS

Recently, canine distemper virus (CDV) has been linked to population declines in the endangered African wild dog (Lycaon pictus). As CDV appears able to persist in wildlife, threats to free-ranging wild dogs cannot be eliminated by vaccinating domestic dogs. Conservation managers may therefore consider CDV vaccination of wild dogs in highly threatened populations. For use in field conservation, the ideal CDV vaccine would be safe, immunogenic, and readily available in Africa. The CDV vaccine type most commonly used for domestic dogs (modified live vaccine) is available in Africa, and apparently immunogenic in wild dogs, but has been linked to fatal vaccine-induced distemper in captive wild dogs. However, alternatives are either ineffective (inactivated vaccine) or difficult to obtain in Africa (recombinant vaccine). Data from a questionnaire survey of zoo vaccination practices were therefore combined with studbook tracing to assess the safety of modified live CDV vaccine in captive African wild dogs. Among 135 wild dog pups given modified live CDV vaccine for the first time, there was a single, unconfirmed, case of potential vaccine-induced distemper. Pups given modified live vaccine survived better than those given inactivated vaccine or no vaccine. Although studbook tracing revealed higher overall pup survival at zoos which responded to the questionnaire than at zoos which did not, tracing of all pups born during a 20-yr period that lived long enough to be vaccinated (n = 698 pups in 155 litters) revealed no mortality events consistent with vaccine-induced distemper. Modified live CDV vaccine thus appears to carry low mortality risks for African wild dog pups in captivity, and may warrant trials in free-ranging populations.

Phylodynamic analysis of two amino acid substitutions in the hemagglutinin protein of canine distemper virus strains detected in fur-bearing animals in China

Canine distemper virus (CDV) causes a highly contagious disease in a wide range of carnivores. The hemagglutinin (H) protein of viruses shows the highest variability and plays an important role in modulation of viral antigenicity, virulence, and receptor recognition. Since 2012, canine distemper (CD) outbreaks in fur-bearing animals (minks, foxes, raccoon dogs) caused by CDV variants with I542N and Y549H substitutions in the H protein have been frequently reported in China. To characterize the molecular evolutionary dynamics and epidemiological dynamics of CDV, 235 H gene sequences of CDV wild-type strains collected from 22 countries between 1975 and 2015, including 44 strains predominant in fur-bearing animals in China, were analyzed. The phylogenetic relationships and evolutionary rates of the CDV strains were determined by Bayesian phylogenetics. The CDV strains clustered into distinct geographic genotypes, irrespective of the species of isolation. All the variant strains formed a distinct monophyletic cluster and belonged to the F sub-genotype within the Asia-1 genotype-currently the predominant sub-genotype in fur-bearing animals in China. Evolutionary analysis suggested that the variant strains originated in 2006. Furthermore, the selection pressure analysis revealed that the Y549H substitution was under positive selection pressure for adaptation toward the fur-bearing animals. The residue at position 549 also showed structural interaction with the V domain of the mink signaling lymphocyte-activation molecule (SLAM) receptor based on the homology modeling of the H-SLAM complex. Our results suggested that the Y549H substitution contributed to the molecular adaptation of CDV variants in the fur-bearing animals during the viral evolutionary phase in China.

Canine and Phocine Distemper Viruses: Global Spread and Genetic Basis of Jumping Species Barriers

Canine distemper virus (CDV) and phocine distemper (PDV) are closely-related members of the Paramyxoviridae family, genus morbillivirus, in the order Mononegavirales. CDV has a broad host range among carnivores. PDV is thought to be derived from CDV through contact between terrestrial carnivores and seals. PDV has caused extensive mortality in Atlantic seals and other marine mammals, and more recently has spread to the North Pacific Ocean. CDV also infects marine carnivores, and there is evidence of morbillivirus infection of seals and other species in Antarctica. Recently, CDV has spread to felines and other wildlife species in the Serengeti and South Africa. Some CDV vaccines may also have caused wildlife disease. Changes in the virus haemagglutinin (H) protein, particularly the signaling lymphocyte activation molecule (SLAM) receptor binding site, correlate with adaptation to non-canine hosts. Differences in the phosphoprotein (P) gene sequences between disease and non-disease causing CDV strains may relate to pathogenicity in domestic dogs and wildlife. Of most concern are reports of CDV infection and disease in non-human primates raising the possibility of zoonosis. In this article we review the global occurrence of CDV and PDV, and present both historical and genetic information relating to these viruses crossing species barriers.

Comparative sequence analysis of morbillivirus receptors and its implication in host range expansion

SLAM (CD150) and nectin-4 are the major morbillivirus receptors responsible for virus pathogenesis and host range expansion. Recently, morbillivirus infections have been reported in unnatural hosts, including endangered species, posing a threat to their conservation. To understand the host range expansion of morbilliviruses, we generated the full-length sequences of morbillivirus receptors (goat, sheep, and dog SLAM, and goat nectin-4) and tried to correlate their role in determining host tropism. A high level of amino acid identity was observed between the sequences of related species, and phylogenetic reconstruction showed that the receptor sequences of carnivores, marine mammals, and small ruminants grouped separately. Analysis of the ligand binding region (V region; amino acid residues 52-136) of SLAM revealed high amino acid identity between small ruminants and bovine SLAMs. Comparison of canine SLAM with ruminants and non-canids SLAM revealed appreciable changes, including charge alterations. Significant differences between feline SLAM and canine SLAM have been reported. The binding motifs of nectin-4 genes (FPAG motif and amino acid residues 60, 62, and 63) were found to be conserved in sheep, goat, and dog. The differences reported in the binding region may be responsible for the level of susceptibility or resistance of a species to a particular morbillivirus.