High rate of viral evolution associated with the emergence of carnivore parvovirus

Novel parvovirus in cats, China

Parvovirus is a common element of the feline virus group and usually causes gastroenteritis and leukopenia in cats. In this study, we identified a novel protoparvovirus from the Chinese domestic cats, which is genetically similar to canine bufavirus (98.0%-99.8%), but sharing low amino acid identities in the viral structural proteins 2 (VP2) (36.1-37.2%) to the well-known canine parvovirus type 2 and feline panleukopenia virus. This virus was provisionally designated as feline bufavirus (FBuV). Screening of fecal samples revealed a prevalence of 7.4% (19/257) in domestic cats. Diarrhea was present in 52.6% (10/19) of cats positive for FBuV. However, statistical analysis showed no association between FBuV and clinical signs. VP2 gene of the 19 field FBuV was sequenced and phylogenetic analysis demonstrated that FBuV determined from China had a genetic diversity. This study will strengthen the understanding of the epidemiology and genetic diversity of bufavirus and provide a foundation for further studies.

Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation

Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5' intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.

Restoring the natural tropism of AAV2 vectors for human liver

Recent clinical successes in gene therapy applications have intensified interest in using adeno-associated viruses (AAVs) as vectors for therapeutic gene delivery. Although prototypical AAV2 shows robust in vitro transduction of human hepatocyte-derived cell lines, it has not translated into an effective vector for liver-directed gene therapy in vivo. This is consistent with observations made in Fah^-/-/Rag2^-/-/Il2rg^-/- (FRG) mice with humanized livers, showing that AAV2 functions poorly in this xenograft model. Here, we derived naturally hepatotropic AAV capsid sequences from primary human liver samples. We demonstrated that capsid mutations, likely acquired as an unintentional consequence of tissue culture propagation, attenuated the intrinsic human hepatic tropism of natural AAV2 and related human liver AAV isolates. These mutations resulted in amino acid changes that increased binding to heparan sulfate proteoglycan (HSPG), which has been regarded as the primary cellular receptor mediating AAV2 infection of human hepatocytes. Propagation of natural AAV variants in vitro showed tissue culture adaptation with resulting loss of tropism for human hepatocytes. In vivo readaptation of the prototypical AAV2 in FRG mice with a humanized liver resulted in restoration of the intrinsic hepatic tropism of AAV2 through decreased binding to HSPG. Our results challenge the notion that high affinity for HSPG is essential for AAV2 entry into human hepatocytes and suggest that natural AAV capsids of human liver origin are likely to be more effective for liver-targeted gene therapy applications than culture-adapted AAV2.

Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses

Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.

Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites

Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity, and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China, while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite's virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite, and Cotton leaf curl Multan betasatellite populations arising from distinct regions exhibit high mutation rates. Although evolutionarily linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.

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.

Genetic Insights into Feline Parvovirus: Evaluation of Viral Evolutionary Patterns and Association between Phylogeny and Clinical Variables

Feline panleukopenia is a severe disease of cats caused by feline parvovirus (FPV), and marginally canine parvovirus (CPV). Despite being less rapid than CPV, FPV evolution deserves attention, especially since outbreaks of particular severity are currently reported. This apparently different virulence needs monitoring from genetic and clinical points of view. This manuscript explored FPV molecular epidemiology at both Italian and international levels and the possible association between viral phylogeny and disease severity. Sequences from clinical cases of feline panleukopenia in Italy were obtained from 2011 to 2019, and the etiological agent was characterized, distinguishing FPV from CPV. Phylogenetic and phylodynamic analyses were conducted on Italian and international sequences. Moreover, the association between the viral sequence and clinical variables was evaluated on a group of highly characterized patients. After its origin in the 1920s, FPV showed a constant population size until a more recent expansion since 2000. Few long-distance introduction events characterized FPV spreading, however, most of its evolution occurred locally. Although without a strong statistical association, several clinical variables appeared influenced by viral phylogeny, suggesting a differential virulence potentially characterizing FPV strains. These results stress the importance of the continuous study of viral evolution and its repercussions on the disease clinical aspects.

Computational based design and tracking of synthetic variants of Porcine circovirus reveal relations between silent genomic information and viral fitness

Viral genomes not only code the protein content, but also include silent, overlapping codes which are important to the regulation of the viral life cycle and affect its evolution. Due to the high density of these codes, their non-modular nature and the complex intracellular processes they encode, the ability of current approaches to decipher them is very limited. We describe the first computational-experimental pipeline for studying the effects of viral silent and non-silent information on its fitness. The pipeline was implemented to study the Porcine Circovirus type 2 (PCV2), the shortest known eukaryotic virus, and includes the following steps: (1) Based on the analyses of 2100 variants of PCV, suspected silent codes were inferred. (2) Five hundred variants of the PCV2 were designed to include various ‘smart’ silent mutations. (3) Using state of the art synthetic biology approaches, the genomes of these five hundred variants were generated. (4) Competition experiments between the variants were performed in Porcine kidney-15 (PK15) cell-lines. (5) The variant titers were analyzed based on novel next-generation sequencing (NGS) experiments. (6) The features related to the titer of the variants were inferred and their analyses enabled detection of various novel silent functional sequence and structural motifs. Furthermore, we demonstrate that 50 of the silent variants exhibit higher fitness than the wildtype in the analyzed conditions.

Molecular Insights into the Genetic Variability of ORF Virus in a Mediterranean Region (Sardinia, Italy)

Orf virus (ORFV) represents the causative agent of contagious ecthyma, clinically characterized by mild papular and pustular to severe proliferative lesions, mainly occurring in sheep and goats. In order to provide hints on the evolutionary history of this virus, we carried out a study aimed to assess the genetic variation of ORFV in Sardinia that hosts a large affected small ruminant population. We also found a high worldwide mutational viral evolutionary rate, which resulted, in turn, higher than the rate we detected for the strains isolated in Sardinia. In addition, a well-supported genetic divergence was found between the viral strains isolated from sheep and those from goats, but no relevant connection was evidenced between the severity of lesions produced by ORFV and specific polymorphic patterns in the two species of hosts. Such a finding suggests that ORFV infection-related lesions are not necessarily linked to the expression of one of the three genes here analyzed and could rather be the effect of the expression of other genes or rather represents a multifactorial character.

Origin, spreading and genetic variability of chicken anaemia virus

Chicken anaemia virus (CAV) is a widespread pathogen that causes immunosuppression in chickens. The virus-induced immunosuppression often results in secondary infections and a sub-optimal response to vaccinations, leading to high mortality rates and significant economic losses in the poultry industry. The small circular ssDNA genome (2.3 kb) has three partially overlapping genes: vp1, vp2 and vp3. VP1 capsid protein is highly variable and contains the neutralizing epitopes. Here, we analysed CAV strains from Uruguay using the full-length vp1 gene and performed a global comparative analysis to provide new evidence about the origin, dispersion and genetic variability of the virus. The phylogenetic analysis classified CAV in three or four major clades. Two clades (II and III) grouped most of the strains circulating worldwide including the Uruguayan strains. The phylodynamic analyses indicated that CAV emerged in the early 1900s and diverged to originate clade II and III. This early period of viral emergence was characterised by local diversification promoted by the extremely high substitution rate inferred for the virus (3.8 × 10^-4 substitutions/site/year). Later, the virus underwent a global spreading by intra- and inter-continental migrations that correlates with a significant rise in the effective population size. In South America, CAV was introduced in three different migratory events and spread across the continent. Our findings suggest that the current CAV distribution is the consequence of its continuous expansion capability that homogenizes the populations and prevents the detection of clear temporal and geographic patterns of evolution in most strains.RESEARCH HIGHLIGHTS Current strains of chicken anaemia virus emerged in Asia in the early 1900s.Chicken anaemia virus has a high substitution rate.The phylogenetic analysis classified chicken anaemia virus in four major clades.Evolution in South America was characterized by long migration and local spreading.

Canine parvovirus type 2c in Vietnam continues to produce distinct descendants with new mutations restricted to Vietnamese variants

Viral protein 2 (VP2) of canine parvovirus (CPV) exhibits a high degree of genetic and antigenic diversity. We analyzed 88 Vietnamese CPV-VP2 sequences (1755 bp), 34 from this study and 54 from previous studies, and discovered a new sublineage, "new var.", within the lineage CPV-2c-"new", characterized by the mutation 5G/447M, which is restricted to the Vietnamese isolates. These new mutants appear to have emerged in recent years, accounting for 65.5% of the total. With strong nodal support (98%), the distinct Vietnamese 2c-"new-var." sublineage (5G/426E/447M) was found to be separate from the 2c-"new" sublineage (5G/426E/447I) within the 2c-(Asia)/Asia-2c lineage. Amino acid changes in epitopes of VP2 might have led to the generation of subvariants and affected the antigenicity, immunogenicity, or virulence of the virus, resulting in vaccine failure worldwide.

Pathogenicity comparison of the SMPV-11 and attenuated mink enteritis virus F61 in mink

Mink enteritis virus (MEV) is a major pathogen inducing acute hemorrhagic enteritis in mink. This study aims to determine the pathogenicity of the isolated MEV strain (SMPV-11) compared with the attenuated MEV strain (MEV-F61) in the mink. The two MEV strains were inoculated in the two mink groups, respectively. Then the clinical symptom, hematological, serological, and histopathological change were evaluated. Our findings showed that there were differences in the clinical features and pathological changes of the SMPV-11 and MEV-F61 in the mink. It indicates that SMPV-11 is a virulent strain, and it can be the potential MEV vaccine strain in the mink.

Molecular survey of parvovirus, astrovirus, coronavirus, and calicivirus in symptomatic dogs

Gastrointestinal disorders caused by enteric viruses are frequently reported in dogs worldwide, with significant mortality rates in unvaccinated individuals. This study reports the identification and molecular characterization of Canine parvovirus (CPV-2), Canine coronavirus (CcoV), Canine astrovirus (AstV), and Canine calicivirus (CcaV) in a panel of dogs showing severe enteric clinical signs sampled in a typical Mediterranean environment (Sardinia, Italy). At least one of these viral species was detected in 92.3% samples. CPV-2 was the most frequently detected virus (87.2%), followed by AsTv (20.5%), CCoV-IIa (18%), and CCoV-I (10.3%). CCoV-IIb and CaCV were not detected in any sample. Single infection was detected in 24 samples (66.7%), mainly related to CPV-2 (91.7%). Coinfections were present in 33.3% samples with constant detection of CPV-2. Canine coronavirus was present only in coinfected animals. The VP2 sequence analysis of CPV-2 positive samples confirmed the presence of all variants, with CPV-2b most frequently detected. Phylogeny based on the CcoV-IIa spike protein (S) gene allowed to identify 2 different clades among Sardinian isolates but failed to distinguish enteric from pantropic viruses. Study on presence and prevalence of enteroviruses in dogs increase our knowledge about the circulation of these pathogens in the Mediterranean area and highlight the need for dedicated routine vaccine prophylaxis. Molecular analyses of enteric viruses are fundamental to avoid failure of vaccines caused by frequent mutations observed in these enteroviruses.

Multi-host dispersal of known and novel carnivore amdoparvoviruses

Amdoparvoviruses (family Parvoviridae) are ssDNA viruses that cause an immune complex-mediated wasting syndrome in carnivores. They are multi-host pathogens and cross-species infection is facilitated by the fact that viral entry is mediated by cellular Fc receptors recognizing antibody-coated viruses. We developed a pan-amdoparvovirus PCR and screened tissue samples from 666 wild carnivores (families Felidae, Canidae, and Mustelidae) from Newfoundland or Labrador (Canada) and molecularly characterized the identified strains. Fifty-four out of 666 (8.1%) animals were amdoparvovirus-positive. Infection rate was the highest in American mink (34/47, 72.3%), followed by foxes (Arctic and red foxes, 13/311, 4.2%), lynx (2/58, 3.5%), and American martens (5/156, 3.4%). No virus was detected in samples from 87 coyotes and 17 ermines. Viruses from Newfoundland were classified as Aleutian mink disease virus (AMDV). Mink harvested near AMDV-affected fur farms had higher prevalence (24/24, 100%) than other mink (10/23, 43.5%; P < 0.001) and their viruses were phylogenetically closely related to those from farms, while most viruses from other mink were in other clades. Strains from three foxes and two lynx were highly related to mink strains. This proves that farms disperse AMDV that subsequently spreads among wild mink (maintenance host) and transmits to other spillover carnivore hosts. In Labrador two novel viruses were identified, Labrador amdoparvovirus 1 (LaAV-1) found in foxes (9/261, 3.5%) and martens (5/156, 3.4%), and LaAV-2 found in one fox (0.4%). LaAV-1 fulfills all requirements to be classified as a novel species. LaAV-1 was most similar to viruses of mink and skunks (AMDV and skunk amdoparvovirus (SKAV)) while LaAV-2 was more closely related to other viruses infecting canids. LaAV-1 capsid proteins were almost indistinguishable from those of AMDV in some regions, suggesting that LaAV-1 could be a virus of mustelids that can infect foxes. While intensive farming practices provide occasions for inter-species transmission in farms, niche overlap or predation could explain cross-species transmission in the wild, but competition among sympatric species reduces the chances of direct contacts, making this an infrequent event. Pan-amdoparvovirus detection methods in wide epidemiological investigations can play a crucial role in defining amdoparvoviral ecology and evolution and discovering novel viruses.

Circulation of diverse protoparvoviruses in wild carnivores, Italy

Protoparvovirus is a monophyletic viral genus that includes the species Carnivore protoparvovirus-1 infecting domestic and wild carnivores. In this paper, the results of an epidemiological survey for Carnivore protoparvovirus-1 in wild carnivores in Italy are reported. Overall, 34 (11.4%) out of 297 tested animals were positive for Carnivore protoparvovirus-1, but the frequency of detection was much higher in intestine (54%) than in spleen samples (2.8%), thus suggesting that the intestine is the best sample to collect from wild animals for parvovirus detection. Feline panleukopenia virus (FPV) was detected in red foxes (Vulpes vulpes) (2.8%, 7/252) and Eurasian badgers (Meles meles) (10%, 1/10), whilst canine parvovirus (CPV) was found in wolves (54.3%, 19/35), Eurasian badgers (60%, 6/10) and one beech marten (Martes foina) (100%, 1/1), with more than one parvovirus type detected in some animals. Protoparvoviral DNA sequences from this study were found to be related to CPV/FPV strains detected in Asia and Europe, displaying some amino acid changes in the main capsid protein VP2 in comparison with other parvovirus strains from wildlife. In particular, the two most common mutations were Ile418Thr and Ala371Gly, which were observed in 6/12 (50%) and 5/12 (41.7%) of the CPV sequences from this study. Continuous surveillance for parvoviruses in wild carnivores and genetic analysis of the detected strains may help obtain new insight into the role of these animals in the evolution and epidemiology of carnivore parvoviruses.

Epidemiology and molecular characterization of Carnivore protoparvovirus-1 infection in the wild felid Leopardus guigna in Chile

Landscape anthropization has been identified as one of the main drivers of pathogen emergence worldwide, facilitating pathogen spillover between domestic species and wildlife. The present study investigated Carnivore protoparvovirus-1 infection using molecular methods in 98 free-ranging wild guignas (Leopardus guigna) and 262 co-occurring owned, free-roaming rural domestic cats. We also assessed landscape anthropization variables as potential drivers of infection. Protoparvovirus DNA was detected in guignas across their entire distribution range, with observed prevalence of 13.3% (real-time PCR) and 9% (conventional PCR) in guignas, and 6.1% (conventional PCR) in cats. Prevalence in guigna did not vary depending on age, sex, study area or landscape variables. Prevalence was higher in juvenile cats (16.7%) than in adults (4.4%). Molecular characterization of the virus by amplification and sequencing of almost the entire vp2 gene (1,746 bp) from one guigna and five domestic cats was achieved, showing genetic similarities to canine parvovirus 2c (CPV-2c) (one guigna and one cat), feline panleukopenia virus (FPV) (one cat), CPV-2 (no subtype identified) (two cats), CPV-2a (one cat). The CVP-2c-like sequence found in a guigna clustered together with domestic cat and dog CPV-2c sequences from South America, suggesting possible spillover from a domestic to a wild species as the origin of infection in guigna. No clinical signs of disease were found in PCR-positive animals except for a CPV-2c-infected guigna, which had haemorrhagic diarrhoea and died a few days after arrival at a wildlife rescue centre. Our findings reveal widespread presence of Carnivore protoparvovirus-1 across the guigna distribution in Chile and suggest that virus transmission potentially occurs from domestic to wild carnivores, causing severe disease and death in susceptible wild guignas.

Detection and molecular epidemiology of canine parvovirus type 2 (CPV-2) circulating in Jilin Province, Northeast China

Canine parvovirus (CPV) is highly contagious and can cause haemorrhagic enteritis and myocarditis in dogs. To understand the current epidemic situation of CPV in Jilin Province, China, a total of 44 fecal or intestinal tissue samples of pet dogs suspected of being infected with CPV from February 2018 to November 2019 in Changchun and Liaoyuan City, Jilin Province were collected.All of the 44 collected samples were tested positive to CPV-2 by a PCR assay. The sequencing and analyzing of complete VP2 genes showed that CPV-2c was the most prevalent variant (n = 31;70.4 %), followed by new-CPV-2a (n = 8;18.2 %), new-CPV-2b (n = 4; 9.1 %) and CPV-2 (n = 1; 2.3 %). Phylogenetic analysis revealed that the 31 CPV-2c strains in our study are closely related to local CPV-2c isolates in cluster I. The VP2 protein of the acquired CPV 2c strains all possessed the substitutions Ala5Gly, Phe267Tyr, Tyr324Ile, and Gln370Arg only one with a novel Arg481Lys mutation. These findings demonstrate that CPV-2c was the most prominent type of CPV circulating in Jilin in 2018-2019, clustered in a separate group that is far from the vaccine strains and suggest that further and extensive epidemiological investigation among pet dogs are warranted to provide information for usage and research of current vaccines.

Porcine circovirus 2 (PCV2) population study in experimentally infected pigs developing PCV2-systemic disease or a subclinical infection

Porcine circovirus 2 (PCV2) is a single stranded DNA virus with one of the highest mutation rates among DNA viruses. This ability allows it to generate a cloud of mutants constantly providing new opportunities to adapt and evade the immune system. This pig pathogen is associated to many diseases, globally called porcine circovirus diseases (PCVD) and has been a threat to pig industry since its discovery in the early 90's. Although 11 ORFs have been predicted from its genome, only two main proteins have been deeply characterized, i.e. Rep and Cap. The structural Cap protein possesses the majority of the epitopic determinants of this non-enveloped virus. The evolution of PCV2 is affected by both natural and vaccine-induced immune responses, which enhances the genetic variability, especially in the most immunogenic Cap region. Intra-host variability has been also demonstrated in infected animals where long-lasting infections can take place. However, the association between this intra-host variability and pathogenesis has never been studied for this virus. Here, the within-host PCV2 variability was monitored over time by next generation sequencing during an experimental infection, demonstrating the presence of large heterogeneity. Remarkably, the level of quasispecies diversity, affecting particularly the Cap coding region, was statistically different depending on viremia levels and clinical signs detected after infection. Moreover, we proved the existence of hyper mutant subjects harboring a remarkably higher number of genetic variants. Altogether, these results suggest an interaction between genetic diversity, host immune system and disease severity.

New genotype classification and molecular characterization of canine and feline parvoviruses

Background

Canine parvovirus (CPV) and feline panleukopenia (FPV) cause severe intestinal disease and leukopenia.

Objectives

In Korea, there have been a few studies on Korean FPV and CPV-2 strains. We attempted to investigate several genetic properties of FPV and CPV-2.

Methods

Several FPV and CPV sequences from around world were analyzed by Bayesian phylo-geographical analysis.

Results

The parvoviruses strains were newly classified into FPV, CPV 2-I, CPV 2-II, and CPV 2-III genotypes. In the strains isolated in this study, Gigucheon, Rara and Jun belong to the FPV, while Rachi strain belong to CPV 2-III. With respect to CPV type 2, the new genotypes are inconsistent with the previous genotype classifications (CPV-2a, -2b, and -2c). The root of CPV-I strains were inferred to be originated from a USA strain, while the CPV-II and III were derived from Italy strains that originated in the USA. Based on VP2 protein analysis, CPV 2-I included CPV-2a-like isolates only, as differentiated by the change in residue S297A/N. Almost CPV-2a isolates were classified into CPV 2-III, and a large portion of CPV-2c isolates was classified into CPV 2-II. Two residue substitutions F267Y and Y324I of the VP2 protein were characterized in the isolates of CPV 2-III only.

Conclusions

We provided an updated insight on FPV and CPV-2 genotypes by molecular-based and our findings demonstrate the genetic characterization according to the new genotypes.

Genetic characterization of feline panleukopenia virus from dogs in Vietnam reveals a unique Thr101 mutation in VP2

Background

Canine parvovirus type 2 (CPV-2) and feline parvovirus (FPV) are known as the main causes of several serious diseases and have a severe impact on puppies and kittens, respectively. FPV and new CPV-2 variants are all able to infect cats, causing diseases indistinguishable from feline panleukopenia. However, FPV only replicates efficiently in feline cells in vitro and replicates in dogs in the thymus and bone marrow without being shed in feces. In our previous study, the genotypes of six parvoviral isolates were unable to be identified using a SimpleProbe^® real-time PCR assay.

Methods

In the present study, we characterized previously unidentified FPV-like viruses isolated from dogs in Vietnam. The six isolates were utilized to complete VP2 gene sequencing and to conduct phylogenetic analyses.

Results

Sequence analysis of the six parvoviral strains identified the species as being similar to FPV. Phylogenetic analysis demonstrated that the complete VP2 genes of the strains are similar to those of FPV. The FPV-like strains contain a Thr101 mutation in the VP2 protein, which is different from prototype FPV strains.

Discussion

Our data provide evidence for the existence of changes in the charge, protein contact potential and molecular surface of the core of the receptor-binding size with an Ile101 to Thr101 mutation. This is also the first study to provide reliable evidence that FPV may be a threat to the Vietnamese dog population.

Detection of canine parvovirus and feline panleukopenia virus in fecal samples by strand exchange amplification

Canine parvovirus 2 (CPV-2) and feline panleukopenia virus (FPLV) often cause acute enteric disease in their hosts. A simple, rapid, and effective method for the on-site detection of these viruses would be useful. We used a denaturation bubble-mediated strand exchange amplification (SEA) method to successfully detect CPV-2 and FPLV in fecal samples. SEA could detect as little as 3.6 pg/μL of CPV-2 and 6.6 pg/μL of FPLV genomic DNA following a 40-min incubation at an isothermal temperature of 61°C. Unlike PCR, SEA does not require complicated equipment, and positive samples produce a color change that can be visualized by the naked eye. Additionally, SEA is simpler than PCR because no extraction is needed, and heating of the fecal sample at 98°C can be performed with a heating block or water bath. This rapid and effective nucleic acid detection platform could be used as a point-of-care test for the detection of CPV-2 and FPLV.

The increasing prevalence of CPV-2c in domestic dogs in China

Background

Canine parvovirus type 2 (CPV-2), a serious pathogen, leads to high morbidity and mortality in dogs and several wild carnivore species. Although it is a DNA virus, it evolves particularly rapidly, with a genomic substitution rate of approximately 10⁻⁴ substitutions/site/year, close to that of some RNA viruses. Tracing the prevalence of CPV-2 in dogs is significant.

Methods

In this study, an aetiological survey was carried out from 2016 to 2019 in Guangdong Province, China, involving Guangzhou, Shenzhen and Dongguan. Furthermore, to systematically analyse the prevalence of CPV-2 in China, the VP2 gene sequences of all Chinese isolates were downloaded from the NCBI nucleotide database in December 2019, and changes in CPV-2 variants were examined.

Results

A total of 55.7% (34/61) of samples were CPV-2 positive by PCR detection and virus isolation. In addition to different variants circulating in dogs, coinfection with multiple variants was identified, as was coinfection with other canine enteric pathogens in some cases. Two previously reported amino acid sites, A5G and Q370R of CPV-2c mutants, reported in variants in China were assessed, and several CPV-2 isolates with P13S and K582N mutations were detected in this study. Finally, we speculate on the prevalence of different CPV-2 variants in China. According to the VP2 gene sequence obtained from the NCBI nucleotide database, the proportion of different variants in China has changed, and CPV-2c appears to be growing rapidly. In conclusion, this aetiology survey suggests that CPV-2 continues to be common in China and that the prevalence of CPV-2c is increasing.

Molecular and phylogenetic analysis of Vietnamese canine parvovirus 2C originated from dogs reveals a new Asia-IV clade

Canine parvovirus type 2 (CPV-2) is a small, single-stranded DNA virus causing fatal haemorrhagic enteritis in dogs. Currently, CPV-2 is classified into CPV-2a, CPV-2b and CPV-2c based on genetic variation in the VP2 gene. The CPV-2c variant has become ubiquitous worldwide and gained attention for monitoring parvoviral evolution. In this study, we characterized the full-length genome sequences of CPV-2c strains obtained from 59 dogs in Vietnam. Molecular analysis revealed that Vietnamese CPV-2c shared a common evolutionary pattern with the Asian CPV-2 clade, which is marked by genetic signature patterns in the structural and nonstructural proteins. In addition, these Vietnamese CPV-2c strains exhibited unique Thr112Ile and Ile447Met mutations in the VP1 and VP2 sequence, respectively. Interestingly, phylogenetic analysis indicated that the mutations of amino acid residues in both the structural and nonstructural genes have contributed to the emergence of a new clade, designated here as the Asia-IV clade. The substitution rates, estimated from a dataset containing 199 sequences over the last 42 years, confirmed that CPV-2 showed a high rate of nucleotide substitution, at about 2.49 × 10^-4 nucleotide substitutions per site per year (nt/s/y), with VP1/2 and NS1/2 estimates of 3.06 × 10^-4 and 3.16 × 10^-4 nt/s/y, respectively. Even though no evidence of genetic recombination in these Vietnamese CPV-2c strains was established, potential positive selection sites were observed in both the structural and nonstructural genes, suggesting the viral evolutionary process has occurred in both the structural and nonstructural proteins. Genetic and evolutionary analysis of the full-length genome sequence is necessary to gain evolutionary insight of CPV-2.

Domestic dog origin of Carnivore Protoparvovirus 1 infection in a rescued free-ranging guiña (Leopardus guigna) in Chile

Carnivore protoparvovirus 1 is one of the most important pathogens affecting both wild and domestic carnivores. Here, we reported the genetic characterization of canine parvovirus (CPV-2) strains from a rescued guiña (Leopardus guigna) and domestic dogs from Chile. Guiña strain was classified as CPV-2c, and phylogenetic analysis of the complete coding genome showed that the guiña CPV-2c strain shares a recent common ancestor with Chilean domestic dogs' strains. These viruses showed >99% identity and exhibited three changes in the NS1 protein (V596A, E661K and L582F). This is the first detection and genetic characterization of CPV-2c infection in guiña worldwide, and one of the few comparative studies that show the source of infection was domestic dogs. The current findings highlight the fact that guiña is a susceptible species to protoparvovirus infection and that domestic dogs represent an important threat to its conservation. The CPV-2 cross-species transmission between domestic dogs and guiña should be taken into account for protection programmes of this endangered species.

Diagnostic Challenges in Canine Parvovirus 2c in Vaccine Failure Cases

In this study, three different diagnostic tests for parvovirus were compared with vaccination status and parvovirus genotype in suspected canine parvovirus cases. Faecal samples from vaccinated (N17) and unvaccinated or unknown vaccination status (N41) dogs that had clinical signs of parvovirus infection were tested using three different assays of antigen tests, conventional and quantitative PCR tests. The genotype of each sample was determined by sequencing. In addition to the suspected parvovirus samples, 21 faecal samples from apparently healthy dogs were tested in three diagnostic tests to evaluate the sensitivity and specificity of the tests. The antigen test was positive in 41.2% of vaccinated dogs and 73.2% of unvaccinated diseased dogs. Conventional PCR and qPCR were positive for canine parvovirus (CPV) in 82.4% of vaccinated dogs and 92.7% of unvaccinated dogs. CPV type-2c (CPV-2c) was detected in 82.75% of dogs (12 vaccinated and 36 unvaccinated dogs), CPV-2b was detected in 5.17% dogs (one vaccinated and two unvaccinated) and CPV-2a in 1.72% vaccinated dog. Mean Ct values in qPCR for vaccinated dogs were higher than the unvaccinated dogs (p = 0.049), suggesting that vaccinated dogs shed less virus, even in clinical forms of CPV. CPV-2c was the dominant subtype infecting dogs in both vaccinated and unvaccinated cases. Faecal antigen testing failed to identify a substantial proportion of CPV-2c infected dogs, likely due to low sensitivity. The faecal samples from apparently healthy dogs (n = 21) showed negative results in all three tests. Negative CPV faecal antigen results should be viewed with caution until they are confirmed by molecular methods.

Molecular characteristics of the capsid protein VP2 gene of canine parvovirus type 2 amplified from raccoon dogs in Hebei province, China

Canine parvovirus type 2 (CPV-2) is currently circulating in domestic and wild animals, but our knowledge about CPV-2 infections in raccoon dogs is limited. In this study, VP2 gene sequences of CPV-2 were amplified from rectal swabs of 14 diarrhetic raccoon dogs (Nyctereutes procyonoides) in Hebei province, China, in 2016 and 2017. Phylogenetic analysis of the VP2 gene sequences revealed that most of these sequences (11 of 14) belonged to the same subclade as raccoon dog strain CPV-2/Raccoon_Dog/China/DP-1/16 isolated from Shandong province in 2016. A comparison of deduced amino acid sequences revealed presence of the substitutions S297A and S27T in 11 of those 14 sequences. I418T was observed in a minority of the sequences (4 of 14). In addition, A300D and T301I, P13S and I219V, and N419K were found in three of the sequences. This study shows that CPV-2 strains with different substitutions in their VP2 amino acid sequences were spreading among raccoon dogs in Hebei during 2016 and 2017 and suggests that further studies are needed to monitor the distribution of these strains in China.

Analysis of canine parvoviruses circulating in Australia reveals predominance of variant 2b and identifies feline parvovirus-like mutations in the capsid proteins

Canine parvovirus (CPV) is a major enteric pathogen of dogs worldwide that emerged in the late 1970s from a feline parvovirus (FPV)-like ancestral virus. Shortly after its emergence, variant CPVs acquired amino acid (aa) mutations in key capsid residues, associated with biological and/or antigenic changes. This study aimed to identify and analyse CPV variants and their capsid mutations amongst Australian dogs, to gain insights into the evolution of CPV in Australia and to investigate relationships between the disease and vaccination status of dogs from which viruses were detected. CPV VP2 sequences were amplified from 79 faecal samples collected from dogs with parvoviral enteritis at 20 veterinary practices in five Australian states. The median age at diagnosis was 4 months (range 1-96 months). Only 3.7% of dogs with vaccination histories had completed recommended vaccination schedules, while 49% were incompletely vaccinated and 47.2% were unvaccinated. For the first time, CPV-2b has emerged as the dominant antigenic CPV variant circulating in dogs with parvoviral enteritis in Australia, comprising 54.4% of viruses, while CPV-2a and CPV-2 comprised 43.1% and 2.5%, respectively. The antigenic variant CPV-2c was not identified. Analysis of translated VP2 sequences revealed a vast repertoire of amino acid (aa) mutations. Several Australian CPV strains displayed signatures in the VP2 protein typical of Asian CPVs, suggesting possible introduction of CPV strains from Asia, and/or CPV circulation between Asia and Australia. Canine parvoviruses were identified containing aa residues typical of FPV at key capsid (VP2) positions, representing reverse mutations or residual mutations retained from CPV-2 during adaptation from an FPV-like ancestor, suggesting that evolutionary intermediates between CPV-2 and FPV are circulating in the field. Similarly, intermediates between CPV-2a-like viruses and CPV-2 were also identified. These findings help inform a better understanding of the evolution of CPV in dogs.

Phylogenetic and Geospatial Evidence of Canine Parvovirus Transmission between Wild Dogs and Domestic Dogs at the Urban Fringe in Australia

Canine parvovirus (CPV) is an important cause of disease in domestic dogs. Sporadic cases and outbreaks occur across Australia and worldwide and are associated with high morbidity and mortality. Whether transmission of CPV occurs between owned dogs and populations of wild dogs, including Canis familiaris, Canis lupus dingo and hybrids, is not known. To investigate the role of wild dogs in CPV epidemiology in Australia, PCR was used to detect CPV DNA in tissue from wild dogs culled in the peri-urban regions of two Australian states, between August 2012 and May 2015. CPV DNA was detected in 4.7% (8/170). There was a strong geospatial association between wild-dog CPV infections and domestic-dog CPV cases reported to a national disease surveillance system between 2009 and 2015. Postcodes in which wild dogs tested positive for CPV were 8.63 times more likely to also have domestic-dog cases reported than postcodes in which wild dogs tested negative (p = 0.0332). Phylogenetic analysis of CPV VP2 sequences from wild dogs showed they were all CPV-2a variants characterized by a novel amino acid mutation (21-Ala) recently identified in CPV isolates from owned dogs in Australia with parvoviral enteritis. Wild-dog CPV VP2 sequences were compared to those from owned domestic dogs in Australia. For one domestic-dog case located approximately 10 km from a wild-dog capture location, and reported 3.5 years after the nearest wild dog was sampled, the virus was demonstrated to have a closely related common ancestor. This study provides phylogenetic and geospatial evidence of CPV transmission between wild and domestic dogs in Australia.

The Potential Role of Endogenous Viral Elements in the Evolution of Bats as Reservoirs for Zoonotic Viruses

Despite a small genome size, bats have comparable diversity of retroviral and non-retroviral endogenous sequences to other mammals. These include Class I and Class II retroviral sequences, foamy viruses, and deltaretroviruses, as well as filovirus, bornavirus, and parvovirus endogenous viral elements. Some of these endogenous viruses are sufficiently preserved in bat genomes to be expressed, with potential effects for host biology. It is clear that the bat immune system differs when compared with other mammals, yet the role that virus-derived endogenous elements may have played in the evolution of bat immunity is poorly understood. In this review, we discuss some of the bat-specific immune mechanisms that may have resulted in a virus-tolerant phenotype and link these to the long-standing virus-host coevolution that may have allowed a large diversity of endogenous retroviruses and other endogenous viral elements to colonize bat genomes. We also consider the possible effects of endogenization in the evolution of the bat immune system.

Impact of Natural or Synthetic Singletons in the Capsid of Human Bocavirus 1 on Particle Infectivity and Immunoreactivity

Human bocavirus 1 (HBoV1) is a parvovirus that gathers increasing attention due to its pleiotropic role as a pathogen and emerging vector for human gene therapy. Curiously, albeit a large variety of HBoV1 capsid variants has been isolated from human samples, only one has been studied as a gene transfer vector to date. Here, we analyzed a cohort of HBoV1-positive samples and managed to PCR amplify and sequence 29 distinct HBoV1 capsid variants. These differed from the originally reported HBoV1 reference strain in 32 nucleotides or four amino acids, including a frequent change of threonine to serine at position 590. Interestingly, this T590S mutation was associated with lower viral loads in infected patients. Analysis of the time course of infection in two patients for up to 15 weeks revealed a gradual accumulation of T590S, concurrent with drops in viral loads. Surprisingly, in a recombinant vector context, T590S was beneficial and significantly increased titers compared to that of T590 variants but had no major impact on their transduction ability or immunoreactivity. Additional targeted mutations in the HBoV1 capsid identified several residues that are critical for transduction, capsid assembly, or DNA packaging. Our new findings on the phylogeny, infectivity, and immunoreactivity of HBoV1 capsid variants improve our understanding of bocaviral biology and suggest strategies to enhance HBoV1 gene transfer vectors.IMPORTANCE The family of Parvoviridae comprises a wide variety of members that exhibit a unique biology and that are concurrently highly interesting as a scaffold for the development of human gene therapy vectors. A most notable example is human bocavirus 1 (HBoV1), which we and others have recently harnessed to cross-package and deliver recombinant genomes derived from another parvovirus, the adeno-associated virus (AAV). Here, we expanded the repertoire of known HBoV1 variants by cloning 29 distinct HBoV1 capsid sequences from primary human samples and by analyzing their properties as AAV/HBoV1 gene transfer vectors. This led to our discovery of a mutational hot spot at HBoV1 capsid position 590 that accumulated in two patients during natural infection and that lowers viral loads but increases vector yields. Thereby, our study expands our current understanding of HBoV1 biology in infected human subjects and concomitantly provides avenues to improve AAV/HBoV1 gene transfer vectors.

Host-virus evolutionary dynamics with specialist and generalist infection strategies: Bifurcations, bistability, and chaos

In this work, we have investigated the evolutionary dynamics of a generalist pathogen, e.g., a virus population, that evolves toward specialization in an environment with multiple host types. We have particularly explored under which conditions generalist viral strains may rise in frequency and coexist with specialist strains or even dominate the population. By means of a nonlinear mathematical model and bifurcation analysis, we have determined the theoretical conditions for stability of nine identified equilibria and provided biological interpretation in terms of the infection rates for the viral specialist and generalist strains. By means of a stability diagram, we identified stable fixed points and stable periodic orbits, as well as regions of bistability. For arbitrary biologically feasible initial population sizes, the probability of evolving toward stable solutions is obtained for each point of the analyzed parameter space. This probability map shows combinations of infection rates of the generalist and specialist strains that might lead to equal chances for each type becoming the dominant strategy. Furthermore, we have identified infection rates for which the model predicts the onset of chaotic dynamics. Several degenerate Bogdanov-Takens and zero-Hopf bifurcations are detected along with generalized Hopf and zero-Hopf bifurcations. This manuscript provides additional insights into the dynamical complexity of host-pathogen evolution toward different infection strategies.

PCR-based detection and genetic characterization of porcine parvoviruses in South Korea in 2018

Background

with the advantage of sequencing technology, many novel porcine parvoviruses (PPV) rather than PPV1 has been reported. This study ultilized specific PCR- based method and gene- based analysis to study the presence and genetic diversity of porcine parvoviruses in South Korea in 2018.

Results

The present study was conducted in 2018 and found PPV1 and PPV7 in nine out of 151 field samples (organs and semen) by the PCR method. Among these, the complete genome sequences of five strains (N2, N91, N108, N133, and N141) were recovered. Phylogenic analysis revealed that the strains N2, N91, and N108 belong to the PPV1 genotype, while N133 and N141 belong to PPV7 genotype. The PPV7 strains collected in this study had deletion mutations in the VP2 gene but differed from that of PPV7 strains collected in 2017. Among the PPV1 strains, the amino acid variations in the B cell epitopes of the VP2 protein were observed between three Korean PPV1 field strains (N2, N91, and N108) and the reference PPV1 strains. Those substitutions resulted in six out of 12 predicted epitopes having significant differences in antigenic index compared to the other PPV1 strains.

Conclusions

This study confirmed the presence of different genotypes of porcine parvoviruses in South Korea. The PPVs circulating in South Korea were phylogenetically classified as PPV1 and PPV7 genotypes. Three Korean PPV1 strains collected in 2018 were predicted to have antigenic alteration in VP2 compared to several reference strains of PPV1.

Unveiling patterns of viral pathogen infection in free-ranging carnivores of northern Portugal using a complementary methodological approach

Pathogen surveillance in free-ranging carnivores presents challenges due to their low densitie and secretive nature. We combined molecular and serological assays to investigate infections by viral pathogens (Canine parvovirus (CPV), Canine distemper virus (CDV) and Canine coronavirus (CCoV)) in Portuguese carnivores (Canis lupus, Vulpes vulpes, Lutra lutra, Martes foina, M. martes, Meles meles, and Genetta genetta) over a period of 16 years. Additionally we explored spatio-temporal patterns of virus occurrence in Canis lupus. Our study identified CPV DNA in all carnivore species with an overall prevalence of 91.9 %. CPV was detected in all sampled years and seasons in Canis lupus, supporting its enzootic nature. CDV RNA was mainly detected in the Canidae family, with viral nucleic acid recorded between 2005 and 2008 with a peak prevalence of 67 % among the wolf population, followed by a sharp decline, suggesting an epizootic behaviour of the virus. Antibodies show that mustelids and viverrids were often exposed to CDV. CCoV was first recorded by molecular methods in wolf samples in 2002, remaining in the wolf populations with marked fluctuations over time. The dual serological and molecular approach provided important epidemiological data on pathogens of wild carnivores in Portugal. These programmes should also include monitoring of other potential reservoir hosts such as domestic cats and dogs.

Genetic characterization of canine parvovirus type 2c from domestic dogs in Korea

Canine parvovirus type 2 (CPV‐2) is an aetiological agent that causes acute haemorrhagic enteritis and fatal myocarditis in dogs. Since CPV‐2 first emerged in the late 1970s, its rapid evolution has resulted in three antigenic variants: CPV‐2a, CPV‐2b and CPV‐2c. Here, we report, for the first time in Korea, two cases of CPV‐2c infection in two dogs with severe diarrhoea. The complete open reading frame (4,269nt) of CPV‐2, encoding both non‐structural (NS) and structural (VP) proteins, was sequenced. Based on the amino acid Gln present at residue 426 of the VP2 gene, these strains were typed as CPV‐2c, and were named Korea CPV‐2c_1 and Korea CPV‐2c_2. These strains shared 99.48% reciprocal nucleotide sequence identity and had the highest nucleotide identity (99.77%–99.34%) with Asian CPV strains isolated in China, Italy (found in a dog imported from Thailand), and Vietnam from 2013 to 2017. Phylogenetic analysis based on the non‐structural (NS1) and capsid (VP2) genes revealed that Korean CPV‐2c strains clustered closely to Asian CPV strains, and separately from strains isolated in Europe, South America and North America. Amino acid changes never reported before were observed in NS1 (Thr70Pro, Cys287Tyr), VP1 (Lys17Arg, Phe33Leu) and VP2 (Gln365His, Ala516Val). Additional observed mutations, including Phe267Tyr, Tyr324Ile and Gln370Arg, have been previously reported in the recent CPV‐2c strains with Asian origins. These results suggest that the Korean CPV‐2c strains were potentially introduced via neighbouring Asian countries.

A Mini-Review on the Epidemiology of Canine Parvovirus in China

Canine viral diarrhea is a severe disease in dogs worldwide. The role of canine parvovirus (CPV) in canine viral diarrhea is a common health problem in dogs, attracting major concern from veterinarians and dog owners across China. In this mini-review, we summarize the CPV epidemiology in China, including its origin, prevalence, coinfection, and the genetic evolution of the virus. The review reveals the correlation between CPV-2 infection and seasonality, a dog's age/gender/breed/vaccination; that CPV-2 is the main causative agent of canine diarrhea in Northeast China and that coinfection with other pathogens is a common occurrence; the predominant CPV epidemic strains were the new CPV-2a, and CPV-2c has shown significant growth trends since 2010. This mini-review will provide valuable information for CPV infections across China and other countries.

Dynamic evolution of canine parvovirus in Thailand

Background and Aim:

According to the previous study, the circulating canine parvovirus (CPV) in Thailand is 2a and 2b. Nowadays, CPV mutants, including CPV-2c, have been identified in many parts of the world. This study aimed to investigate the genetic diversity of the circulating CPV in Thailand.

Materials and Methods:

Eighty-five CPV-positive fecal samples were obtained from dogs with either acute hemorrhagic diarrhea or diarrhea. The complete VP2 gene of these samples was amplified using VP2 specific primers and polymerase chain reaction (PCR). The obtained full-length VP2 sequences were analyzed and a phylogenetic tree was constructed.

Results:

Sixty and 25 CPV-positive fecal samples were collected in 2010 and 2018, respectively. Thirty-four samples were new CPV-2a and 31 samples were new CPV-2b due to amino acids substitution at position 297 (Ser-Ala). In 2018, 5 new CPV-2a, 19 CPV-2c, and 1 feline panleukopenia virus (FPV) were found, but no new CPV-2b was detected. Moreover, most of the CPV in this study had amino acids mutations at positions 324 and 440. The phylogenetic construction demonstrated the close relationship between the current new CPV-2a with the previous CPV-2a reported from Thailand, China, Uruguay, Vietnam, Singapore, and India. Interestingly, the current new CPV-2b in this study was not closely related to the previous CPV-2b reported in Thailand. The CPV-2c in this study was closer to Asian CPV-2c and further from either European or South America CPV-2c. Interestingly, FPV was identified in a diarrhea dog.

Conclusion:

The evolution of CPV in Thailand is very dynamic. Thus, it is important to monitor for CPV mutants and especially the clinical signs relating to these mutants to conduct surveillance for the emergence of new highly pathogenic CPV in the future.

Broad diversity of simian immunodeficiency virus infecting Chlorocebus species (African green monkey) and evidence of cross-species infection in Papio anubis (olive baboon) in Kenya

BACKGROUND

Simian immunodeficiency virus (SIV) naturally infects African non-human primates (NHPs) and poses a threat of transmission to humans through hunting and consumption of monkeys as bushmeat. This study investigated the as of yet unknown molecular diversity of SIV in free-ranging Chlorocebus species (African green monkeys-AGMs) and Papio anubis (olive baboons) within Mombasa, Kisumu and Naivasha urban centres in Kenya.

METHODS

We collected blood samples from 124 AGMs and 65 olive baboons in situ, and detected SIV by high-resolution melting analysis and sequencing of PCR products.

RESULTS

Simian immunodeficiency virus prevalence was 32% in AGMs and 3% in baboons. High-resolution melting (HRM) analysis demonstrated distinct melt profiles illustrating virus diversity confirmed by phylogenetic analysis.

CONCLUSIONS

There is persistent evolutionary diversification of SIVagm strains in its natural host, AGMs and cross-species infection to olive baboons is occurring. Further study is required to establish pathogenesis of the diverse SIVagm variants and baboon immunological responses.

Regional adaptations and parallel mutations in Feline panleukopenia virus strains from China revealed by nearly-full length genome analysis

Protoparvoviruses, widespread among cats and wild animals, are responsible for leukopenia. Feline panleukopenia virus (FPLV) in domestic cats is genetically diverse and some strains may differ from those used for vaccination. The presence of FPLV in two domestic cats from Hebei Province in China was identified by polymerase chain reaction. Samples from these animals were used to isolate FPLV strains in CRFK cells for genome sequencing. Phylogenetic analysis was performed to compare our isolates with available sequences of FPLV, mink parvovirus (MEV) and canine parvovirus (CPV). The isolated strains were closely related to strains of FPLV/MEV isolated in the 1960s. Our analysis also revealed that the evolutionary history of FPLV and MEV is characterized by local adaptations in the Vp2 gene. Thus, it is likely that new FPLV strains are emerging to evade the anti-FPLV immune response.

Prisoners of war - host adaptation and its constraints on virus evolution

Recent discoveries of contemporary genotypes of hepatitis B virus and parvovirus B19 in ancient human remains demonstrate that little genetic change has occurred in these viruses over 4,500-6,000 years. Endogenous viral elements in host genomes provide separate evidence that viruses similar to many major contemporary groups circulated 100 million years ago or earlier. In this Opinion article, we argue that the extraordinary conservation of virus genome sequences is best explained by a niche-filling model in which fitness optimization is rapidly achieved in their specific hosts. Whereas short-term substitution rates reflect the accumulation of tolerated sequence changes within adapted genomes, longer-term rates increasingly resemble those of their hosts as the evolving niche moulds and effectively imprisons the virus in co-adapted virus-host relationships. Contrastingly, viruses that jump hosts undergo strong and stringent adaptive selection as they maximize their fit to their new niche. This adaptive capability may paradoxically create evolutionary stasis in long-term host relationships. While viruses can evolve and adapt rapidly, their hosts may ultimately shape their longer-term evolution.

Interaction of virus populations with their hosts

Viral population numbers are extremely large compared with those of their host species. Population bottlenecks are frequent during the life cycle of viruses and can reduce viral populations transiently to very few individuals. Viruses have to confront several types of constraints that can be divided into basal, cell-dependent, and organism-dependent constraints. Viruses overcome them exploiting a number of molecular mechanisms, with an important contribution of population numbers and genome variation. The adaptive potential of viruses is reflected in modifications of cell tropism and host range, escape to components of the host immune response, and capacity to alternate among different host species, among other phenotypic changes. Despite a fitness cost of most mutations required to overcome a selective constraint, viruses can find evolutionary pathways that ensure their survival in equilibrium with their hosts.

Duplex PCR for Detection of Aleutian Disease Virus from Biological and Environmental Samples

Aleutian disease is one of the most serious disease entities affecting mink farms. The disease causes significant economic losses in mink breeding countries. The aim of the study was to optimize a diagnostic test based on duplex PCR to enable detection of Aleutian disease virus in biological and environmental samples.

Blood (n = 40) and spleen (n = 40) samples from animals with suspected infection, and swabs from cages in which infected animals were kept (n = 20) were used for analysis. DNA was isolated from the samples, followed by optimization of the duplex PCR reaction targeting sequences coding NS1 and VP2 proteins. The qPCR method was used to determine the sensitivity of the reaction. The specificity of the analysis was confirmed by the sequencing results.

Optimized duplex PCR enabled detection of Aleutian Mink Disease Virus (AMDV) genetic material in biological and environmental samples. Testing of the sensitivity of the method indicated clear amplification for both primer pairs at 102 copies of viral DNA in a reaction. Sequencing confirmed the specificity of the reaction, which in the case of both primer pairs indicated an over 90% agreement between the isolates and the variants of the virus from the databases.

The use of duplex PCR to detect two regions of the AMDV genome may increase the sensitivity and specificity of the method and significantly expand the possibilities of further analysis based on sequencing.

Limited Intrahost Diversity and Background Evolution Accompany 40 Years of Canine Parvovirus Host Adaptation and Spread

Canine parvovirus (CPV) is a highly successful pathogen that has sustained pandemic circulation in dogs for more than 40 years. Here, integrating full-genome and deep-sequencing analyses, structural information, and in vitro experimentation, we describe the macro- and microscale features that accompany CPV's evolutionary success. Despite 40 years of viral evolution, all CPV variants are more than ∼99% identical in nucleotide sequence, with only a limited number (<40) of substitutions becoming fixed or widespread during this time. Notably, most substitutions in the major capsid protein (VP2) gene are nonsynonymous, altering amino acid residues that fall within, or adjacent to, the overlapping receptor footprint or antigenic regions, suggesting that natural selection has channeled much of CPV evolution. Among the limited number of variable sites, CPV genomes exhibit complex patterns of variation that include parallel evolution, reversion, and recombination, compromising phylogenetic inference. At the intrahost level, deep sequencing of viral DNA in original clinical samples from dogs and other host species sampled between 1978 and 2018 revealed few subconsensus single nucleotide variants (SNVs) above ∼0.5%, and experimental passages demonstrate that substantial preexisting genetic variation is not necessarily required for rapid host receptor-driven adaptation. Together, these findings suggest that although CPV is capable of rapid host adaptation, a relatively low mutation rate, pleiotropy, and/or a lack of selective challenges since its initial emergence have inhibited the long-term accumulation of genetic diversity. Hence, continuously high levels of inter- and intrahost diversity are not necessarily required for virus host adaptation.IMPORTANCE Rapid mutation rates and correspondingly high levels of intra- and interhost diversity are often cited as key features of viruses with the capacity for emergence and sustained transmission in a new host species. However, most of this information comes from studies of RNA viruses, with relatively little known about evolutionary processes in viruses with single-stranded DNA (ssDNA) genomes. Here, we provide a unique model of virus evolution, integrating both long-term global-scale and short-term intrahost evolutionary processes of an ssDNA virus that emerged to cause a pandemic in a new host animal. Our analysis reveals that successful host jumping and sustained transmission does not necessarily depend on a high level of intrahost diversity nor result in the continued accumulation of high levels of long-term evolution change. These findings indicate that all aspects of the biology and ecology of a virus are relevant when considering their adaptability.

Evolution and phylogeography of Culex pipiens densovirus

Viruses of the Parvoviridae family infect a wide range of animals including vertebrates and invertebrates. So far, our understanding of parvovirus diversity is biased towards medically or economically important viruses mainly infecting vertebrate hosts, while invertebrate infecting parvoviruses—namely densoviruses—have been largely neglected. Here, we investigated the prevalence and the evolution of the only mosquito-infecting ambidensovirus, Culex pipiens densovirus (CpDV), from laboratory mosquito lines and natural populations collected worldwide. CpDV diversity generally grouped in two clades, here named CpDV-1 and -2. The incongruence of the different gene trees for some samples suggested the possibility of recombination events between strains from different clades. We further investigated the role of selection on the evolution of CpDV genome and detected many individual sites under purifying selection both in non-structural and structural genes. However, some sites in structural genes were under diversifying selection, especially during the divergence of CpDV-1 and -2 clades. These substitutions between CpDV-1 and -2 clades were mostly located in the capsid protein encoding region and might cause changes in host specificity or pathogenicity of CpDV strains from the two clades. However, additional functional and experimental studies are necessary to fully understand the protein conformations and the resulting phenotype of these substitutions between clades of CpDV.

Detection of canine parvovirus types 2b and 2c in canine faecal samples contaminating urban thoroughfares in Brazil

Canine parvovirus type 2 (CPV-2) is a highly contagious virus that causes acute gastroenteritis in dogs all over the world. Because of its stability in the environment, CPV-2 can remain infective for a long time, especially if protected in organic matter. To demonstrate CPV-2's potential as an environmental hazard for nonimmunized susceptible hosts, we investigated 50 faecal samples collected from public areas in a municipality of Paraná state, Brazil. Seven samples tested positive for CPV by a PCR assay targeting the partial VP2 gene, with three strains being confirmed as CPV-2b variant and one as CPV-2c variant by sequence analysis. These findings were supported by phylogenetic analysis, and the species identity of faecal samples source was confirmed by canine mitochondrial DNA amplification and sequencing. Our results demonstrate the presence of CPV in canine faeces contaminating urban thoroughfares and reinforce the importance of environmental control to reduce the potential exposure risks to susceptible hosts.

Socioeconomic, geographic and climatic risk factors for canine parvovirus infection and euthanasia in Australia

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11 % of Australian veterinary hospitals reported >40 canine parvovirus cases in 2016.

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Socioeconomic disadvantage was the strongest risk factor for canine parvovirus.

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Euthanasia is the leading cause of fatality for canine parvovirus related disease.

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Hottest month of the year is associated with canine parvovirus case occurrence.

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Low rainfall is associated with higher canine parvovirus cases.

Infection of canids with canine parvovirus (CPV) can result in severe, often fatal disease. This study aimed to examine climatic, socioeconomic and geographic risk factors for CPV infection and CPV-associated euthanasia in Australia. Australian veterinary hospital responses (534; 23.5 %) to a national veterinary survey of CPV case occurrences and euthanasias in 2016 were used. Severe caseloads (>40 cases per annum) were reported by 26 (11 %) hospitals (median 60 cases; IQR 50–110). Case reporting, case numbers, and without-treatment euthanasia were significantly associated with disadvantage across all Socio-Economic Index for Areas quintiles (p < 0.0001) – the greater the disadvantage, the more reports. Strong negative correlations were found between case numbers and the Index of Relative Socioeconomic Disadvantage (r_SP = –0.3357, p < 0.0001) and also between euthanasia and the Index of Education and Occupation (r_SP = –0.3762, p < 0.0001). Hospitals in more remote areas were also more likely to report cases and to euthanize without treatment (p < 0.0001). Of the climate variables, temperature of the hottest month was most strongly positively correlated with case numbers (r_SP = 0.421, p < 0.0001), and lower annual rainfall was associated with more case-reporting hospitals (p < 0.0001). These results confirm that socioeconomic disadvantage is a significant risk-factor for CPV infection and outcome, and high temperature may also contribute to risk.

Molecular epidemiology of canine parvovirus type 2 in Italy from 1994 to 2017: recurrence of the CPV-2b variant

Background

Canine parvovirus type 2 (CPV-2) is the most important enteric virus infecting canids. It is a rapidly evolving virus; after its emergence in the 1970s, new antigenic variants (called CPV-2a, 2b and 2c) emerged and replaced the original antigenic type. The three antigenic variants are globally distributed with different frequencies and levels of genetic variability. This study focused on VP2 gene sequence analysis and the phylodynamics of CPV-2 which were detected in 123 dogs showing clinical signs of gastroenteritis collected in Italy from 1994 to 2017.

Results

For the most part, the sick dogs were young, and a third of them (32.5%) had been vaccinated. No statistical association was found between the CPV-2 antigenic variants, and sex, age, breed and vaccination status. Sequence analysis showed that all three antigenic types circulated in Italy; the CPV-2a type was the prominent genotype, followed by CPV-2c and CPV-2b, with notable differences regarding regional bases and significant fluctuations over time. Nucleotide sequence data showed high genetic heterogeneity with 67 nucleotide sequence types (ntSTs) identified, corresponding to 21 amino acid sequence types (aaSTs). The aaSTs and ntSTs obtained were distributed differently among the three CPV-2 antigenic variants: CPV-2a grouped 12/21 (57.1%) aaSTs and 41/67 (61.2%) ntSTs; CPV-2b grouped 5/21 (23.8%) aaSTs and 6/67 (8.9%) ntSTs, and CPV-2c grouped 4/21 (19.1%) aaSTs and 20/67 (29.9%) ntSTs. Canine parvovirus 2a was characterised by the highest genetic variability while CPV-2c was characterised by notable stability with a predominant amino acid profile during the entire sampling time. Canine parvovirus 2b re-emerged in recent years, showing a new and distinctive amino acid profile of the VP2 protein.

Conclusions

The findings of the present study provided new insights regarding the phylodynamics and evolution of CPV-2 in Italy, pointing out notable differences at the local level in the distribution of the CPV-2 variants and the selection of genetic subtypes. The evolution of CPV-2 has raised questions regarding the efficacy of vaccination; therefore, continuous monitoring regarding the evolution and spread of new CPV-2 variants should be a key aim of ongoing research.

Genetic characterization of Carnivore Parvoviruses in Spanish wildlife reveals domestic dog and cat-related sequences

The impact of carnivore parvovirus infection on wild populations is not yet understood; disease signs are mainly developed in pups and assessing the health of litters in wild carnivores has big limitations. This study aims to shed light on the virus dynamics among wild carnivores thanks to the analysis of 213 samples collected between 1994 and 2013 in wild ecosystems from Spain. We determined the presence of carnivore parvovirus DNA by real-time PCR and sequenced the vp2 gen from 22 positive samples to characterize the strains and to perform phylogenetic analysis. The presence of carnivore parvovirus DNA was confirmed in 18% of the samples, with a higher prevalence detected in wolves (Canis lupus signatus, 70%). Fourteen sequences belonging to nine wolves, three Eurasian badgers (Meles meles), a common genet (Genetta genetta) and a European wildcat (Felis silvestris) were classified as canine parvovirus 2c (CPV-2c); five sequences from three wolves, a red fox (Vulpes vulpes) and a stone marten (Martes foina) as CPV-2b; and three sequences from a badger, a genet and a stone marten as feline parvovirus (FPV). This was the first report of a wildcat infected with a canine strain. Sequences described in this study were identical or very close related to others previously found in domestic carnivores from distant countries, suggesting that cross-species transmission takes place and that the parvovirus epidemiology in Spain, as elsewhere, could be influenced by global factors.

Nearly full-length genome characterization of canine parvovirus strains circulating in Nigeria

Canine parvovirus type 2 (CPV‐2) emerged suddenly in the late 1970s as pathogen of dogs, causing a severe and often fatal gastroenteric disease. The original CPV‐2 was replaced by three antigenic variants, CPV‐2a, CPV‐2b and CPV‐2c, which to date have gained a worldwide distribution with different relative proportions. All previous studies conducted in Africa were based on partial VP2 gene sequences. The aim of this study was to provide a genome analysis to characterize the CPV strains collected in Nigeria, Africa. Rectal swab samples (n = 320) were collected in 2018 and tested by means of an immunochromatographic assay. Among the 144 positive samples, 59 were selected for further analyses using different molecular assays. The results revealed a high prevalence of CPV‐2c (91.5%) compared to the CPV‐2a variant (8.5%). The VP2 gene sequences showed a divergence from the strains analysed in 2010 in Nigeria and a closer connection with CPV strains of Asian origin. The non‐structural gene analysis evidenced amino acid changes never previously reported. The molecular analysis based on genomic sequences evidenced a geographical pattern of distribution of the analysed strains, suggesting a potential common evolutionary origin with CPV of Asian origin. This study represents the first CPV molecular characterization including all the encoding gene sequences conducted in the African continent and contributes to define the current geographical spread of the CPV variants worldwide.

Novel Primate Bocaparvovirus Species 3 Identified in Wild Macaca Mulatta in China

Primate bocaparvovirus (BOV) is a possible cause of respiratory disorders and gastroenteritis in humans. However, the diversity and evolution of these viruses remain largely unknown, despite the identification of a growing number of BOVs in non-human primates (NHPs). Here, we report the identification of a novel BOV (provisionally named Macaca mulatta bocaparvovirus [MmBOV]) in the feces of wild Macaca mulatta in China by viral metagenomic analysis. Seven of 400 fecal samples from Macaca mulatta were positive for MmBOV. An almost complete genome sequence of 4,831 nucleotides was obtained, which had genomic organization and protein motifs similar to human bocaviruses (HOBVs), and shared characteristically low G/C content and weak codon usage bias. Sequence analyses of NS1, NP1, and VP1 revealed that MmBOV was most closely related to HBOV4 of Primate bocaparvovirus 2 (approximately 68.4%/70.6%, 73.3%/67.6%, and 70.4%/73.1% nucleotide/amino acid identities, respectively). Additionally, phylogenetic analysis revealed that MmBOV formed an independent peripheral branch, but clustered closely with those of the Primate bocaparvovirus species in the BOV genus (particularly HBOV4). These data strongly suggest that HBOV4 originated from NHP bocaparvoviruses around 200-300 years ago, and that NHPs may act as HBOV reservoirs. Following the International Committee of Taxonomy for Viruses guidelines, we propose MmBOV as a new species (tentatively named Primate bocaparvovirus 3) in the genus Bocaparvovirus, which is the first report of a novel species of primate BOV. Our data facilitate future research on the genetic diversity and evolution of primate bocaparvoviruses and highlight the importance of bocaparvovirus surveys in wild NHPs.

Transferrin receptor binds virus capsid with dynamic motion

Canine parvovirus (CPV) is an important pathogen causing severe diseases in dogs, including acute hemorrhagic enteritis, myocarditis, and cerebellar disease. Cross-species transmission of CPV occurs as a result of mutations on the viral capsid surface that alter the species-specific binding to the host receptor, transferrin receptor type-1 (TfR). The interaction between CPV and TfR has been extensively studied, and previous analyses have suggested that the CPV-TfR complex is asymmetric. To enhance the understanding of the underlying molecular mechanisms, we determined the CPV-TfR interaction using cryo-electron microscopy to solve the icosahedral (3.0-Å resolution) and asymmetric (5.0-Å resolution) complex structures. Structural analyses revealed conformational variations of the TfR molecules relative to the binding site, which translated into dynamic molecular interactions between CPV and TfR. The precise footprint of the receptor on the virus capsid was identified, along with the identity of the amino acid residues in the virus-receptor interface. Our "rock-and-roll" model provides an explanation for previous findings and gives insights into species jumping and the variation in host ranges associated with new pandemics in dogs.