Evolutionary and genetic analysis of the VP2 gene of canine parvovirus

Comparative genomics of canine parvovirus in South America: Diversification patterns in local populations

Canine parvovirus (CPV) is a significant pathogen in domestic dogs worldwide, causing a severe and often fatal disease. CPV comprises three antigenic variants (2a, 2b, and 2c) distributed unevenly among several phylogenetic groups. The present study compared genetic variability and evolutionary patterns in South American CPV populations. We collected samples from puppies suspected of CPV infection in the neighboring Argentina and Uruguay. Antigenic variants were preliminarily characterized using PCR-RFLP and partial vp2 sequencing. Samples collected in Argentina during 2008-2018 were mainly of the 2c variant. In the Uruguayan strains (2012-2019), the 2a variant wholly replaced the 2c from 2014. Full-length coding genome and vp2 sequences were compared with global strains. The 2c and 2a strains fell by phylogenetic analysis into two phylogroups (Europe I and Asia I). The 2c strains from Argentina and Uruguay clustered in the Europe I group, with strains from America, Europe, Asia, and Oceania. Europe I is widely distributed in South America in the dog population and is also being detected in the wildlife population. The 2a strains from Uruguay formed the distinct Asia I group with strains from Asia, Africa, America, and Oceania. This Asia I group is increasing its distribution in South America and worldwide. Our research reveals high genetic variability in adjacent synchronic samples and different evolutionary patterns in South American CPV. We also highlight the importance of ancestral migrations and local diversification in the evolution of global CPV strains.

Molecular characterization of full-length VP2 gene of canine parvovirus type 2 strains circulating in Egypt 2019-2021

Canine parvovirus type 2 (CPV-2) is a major cause of fatal gastroenteritis and myocarditis in puppies of domestic and wild carnivores. CPV-2 has accumulated changes over time lead to the emergence of three antigenic variants CPV-2a, CPV-2b, and CPV-2c. VP2 is the major capsid protein that determines virus antigenicity, and host range. Although the three CPV-2 variants were previously identified in Egypt, most reports covered a restricted geographic region and/or time period, and only analyzed partial fragments of VP2 gene. Therefore, this study was designed to test 100 rectal swabs collected from 7 Egyptian governorates between 2019 and 2021 for CPV-2 using PCR. A total of 65 positive samples were identified, mostly in pure dog breeds of young age. The three variants co-circulated in 2019, while CPV-2b was not detected in 2020 and 2021. The frequency of CPV-2b and CPV-2c was higher in 2019 and 2021, respectively. Analysis of CPV-2 full-length VP2 gene sequence from 19/65 positive samples has identified four common amino acid substitutions F267Y, S297A, A300G, Y324I, which are characteristic for the new CPV-2 variants currently circulating worldwide. Unique substitutions including A5G, G36R, V38E, Q370R, and G392V were recognized in certain samples, and appears to have distinct effect on receptor binding, nuclear translocation, and inter-species transmission. Phylogenetic analysis showed separation of CPV-2 strains into two clades. All strains of this study were classified in clade I with Asian strains. In conclusion, this study provides updated comprehensive molecular analysis of CPV-2 variants in Egypt.

Genetic characterization of the parvovirus full-length VP2 gene in domestic cats in Brazil

Feline parvovirus (FPV) and canine parvovirus (CPV) are over 98% identical in their DNA sequences, and the new variants of CPV (2a/2b/2c) have gained the ability to infect and replicate in cats. The aim of this study was to determine the genetic diversity in the VP2 gene of parvovirus strains circulating in domestic cats in Brazil during a 10-year period (2008-2017). For parvovirus screening, specific PCR was performed, and 25 (34.7%) of 72 cats tested positive. The PCR-positive samples were further subjected to full-length VP2 sequencing (1755 bp), and eight sequences (36%) were characterized as FPV, seven (28%) as CPV-2a and (32%) nine (36%) as CPV-2b. One sequence (RJ1085/11) showing typical CPV amino acid (aa) at residues 80 R, 93 N, 103 A, 232 I, and 323 N could not be characterized at this time. The sequences in this study displayed aa changes previously described for FPV (A14T, A91S, I101T, N564S, and A568G) from cats and CPV-2a/2b (S297N and Y324L) from dogs. However, the Y324L mutation has not yet been reported in any CPV-2a/2b strains from cats. Phylogenetic analysis supported the division of these sequences into two well-defined clades, clade 1 for FPV and clade 2 for CPV2a/2b. Unusually, the sequence RJ1085/11 was grouped separately. Two recombination breakpoints were detected by Bootscan and 3Seq methods implemented in the RDP4. This study is the first report of CPV-2a/2b in cats in Brazil. The detection of FPV strains with mutations characteristic of CPV indicates that Brazilian FPV strains have undergone genetic changes.

Codon usage bias analysis of the spike protein of human coronavirus 229E and its host adaptability

Human coronavirus 229E (HCoV-229E) represents one of the known coronaviruses capable of infecting humans and causes mild respiratory symptoms. It is also considered to have a zoonotic source, originating from animals and being transmitted the humans. In this study, a comprehensive phylogenetic and codon usage analysis of the spike (S) gene of HCoV-229E was conducted. Utilizing phylogenetic analysis and principal component analysis, HCoV-229E was categorized into four distinct clusters, each demonstrating unique host affiliations. Furthermore, it was observed that the codon usage bias within the S gene of HCoV-229E is relatively low, primarily influenced by natural selection patterns, with contributions from mutation pressure and dinucleotide abundance. Comparative analysis involving Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) revealed that the codon usage pattern of HCoV-229E mirrors more closely that of camels, as opposed to alpacas and humans. The elucidation of the codon usage pattern within HCoV-229E, which we have meticulously examined, offers valuable insights for a more comprehensive comprehension of viral features, history, and evolutionary trajectory.

Mutation and codon bias analysis of the spike protein of Omicron, the recent variant of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is a heavily mutated virus and designated as a variant of concern. To investigate the codon usage pattern of this new variant, we performed mutation and codon bias analysis for Omicron as well as for its sub-lineages BA.1 and BA.2 and compared them with the original SARS-CoV-2 and the Delta variant sequences obtained in this study. Our results indicate that the sub-lineage BA.1 and BA.2 have up to 23 sites of difference on the spike protein, which have minimal impact on function. The Omicron variant and its sub-lineages have similar codon usage patterns and A/U ending codons appear to be preferred over G/C ending codons. The Omicron has a lower degree of codon usage bias in spite of evidence that natural selection, mutation pressure and dinucleotide abundance shape the codon usage bias of Omicron, with natural selection being more significant on BA.2 than the other sub-lineages of Omicron. The codon usage pattern of Omicron variant that we explored provides valid information for a clearer understanding of Omicron and its sub-lineages, which could find application in vaccine development and optimization.

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

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

Molecular characterization of Canine parvovirus type 2 from diarrheic dogs in Serbia from 2008 to 2020

Canine parvovirus 2 (CPV-2) is the causal agent of canine parvovirosis an infectious disease with the high fatality rate among dogs. However, in Serbia, it has never been investigated thoroughly. This study was conducted on samples collected from dogs with diarrhea in anamnesis, submitted for various reasons to the Institute of Veterinary Medicine of Serbia, and stored in the sample bank. In total, 50 rectal swab samples were collected from the period 2008 to 2020, and consequently tested. Out of 50 rectal swab samples, the CPV-2 genome was detected in 14 (28%). This retrospective study showed the presence of three different subtypes of CPV-2 in diarrheic dogs during the last 12 years in Serbia. CPV-2a was the most prevalent subtype (60%) followed by CPV-2b (30%), and CPV-2c (10%). Interestingly, CPV-2a had been the predominantly detected subtype up until 2018. Nevertheless in 2019, there was the first detected occurrence of the CPV-2b, followed by the first detection of the CPV-2c in 2020. This study reports the evidence and distribution of CPV-2 from 2008 to 2020, providing new information about the presence of virus strains in Serbia.

Characterization of the VP2 and NS1 genes from canine parvovirus type 2 (CPV-2) and feline panleukopenia virus (FPV) in Northern China

Canine parvovirus type 2 (CPV-2) and feline panleukopenia virus (FPV) cause severe disease in young animals, pups, and kittens. CPV-2 evolved from FPV by altering the species-specific binding of the viral capsid to the host receptor, i.e., the transferrin receptor (TfR), and CPV-2 genetic variants have been identified by specific VP2 amino acid residues (297, 426). Early studies focused on the main capsid protein VP2; however, there have been limited studies on the non-structural protein NS1. In this study, we identified the genetic variants of clinical samples in dogs and cats in northern China during 2019-2020. The genetic characterization and phylogenetic analyses of VP2 and NS1 gene were also conducted. The results revealed that the CPV-2c was identified as the major genetic variant. One new CPV-2b and two CPV-2c strains were collected from cats. Four mutation sites (60, 630, 443, and 545 amino acid residues) were located in the functional domains of the NS1 protein. The phylogenetic analysis of VP2 and NS1 genes showed that they were clustered by geographical regions and genotypes. The gene mutation rate of CPV-2 was increasing in recent years, resulting in a complex pattern of gene evolution in terms of host preference, geographical selection, and new genetic variants. This study emphasizes that continuous molecular epidemiological surveillance is required to understand the genetic diversity of FPV and CPV-2 strains.

Exclusive circulation of canine parvovirus type 2c in the Guadalajara metropolitan area in western Mexico: a five-year study

Canine parvovirus type 2 (CPV-2) infection in dogs is associated with severe gastroenteritis, bloody diarrhea, and vomiting, resulting in high rates of death, especially in unvaccinated puppies within the first months of age. There are three variants, called CPV-2a, CPV-2b, and CPV-2c, co-circulating worldwide. Our group previously reported that the only circulating CPV-2 variant in the Guadalajara metropolitan area in western Mexico was type 2c. Now, a five-year study was performed in order to investigate the possible dominance of CPV-2c in our region. Rectal swabs were collected from 146 dogs with clinical gastroenteritis from May 2014 to August 2019 at the Veterinary Hospital of the University of Guadalajara. Of these, 90 dogs tested positive for canine parvovirus by PCR. Most of the infected dogs with CPV-2 had a partial or incomplete vaccination status (n = 88, 97.8%). Approximately 65% (n = 59) of them were mixed-breed dogs, 77.8% (n = 70) were under 6 months of age, and 37.8% (n = 34) of them died from clinical complications. RFLP analysis of amplicons derived from the vp2 gene showed that all 90 DNA samples corresponded to CPV-2c, with no evidence of the presence of CPV-2a or CPV-2b variants. Twenty-nine of the 90 DNA samples were selected for amplification of a portion of the vp2 gene, and sequencing of these amplicons showed that all of them had the sequence GAA at codon 426, encoding the amino acid glutamic acid, which is characteristic of CPV-2c. Phylogenetic analysis showed that the CPV-2c sequences were related to those of viruses from Europe and South America. The present study indicates that CPV-2c is still the only variant circulating in the dog population of the Guadalajara metropolitan area.

Carnivore protoparvovirus 1 in Peruvian dogs: Temporal/geographical and evolutionary dynamics of virus

Canine parvovirus (CPV) has been recognized all around the world as the causal agent of a contagious and highly mortal disease in domestic dogs. In Peru, the infection is endemic and unvaccinated animals and puppies are the most at risk. In order to analyze viral diversity and determine the evolutionary genetic relationships and transmission dynamic of Peruvian CPV-2, were collected during the period of 2016-2017 rectal swabs from puppies with parvovirosis compatible symptoms. Viral DNA was amplified by PCR using primers that flanked the ends of the viral genome and sequenced by Illumina Miseq platform. Twenty-six genomic sequences (NSP1-VP1) of CPV from several districts in Lima Metropolitan area were obtained. The VP2 gene analysis demonstrated the presence of the New CPV-2a, New CPV-2b and 2c variants. The phylodynamic analysis of the viral genomes determined that all Peruvian sequences were clustered into a big clade named South American clade that emerged from the west region of Europe (Italy). The Time to the Most Recent Common Ancestor (TMRCA) of the South American clade was dated to 1993. Peruvian sequences were distributed into three subclades, and the 92% of these sequences were related to Ecuadorian CPV-2. The results suggests that three independent introduction events of virus from other countries could have occurred, in two of these events, CPV-2 from Ecuador were introduced in Peru in 2003 and 2009, and another introduction event, in 2000, from Europe. Overall, these results indicate a viral genetic relationship between Peruvian with Ecuadorian and European virus, and the circulation of several viral subpopulations in Lima Metropolitan.

Isolation and Genetic Characterization of Canine Parvovirus in a Malayan Tiger

Naïve Felidae in the wild may harbor infectious viruses of importance due to cross-species transmission between the domesticated animals or human–wildlife contact. However, limited information is available on virus shedding or viremia in the captive wild felids, especially in Malaysia. Four infectious viruses of cat, feline herpesvirus (FHV), feline calicivirus (FCV), canine distemper virus (CDV), and canine parvovirus (CPV), were screened in leopards, feral cats, and tigers in Malaysia based on virus isolation in Crandell-Rees feline kidney (CRFK) cells, PCR/RT-PCR, and whole-genome sequencing analysis of the positive isolate. From a total of 36 sera collected, 11 samples showed three consecutive cytopathic effects in the cell culture and were subjected to PCR using specific primers for FHV, FCV, CDV, and CPV. Only one sample from a Malayan tiger was detected positive for CPV. The entire viral genome of CPV (UPM-CPV15/P. tigris jacksoni; GenBank Accession number MW380384) was amplified using the Sanger sequencing approach. Genome sequencing of the isolate revealed 99.13, 98.65, and 98.40% close similarity to CPV-31, CPV-d Cornell #320, and CPV-15 strains, respectively, and classified as CPV-2a. Time-scaled Bayesian Maximum Clade Credibility tree for the non-structural (NS) genes of CPV showed a close relationship to the isolates CPV-CN SD6_2014 and KSU7-SD_2004 from China and USA, respectively, while the capsid gene showed the same ancestor as the FPV-BJ04 strain from China. The higher evolution rate of the capsid protein (CP) (VP 1 and VP2) [1.649 × 10⁻⁵ (95% HPD: 7.626 × 10⁻³ to 7.440 × 10⁻³)] as compared to the NS gene [1.203 × 10⁻⁴ (95% HPD: 6.663 × 10⁻³ to 6.593 × 10⁻³)] was observed in the CPV from this study, and fairly higher than other parvovirus species from the Protoparvovirus genus. Genome sequencing of the isolated CPV from a Malayan tiger in the present study provides valuable information about the genomic characteristics of captive wild felids, which may add information on the presence of CPV in species other than dogs.

Predominance of canine parvovirus 2b in Japan: an epidemiological study during 2014-2019

Canine parvovirus 2 (CPV-2) is an important pathogen of domestic dogs and wild canids. In Japan, CPV-2 infection is one of the most common infectious diseases of dogs. We analyzed samples collected between 2014 and 2019 to identify antigenic variants of CPV-2 in dogs in Japan. Our results demonstrated that the CPV-2b variant was predominant. The CPV-2c variant was not found among our samples. Our findings demonstrate that the distribution of CPV-2 antigenic variants in Japan was more similar to that in Australia than to that in neighboring countries in Asia.

Molecular Analysis of Full-Length VP2 of Canine Parvovirus Reveals Antigenic Drift in CPV-2b and CPV-2c Variants in Central Chile

Simple Summary

Canine parvovirus (CPV) is a relevant pathogen, mainly affecting unvaccinated puppies, causing severe and fatal disease. CPV is classified into three variants (CPV-2a, CPV-2b and CPV-2c), which are widely distributed worldwide. These variants may be mutated at specific sites relevant to the immune response against CPV in dogs, and thus previously characterized vaccines may not be effective against new mutants. Therefore, the aim of the present study was to perform a molecular characterization of CPV variants. For this purpose, blood samples from canine patients in central Chile were used. The results of this study showed that the circulating variants were mainly CPV-2c followed by CPV-2b. In addition, genetic mutations were found in regions important for the immune response against CPV, which possibly has implications for the protective immunity generated by available vaccines.

Abstract

Canine parvovirus (CPV) is a major pathogen in canines, with a high mortality rate in unvaccinated puppies. CPV is traditionally classified into three antigenic variants (CPV-2a, CPV-2b and CPV-2c) based on the amino acid sequence of the VP2 protein. Currently, various mutations are described in the receptor-binding area or in the regions of greatest antigenicity of the VP2 protein, giving rise to new viral variants that are capable of immunological escape, affecting the protective immunity of traditional vaccines. In the present study, a molecular characterization of the VP2 gene was performed, which included phylogenetic analysis, amino acid characterization and determination of selection pressures. Blood samples were initially collected from canine patients with clinical signs of gastrointestinal infection, of which 69 were positive for CPV as measured by means of PCR and 18 samples were selected for the amplification of the complete VP2 gene. The analysis revealed a higher rate of CPV-2c-positive patients compared to CPV-2b. Furthermore, the amino acid characterization of VP2 indicated mutations in the regions of highest antigenicity previously described in the literature (CPV-2b: 297 and 324; CPV-2c: 440), as well as others not previously documented (CPV-2b: 514; CPV-2c: 188, 322, 379, 427 and 463). Our analysis of selection pressure showed that the VP2 gene is under negative selection. However, positive selection point sites were identified, both in CPV-2c (324, 426 and 440) and CPV-2b (297 and 324), at sites that have been associated with evasion of the immune response via antigenic drift, which possibly has implications for the protective immunity generated by traditional vaccines.

Genetic diversity of canine parvovirus variants circulating in Nigeria

Canine parvovirus (CPV) is a fast-evolving single-stranded DNA virus that causes severe and fatal gastrointestinal disease in dogs. Lately, several mutations affecting viral protein (VP) capsid resulting in highly pathogenic variants with distinctive immunological and clinicopathological characteristics abound. This study involved screening stools of 44 randomly selected clinical cases of canine gastroenteritis from 4 cities (Ibadan, Jos, Makurdi, and Zaria) in Nigeria for CPV antigen using an on-the-spot immunoassay test kit, as well as, molecular detection of viral nucleic acid by polymerase chain reaction. Subsequently, nucleic acid sequencing of 1195-bp amplicons encompassing the VP2 encoding region was done. The resultant 40 high-quality amino acid sequences obtained were analysed for the identification and grouping of the viruses into their discrete variants - CPV-2a, CPV-2b, or CPV-2c, using key amino acids substitutions - Asn, Asp, or Glu respectively at position 426 of the VP2 gene. One-third (11/40; 27.5%) of the analysed sequences were identified as CPV-2a and two-third (29/40; 72.5%) as CPV-2c. The original CPV and CPV-2b were not detected. Also, the "new CPV-2a variant" with mutation S297A identified had two additional mutations (Y324I and T440A) associated with selective pressure and vaccination failure in their sequences. Similarly, unique CPV-2c mutants carrying genetic markers (S297A, Y324I, and Q370R) that are highly related to CPVs of Asian origin were observed. These findings revealed a high level of divergence of existing CPVs in circulation; suggesting that CPV is rapidly evolving in Nigeria lately.

Phylogenetic analysis and evolution of feline bocavirus in Anhui Province, eastern China

To understand the epidemic status of feline bocavirus (FBoV) in Anhui Province, eastern China, FBoV was successfully extracted from fecal samples of domestic cats, and five complete genomes were amplified in this study. Phylogenetic analysis showed that these five strains belong to three different FBoV genotypes. Recombination analysis showed that inter- and intra-genotype recombination events occurred. Selection pressure and codon usage bias analyses indicated that FBoV-1 and FBoV-3 continuously evolve toward adaptation, and selection pressure is the main factor for codon usage bias during evolution. This study provides the first molecular evidence of FBoV prevalence in eastern China, further enriching the available information on its genetics and evolutionary characteristics and providing a basis for further research on its evolution.

Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus

Novel H7N9 influenza virus transmitted from birds to human and, since March 2013, it has caused five epidemic waves in China. Although the evolution of H7N9 viruses has been investigated, the evolutionary changes associated with codon usage are still unclear. Herein, the codon usage pattern of two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA), was studied to understand the evolutionary changes in relation to host, epidemic wave, and pathogenicity. Both genes displayed a low codon usage bias, with HA higher than NA. The codon usage was driven by mutation pressure and natural selection, although the main contributing factor was natural selection. Additionally, the codon adaptation index (CAI) and deoptimization (RCDI) illustrated the strong adaptability of H7N9 to Gallus gallus. Similarity index (SiD) analysis showed that Homo sapiens posed a stronger selection pressure than Gallus gallus. Thus, we assume that this may be related to the gradual adaptability of the virus to human. In addition, the host strong selection pressure was validated based on CpG dinucleotide content. In conclusion, this study analyzed the usage of codons of two genes of H7N9 and expanded our understanding of H7N9 host specificity. This aids into the development of control measures against H7N9 influenza virus.

Molecular characterisation of canine parvoviruses from clinical samples and vaccines in Nigeria

Canine parvovirus (CPV) the causative agent of canine parvovirus enteritis is an intractable pathogen of dogs characterised by mutations, evolutionary changes and eventual vaccine failure. The disease is a serious problem in dogs with limited studies conducted in Nigeria. Therefore, this study was designed to characterise the subtypes of CPV isolates in six commonly used vaccines and 157 clinical samples collected from seven states in Nigeria from June 2016 to March 2018. Faecal samples collected from the clinical cases were subjected to in-clinic immunoassay to detect viral antigens. Polymerase chain reaction (PCR) was used to amplify viral VP2 gene in the samples and commonly used vaccines in Nigeria. Thereafter, PCR products were sequenced and analysed. The result showed that 93.0% of the dogs tested positive for CPV in both assays; 72.8% were puppies less than six months old, with 58.3% of them vaccinated. Partial VP2 gene sequence and phylogenetic analysis of 11 random clinical samples showed that CPV-2c 7(63.6%) and CPV-2a 4(36.4%) were the predominant subtypes in Nigeria; with genetic signatures that are 98.7% to 99.9% closely related to Asian and European strains, respectively. No CPV-2b was detected. Amino acid mutation analysis divulged some imperative transmutation sites: D305Y, Y324I, Q370R, N375D, T440A, Y444S, I447M and Y451C in the isolates. The viruses in the vaccines were characterised as the wild-type CPV. The genetic variability, viral population heterogeneity and phylogenetic linkage with isolates from other countries probably suggest transboundary migrations and local differentiations are contributing to continuous CPV evolution and vaccine failure in Nigeria.

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.

Study of the immunogenicity of the VP2 protein of canine parvovirus produced using an improved Baculovirus expression system

BACKGROUND

Canine parvovirus (CPV) is now recognized as a serious threat to the dog breeding industry worldwide. Currently used CPV vaccines all have their specific drawbacks, prompting a search for alternative safe and effective vaccination strategies such as subunit vaccine. VP2 protein is the major antigen targeted for developing CPV subunit vaccine, however, its production in baculovirus expression system remains challenging due to the insufficient yield. Therefore, our study aims to increase the VP2 protein production by using an improved baculovirus expression system and to evaluate the immunogenicity of the purified VP2 protein in mice.

RESULTS

The results showed that high-level expression of the full length VP2 protein was achieved using our modified baculovirus expression system. The recombinant virus carrying two copies of VP2 gene showed the highest expression level, with a productivity of 186 mg/L, which is about 1.4-1.6 fold that of the recombinant viruses carrying only one copy. The purified protein reacted with Mouse anti-His tag monoclonal antibody and Rabbit anti-VP2 polyclonal antibody. BALB/c mice were intramuscularly immunized with purified VP2 protein twice at 2 week intervals. After vaccination, VP2 protein could induce the mice produce high level of hemagglutination inhibition antibodies.

CONCLUSIONS

Full length CPV VP2 protein was expressed at high level and purified efficiently. Moreover, it stimulated mice to produce high level of antibodies with hemmaglutination inhibition properties. The VP2 protein expressed in this study could be used as a putative economic and efficient subunit vaccine against CPV infection.

Genetic analysis and emergence of canine parvovirus type 2c in South Eastern Nigeria

BACKGROUND

Genetic analysis of canine parvovirus type 2 (CPV-2) variants circulating in South Eastern Nigeria was investigated. The original strain of CPV-2 emerged in 1978, mutated later to CPV-2a and has continued to be evolved.

AIMS

To genetically characterize CPV-2 strains detected in dogs in South Eastern Nigeria and to phylogenetically group the viruses with existing sequencing data.

METHODS

A total number of 82 rectal swabs were collected and stored in virus transport medium (VTM) from suspected cases of CPV-2 within the study area and were tested with polymerase chain reaction (PCR).

RESULTS

Seventy-nine samples (96.3%) were positive for CPV-2 and sequence analysis of partial VP2 gene of 20 amplicons revealed circulation of CPV-2a (n=4) and CPV-2c (n=16) in the region. The obtained strains clustered together. However, the group was further divided into two clear clusters comprising of 2a and 2c strains. The vaccine strain and the CPV-2 reference strains from USA formed a monophyletic cluster.

CONCLUSION

Canine parvovirus types 2a and 2c are co-circulating in South Eastern region of Nigeria and therefore, there is an urgent need for an improved vaccine to cover for the emerging strain (CPV-2c) in Nigeria.

Carnivore Protoparvovirus 1 at the Wild-Domestic Carnivore Interface in Northwestern Mexico

Eighty-three wild and domestic carnivores of nine species from Janos Biosphere Reserve (JBR), Mexico, were tested by serologic and molecular assays to determine exposure and infection rates of carnivore protoparvovirus 1. Overall, 50.8% (33/65) of the wild carnivores and 100% (18/18) of the domestic dogs tested were seropositive for Canine protoparvovirus 1 (CPV), while 23% (15/65) of the wild carnivores and 22.2% (4/18) of the domestic dogs were PCR positive for CPV. Phylogenetic analysis confirmed circulation of CVP-2 with residues 426 Asn (CPV2a = 1/19) and 426 Glu (CPV-2c = 18/19) among carnivores in JBR. The prevalence of both PCR positivity and antibodies to CPV varied significantly among wild host species. Of the six identified haplotypes, three were unique to kit foxes (Vulpes macrotis) (the species with higher haplotype richness) and two to striped skunks (Mephitis mephitis). The remaining haplotype was shared among all carnivore species including dogs suggesting non-host specificity and bidirectional and continuous viral transmission cycle in the JBR. The phylogenetic similarity of CPV strains from dogs and wild carnivores and the higher prevalence of CPV in wild carnivores captured near towns relative to those captured far from towns suggest that dogs might be an important source of CPV infection for wild carnivores in the JBR. We provide evidence that cross-species transmission occurs at the domestic-wildlife interface in JBR.

Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus

The torque teno sus virus (TTSuV) is an emerging virus threating the Suidae species of unclear pathogenicity, although it was previously reported as a worsening factor of other porcine diseases, in particular, porcine circovirus associated disease (PCVAD). Here, a comprehensive codon usage analysis of the open reading frame 1 (ORF1), which encodes the viral capsid protein, was undertaken for the first time to reveal its evolutionary history. We revealed independent phylogenetic processes for the two genera during TTSuV evolution, which was confirmed by principal component analysis (PCA). A low codon usage bias was observed in different genera and different species, with Kappatorquevirus a (TTSuVk2a) displaying the highest, which was mainly driven by mutation pressure and natural selection, especially natural selection. Overall, ATs were more abundant than GCs, along with more A-ended synonymous codons in relative synonymous codon usage (RSCU) analysis. To further confirm the role of natural selection and TTSuV adaptation to the Suidae species, codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses were performed, which showed different adaptations for different TTSuVs. Importantly, we identified a more dominant role of Sus scrofa in the evolution of Iotatorquevirus (TTSuV1), with the highest CAI values and lowest RCDI values compared to Sus scrofa domestica. However, in TTSuVk2, the roles of Sus scrofa and Sus scrofa domestica were the same, regarding codon usage, with similar CAI and RCDI values. Our study provides a new perspective of the evolution of TTSuV and valuable information to develop control measures against TTSuV.

Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern

The codon usage pattern can reveal the adaptive changes that allow virus survival and fitness adaptation to their particular host, as well as the external environment. Although still considered a novel influenza virus, there is an increasing number of influenza D viruses (IDVs) reported. Considering the vital role of the hemagglutinin-esterase fusion (HEF) gene in receptor binding, receptor degradation, and membrane fusion, we investigated the codon usage pattern of the IDV HEF gene to better understand its adaptive changes during evolution. Based on the HEF gene, three groups including, D/OK, D/660, and D/Japan were identified. We found a low codon usage bias, which allowed IDV to replicate in the corresponding hosts by reducing competition during evolution, that was mainly driven by natural selection and mutation pressure, with a profound role of natural selection. Furthermore, the interaction between the codon adaption index (CAI) and the relative codon deoptimization index (RCDI) revealed the adaption of IDV to multiple hosts, especially cattle which is currently considered its reservoir. Additionally, similarity index (SiD) analysis revealed that the swine exerted a stronger evolutionary pressure on IDV than cattle, though cattle is considered the primary reservoir. In addition, the conserved PB1 gene showed a similar pattern of codon usage compared to HEF. Therefore, we hypothesized that IDV has a preference to maintain infection in multiple hosts. The study aids the understanding of the evolutionary changes of IDV, which could assist this novel virus prevention and control.

First identification of a novel parvovirus distantly related to human bufavirus from diarrheal dogs in China

Bufaviruses are small, nonenveloped, single-stranded DNA viruses belonging to the subfamily Parvovirinae. Human bufaviruses were first identified in 2012 in fecal samples from children with diarrhea. A new parvovirus of canines that was first detected in various samples from dogs with enteric and respiratory symptoms in Italy between 2014 and 2018 is closely related to the newly described human bufavirus. To explore the prevalence and genetic diversity of CBuV in Chinese dogs, 540 canine parvovirus (CPV)-positive serum and diarrhea samples were collected in Guangxi Province between 2016 and 2018. Among the samples, 6.25% (5/80) of rectal swabs and 2.5% (5/200) of CPV PCR-positive samples were positive for CBuV. However, the virus was not detected in CPV PCR-negative samples or nasal swabs. Two CBuV isolates were identified from CPV-positive fecal and serum samples by complete sequence analysis, with 99.8%-99.9% NS1 and VP2 protein identity to each another. Sequence analysis indicated that the CBuV GXNN01-2018 isolate VP2 protein shares 99.6% identity with the Italian CBuV ITA/2015/297 isolate and 62.3%-65.5% identity with human bufavirus. Phylogenetic analysis showed that CBuV was significantly distinct from other known bufaviruses and was most closely related to CBuV ITA/2015/297. This is the first report of the existence of CBuV in China, and our findings will strengthen the understanding of the epidemiology of bufaviruses in different animals.

New variants of canine parvovirus in dogs in southern Brazil

Carnivore protoparvovirus 1 (canine parvovirus 2, CPV-2) has undergone a rapid evolution through mutations in the capsid protein VP2, giving rise to variants associated with unique clinicopathological and immunological features. VP2 is a major capsid protein involved in key steps of virus biology, including interactions with cellular receptors and with the immune system. This study analyzed the complete VP2 coding sequence of 38 CPV-2 isolates obtained from dogs with clinical parvovirosis in southern Brazil. Amplicons encompassing the whole VP2 coding region were subjected to nucleotide sequencing, and predicted amino acid sequences were analyzed to identify molecular markers of viral variants. Viral variants were classified as CPV-2a, -2b or -2c based on the presence of the amino acid Asn, Asp or Glu, respectively, at VP2 residue 426. Amino acid sequence analysis identified 20 CPV-2c and four CPV-2b isolates. Eleven viruses were identified as New CPV-2a, two as New CPV-2b, and one resembled the original CPV-2 and was designated CPV-2-like. In addition to the mutation at amino acid 426 of VP2, new 2a/2b variants containing a Ser297Ala mutation at residue 297 were identified. CPV-2-like samples contained some mutations that were also present in the original CPV-2 isolate, including as Leu, Thr, Ala and Asp at residues 87, 101, 300 and 305, respectively. The New CPV-2a isolates had three additional mutations (Phe267Tyr, Tyr324Ile and Thr440Ala) associated with selective pressure and development of disease in vaccinated dogs. The resemblance of the CPV-2-like isolate to CPV-2 suggests reemergence of CPV-2 and/or evolution from vaccine strains. Phylogenetic analysis grouped the variants with their respective reference strains, in general, according to amino acid changes. These results demonstrate the high VP2 diversity of CPV circulating in dogs in southern Brazil and indicate the emergence of new viral variants that differ markedly from the current vaccine strains.

The adaptation of codon usage of +ssRNA viruses to their hosts

Viruses depend on their host's cellular structure to survive. Most of them do not have tRNAs, their translation relies on hosts' tRNA pools. Over the course of evolution, viruses needed to optimally exploit cellular processes of their host. Thus, codon usage of a virus should coevolve with its host to efficiently and rapidly replicate. Some viruses can invade a broad spectrum of hosts (BSTVs), while others can invade a narrow spectrum only (NSTVs). Consequently, we test the hypothesis that similarity of codon usage preference and the degree of matching between BSTVs and their hosts will be lower than that of NSTVs, which only need to coevolve with few hosts. We compare the patterns of codon usage in 255 virus genomes to test this hypothesis. Our results show that NSTVs have a higher degree of matching to their hosts' tRNA pools than BSTVs. Further, analysis of the effective number of codons (ENC) infers that codon usage bias of NSTVs is relatively stronger than that of BSTVs. Thus, codon usage of NSTVs tends to better match their host than that of BSTVs. This supports the hypothesis that viruses adapt to the expression system of their host(s).

Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses

Rabies virus (RABV) and other lyssaviruses can cause rabies and rabies-like diseases, which are a persistent public health threat to humans and other mammals. Lyssaviruses exhibit distinct characteristics in terms of geographical distribution and host specificity, indicative of a long-standing diversification to adapt to the environment. However, the evolutionary diversity of lyssaviruses, in terms of codon usage, is still unclear. We found that RABV has the lowest codon usage bias among lyssaviruses strains, evidenced by its high mean effective number of codons (ENC) (53.84 ± 0.35). Moreover, natural selection is the driving force in shaping the codon usage pattern of these strains. In summary, our study sheds light on the codon usage patterns of lyssaviruses, which can aid in the development of control strategies and experimental research.

Bacterial diversity in the feces of dogs with CPV infection

Canine parvovirus (CPV) is a contagious disease in dogs that has high morbidity and mortality. In cases of infection, the pups tend to have a higher mortality and more severe clinical symptoms than the adult dogs because the dehydration is difficult for pups to bear. Following the natural infection, there is a rapid antibody response neutralizing the extracellular virus. As a result, virus titers in tissue and feces become markedly reduced. Hence, it is important to have an effective symptomatic therapy of supporting animals to survive in the early stages of CPV infection. Furthermore, the co-infection with bacteria could increase the severity of lesions and clinical signs as well. In this paper, we obtained the bacterial diversity in feces of CPV infected dogs with the enrichment of five bacteria genera (Shigella, Peptoclostridium, Peptostreptococcus, Streptococcus, Fusobacterium). These microorganisms may partly result in the intestinal pathology of the infection. In summary, the discussion of the bacterial biodiversity in feces of CPV infected dogs provides further insights into the pathology of CPV disease and the targets of developing more effective treatment strategies.

Molecular typing of a novel canine parvovirus type 2a mutant circulating in Italy

Canine parvovirus (CPV) is the etiological agent of a severe viral disease of dogs. After its emergence in late 1970s, the CPV original type (CPV-2) was rapidly and totally replaced by three antigenic variants named CPV-2a, CPV-2b and CPV-2c. CPV has an evolutionary rate nearest to those of RNA viruses, with consequences on disease diagnosis and epidemiology. This paper reports the molecular characterization of eight CPV-2a strains collected from dogs in Italy in 2016–2017. Genetic analysis was conducted on a CPV genomic region encompassing both open reading frames (ORFs) encoding for nonstructural (NS1-NS2) and structural proteins (VP1-VP2). Sequence analysis indicates new and unreported sequence changes, mainly affecting the VP2 gene, which included the mutation Tyr324Leu. This study represents the first evidence of a new CPV-2a mutant (VP2 324Leu) and illustrates the importance of a continuous molecular survey in order to obtain more information on effective spread of new CPV mutants.

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Canine parvovirus strains collected from dogs in southern Italy were analyzed.

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Nearly complete genome sequences of the CPV strains were obtained and comparatively analyzed.

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A novel CPV-2a mutant with unreported sequence changes has been characterized.

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This study reports a novel CPV-2a mutant in genus Protoparvovirus.

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Our data confirmed the importance of the continuous epidemiological survey.

Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus

Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which first broken out in Jeddah in 2012, causes a severe acute respiratory illness with a high mortality rate. To better understand the molecular characteristics of isolated MERS-CoV genomes, we first analysed the codon usage pattern of the zoonotic MERS-CoV strains comprehensively to gain an insight into the mechanism of cross-species transmission. We found that MERS human/camel isolates showed a low codon usage bias. Both mutation and nature selection pressure have contributed to this low codon usage bias, with the former being the main determining factor. We also observed that gene function, evolution time and the different host species of the virus all contributed to the bias of MERS-CoV, to some extent. Additionally, the codon usage pattern of MERS-CoV isolates is different from other related Nidovirales viruses isolated from bats and hedgehogs. In the future, more epidemiological surveys are required to examine the factors that resulted in the emergence and outbreak of this virus.

Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus

BACKGROUND

The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of several members of the Varicellovirus genus. Here, currently available varicellovirus genomic sequences were used for phylogenetic, recombination, and genetic distance analysis.

RESULTS

A phylogenetic network including genomic sequences of individual species, was generated and suggested a potential restriction between the ungulate and non-ungulate viruses. Intraspecies genetic distances were higher in the ungulate viruses (pseudorabies virus (SuHV-1) 1.65%, bovine herpes virus type 1 (BHV-1) 0.81%, equine herpes virus type 1 (EHV-1) 0.79%, equine herpes virus type 4 (EHV-4) 0.16%) than non-ungulate viruses (feline herpes virus type 1 (FHV-1) 0.0089%, canine herpes virus type 1 (CHV-1) 0.005%, varicella-zoster virus (VZV) 0.136%). The G + C content of the ungulate viruses was also higher (SuHV-1 73.6%, BHV-1 72.6%, EHV-1 56.6%, EHV-4 50.5%) compared to the non-ungulate viruses (FHV-1 45.8%, CHV-1 31.6%, VZV 45.8%), which suggests a possible link between G + C content and intraspecies genetic diversity. Varicellovirus clade nomenclature is variable across different species, and we propose a standardization based on genomic genetic distance. A recent study reported no recombination between sequenced FHV-1 strains, however in the present study, both splitstree, bootscan, and PHI analysis indicated recombination. We also found that the recently sequenced Brazilian CHV-1 strain BTU-1 may contain a genetic signal in the UL50 gene from an unknown varicellovirus.

CONCLUSION

Together, the data contribute to a greater understanding of varicellovirus genomics, and we also suggest a new clade nomenclature scheme based on genetic distances.

Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Senecavirus A evolution

Senecavirus A (SVA) infection was recently confirmed in pigs in Brazil, United States of America and Canada. To better understand the molecular characteristics of isolated SVA genomes, we first reported genome-wide comprehensive analyses of codon usage and various factors that have contribute to the molecular evolution in SVA. The effective number of codons (ENC) ranged from 54.51 to 55.54 with an average of 54.87 ± 0.285, which reveals a relatively stable nucleotide composition. We found that codon usage bias of the SVA was low. Mutational pressure acted as an increasingly dominant factor for the evolution of the virus compared with the natural selection. Notably, codon usage bias was also affected by the geographic distribution and isolated time. The first systemic analysis on the codon usage bias of the SVA provides important information for the understanding of the evolution of the SVA and has fundamental and theoretical benefits.

Identification and function analysis of canine stimulator of interferon gene (STING)

Stimulator of interferon gene (STING) plays an important role in the cyclic GMP-AMP synthase (cGAS)-mediated activation of type I IFN responses. In this study, we identified and cloned canine STING gene. Full-length STING encodes a 375 amino acid product that shares the highest similarity with feline STING. Highest levels of mRNA of canine STING were detected in the spleen and lungs while the lowest levels in the heart and muscle. Analysis of its cellular localization showed that STING is localizes to the endoplasmic reticulum. STING overexpression induced the IFN response via the IRF3 and NF-κB pathways and up-regulated the expression of ISG15 and viperin. However, knockdown of STING did not inhibit the IFN-β response triggered by poly(dA:dT), poly(I:C), or SeV. Finally, overexpression of STING significantly inhibited the replication of canine influenza virus H3N2. Collectively, our findings indicate that STING is involved in the regulation of the IFN-β pathway in canine.

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Here we first identified and cloned canine STING gene.

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STING overexpression induced the IFN response via the IRF3 and NF-kB pathways.

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Overexpression of STING inhibited the replication of H3N2 CIV.

Comprehensive analysis of the codon usage patterns in the envelope glycoprotein E2 gene of the classical swine fever virus

The classical swine fever virus (CSFV), circulating worldwide, is a highly contagious virus. Since the emergence of CSFV, it has caused great economic loss in swine industry. The envelope glycoprotein E2 gene of the CSFV is an immunoprotective antigen that induces the immune system to produce neutralizing antibodies. Therefore, it is essential to study the codon usage of the E2 gene of the CSFV. In this study, 140 coding sequences of the E2 gene were analyzed. The value of effective number of codons (ENC) showed low codon usage bias in the E2 gene. Our study showed that codon usage could be described mainly by mutation pressure ENC plot analysis combined with principal component analysis (PCA) and translational selection-correlation analysis between the general average hydropathicity (Gravy) and aromaticity (Aroma), and nucleotides at the third position of codons (A3s, T3s, G3s, C3s and GC3s). Furthermore, the neutrality analysis, which explained the relationship between GC12s and GC3s, revealed that natural selection had a key role compared with mutational bias during the evolution of the E2 gene. These results lay a foundation for further research on the molecular evolution of CSFV.