Identification of recombination in the NS1 and VPs genes of parvovirus B19

Equine Parvovirus-Hepatitis in China: Characterization of Its Genetic Diversity and Evidence for Natural Recombination Events Between the Chinese and American Strains

Equine parvovirus-hepatitis (EqPV-H) was first reported in a horse that died of equine serum hepatitis in the USA in 2018, and was determined having a strong association with equine serum hepatitis in the following studies. As a newly discovered virus, the genomic sequences of only seven EqPV-H strains have been reported. Considering this, an epidemiological study was performed to investigate the prevalence of EqPV-H in equines in Guangdong Province in China, and obtain genomic sequences of the field prevalent EqPV-H strains. The detection rate of EqPV-H was finally determined to be 8.33% (95% CI: 2.8-18.4%), and EqPV-H's coinfection with equine hepacivirus and equine pegivirus was also determined. Then, the genomes of the Chinese field EqPV-H strains were obtained by PCR, sequencing, and assembly. Through bootscanning analysis, Simplot analysis, and phylogenetic analysis, strong evidence for natural recombination events were found in two Chinese field EqPV-H strains. The natural recombination events occurred between the Chinese and American strains, and were determined within VP protein. Finally, the genetic distance of EqPV-H strains was investigated. Nucleotide identities of 97.1-99.9% and 95.2-100% were found for NS and VP between EqPV-H strains, respectively. Together with other molecular evidence obtained in the present study, the genetic diversity of EqPV-H was determined. Taken together, the results of the present study expand our knowledge on the epidemiological characteristics, genetic variability, and evolution of EqPV-H.

Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans

Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to ∼70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9-99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from ∼0.5 to ∼6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed ∼12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to ∼5.0-6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics.

Echovirus plays major roles in the natural recombination of Coxsackievirus B3

Coxsakievirus B3 (CVB3) is a member of enterovirus B (EVB) group, which can cause serious heart diseases such as viral myocarditis. In order to analyze the evolution of CVB3, we performed a recombination analysis of all viral genomes of enterovirus B, and found that there were 19 putative recombination events that produced CVB3. A total of 11 serotypes were found to be involved in the generation of CVB3 progeny virus. These recombination events involved echovirus, EcoV (which includes EcoV6, EcoV9, EcoV14, EcoV15, EcoV17, EcoV21, EcoV24, and EcoV25), CVB4, CVB5, and EVB81, as major or minor parents. The most active, EcoV, which was involved in the 14 of 19 recombination events, acts as one of the parental viruses for CVB3 strains among molecular evolution and recombination events in circulating CVB3. Our study indicates that, EcoV plays major roles in CVB3 recombination, and is involved in the production of 11 new CVB3 recombinant strains.

Transcription-associated mutational pressure in the Parvovirus B19 genome: Reactivated genomes contribute to the variability of viral populations

In this study we used non-overlapping parts of the two long open reading frames coding for nonstructural (NS) and capsid (VP) proteins of all available sequences of the Parvovirus B19 subgenotype 1a genome and found out that the rates of A to G, C to T and A to T mutations are higher in the first long reading frame (NS) of the virus than in the second one (VP). This difference in mutational pressure directions for two parts of the same viral genome can be explained by the fact of transcription of just the first long reading frame during the lifelong latency in nonerythroid cells. Adenine deamination (producing A to G and A to T mutations) and cytosine deamination (producing C to T mutations) occur more frequently in transcriptional bubbles formed by DNA "plus" strand of the first open reading frame. These mutations can be inherited only in case of reactivation of the infectious virus due to the help of Adenovirus that allows latent Parvovirus B19 to start transcription of the second reading frame and then to replicate its genome by the rolling circle mechanism using the specific origin. Results of this study provide evidence that the genomes reactivated from latency make significant contributions to the variability of Parvovirus B19.

Human Parvoviruses

Parvovirus B19 (B19V) and human bocavirus 1 (HBoV1), members of the large Parvoviridae family, are human pathogens responsible for a variety of diseases. For B19V in particular, host features determine disease manifestations. These viruses are prevalent worldwide and are culturable in vitro, and serological and molecular assays are available but require careful interpretation of results. Additional human parvoviruses, including HBoV2 to -4, human parvovirus 4 (PARV4), and human bufavirus (BuV) are also reviewed. The full spectrum of parvovirus disease in humans has yet to be established. Candidate recombinant B19V vaccines have been developed but may not be commercially feasible. We review relevant features of the molecular and cellular biology of these viruses, and the human immune response that they elicit, which have allowed a deep understanding of pathophysiology.

Existence of various human parvovirus B19 genotypes in Chinese plasma pools: genotype 1, genotype 3, putative intergenotypic recombinant variants and new genotypes

Background

Human parvovirus B19 (B19V) is a frequent contaminant of blood and plasma-derived medicinal products. Three distinct genotypes of B19V have been identified. The distribution of the three B19V genotypes has been investigated in various regions or countries. However, in China, data on the existence of different B19V genotypes are limited.

Methods

One hundred and eighteen B19V-DNA positive source plasma pool samples collected from three Chinese blood products manufacturers were analyzed. The subgenomic NS1/VP1u region junction of B19V was amplified by nested PCR. These amplified products were then cloned and subsequently sequenced. For genotyping, their phylogenetic inferences were constructed based on the NS1/VP1-unique region. Then putative recombination events were analyzed and identified.

Results

Phylogenetic analysis of 118 B19V sequences attributed 61.86 % to genotype 1a, 10.17 % to genotype 1b, and 17.80 % to genotype 3b. All the genotype 3b sequences obtained in this study grouped as a specific, closely related cluster with B19V strain D91.1. Four 1a/3b recombinants and 5 new atypical B19V variants with no recombination events were identified.

Conclusions

There were at least 3 subtypes (1a, 1b and 3b) of B19V circulating in China. Furthermore, putative B19V 1a/3b recombinants and unclassified strains were identified as well. Such recombinant and unclassified strains may contribute to the genetic diversity of B19V and consequently complicate the B19V infection diagnosis and NAT screening. Further studies will be required to elucidate the biological significance of the recombinant and unclassified strains.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-016-0611-6) contains supplementary material, which is available to authorized users.