Comparative analysis reveals frequent recombination in the parvoviruses

Shackelton, Laura A.; Hoelzer, Karin; Parrish, Colin R.; Holmes, Edward C.

doi:10.1099/vir.0.83255-0

Cited by 95 publications

(83 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Consequently, it was natural to consider that a recombinant among FPV subspecies would be discovered in time. As previously discussed by Shackelton et al [31], recombination might be a rare event for FPV subspecies which cause acute disease because early elimination of the virus by an immune response might reduce the chance of dual infection.…”

Section: Discussionmentioning

confidence: 97%

“…These results suggested that recombination is a more frequent event than previously believed for the FPV subspecies that generally cause acute infection. This observation prompted us to search for further evidence of natural recombination among FPV subspecies using similar methods to those employed by Shackelton et al [31]. As a result we found evidence for inter-FPV subspecies recombination between FPLV and CPV.…”

mentioning

confidence: 86%

“…This applies also to RNA viruses infecting cats and dogs; for example, group 1 feline and canine coronaviruses [8,21], feline calicivirus [4], feline immunodeficiency virus [2,7,10,29], and canine distemper virus [6]. Recently Shackelton et al [31] found some evidence of natural recombination among porcine, mink, and rodent parvoviruses by analyzing the genetic data deposited in databases, and discussed the possibility that recombination may be important in the natural evolution of parvoviruses, especially in circumstances where parvoviruses cause persistent infections. However, in their previous study they found no evidence for recombination of any carnivore parvovirus, including CPV and FPLV [32].…”

mentioning

confidence: 99%

See 2 more Smart Citations

Evidence for Recombination Between Feline Panleukopenia Virus and Canine Parvovirus Type 2

Ohshima

Mochizuki

2009

The Journal of Veterinary Medical Science

View full text Add to dashboard Cite

ABSTRACT. Canine parvovirus type 2 (CPV) is a virulent pathogen that emerged in the late 1970s, probably originating from feline panleukopenia virus (FPLV) or a closely related carnivore parvovirus belonging to the feline parvovirus (FPV) subspecies. In contrast to FPLV, CPV has evolved rapidly since its emergence. The original antigenic type of CPV disappeared more than two decades ago and several new antigenic as well as genetic CPV variants have appeared and spread in the field. Both high mutation rate and positive selection of mutations in the capsid gene appear to be the driving force for such rapid evolution. In addition, genetic recombination has been assessed as a factor in parvovirus evolution. Recently, we provided the first evidence of inter-antigenic type recombination of CPV in nature. Here, an inter-FPV subspecies recombinant was revealed by analyzing the genetic data deposited in databases with several recombination detection programs, and by phylogeny. FPLV strain XJ-1, submitted by Su et al., Harbin, China in 2007 (GenBank accession no. EF988660), was most likely generated by recombination between CPV and FPLV. Its genome was generally composed of the NS1 gene of CPV origin and the VP1 gene of FPLV origin. This is the first demonstration of recombination between different FPV subspecies in nature. Consequently, recombination should be considered as an element in the generation and evolution of parvoviruses of the FPV subspecies.

show abstract

Section: Discussionmentioning

confidence: 97%

mentioning

confidence: 86%

mentioning

confidence: 99%

See 1 more Smart Citation

Evidence for Recombination Between Feline Panleukopenia Virus and Canine Parvovirus Type 2

Ohshima

Mochizuki

2009

The Journal of Veterinary Medical Science

View full text Add to dashboard Cite

show abstract

“…Recombination is known to occur in the parvoviruses (19,43,70), microviruses (66), anelloviruses (40,46), circoviruses (11,26,60), nanoviruses (30), geminivirus DNA-B components, and geminivirus satellite molecules (2,62). Given that most, if not all, of these ssDNA replicons are evolutionarily related to and share many biological features with the geminiviruses (22,31,36), it is of interest to determine whether conserved recombination patterns observed in the geminiviruses (61,81) are evident in these other groups.…”

mentioning

confidence: 99%

Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses

Lefeuvre

Lett

Varsani

et al. 2009

J Virol

225

179

View full text Add to dashboard Cite

The combinatorial nature of genetic recombination can potentially provide organisms with immediate access to many more positions in sequence space than can be reached by mutation alone. Recombination features particularly prominently in the evolution of a diverse range of viruses. Despite rapid progress having been made in the characterization of discrete recombination events for many species, little is currently known about either gross patterns of recombination across related virus families or the underlying processes that determine genome-wide recombination breakpoint distributions observable in nature. It has been hypothesized that the networks of coevolved molecular interactions that define the epistatic architectures of virus genomes might be damaged by recombination and therefore that selection strongly influences observable recombination patterns. For recombinants to thrive in nature, it is probably important that the portions of their genomes that they have inherited from different parents work well together. Here we describe a comparative analysis of recombination breakpoint distributions within the genomes of diverse single-stranded DNA (ssDNA) virus families. We show that whereas nonrandom breakpoint distributions in ssDNA virus genomes are partially attributable to mechanistic aspects of the recombination process, there is also a significant tendency for recombination breakpoints to fall either outside or on the peripheries of genes. In particular, we found significantly fewer recombination breakpoints within structural protein genes than within other gene types. Collectively, these results imply that natural selection acting against viruses expressing recombinant proteins is a major determinant of nonrandom recombination breakpoint distributions observable in most ssDNA virus families.

show abstract

“…The 5= nontranslated region (NTR) has 291 nucleotides (nt) and the 3= NTR 527 nt; the complete coding sequence contains 4,258 nt. The PPV genome includes two open reading frames (ORFs) (6); ORF1 locates at the 5= end and ORF2 at the 3= end. ORF1 encodes the nonstructural proteins NS1 (663 amino acids [aa]), NS2 (162 aa), and NS3 (108 aa); ORF2 encodes the structural proteins VP1 (730 aa) and VP2 (580 aa).…”

mentioning

confidence: 99%

Genome Sequence of Chinese Porcine Parvovirus Strain PPV2010

Cui

Wang

Ren

et al. 2012

J Virol

View full text Add to dashboard Cite

Porcine parvovirus (PPV) isolate PPV2010 has recently emerged in China. Herein, we analyze the complete genome sequence of PPV2010. Our results indicate that the genome of PPV2010 bears mixed characteristics of virulent PPV and vaccine strains. Importantly, PPV2010 has the potential to be a naturally attenuated candidate vaccine strain. P orcine parvovirus (PPV) is a member of the genus Parvovirus and the family Parvoviridae (8). PPV is a negative-oriented, single-stranded DNA virus that causes porcine reproductive failure characterized by infertility, embryonic and fetal death, mummified fetuses, and stillbirth in swine (5). Currently, three complete genome sequences of attenuated PPVs, including the prototype strain NADL-2 (USA, 1976) and the N (China, 1989) and China (China) strains, are available in GenBank. The role of attenuated PPV in disease is not fully understood.In March of 2010, a PPV with low virulence, named PPV2010, was isolated from a disease outbreak in a hoggery in Jilin Province, northeastern China. Tissue samples tested positive for PPV by PCR using primers targeting viral VP2. Sequence alignment was performed using MUSCLE software (2, 3).The whole genome of PPV2010 was sequenced with an ABI 3730xl genetic analyzer using the Sanger method, based on five overlapping DNA fragments amplified by PCR. The genome is comprised of 5,076 bp with a GC content of 37.9%, which is similar to that of the other sequenced PPV strains. The 5= nontranslated region (NTR) has 291 nucleotides (nt) and the 3= NTR 527 nt; the complete coding sequence contains 4,258 nt. The PPV genome includes two open reading frames (ORFs) (6); ORF1 locates at the 5= end and ORF2 at the 3= end. ORF1 encodes the nonstructural proteins NS1 (663 amino acids [aa]), NS2 (162 aa), and NS3 (108 aa); ORF2 encodes the structural proteins VP1 (730 aa) and VP2 (580 aa). PPV2010 has 99.6% and 99.9% sequence homology with the BQ strain (China), a virulent Chinese PPV, at the amino acid and nucleotide levels, respectively. The NADL-2 and Kresse strains differ in the VP2 protein by six amino acids, which have been demonstrated to be responsible for the replication efficiency of PPV in cell culture (4). The six amino acids are the same in PPV strain PPV2010 and the virulent Kresse strain; however, they are different from the amino acid sequences at the same location in PPV vaccine strains N and NADL-2. Even more interesting, by comparing the 3= NTRs, we found that PPV2010 has two complete repeat units that are the same as those of the attenuated strains NADL-2 and N; however, the highly virulent Kresse strain has only one repeat unit and the moderately virulent BQ strain, which is very similar to PPV2010 in the coding regions, lacks 63 nt in the first repeat unit (7). PPV virulence is related to a 127-bp repeat in the 3= NTR (1). PPV2010 shares the highest similarity with BQ in complete ORFs; however, in the 3= NTR, PPV2010 has 99.9% homology with vaccine strain NADL-2. These data indicate that PPV2010 bears the characteristics of virulent and ...

show abstract

Comparative analysis reveals frequent recombination in the parvoviruses

Cited by 95 publications

References 37 publications

Evidence for Recombination Between Feline Panleukopenia Virus and Canine Parvovirus Type 2

Evidence for Recombination Between Feline Panleukopenia Virus and Canine Parvovirus Type 2

Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses

Genome Sequence of Chinese Porcine Parvovirus Strain PPV2010

Contact Info

Product

Resources

About