Nearly 20 Years of Genetic Diversity and Evolution of Porcine Circovirus-like Virus P1 from China

Abstract

Porcine circovirus-like virus P1 can infect many kinds of animals and mainly causes postweaning multisystemic wasting syndrome. In China, the genetic diversity, variation, and evolutionary processes of this virus have not been described yet. To improve our knowledge of its genetic diversity, evolution, and gene flow, we performed a bioinformatics analysis using the available nucleotide sequences of the P1 virus; among them, 12 nucleotide sequences were from ten pig farms in Jiangsu Province in this epidemiological survey, and 84 sequences were downloaded from GenBank. The P1 sequences showed a rich composition of AT nucleotides. Analyses of the complete genomic sequences were polymorphic and revealed high haplotype (gene) diversity and nucleotide diversity. A phylogenetic analysis based on the NJ method showed that all P1 virus sequences formed two distinct groups: A and B. High genetic differentiation was observed between strains from groups A and B. The codon usage pattern of P1 was affected by dinucleotide compositions. Dinucleotide UU/CC was overrepresented, and dinucleotide CG was underrepresented. The mean evolutionary rate of the P1 virus was estimated to be 3.64 × 10−4 nucleotide substitutions per site per year (subs/site/year). The neutrality tests showed negative values. The purifying selection and recombination events may play a major driving role in generating the genetic diversity of the P1 population. The information from this research may be helpful to obtain new insights into the evolution of P1.

Vertical transmission of porcine circovirus-like virus P1 in BALB/c mice

“…The P1 virus was discovered nearly 20 years ago, but there is still no suitable cell line for its propagation [ 14 ]. Infectious molecular clones of the virus or rescue virus can be used in the research of virus pathogenesis.…”

Transcriptomic and Proteomic Approaches Reveal the Biological Functions of Two Novel Porcine-Origin Noncoding DNA Molecules

“…Porcine circoviruses (PCVs), belonging to the genus Circovirus of the family Circoviridae, are small nonenveloped viruses (17)(18)(19)(20)(21)(22) nm in diameter) with single-stranded circular DNA (∼2,000 nt). To date, four types of PCVs (PCV1-PCV4) have been identified [1][2][3][4][5].…”

Special Issue “State-of-the-Art Porcine Virus Research in China”

“…The original studies mainly focus on the pathogenicity, evolution, and detection of porcine reproductive and respiratory syndrome virus (PRRSV), coronaviruses, and circoviruses, which are the top porcine viruses circulating in China to date [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 ]. As reported, PRRSV regulates the expression of poly- N -acetyllactosamine and complex N -glycan in porcine pulmonary microvascular endothelial cells [ 1 ].…”

“…Furthermore, codon usage contributes to genetic diversity and evolutionary dynamics [ 10 , 11 , 19 ]. For example, PCV2 can be divided into nine genotypes, PCV2a to 2i [ 20 ].…”

“…In contrast, PCV2b, PCV2d, and the newly emerged PCV2e are circulating in China, indicating that PCV2 genotypes in China are more abundant [ 9 ]. Further research showed that the PCVs and PCV-like virus genomes possess an overrepresentation of AT pairs and codon usage bias caused by natural selection and mutation pressure [ 10 , 11 ]. In addition, host restriction factors, such as interferon-inducible transmembrane proteins (IFITMs) [ 21 ] and Mx1 [ 22 ], and cholesterol biosynthesis [ 23 ] also play vital roles in host–virus interactions.…”