Porcine Parvovirus 7: Evolutionary Dynamics and Identification of Epitopes toward Vaccine Design

Abstract

Porcine parvovirus 7 (PPV7) belonging to the genus Chapparvovirus in the family Parvoviridae, has been identified in the USA, Sweden, Poland, China, South Korea and Brazil. Our objective was to determine the phylogeny, estimate the time of origin and evolutionary dynamics of PPV7, and use computer-based immune-informatics to assess potential epitopes of its Cap, the main antigenic viral protein, for vaccines or serology. Regarding evolutionary dynamics, PPV7 had 2 major clades, both of which possibly had a common ancestor in 2004. Furthermore, PPV7 strains from China were the most likely ancestral strains. The nucleotide substitution rates of NS1 and Cap genes were 8.01 × 10^-4 and 2.19 × 10^-3 per site per year, respectively, which were higher than those reported for PPV1-4. The antigenic profiles of PPV7 Cap were revealed and there were indications that PPV7 used antigenic shift to escape from the host's immune surveillance. Linear B cell epitopes and CD8 T cell epitopes of Cap with good antigenic potential were identified in silico; these conserved B cell epitopes may be candidates for the PPV7 vaccine or for the development of serological diagnostic methods.

Keywords: B cell and T cell epitopes; Cap; PPV7; evolution; vaccine.

Figure 1

Phylogenetic analysis of viruses in the Parvoviridae family. Trees were constructed based on the NS1 (A) and Cap (B) amino acid sequences by the neighbor joining (NJ) phylogenetic method, using the p-distance model with 1000 bootstrap replicates and bootstrap > 50%.

Figure 2

Maximum clade credibility (MCC) tree for the complete genome sequences of PPV7. The tree contained 2 major clades: Clade 1 (red) and Clade 2 (blue).

Figure 3

Sequence alignment of Ca²⁺ binding loop and putative secretory phospholipase A2 (PLA2) motif of PPV7. The conserved amino acids of the Ca²⁺ binding loop (²⁶⁷YXGXXG²⁷²) and the catalytic residues (³⁰⁰HDXXN³⁰⁴) are indicated at the bottom of the alignment.

Figure 4

Sequence alignment of predicted PPV7 and identified PPV1 linear B cell epitopes from Cap. Blue lines represent predicted PPV7 B cell epitopes and green lines represent identified PPV1 B cell epitopes.

Figure 5

Molecular interaction analysis of PPV7 peptides (shown as red) to SLA-2*0402 (A) and SLA-3*0401 (B) protein (shown as gray). Interacting residues are shown and are consistent with the information in Table 4.