Identification of a natural human serotype 3 parainfluenza virus

Abstract

Parainfluenza virus is an important pathogen threatening the health of animals and human, which brings human many kinds of disease, especially lower respiratory tract infection involving infants and young children. In order to control the virus, it is necessary to fully understand the molecular basis resulting in the genetic diversity of the virus. Homologous recombination is one of mechanisms for the rapid change of genetic diversity. However, as a negative-strand virus, it is unknown whether the recombination can naturally take place in human PIV. In this study, we isolated and identified a mosaic serotype 3 human PIV (HPIV3) from in China, and also provided several putative PIV mosaics from previous reports to reveal that the recombination can naturally occur in the virus. In addition, two swine PIV3 isolates transferred from cattle to pigs were found to have mosaic genomes. These results suggest that homologous recombination can promote the genetic diversity and potentially bring some novel biologic characteristics of HPIV.

Figure 1

(A, B) Results of Similarity and BootScanning analysis of the genome of LZ22_FJ455842. The y-axis in Similarity plot (A) gives the percentage of sequence identity within a sliding window of 400 bp wide centered on the position plotted, with a step size between plots of 20 bp, while in BootScanning plot (B) represents the percentage of permuted trees. The χ2 of maximization and P value of Fisher's Exact test are shown near (or on) the vertical line. GP and ZHYMgz01 are used as two parental lineage sequences and JS_U51116 an outgroup sequence. The breakpoint is identified and located at position 485, with χ² value maximized. The query sequence LZ22_FJ455842 demonstrates greater sequence identity and BootScanning support with GP in the beginning region while otherwise with ZHYMgz01_EU326526 in the complementary regions.

Figure 2

Phylogenetic profiles of separate regions of LZ22_FJ455842 partitioned by cross-over events. The scale corresponds to the number of nucleotide substitutions per site. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches (only N > 70% is shown). The putative recombinants were showed with "black square". The putative parent lineages were marked with "black triangle". (A) and (B) respectively represent the phylogeny of pre- (1-485) and post- (486-15536) part of complete segments delimited by the breakpoint. The pre-part of mosaics demonstrated higher level of congruence with the GP lineage, while the post-part converge with ZHYMgz01_EU326526.