Divergent Viruses Discovered in Swine Alter the Understanding of Evolutionary History and Genetic Diversity of the Respirovirus Genus and Related Porcine Parainfluenza Viruses

Abstract

Paramyxoviridae is a rapidly growing family of viruses, whose potential for cross-species transmission makes it difficult to predict the harm of newly emerging viruses to humans and animals. To better understand their diversity, evolutionary history, and co-evolution with their hosts, we analyzed a collection of porcine parainfluenza virus (PPIV) genomes to reconstruct the species classification basis and evolutionary history of the Respirovirus genus. We sequenced 17 complete genomes of porcine respirovirus 1 (also known as porcine parainfluenza virus 1; PPIV-1), thereby nearly tripling the number of currently available PPIV-1 genomes. We found that PPIV-1 was widely prevalent in China with two divergent lineages, PPIV-1a and PPIV-1b. We further provided evidence that a new species, porcine parainfluenza virus 2 (PPIV-2), had recently emerged in China. Our results pointed to a need for revising the current species demarcation criteria of the Respirovirus genus. In addition, we used PPIV-1 as an example to explore recombination and diversity of the Respirovirus genus. Interestingly, we only detected heterosubtypic recombination events between PPIV-1a and PPIV-1b with no intrasubtypic recombination events. The recombination hotspots highlighted a diverse geography-dependent genome structure of paramyxovirus infecting swine in China. Furthermore, we found no evidence of co-evolution between respirovirus and its host, indicating frequent cross-species transmission. In summary, our analyses showed that swine can be infected with a broad range of respiroviruses and recombination may serve as an important evolutionary mechanism for the Respirovirus genus' greater diversity in genome structure than previously anticipated. IMPORTANCE Livestock have emerged as critically underrecognized sources of paramyxovirus diversity, including pigs serving as the source of Nipah virus (NiV) and swine parainfluenza virus type 3, and goats and bovines harboring highly divergent viral lineages. Here, we identified a new species of Respirovirus genus named PPIV-2 in swine and proposed to revise the species demarcation criteria of the Respirovirus genus. We found heterosubtypic recombination events and high genetic diversity in PPIV-1. Further, we showed that genetic recombination may have occurred in the Respirovirus genus which may be associated with host range expansion. The continued expansion of Respirovirus genus diversity in livestock with relatively high human contact rates requires enhanced surveillance and ongoing evaluation of emerging cross-species transmission threats.

Keywords: divergent viruses discovered; genetic diversity; porcine parainfluenza virus 2.

FIG 1

Diversity of newly sequenced porcine paramyxovirus. (A) Provinces of the PPIV strains sequenced in this study. (B) Pairwise distance of the whole genomes of newly sequenced porcine paramyxovirus and available PPIV-1 sequences. We used SSE1.4 with a sliding window of 250 nucleotides, and a step size of 25 nucleotides to plot the pairwise distance. Different colored lines represent different groups. (C) The reconstructed maximum-likelihood phylogenetic tree based on the nucleotide sequences of L gene with HPIV-1 as the outer group. The unique branches formed by ZJ14 and ZJ19 are shown in blue green. (D) The reconstructed maximum-likelihood phylogeny of PPIV-1 whole genome, after removing ZJ14 and ZJ19. Strains in colored regions represent the different clades of PPIV-1. The red dots represent the strains sequenced in this study.

FIG 2

Genetic diversity and evolutionary history reconstruction of Respirovirus genus. (A) Maximum-likelihood phylogeny of Respirovirus genus based on the amino acid sequences of L gene. The number represents the branch length from the tip of the same species to their MRCA. The number between species represents the genetic distance (in average number of substitutions per site) between species. (B to D) Enlarged branches where PPIV-1, PPIV-2, CPIV-3, and BPIV-3 are located, and the number on each branch represents the branch length. (E) Time-calibrated phylogeny of the Respirovirus genus. Different colors represent different species.

FIG 3

Recombinant features of PPIV-1 phylogenies. (A to D) Maximum-likelihood phylogenetic trees inferred for different recombination regions. The red dots represent the strains sequenced here. The strains highlighted in blue green are recombinant strains. The colors on the branches represent different clades.

FIG 4

Maximum-likelihood phylogenetic trees of F and L genes, and analysis of amino acid differences. (A) Maximum-likelihood phylogeny and analysis amino acid difference of F gene. (B) Maximum-likelihood phylogeny and analysis amino acid difference of L gene. Branches of different colors represent different genotypes. The sequences obtained in this study are marked with red dots. The number represents the amino acid position in the protein, and the number highlighted in red represents the amino acid here that can be used to distinguish genotypes. Different countries are marked with different color blocks.

FIG 5

Events that may occur in evolution inferred by the eMPRess software package. The orange dot represents co-evolution, the blue-violet diamond represents duplication, the purple square represents host transfer, and the dashed line represents loss. In the tree, the number above each color block represents the number of occurrences in 100 randomizations, and as such represents the probability of occurrence of the event.