Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant

Abstract

While the widespread and endemic circulation of porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) causes persistent economic losses to the U.S. swine industry, unusual increases of severe cases associated with the emergence of new genetic variants are a major source of concern for pork producers. Between 2020 and 2021, such an event occurred across pig production sites in the Midwestern U.S. The emerging viral clade is referred to as the novel sub-lineage 1C (L1C) 1-4-4 variant. This genetic classification is based on the open reading frame 5 (ORF5) gene. However, although whole genome sequence (WGS) suggested that this variant represented the emergence of a new strain, the true evolutionary history of this variant remains unclear. To better elucidate the variant's evolutionary history, we conducted a recombination detection analysis, time-scaled phylogenetic estimation, and discrete trait analysis on a set of L1C-1-4-4 WGSs (n = 19) alongside other publicly published WGSs (n = 232) collected over a 26-year period (1995-2021). Results from various methodologies consistently suggest that the novel L1C variant was a descendant of a recombinant ancestor characterized by recombination at the ORF1a gene between two segments that would be otherwise classified as L1C and L1A in the ORF5 gene. Based on analysis of different WGS fragments, the L1C-1-4-4 variant descended from an ancestor that existed around late 2018 to early 2019, with relatively high substitution rates in the proximal ORF1a as well as ORF5 regions. Two viruses from 2018 were found to be the closest relatives to the 2020-21 outbreak strain but had different recombination profiles, suggesting that these viruses were not direct ancestors. We also assessed the overall frequency of putative recombination amongst ORF5 and other parts of the genome and found that recombination events which leave detectable numbers of descendants are not common. However, the rapid spread and high virulence of the L1C-1-4-4 recombinant variant demonstrates that inter-sub-lineage recombination occasionally found amongst the U.S. PRRSV-2 might be an evolutionary mechanisms that contributed to this emergence. More generally, recombination amongst PRRSV-2 accelerates genetic change and increases the chance of the emergence of high fitness variants.

Keywords: epidemics; porcine reproductive and respiratory syndrome virus 2; variant emergence; viral recombination; whole genome sequencing.

Figure 1

Recombination profile of the novel L1C-1-4-4 viruses in relation to PRRSV-2 genomic organization. (A) PRRSV-2 genomic organization. (B) Putative recombinant regions and minor parents of the 2020–21 (n = 18) and the 2018 (n = 1) L1C-1-4-4 variants. The long bar across the top represents the viral genomic backbone. The smaller bars below represent putative minor parents labeled according to the ORF5-based sub-lineages. (C) Recombination breakpoint distribution of the novel L1C-1-4-4 WGSs as queries against other PRRSV-2 WGSs. (D) Overall recombination breakpoint distribution of the 251 PRRSV-2 WGSs. Recombination hotspots defined by the local density plot are highlighted in red. (E) Genomic fragments with low within-fragment recombination rates used for phylogenetic analyses. Nucleotide positions in the alignment are shown in the parenthesis.

Figure 2

Discrete trait analysis of PRRSV-2 lineage/sub-lineage recombination. (A) Heat map showing number of potential ancestral recombination between lineages/sub-lineages of each genomic fragment estimated from the trait transitions. Cell border thickness represents Bayes factor (BF) support for each recombination. (B) Bayesian MCC trees colored by ancestral ORF5-based lineage or sub-lineage. Asterisks locate the phylogenetic position of taxa of interest.