Complete Genome and Recombination Analysis of a Novel Porcine Reproductive and Respiratory Syndrome Virus 2 (Variant 1H.18) Identified in the Midwestern USA

Abstract

Porcine Reproductive and Respiratory Syndrome Virus 2 (PRRSV-2) represents one of the greatest threats to global pork production. Increased incidence of a genetic variant of Porcine Reproductive and Respiratory Syndrome Virus (variant 1H.18) was recently reported in the Midwestern USA Sequence comparisons in the ORF5 region indicate that 1H.18 was closely related to both sub-lineages L1H and L1C. To expand our understanding and attempt to elucidate the origin of the 1H.18, we sequenced a near-complete genome, covering all coding regions, and investigated the occurrence of recombination events that may have contributed to the emergence of the new variant. At least six distinct recombination events were identified across the coding portion of the genome. Evidence of recombination in the ORF5 region between variants 1H.31 and 1C.3 was detected. Our results suggest a likely origin of 1H.18 driven by recombination.

Keywords: PRRSV-2; recombination; variant 1H.18; variant emergence.

Figure 1

Phylogenetic tree constructed by maximum likelihood using IQ-TREE2, with 1000 bootstrap replicates and the GTR+I+G4 substitution model. Colors indicate ORF5-based lineage assignments determined by PRRSLoom [6]. Isolate PQ252345 is indicated by a red star. (A) Whole-genome phylogenetic tree. (B) ORF5 phylogenetic tree.