Phylogenetic Structure and Sequential Dominance of Sub-Lineages of PRRSV Type-2 Lineage 1 in the United States

• Published in: Vaccines (Basel) 2021-06, Vol.9 (6), p.608
• Main Authors: Paploski, Igor A D, Pamornchainavakul, Nakarin, Makau, Dennis N, Rovira, Albert, Corzo, Cesar A, Schroeder, Declan C, Cheeran, Maxim C-J, Doeschl-Wilson, Andrea, Kao, Rowland R, Lycett, Samantha, VanderWaal, Kimberly
• Format: Article
• Language: English
• Subjects: Amino acids; Animal diseases; Animals; Antigens; Autosomal dominant inheritance; Bayesian analysis; Bioinformatics; Classification; Datasets; Discriminant analysis; Epidemics; Evolution; Genetic diversity; Genetic variance; Genomes; Hogs; Mathematical models; Mortality; mutations; phylogenetic analysis; Phylogenetics; Phylogeny; Population; Population number; porcine reproductive and respiratory syndrome virus; principal component analyses; Principal components analysis; Vaccines; viral population dynamics; Viruses; Weaning; whole genome
• ISSN: 2076-393X; 2076-393X
• DOI: 10.3390/vaccines9060608

The genetic diversity and frequent emergence of novel genetic variants of porcine reproductive and respiratory syndrome virus type-2 (PRRSV) hinders control efforts, yet drivers of macro-evolutionary patterns of PRRSV remain poorly documented. Utilizing a comprehensive database of >20,000 sequences, our objective was to classify variants according to the phylogenetic structure of PRRSV co-circulating in the U.S., quantify evolutionary dynamics of sub-lineage emergence, and describe potential antigenic differences among sub-lineages. We subdivided the most prevalent lineage (Lineage 1, accounting for approximately 60% of available sequences) into eight sub-lineages. Bayesian coalescent SkyGrid models were used to estimate each sub-lineage's effective population size over time. We show that a new sub-lineage emerged every 1 to 4 years and that the time between emergence and peak population size was 4.5 years on average (range: 2-8 years). A pattern of sequential dominance of different sub-lineages was identified, with a new dominant sub-lineage replacing its predecessor approximately every 3 years. Consensus amino acid sequences for each sub-lineage differed in key GP5 sites related to host immunity, suggesting that sub-lineage turnover may be linked to immune-mediated competition. This has important implications for understanding drivers of genetic diversity and emergence of new PRRSV variants in the U.S.