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

Igor A. D. Paploski, Nakarin Pamornchainavakul, Dennis N. Makau, Albert Rovira, Cesar A. Corzo, Declan C. Schroeder, Maxim C-J Cheeran, Andrea Doeschl-Wilson, Rowland R. Kao, Samantha Lycett, Kimberly VanderWaal*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

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 orf5 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-lineageemergence, 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.
Original languageEnglish
Article number608
JournalVaccines
Volume9
Issue number6
DOIs
Publication statusPublished - 5 Jun 2021

Keywords

  • PHYLOGENETIC DIVERSITY

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