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

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

doi:10.3390/vaccines9060608

Igor A D Paploski, Andrea Doeschl-Wilson + Show 9 more

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https://doi.org/10.3390/vaccines9060608

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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-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.

Highlights

Introduction published maps and institutional affilPorcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important pathogens affecting swine globally [1,2,3,4]
By applying a genetic clustering algorithm to more than 7000 orf5 porcine reproductive and respiratory syndrome virus type-2 (PRRSV) Lineage 1 sequences, we found that the best delineation of genetic diversity with Lineage 1 was achieved by grouping sequences into eight sub-lineages
While whole genome sequencing (WGS) data would unveil a broader perspective on PRRSV evolution, recent data has shown that sequences grouped together as sub-lineages in orf5 phylogenies largely remain grouped by WGS [48], suggesting that orf5-based lineage classification does reveal groups of viruses with shared ancestry

Summary

Introduction

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important pathogens affecting swine globally [1,2,3,4]. In the United States, the annual estimated economic losses due to PRRS are approximately USD 664 million [5], with economic losses stemming from reproductive failure, abortion, premature farrowing, increased rate of stillborn piglets [6], pre-weaning mortality as extreme as 70% among piglets [7], and losses in production parameters such as post-weaning mortality, daily gain, and feed conversion [8,9]. Up to 40% of the U.S breeding herd experience outbreaks annually [10], which exemplifies the widespread impact of this virus in the U.S. As demonstrated by the continued endemicity of PRRS in the U.S, efforts to control. Current PRRSV vaccines display varying protection against homologous and heterologous challenges [13,14,15,16], and the diversity of wild-type PRRSV iations.

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