Emergence of a New Lineage 1C Variant of Porcine Reproductive and Respiratory Syndrome Virus 2 in the United States

Kikuti, Mariana; Paploski, Igor Adolfo Dexheimer; Pamornchainavakul, Nakarin; Picasso-Risso, Catalina; Schwartz, Mark; Yeske, Paul; Leuwerke, Brad; Bruner, Laura; Murray, Deborah; Roggow, Brian D.; Thomas, Pete; Feldmann, Lori; Allerson, Matt; Hensch, Melissa; Bauman, Tyler M.; Sexton, Brent; Rovira, Albert; VanderWaal, Kimberly; Corzo, Cesar

doi:10.3389/fvets.2021.752938

Cited by 29 publications

(39 citation statements)

References 19 publications

(22 reference statements)

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“…Case A : A 1700 breed‐to‐wean farm operating on a continuous breed‐farrow system, classified as Positive Stable (II‐A) for PRRSV according to the AASV scheme (Holtkamp et al., 2011 ), went through a PRRS rebreak with a Lineage 1A RFLP 1‐7‐4 PRRSV strain in October of 2020. Another introduction occurred in the same breed‐to‐wean farm in May 2021, with a strain sharing 99.4% with the PRRSV L1C variant strain (Kikuti et al., 2021 ; Trevisan et al., 2021a ) and 92.8% nucleotide identity with the farm's referent strain. The farm had no reported PRRSV MLV use prior to or after the October 2020 outbreak.…”

Section: Resultsmentioning

confidence: 99%

Implementing a user‐friendly format to analyze PRRSV next‐generation sequencing results and associating breeding herd production performance with number of PRRSV strains and recombination events

Trevisan

Zeller

et al. 2022

Transbounding Emerging Dis

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The open reading frames (ORF)5 represents approximately 4% of the porcine reproductive and respiratory syndrome virus (PRRSV)-2 genome (whole-PRRSV) and is often determined by the Sanger technique, which rarely detects >1 PRRSV strain if present in the sample. Next-generation sequencing (NGS) may provide a more appropriate method of detecting multiple PRRSV strains in one sample. This work assessed the effect of PRRSV genetic variability and recombination events, using NGS, on the time-to-low prevalence (TTLP) and total losses in breeding herds (n 20) that detected a PRRSV outbreak and adopted measures to eliminate PRRSV. Serum, lung or live virus inoculation material collected within 3-weeks of outbreak, and subsequently, processing fluids (PFs) were tested for PRRSV by RT-qPCR and NGS. Recovered whole-PRRSV or partial sequences were used to characterize within and between herd PRRSV genetic variability. Whole-PRRSV was recovered in five out of six (83.3%) lung, 16 out of 22 (72.73%) serum and in five out of 95 (5.26%) PF. Whole-PRRSV recovered from serum or lung were used as farm referent strains in 16 out of 20 (80%) farms.In four farms, only partial genome sequences were recovered and used as farm referent strains. At least two wild-type PRRSV strains (wt-PRRSV) were circulating simultaneously in 18 out of 20 (90%) and at least one vaccine-like strain co-circulating in eight out of 20 (40%) farms. PRRSV recombination events were detected in 12 farms (59%), been 10 out of 12 between wt-PRRSV and two out of 12 between wt-PRRSV and vaccine-like strains. Farms having ≥3 strains had a 12-week increase TTLP versus herds ≤2 strains detected. Farms with ≤2 strains (n 10) had 1837 and farms with no recombination events detected (n 8) had 1827 fewer piglet losses per 1000 sows versus farms with ≥3 PRRSV strains (n 8) or detected recombination (n 10), respectively. NGS outcomes and novel visualization methods provided more thorough insightThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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Section: Resultsmentioning

confidence: 99%

Implementing a user‐friendly format to analyze PRRSV next‐generation sequencing results and associating breeding herd production performance with number of PRRSV strains and recombination events

Trevisan

Zeller

et al. 2022

Transbounding Emerging Dis

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“…Potential N-glycosylation of nine residues was identified (residues 30,32,33,34,35,44,51, 57, and 59), with different combinations of glycosylated sites being prevalent over time (Figure 2A). Even though the glycosylation pattern of a sequence is not necessarily lineagedefining, the emergence of certain constellations of potential N-glycosylations coincides with past PRRSV epidemics in the U.S., as can be seen in Figure 3 for L1A, L1C, and L1H.…”

Section: Resultsmentioning

confidence: 99%

Potential Novel N-Glycosylation Patterns Associated with the Emergence of New Genetic Variants of PRRSV-2 in the U.S

et al. 2022

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Glycosylation of proteins is a post-translational process where oligosaccharides are attached to proteins, potentially altering their folding, epitope availability, and immune recognition. In Porcine reproductive and respiratory syndrome virus-type 2 (PRRSV-2), positive selection pressure acts on amino acid sites potentially associated with immune escape through glycan shielding. Here, we describe the patterns of potential N-glycosylation sites over time and across different phylogenetic lineages of PRRSV-2 to better understand how these may contribute to patterns of coexistence and emergence of different lineages. We screened 19,179 PRRSV GP5 sequences (2004–2021) in silico for potential N-glycosylated sites. The emergence of novel combinations of N-glycosylated sites coincided with past PRRSV epidemics in the U.S. For lineage L1A, glycosylation at residues 32, 33, 44, 51, and 57 first appeared in 2012, but represented >62% of all L1A sequences by 2015, coinciding with the emergence of the L1A 1-7-4 strain that increased in prevalence from 8 to 86% of all L1A sequences from 2012 to 2015. The L1C 1-4-4 strain that emerged in 2020 also had a distinct N-glycosylation pattern (residues 32, 33, 44, and 51). From 2020 to 2021, this pattern was responsible for 44–47% of the L1C sequences, contrasting to <5% in years prior. Our findings support the hypothesis that antigenic evolution contributes to the sequential dominance of different PRRSV strains and that N-glycosylation patterns may partially account for antigenic differences amongst strains. Further studies on glycosylation and its effect on PRRSV GP5 folding are needed to further understand how glycosylation patterns shape PRRSV occurrence.

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“…Viral strains associated with PRRS outbreaks were not assessed in this study. The new L1C 144 PRRS variant ( 15 ) only emerged as a significant health problem in late 2020 and remains restricted to one region of the U.S. Thus, we expect its effect in PRRS prevalence trends would be minimal in this study.…”

Section: Discussionmentioning

confidence: 89%

Porcine reproductive and respiratory syndrome prevalence and processing fluids use for diagnosis in United States breeding herds

et al. 2022

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IntroductionProcessing fluids have been recently adopted by the U.S. swine industry as a breeding herd PRRS monitoring tool due to their increased representativeness of animals within the herd. Here, we use the Morrison Swine Health Monitoring Project (MSHMP) database, representative of ~50% of the U.S. swine breeding herd, to describe processing fluids submissions for PRRS diagnosis and their relation to PRRS prevalence and time to stability over time between 2009 and 2020.MethodsAn ecological time series Poisson regression modeling the number of status 1 farms and weekly percentage of processing fluids submissions for PRRS diagnosis was done. Time to stability was calculated for sites that detected a PRRS outbreak within the study period and modeled through a proportional hazards mixed effect survival model using production system as a random-effect factor and epiweek as a panel variable.ResultsProcessing fluids diagnosis submissions increased starting in 2017. The difference between each year's highest and lowest weekly prevalence averaged 10.9% between 2009 and 2017, whereas it averaged 5.0% in 2018–2020 period. Each year's lowest weekly prevalence ranged from 11.3 to 19.5% in 2009–2017 and from 22.4 to 29.2% in 2018–2020. We also detected an increasing proportion of breeding sites that did not reach stability within 1 year of reporting an outbreak (chi-square for trend p < 0.0001). The total time to stability was not associated with the region of the country in which the site was located, the site’s air filtration status, its PRRS status before the outbreak, or the different statuses a site achieved to be classified as stable, when accounting for the production system in the multivariate model. However, a higher proportion of system-wide processing fluids use was associated with increased time to stability.DiscussionAltogether, the temporal concurrence of processing fluids used for PRRS virus monitoring suggests that the adoption of this sampling strategy may help explain the changes observed in PRRS status 1 prevalence since 2018, although further studies are still needed.

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Emergence of a New Lineage 1C Variant of Porcine Reproductive and Respiratory Syndrome Virus 2 in the United States

Cited by 29 publications

References 19 publications

Implementing a user‐friendly format to analyze PRRSV next‐generation sequencing results and associating breeding herd production performance with number of PRRSV strains and recombination events

Implementing a user‐friendly format to analyze PRRSV next‐generation sequencing results and associating breeding herd production performance with number of PRRSV strains and recombination events

Potential Novel N-Glycosylation Patterns Associated with the Emergence of New Genetic Variants of PRRSV-2 in the U.S

Porcine reproductive and respiratory syndrome prevalence and processing fluids use for diagnosis in United States breeding herds

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