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Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant

While the widespread and endemic circulation of porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) causes persistent economic losses to the U.S. swine industry, unusual increases of severe cases associated with the emergence of new genetic variants are a major source of concern for...

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Autores principales: Pamornchainavakul, Nakarin, Kikuti, Mariana, Paploski, Igor A. D., Makau, Dennis N., Rovira, Albert, Corzo, Cesar A., VanderWaal, Kimberly
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8990846/
https://www.ncbi.nlm.nih.gov/pubmed/35400102
http://dx.doi.org/10.3389/fvets.2022.846904
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author Pamornchainavakul, Nakarin
Kikuti, Mariana
Paploski, Igor A. D.
Makau, Dennis N.
Rovira, Albert
Corzo, Cesar A.
VanderWaal, Kimberly
author_facet Pamornchainavakul, Nakarin
Kikuti, Mariana
Paploski, Igor A. D.
Makau, Dennis N.
Rovira, Albert
Corzo, Cesar A.
VanderWaal, Kimberly
author_sort Pamornchainavakul, Nakarin
collection PubMed
description While the widespread and endemic circulation of porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) causes persistent economic losses to the U.S. swine industry, unusual increases of severe cases associated with the emergence of new genetic variants are a major source of concern for pork producers. Between 2020 and 2021, such an event occurred across pig production sites in the Midwestern U.S. The emerging viral clade is referred to as the novel sub-lineage 1C (L1C) 1-4-4 variant. This genetic classification is based on the open reading frame 5 (ORF5) gene. However, although whole genome sequence (WGS) suggested that this variant represented the emergence of a new strain, the true evolutionary history of this variant remains unclear. To better elucidate the variant's evolutionary history, we conducted a recombination detection analysis, time-scaled phylogenetic estimation, and discrete trait analysis on a set of L1C-1-4-4 WGSs (n = 19) alongside other publicly published WGSs (n = 232) collected over a 26-year period (1995–2021). Results from various methodologies consistently suggest that the novel L1C variant was a descendant of a recombinant ancestor characterized by recombination at the ORF1a gene between two segments that would be otherwise classified as L1C and L1A in the ORF5 gene. Based on analysis of different WGS fragments, the L1C-1-4-4 variant descended from an ancestor that existed around late 2018 to early 2019, with relatively high substitution rates in the proximal ORF1a as well as ORF5 regions. Two viruses from 2018 were found to be the closest relatives to the 2020-21 outbreak strain but had different recombination profiles, suggesting that these viruses were not direct ancestors. We also assessed the overall frequency of putative recombination amongst ORF5 and other parts of the genome and found that recombination events which leave detectable numbers of descendants are not common. However, the rapid spread and high virulence of the L1C-1-4-4 recombinant variant demonstrates that inter-sub-lineage recombination occasionally found amongst the U.S. PRRSV-2 might be an evolutionary mechanisms that contributed to this emergence. More generally, recombination amongst PRRSV-2 accelerates genetic change and increases the chance of the emergence of high fitness variants.
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spelling pubmed-89908462022-04-09 Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant Pamornchainavakul, Nakarin Kikuti, Mariana Paploski, Igor A. D. Makau, Dennis N. Rovira, Albert Corzo, Cesar A. VanderWaal, Kimberly Front Vet Sci Veterinary Science While the widespread and endemic circulation of porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) causes persistent economic losses to the U.S. swine industry, unusual increases of severe cases associated with the emergence of new genetic variants are a major source of concern for pork producers. Between 2020 and 2021, such an event occurred across pig production sites in the Midwestern U.S. The emerging viral clade is referred to as the novel sub-lineage 1C (L1C) 1-4-4 variant. This genetic classification is based on the open reading frame 5 (ORF5) gene. However, although whole genome sequence (WGS) suggested that this variant represented the emergence of a new strain, the true evolutionary history of this variant remains unclear. To better elucidate the variant's evolutionary history, we conducted a recombination detection analysis, time-scaled phylogenetic estimation, and discrete trait analysis on a set of L1C-1-4-4 WGSs (n = 19) alongside other publicly published WGSs (n = 232) collected over a 26-year period (1995–2021). Results from various methodologies consistently suggest that the novel L1C variant was a descendant of a recombinant ancestor characterized by recombination at the ORF1a gene between two segments that would be otherwise classified as L1C and L1A in the ORF5 gene. Based on analysis of different WGS fragments, the L1C-1-4-4 variant descended from an ancestor that existed around late 2018 to early 2019, with relatively high substitution rates in the proximal ORF1a as well as ORF5 regions. Two viruses from 2018 were found to be the closest relatives to the 2020-21 outbreak strain but had different recombination profiles, suggesting that these viruses were not direct ancestors. We also assessed the overall frequency of putative recombination amongst ORF5 and other parts of the genome and found that recombination events which leave detectable numbers of descendants are not common. However, the rapid spread and high virulence of the L1C-1-4-4 recombinant variant demonstrates that inter-sub-lineage recombination occasionally found amongst the U.S. PRRSV-2 might be an evolutionary mechanisms that contributed to this emergence. More generally, recombination amongst PRRSV-2 accelerates genetic change and increases the chance of the emergence of high fitness variants. Frontiers Media S.A. 2022-03-25 /pmc/articles/PMC8990846/ /pubmed/35400102 http://dx.doi.org/10.3389/fvets.2022.846904 Text en Copyright © 2022 Pamornchainavakul, Kikuti, Paploski, Makau, Rovira, Corzo and VanderWaal. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Veterinary Science
Pamornchainavakul, Nakarin
Kikuti, Mariana
Paploski, Igor A. D.
Makau, Dennis N.
Rovira, Albert
Corzo, Cesar A.
VanderWaal, Kimberly
Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant
title Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant
title_full Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant
title_fullStr Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant
title_full_unstemmed Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant
title_short Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant
title_sort measuring how recombination re-shapes the evolutionary history of prrsv-2: a genome-based phylodynamic analysis of the emergence of a novel prrsv-2 variant
topic Veterinary Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8990846/
https://www.ncbi.nlm.nih.gov/pubmed/35400102
http://dx.doi.org/10.3389/fvets.2022.846904
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