Refining PRRSV-2 genetic classification based on global ORF5 sequences and investigation of their geographic distributions and temporal changes

Yim-im, Wannarat; Anderson, Tavis K.; Paploski, Igor A. D.; VanderWaal, Kimberly; Gauger, Phillip; Krueger, Karen; Shi, Mang; Main, Rodger; Zhang, Jianqiang

doi:10.1128/spectrum.02916-23

Cited by 19 publications

(17 citation statements)

References 67 publications

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“…c) A priori defined outbreak variant: Since 2020, the swine industry in the Midwestern U.S. has witnessed large-scale spread of a novel PRRSV-2 variant, denoted as either L1C.5 or alternatively L1C-1-4-4 variant based on its sub-lineage and RFLP pattern (15, 23). A previous study used the inclusion criteria of >98% nucleotide identity to any of other sequences to define this clade.…”

Section: Methodsmentioning

confidence: 99%

“…Thus, relying on universal classifications assures standardization between different users. Currently, the naming method used by the industry to discriminate between sequences is RFLP-typing (Restriction Fragment Length Polymorphisms), sometimes in combination with an additional label corresponding to phylogenetic lineage (3, 14, 15, 23, 24). However, using RFLP-types to refer to PRRSV-2 viruses often leads to misleading or even erroneous conclusions (e.g., viruses assigned to the same RFLP-type often are not closely related, and vice versa)(15, 25).…”

Section: Introductionmentioning

confidence: 99%

“…However, using RFLP-types to refer to PRRSV-2 viruses often leads to misleading or even erroneous conclusions (e.g., viruses assigned to the same RFLP-type often are not closely related, and vice versa)(15, 25). Moreover, only 6 sub-lineages are currently prevalent in the U.S. (at least 5% of detected sequences from 2019-23, (26)), each typically having a mean genetic distance of <8.5% (but occasionally higher than 10%) for sequences belonging to the sub-lineage (23), making these classifications too coarse for on-farm disease monitoring and decision-making.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility

VanderWaal,

Pamornchainvakul,

Kikuti

et al. 2024

Preprint

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Disease management and epidemiological investigations of porcine reproductive and respiratory syndrome virus-type 2 (PRRSV-2) often rely on grouping together highly related sequences. In the USA, the last five years have seen a major paradigm shift within the swine industry when classifying PRRSV-2, beginning to move away from RFLP (restriction fragment length polymorphisms)-typing and adopting the use of phylogenetic lineage-based classification. However, lineages and sub-lineages are large and genetically diverse, and the rapid mutation rate of PRRSV coupled with the global prevalence of the disease has made it challenging to identify new and emerging variants. Thus, within the lineage system, a dynamic fine-scale classification scheme is needed to provide better resolution on the relatedness of PRRSV-2 viruses to inform disease management and monitoring efforts and facilitate research and communication surrounding circulating PRRSV viruses. Here, we compare potential fine-scale systems for classifying PRRSV-2 variants (i.e., genetic clusters of closely related ORF5 sequences at finer scales than sub-lineage) using a database of 28,730 sequences from 2010 to 2021, representing >55% of the U.S. pig population. In total, we compared 140 approaches that differed in their tree-building method, criteria, and thresholds for defining variants within phylogenetic trees using TreeCluster. Three approaches produced epidemiologically meaningful variants (i.e., ≥5 sequences per cluster), and resulted in reproducible and robust outputs even when the input data or input phylogenies were changed. In the three best performing approaches, the average genetic distance amongst sequences belonging to the same variant was 2.1-2.5%, and the genetic divergence between variants was 2.5-2.7%. Machine learning classification algorithms were also trained to assign new sequences to an existing variant with >95% accuracy, which shows that newly generated sequences could be assigned without repeating the phylogenetic and clustering analyses. Finally, we identified 73 sequence-clusters (dated <1 year apart with close phylogenetic relatedness) associated with circulation events on single farms. The percent of farm sequence-clusters with an ID change was 6.5-8.7% for our best approaches. In contrast, ~43% of farm sequence-clusters had variation in their RFLP-type, further demonstrating how our proposed fine-scale classification system addresses shortcomings of RFLP-typing. Through identifying robust and reproducible classification approaches for PRRSV-2, this work lays the foundation for a fine-scale system that would more reliably group related field viruses and provide better improved clarity for decision-making surrounding disease management.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility

VanderWaal,

Pamornchainvakul,

Kikuti

et al. 2024

Preprint

Self Cite

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“…ORF2a, ORF2b, ORF3-5, ORF5a, ORF6, and ORF7 encode eight viral structural proteins (Pujhari and Zakhartchouk., 2016;Liu et al, 2019). Notably, ORF5 has been extensively used in molecular epidemiologic research, as well as for the classification of PRRSV field strains due to its marked genetic variation (Larochelle et al, 2003;Zhu et al, 2021;Yim-Im et al, 2023). Owing to this genetic divergence, PRRSV was divided into two primary genotypesgenotypes 1 and 2, recognized as the European type and the North American type, respectively (Bálint et al, 2021;Wang et al, 2021).…”

Section: Open Access Edited Bymentioning

confidence: 99%

Development and biological characterization of an infectious cDNA clone of NADC34-like PRRSV

Lin,

Zhou,

Xiao

et al. 2024

Front. Microbiol.

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IntroductionPorcine Reproductive and Respiratory Syndrome virus (PRRSV) causes high abortion rates in gestating sows and stillbirths, as well as high piglet mortality, seriously jeopardizing the pig industry in China and worldwide.MethodsIn this study, an infectious clone containing the full-length genome of NADC34-like PRRSV was constructed for the first time using reverse genetic techniques. The gene was amplified segmentally onto a plasmid, transfected into BHK-21 cells, and the transfected supernatant was harvested and transfected into PAM cells, which showed classical cytopathic effects (CPE).ResultsThe virus rJS-KS/2021 was successfully rescued which could be demonstrated by Western Blot and indirect immunofluorescence assays. Its growth curve was similar to the original strain. Replace the 5’UTR and 3’UTR of rJS-KS/2021 with 5’UTR and 3’UTR of HP-PRRSV (strain SH1) also failed to propagate on MARC-145.DiscussionIn this study, an infectious clone of NADC34-like was constructed by reverse genetics, replacing the UTR and changing the cellular tropism of the virus. These findings provide a solid foundation for studying the recombination of different PRRSVs and the adaption of PRRSVs on MARC-145 in the future.

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“…Porcine reproductive and respiratory syndrome virus (PRRSV), belonging to the family Arteriviridae, is an enveloped, positive, single-stranded RNA virus [1][2][3]. As the causative agent of porcine reproductive and respiratory syndrome (PRRS), PRRSV is notorious for causing reproductive failures in sows and severe respiratory symptoms in pigs of all ages [4][5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Innate Immune Evasion of PRRSV nsp11 through Degradation of the HDAC2 by Its Endoribonuclease Activity

Zhang,

Chen,

et al. 2024

Viruses

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Porcine reproductive and respiratory syndrome virus (PRRSV), a member of the Arteriviridae family, represents a persistent menace to the global pig industry, causing reproductive failure and respiratory disease in pigs. In this study, we delved into the role of histone deacetylases (HDAC2) during PRRSV infection. Our findings revealed that HDAC2 expression is downregulated upon PRRSV infection. Notably, suppressing HDAC2 activity through specific small interfering RNA led to an increase in virus production, whereas overexpressing HDAC2 effectively inhibited PRRSV replication by boosting the expression of IFN-regulated antiviral molecules. Furthermore, we identified the virus’s nonstructural protein 11 (nsp11) as a key player in reducing HDAC2 levels. Mutagenic analyses of PRRSV nsp11 revealed that its antagonistic effect on the antiviral activity of HDAC2 is dependent on its endonuclease activity. In summary, our research uncovered a novel immune evasion mechanism employed by PRRSV, providing crucial insights into the pathogenesis of this virus and guiding the development of innovative prevention strategies against PRRSV infection.

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Refining PRRSV-2 genetic classification based on global ORF5 sequences and investigation of their geographic distributions and temporal changes

Cited by 19 publications

References 67 publications

Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility

Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility

Development and biological characterization of an infectious cDNA clone of NADC34-like PRRSV

Innate Immune Evasion of PRRSV nsp11 through Degradation of the HDAC2 by Its Endoribonuclease Activity

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