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      Full genome sequence analysis of a 1-7-4-like PRRSV strain in Fujian Province, China

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          Abstract

          PRRS virus (PRRSV) has undergone rapid evolution and resulted in immense economic losses worldwide. In the present study, a PRRSV strain named FJ0908 causing high abortion rate (25%) and mortality (40%) was detected in a swine herd in China. To determine if a new PRRSV genotype had emerged, we characterized the genetic characteristics of FJ0908. Phylogenetic analysis indicated that FJ0908 was related to 1-7-4-like strains circulating in the United States since 2014. Furthermore, the ORF5 sequence restriction fragment length polymorphism (RFLP) pattern of FJ0908 was 1-7-4. Additionally, FJ0908 had a 100 aa deletion (aa329–428) within nsp2, as compared to VR-2332, and the deletion pattern was consistent with most of 1-7-4 PRRSVs. Collectively, the data of this study contribute to the understanding of 1-7-4-like PRRSV molecular epidemiology in China.

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          Assessment of the economic impact of porcine reproductive and respiratory syndrome on swine production in the United States.

          Eric Neumann, James Kliebenstein, Colin Johnson … (2005)
          To estimate the annual cost of infections attributable to porcine reproductive and respiratory syndrome (PRRS) virus to US swine producers. Economic analysis. Data on the health and productivity of PRRS-affected and PRRS-unaffected breeding herds and growing-pig populations were collected from a convenience sample of swine farms in the midwestern United States. Health and productivity variables of PRRS-affected and PRRS-unaffected swine farms were analyzed to estimate the impact of PRRS on specific farms. National estimates of PRRS incidence were then used to determine the annual economic impact of PRRS on US swine producers. PRRS affected breeding herds and growing-pig populations as measured by a decrease in reproductive health, an increase in deaths, and reductions in the rate and efficiency of growth. Total annual economic impact of these effects on US swine producers was estimated at dollar 66.75 million in breeding herds and dollar 493.57 million in growing-pig populations. PRRS imposes a substantial financial burden on US swine producers and causes approximately dollar 560.32 million in losses each year. By comparison, prior to eradication, annual losses attributable to classical swine fever (hog cholera) and pseudorabies were estimated at dollar 364.09 million and dollar 36.27 million, respectively (adjusted on the basis of year 2004 dollars). Current PRRS control strategies are not predictably successful; thus, PRRS-associated losses will continue into the future. Research to improve our understanding of ecologic and epidemiologic characteristics of the PRRS virus and technologic advances (vaccines and diagnostic tests) to prevent clinical effects are warranted.
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            The PRRSV replicase: Exploring the multifunctionality of an intriguing set of nonstructural proteins

            Ying Fang, Eric Snijder (2010)
            Our knowledge about the structure and function of the nonstructural proteins (nsps) encoded by the arterivirus replicase gene has advanced in recent years. The continued characterization of the nsps of the arterivirus prototype equine arteritis virus has not only corroborated several important functional predictions, but also revealed various novel features of arteriviral replication. For porcine reproductive and respiratory syndrome virus (PRRSV), based on bioinformatics predictions and experimental studies, a processing map for the pp1a and pp1ab replicase polyproteins has been developed. Crystal structures have been resolved for two of the PRRSV nonstructural proteins that possess proteinase activity (nsp1α and nsp4). The functional characterization of the key enzymes for arterivirus RNA synthesis, the nsp9 RNA polymerase and nsp10 helicase, has been initiated. In addition, progress has been made on nsp functions relating to the regulation of subgenomic mRNAs synthesis (nsp1), the induction of replication-associated membrane rearrangements (nsp2 and nsp3), and an intriguing replicative endoribonuclease (nsp11) for which the natural substrate remains to be identified. The role of nsps in viral pathogenesis and host immunity is also being explored, and specific nsps (including nsp1α/β, nsp2, nsp4, nsp7, and nsp11) have been implicated in the modulation of host immune responses to PRRSV infection. The nsp3–8 region was identified as containing major virulence factors, although mechanistic information is scarce. The biological significance of PRRSV nsps in virus-host interactions and the technical advancements in engineering the PRRSV genome by reverse genetics are also reflected in recent developments in the area of vaccines and diagnostic assays.
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              Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses.

              Chung-Chau Hon, G. Davies, Li Li … (2010)
              Type 2 (or North American-like) porcine reproductive and respiratory syndrome virus (PRRSV) was first recorded in 1987 in the United States and now occurs in most commercial swine industries throughout the world. In this study, we investigated the epidemiological and evolutionary behaviors of type 2 PRRSV. Based on phylogenetic analyses of 8,624 ORF5 sequences, we described a comprehensive picture of the diversity of type 2 PRRSVs and systematically classified all available sequences into lineages and sublineages, including a number of previously undescribed lineages. With the rapid growth of sequence deposition into the databases, it would be technically difficult for veterinary researchers to genotype their sequences by reanalyzing all sequences in the databases. To this end, a set of reference sequences was established based on our classification system, which represents the principal diversity of all available sequences and can readily be used for further genotyping studies. In addition, we further investigated the demographic histories of these lineages and sublineages by using Bayesian coalescence analyses, providing evolutionary insights into several important epidemiological events of type 2 PRRSV. Moreover, by using a phylogeographic approach, we were able to estimate the transmission frequencies between the pig-producing states in the United States and identified several states as the major sources of viral spread, i.e., "transmission centers." In summary, this study represents the most extensive phylogenetic analyses of type 2 PRRSV to date, providing a basis for future genotyping studies and dissecting the epidemiology of type 2 PRRSV from phylogenetic perspectives.
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                Author and article information

                Contributors
                Jiankui Liu
                Chunhua Wei
                Journal
                Journal ID (nlm-ta): PeerJ
                Journal ID (iso-abbrev): PeerJ
                Journal ID (publisher-id): peerj
                Journal ID (pmc): peerj
                Title: PeerJ
                Publisher: PeerJ Inc. (San Diego, USA )
                ISSN (Electronic): 2167-8359
                Publication date (Electronic): 16 October 2019
                Publication date Collection: 2019
                Volume: 7
                Electronic Location Identifier: e7859
                Affiliations
                [1 ]College of Life Sciences, Longyan University , Longyan, China
                [2 ]Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University , Longyan, China
                [3 ]College of Animal Science, Fujian Agriculture and Forestry University , Fuzhou, China
                Article
                Publisher ID: 7859
                DOI: 10.7717/peerj.7859
                PMC ID: 6800524
                PubMed ID: 31637126
                SO-VID: e105c26f-3e18-43ab-ad61-c2a1fba5c11c
                Copyright © ©2019 Liu et al.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                Date received : 11 February 2019
                Date accepted : 9 September 2019
                Funding
                Funded by: Leading Project Foundation of Science Department of Fujian Province
                Award ID: 2018N0022
                Funded by: Major Project of Science and Technology Program of Fujian Province, China
                Award ID: 2019NZ09005
                Funded by: Fujian Natural Science Foundation, Fujian Province, China
                Award ID: 2016J01168
                This study was supported by the Leading Project Foundation of Science Department of Fujian Province (2018N0022), the Major Project of Science and Technology Program of Fujian Province, China (2019NZ09005) and the Fujian Natural Science Foundation, Fujian Province, China (2016J01168). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Bioinformatics
                Subject: Genomics
                Subject: Veterinary Medicine
                Subject: Virology

                Keywords: prrsv,genome sequence,1-7-4,molecular characteristic
                Data availability:
                Keywords: prrsv, genome sequence, 1-7-4, molecular characteristic

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