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Yim-im W, Anderson TK, Paploski IAD, VanderWaal K, Gauger P, Krueger K, Shi M, Main R, Zhang J. Refining PRRSV-2 genetic classification based on global ORF5 sequences and investigation of their geographic distributions and temporal changes. Microbiol Spectr 2023; 11:e0291623. [PMID: 37933982 PMCID: PMC10848785 DOI: 10.1128/spectrum.02916-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/01/2023] [Indexed: 11/08/2023] Open
Abstract
IMPORTANCE In this study, comprehensive analysis of 82,237 global porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) open reading frame 5 sequences spanning from 1989 to 2021 refined PRRSV-2 genetic classification system, which defines 11 lineages and 21 sublineages and provides flexibility for growth if additional lineages, sublineages, or more granular classifications are needed in the future. Geographic distribution and temporal changes of PRRSV-2 were investigated in detail. This is a thorough study describing the molecular epidemiology of global PRRSV-2. In addition, the reference sequences based on the refined genetic classification system are made available to the public for future epidemiological and diagnostic applications worldwide. The data from this study will facilitate global standardization and application of PRRSV-2 genetic classification.
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Affiliation(s)
- Wannarat Yim-im
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Tavis K. Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | - Igor A. D. Paploski
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Phillip Gauger
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Karen Krueger
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Mang Shi
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Rodger Main
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Jianqiang Zhang
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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Wallace ZS, Davis J, Niewiadomska AM, Olson RD, Shukla M, Stevens R, Zhang Y, Zmasek CM, Scheuermann RH. Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation. FRONTIERS IN BIOINFORMATICS 2022; 2:1020189. [PMCID: PMC9638046 DOI: 10.3389/fbinf.2022.1020189] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022] Open
Abstract
Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has demonstrated its ability to rapidly and continuously evolve, leading to the emergence of thousands of different sequence variants, many with distinctive phenotypic properties. Fortunately, the broad application of next generation sequencing (NGS) across the globe has produced a wealth of SARS-CoV-2 genome sequences, offering a comprehensive picture of how this virus is evolving so that accurate diagnostics, reliable therapeutics, and prophylactic vaccines against COVID-19 can be developed and maintained. The millions of SARS-CoV-2 sequences deposited into genomic sequencing databases, including GenBank, BV-BRC, and GISAID, are annotated with the dates and geographic locations of sample collection, and can be aligned to and compared with the Wuhan-Hu-1 reference genome to extract their constellation of nucleotide and amino acid substitutions. By aggregating these data into concise datasets, the spread of variants through space and time can be assessed. Variant tracking efforts have initially focused on the Spike protein due to its critical role in viral tropism and antibody neutralization. To identify emerging variants of concern as early as possible, we developed a computational pipeline to process the genomic data and assign risk scores based on both epidemiological and functional parameters. Epidemiological dynamics are used to identify variants exhibiting substantial growth over time and spread across geographical regions. Experimental data that quantify Spike protein regions targeted by adaptive immunity and critical for other virus characteristics are used to predict variants with consequential immunogenic and pathogenic impacts. The growth assessment and functional impact scores are combined to produce a Composite Score for any set of Spike substitutions detected. With this systematic method to routinely score and rank emerging variants, we have established an approach to identify threatening variants early and prioritize them for experimental evaluation.
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Affiliation(s)
- Zachary S. Wallace
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States
| | - James Davis
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, United States
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | | | - Robert D. Olson
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, United States
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | - Maulik Shukla
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, United States
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | - Rick Stevens
- Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, United States
- Department of Computer Science, University of Chicago, Chicago, IL, United States
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Christian M. Zmasek
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Richard H. Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
- Global Virus Network, Baltimore, MD, United States
- *Correspondence: Richard H. Scheuermann,
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Hoffman KS, Humphrey NL, Korslund JA, Anderson TK, Faaberg KS, Lager KM, Buckley AC. Characterization of Senecavirus A Isolates Collected From the Environment of U.S. Sow Slaughter Plants. Front Vet Sci 2022; 9:923878. [PMID: 35812884 PMCID: PMC9257094 DOI: 10.3389/fvets.2022.923878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Vesicular disease caused by Senecavirus A (SVA) is clinically indistinguishable from foot-and-mouth disease (FMD) and other vesicular diseases of swine. When a vesicle is observed in FMD-free countries, a costly and time-consuming foreign animal disease investigation (FADI) is performed to rule out FMD. Recently, there has been an increase in the number of FADIs and SVA positive samples at slaughter plants in the U.S. The objectives of this investigation were to: (1) describe the environmental burden of SVA in sow slaughter plants; (2) determine whether there was a correlation between PCR diagnostics, virus isolation (VI), and swine bioassay results; and (3) phylogenetically characterize the genetic diversity of contemporary SVA isolates. Environmental swabs were collected from three sow slaughter plants (Plants 1-3) and one market-weight slaughter plant (Plant 4) between June to December 2020. Of the 426 samples taken from Plants 1-3, 304 samples were PCR positive and 107 were VI positive. There was no detection of SVA by PCR or VI at Plant 4. SVA positive samples were most frequently found in the summer (78.3% June-September, vs. 59.4% October-December), with a peak at 85% in August. Eighteen PCR positive environmental samples with a range of Ct values were selected for a swine bioassay: a single sample infected piglets (n = 2). A random subset of the PCR positive samples was sequenced; and phylogenetic analysis demonstrated co-circulation and divergence of two genetically distinct groups of SVA. These data demonstrate that SVA was frequently found in the environment of sow slaughter plants, but environmental persistence and diagnostic detection was not indicative of whether a sampled was infectious to swine. Consequently, a more detailed understanding of the epidemiology of SVA and its environmental persistence in the marketing chain is necessary to reduce the number of FADIs and aide in the development of control measures to reduce the spread of SVA.
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Affiliation(s)
- Kyle S. Hoffman
- Virus and Prion Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, IA, United States
| | - Nicki L. Humphrey
- Veterinary Services, U.S. Department of Agriculture, Animal Plant Health Inspection Service, Fort Collins, CO, United States
| | - John A. Korslund
- Veterinary Services, U.S. Department of Agriculture, Animal Plant Health Inspection Service, Riverdale, MD, United States
| | - Tavis K. Anderson
- Virus and Prion Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, IA, United States
| | - Kay. S. Faaberg
- Virus and Prion Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, IA, United States
| | - Kelly M. Lager
- Virus and Prion Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, IA, United States
| | - Alexandra C. Buckley
- Virus and Prion Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, IA, United States
- *Correspondence: Alexandra C. Buckley
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