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. 2025 Mar 6:12:1571020.
doi: 10.3389/fvets.2025.1571020. eCollection 2025.

Harnessing sequencing data for porcine reproductive and respiratory syndrome virus (PRRSV): tracking genetic evolution dynamics and emerging sequences in US swine industry

Srijita Chandra  1 , Guilherme Cezar  2 , Kinath Rupasinghe  2 , Edison Magalhães  2 , Gustavo S Silva  2 , Marcelo Almeida  2 , Bret Crim  2 , Eric Burrough  2 , Phillip Gauger  2 , Darin Madson  2 , Joseph Thomas  2 , Michael Zeller  2 , Jianqiang Zhang  2 , Rodger Main  2 , Albert Rovira  3 , Mary Thurn  3 , Paulo Lages  3 , Cesar Corzo  3 , Matthew Sturos  3 , Kimberly VanderWaal  3 , Hemant Naikare  3 , Franco Matias-Ferreyra  4 , Rob McGaughey  4 , Jamie Retallick  4 , Sara McReynolds  4   5 , Jordan Gebhardt  6 , Angela Pillatzki  7 , Jon Greseth  7 , Darren Kersey  7 , Travis Clement  7 , Jane Christopher-Hennings  7 , Beth Thompson  7   8 , Jonah Perkins  9 , Melanie Prarat  9 , Dennis Summers  9 , Craig Bowen  10 , Joseph Boyle  10 , Kenitra Hendrix  10 , James Lyons  10 , Kelli Werling  11 , Andreia G Arruda  12 , Mark Schwartz  3   13 , Paul Yeske  14 , Deborah Murray  15 , Brigitte Mason  16 , Peter Schneider  17 , Samuel Copeland  18 , Luc Dufresne  19 , Daniel Boykin  20 , Corrine Fruge  21 , William Hollis  22 , Rebecca Robbins  23 , Thomas Petznick  24 , Kurt Kuecker  25 , Lauren Glowzenski  26 , Megan Niederwerder  27 , Xiaoqiu Huang  1 , Daniel C L Linhares  2 , Giovani Trevisan  2
Affiliations

Harnessing sequencing data for porcine reproductive and respiratory syndrome virus (PRRSV): tracking genetic evolution dynamics and emerging sequences in US swine industry

Srijita Chandra et al. Front Vet Sci. .

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is the most important swine pathogen affecting the United States of America (USA), leading to significant economic losses. Despite advances in diagnostic testing, there remains a gap in understanding the genetic evolution of PRRSV, especially in tracking the emergence of novel sequences and their spread across different regions and production stages. This research addresses this gap by developing a systematic methodology for directly collecting and analyzing PRRSV ORF5 sequences from veterinary diagnostic laboratories. The study aimed to identify trends among collected sequences and emerging PRRSV sequences by integrating nucleotide sequence data with metadata, providing critical insights into their geographic distribution, collected specimens, swine age groups, lineages, variants, and restriction fragment length polymorphism (RFLP) patterns. As of December 2024, the database housed 115,643 PRRSV ORF5 sequences. Sublineages 1B, 1A, 1H, and 1C.5 were the major wild-type PRRSV sequences detected over time, whereas vaccine-like strains comprised mostly of sublineages 5A and 8A. A novel sequence detection system was implemented, categorizing sequences based on similarity thresholds, ambiguities, and length criteria, identifying 167 novel sequences for the period between 2010 and 2024, whereas only three had continued detection in the field over time, forming clusters of detection. The analysis of these novel sequences highlighted significant trends, including the dominance of grow-finish animals in sequence origin and the high number of detections of sublineage 5A. Production sites located in states with the largest swine inventory have contributed to the most frequent detection of new PRRSV strains. Additionally, the development of a web-based tool provides end users with the capability to search sequences similar to their query sequence, providing macroepidemiological information and genetic sequence features to support PRRSV management and control. Real-time PRRSV sequencing data analysis informs producers and veterinarians of any upcoming novel sequences and trends of detection. The findings are intended to enhance current surveillance efforts and support more effective strategies for managing PRRSV outbreaks, ultimately safeguarding animal health, economic sustainability in the swine industry, and ultimately contributing to national food production sovereignty through pork-derived products.

Keywords: BLAST; PRRSV; database; epidemiology; genetics; surveillance.

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Conflict of interest statement

MSc was employed by Schwartz Farms Inc. CF was employed by The Maschhoffs LLC. WH was employed by Carthage Veterinary Service LTD. RR was employed by Pig Improvement Company. KK was employed by The Hanor Company. DM was employed by New Fashion Pork. BM was employed by Country View Family Farms. PS was employed by Innovative Agriculture Solutions, LLC. LD was employed by Swine Veterinary Partners. DB was employed by Smithfield Foods. SC was employed by Prestage Farms. MN serves on the SDRS Advisory Board and also as Executive Director of Swine Health Information Center which has provided funding to this project under competitive grants evaluated by a panel of reviewers. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

Figure 1
Figure 1
The data accumulation, processing, and updating mechanisms of the SDRS PRRSV Sequencing Database involve a sophisticated interplay between participating laboratories and the database infrastructure. Laboratories transmit their real-time sequencing data either through Comma Separated Value (CSV) files, denoted by red lines, or via Health Level Seven (HL7) messaging, represented by blue lines. This collaborative effort ensures a continuous flow of data, facilitating real-time updates and maintenance of a comprehensive repository for PRRSV genetic information.
Figure 2
Figure 2
Swine age group distribution of complete sequences received between January 2006 and December 2024.
Figure 3
Figure 3
Specimen distribution of samples received. The ‘Others’ section consists of all specimen types which were received less than 5,000 times.
Figure 4
Figure 4
PRRSV ORF5 sequence detections by lineage classification between January 2006 and December 2024.
Figure 5
Figure 5
Novel PRRSV ORF5 sequences identified and distributed by swine age group from January 2010 to December 2024. The number of novel sequences classified as ‘unknown’ swine age group has decreased over the years.
Figure 6
Figure 6
Distribution of novel sequences between January 2010 and December 2024. 53 of the novel sequences had no state information and were labeled as “unknown” locations.
Figure 7
Figure 7
(A) Illustration of the lineage or sublineage classification for 167 novel sequences. Sequences were assigned as novel if they had less than or equal to 6 ambiguities and length between 597 and 606 nucleotides. (B) Variant classification of the novel sequences with all unclassified sequences included under the ‘unclassified’ variant label. (C) Most frequent RFLP pattern seen in the novel sequences. The ‘Others’ section in the pie chart reflects the RFLP patterns seen twice or less.
Figure 8
Figure 8
Yearly and monthly number of novel sequence detections displayed in a heatmap. December 2011 had the highest number of detections recorded, followed closely by October 2013 and January 2020, with 5 detections each.
See this image and copyright information in PMC

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