SHIC-Funded MSHMP Monitoring Detection of PRRSV variant 1H.18

The Swine Health Information Center-funded Morrison Swine Health Monitoring Project (MSHMP) noted an increase in occurrence of a novel PRRSV variant in December 2023 and January 2024. In the May 10, 2024, MSHMP report, a total of 61 sequences belonging to the novel PRRSV variant 1H.18 have been reported as of week 19 of 2024 in the MSHMP database. This variant has been identified in nine production systems located mostly in Iowa (n=23) and Minnesota (n=22), along with one sequence detected in Illinois.

The 61 1H.18 sequences originated from 46 unique sites, including five breeding, 10 grow-finish, 11 others, and 20 unknown. Assessing MSHMP data for changing trends in PRRSV strain occurrence can serve as an early warning for the presence of new or emerging viral variants. Close monitoring of PRRSV 1H.18 by the MSHMP team is ongoing. See the full report for contributing authors and figures and visit the MSHMP science page as well.

During initial analysis, the sequences belonging to this group were classified as a somewhat rare RFLP pattern (1-12-2) and consequently assigned to sub-lineage L1C or L1H, dependent on the classification method used. When the new variant classification (see below) was applied, a novel clade comprised of sequences positioned between sub-lineages L1H and L1C on the phylogenetic tree was identified. Per the MSHMP report, most of the 61 PRRSV 1H.18 sequences have now been classified as either RFLP 1-8-4 (n=32), 1-12-2 (n=20), or 1-12-1 (n=1). Sporadic detections of the 1H.18 variant date back to 2018 and a slight increase in cases has been noted since late 2023 and early 2024. MSHMP staff point out the surge in 1H.18 sequences in 2020 likely went undetected due to sequences at the time being classified as RFLP 1-8-4 and 1-4-4 L1C, common RFLP types that occur in many different lineages and sub-lineages, and many of the sequences originated from a single site.  The production impact of this variant has not yet been formally assessed, although both mild and more severe clinical presentation have been reported by MSHMP participants.

In reporting on the new variant, MSHMP staff commented they do not currently have enough evidence to suggest this variant is of immediate concern to the swine industry, but prospective monitoring is warranted given the sudden increase in cases. The authors recommend careful consideration when interpreting isolated case reports and sequence counts, as they may lead to erroneous conclusions due to reporting biases. MSHMP staff will continue to proactively monitor this variant, and additional reports will be issued as the situation unfolds.

In their report on the PRRSV variant, MSHMP staff included relevant observations, saying RFLP may erroneously group genetically dissimilar PRRS viruses while segregating closely related ones. Phylogenetic methods organize PRRS viruses into ancestral “families,” commonly called lineages and sub-lineages that tend to form broad groups. Recognizing the need for a comprehensive fine-scale variant classification system across all sub-lineages, an American Association of Swine Veterinarians-funded working group, comprised of researchers from the University of Minnesota, Iowa State University, and USDA, is developing and testing a new variant classification method. The new variant nomenclature was used throughout the MSHMP Science Page, since lineage/sub-lineage and RFLP (either separately or combined) were not initially accurate when used as case definition to identify this novel 1H.18 clade.

These observations underscore the challenge faced by both RFLPs and sub-lineages in confidently labeling sequences belonging to this group. With a recent influx of sequences belonging to this variant, the report has compiled current available data to ensure stakeholders and industry are informed. Critical evaluation of routine herd health monitoring data provides a mechanism to detect changes in pathogen occurrence that could indicate a new or emerging disease.

The Swine Health Information Center, launched in 2015 with Pork Checkoff funding, protects and enhances the health of the US swine herd by minimizing the impact of emerging disease threats through preparedness, coordinated communications, global disease monitoring, analysis of swine health data, and targeted research investments. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. For more information, visit http://www.swinehealth.org or contact Dr. Megan Niederwerder at [email protected] or Dr. Lisa Becton at [email protected].