First reported in the Swine Health Information Center June 2024 domestic disease monitoring report, an emerging PRRSV Lineage 1C.5 subclade has continued to expand, with increased detection through the fall and winter months of 2024. A team of diagnosticians at Iowa State University have led the investigation into the changing diagnostic trends of the detection of an emergent and clinically significant PRRSV-2 Lineage 1C.5 clonally expanded clade. Investigative team members Rabsa Naseer, and Drs. Jianqiang Zhang, Phillip Gauger, Giovani Trevisan and Michael Zeller have provided an update on the current situation herein.
Since its emergence in 2020, the PRRSV-2 Lineage 1C.5 has become the dominant lineage in circulation, replacing the prior dominant Lineage 1A in the US. The ISU Veterinary Diagnostic Laboratory has sequenced over 6,000 unique Lineage 1C.5 cases to date, accounting for approximately 72% of the total Lineage 1C cases sequenced at their facility from January 2020 to mid-December 2024. Many of these cases are associated with clinical disease in production systems experiencing PRRS outbreaks. The ISU VDL regularly tracks the diversity of circulating PRRSV strains using both phylogenetic and epidemiological methods, which led to the discovery of an emerging divergent clade within Lineage 1C.5. This clade was notable due to a surge in genetically similar sequences detected over a short period of time and was deemed to be clonally expanding through the swine population. Here, the ISU team has tentatively called it Lineage 1C.5 clonally expanded clade.
From July 2023 to December 2024, 945 cases of PRRSV with ORF5 sequences belonging to this clade have been identified. The ORF5 sequences of this clade exhibit high genetic similarity, with an average nucleotide difference of seven nucleotide bases (98.8% nucleotide similarity), though the entirety of the clade is within 96%. The index case was detected from a grow-finish farm in Iowa on July 20, 2023, and the majority of subsequent cases have been detected in Iowa swine farms (838), indicating a regional outbreak. This Lineage 1C.5 clonally expanded clade was first detected outside Iowa in March 2024, signaling its potential for national spread. To date, this clade has been detected in the states of Minnesota (36 cases), Illinois (17), Missouri (15), Indiana (1), Nebraska (1), South Dakota (1), and Wisconsin (1), highlighting its transmission within the swine population. This clade has been detected primarily in grow-finish farms (464), with fewer cases from breeding farms (101) and nurseries (62); however, this distribution may reflect sampling biases rather than the true prevalence across farm types.
The detection frequency of cases related to this clade of Lineage 1C.5 steadily increased throughout the fall months. After a modest but noticeable rise in cases during November and December of 2023, a significant surge occurred in early 2024. Case numbers climbed from 13 in February to 110 detections by April, nearly a tenfold increase. Although detections declined during the summer months, the strain persisted and resurged in the fall of 2024. By October, case numbers rose to 154, followed by 145 in November, and 110 as of December 26. Notably, an increasing proportion of these detections were reported outside Iowa, suggesting the strain’s expanding geographic reach.
As no swine studies have yet been conducted on this clonally expanded clade of Lineage 1C.5, cycle threshold (Ct) values were used to assess potential differences that might suggest changes in the virus’s clinical impact. The Ct value, a diagnostic measure from real-time PCR, indicates whether a sample is positive and semi-quantitatively reflects the amount of virus present. Median Ct values for the entire Lineage 1C.5 are dependent on sample type, with Ct’s of approximately 17.3 being observed in lung specimens and 28.9 in oral fluid specimens. The emergent Lineage 1C.5 clonally expanded clade shows a similar pattern, with Ct values of 16.8 for lung and 27.9 for oral fluid. Average Ct values for lung and oral fluid specimens from Lineage 1C.5 as a whole are generally lower than those of Lineage 1A, indicating higher viral loads. The median Ct values for Lineage 1A are 18.4 for lung specimens and 31.4 for oral fluid specimens. This indicates a higher viral load on average in the samples positive for Lineage 1C.5 compared to Lineage 1A.
Bayesian phylodynamic analysis revealed that the genetic diversity of Lineage 1C.5 peaked in February 2023 but declined steadily throughout 2024, with a sharp drop in November 2023. This pattern of decreasing genetic diversity paired with persistent high levels of detection, suggests genetic selection favoring a strain with a transmission advantage. The effective reproduction number, which reflects the expected number of new cases generated from a single positive case, was estimated with phylogenetic methods. During the first wave in November 2023, each detected case led to about 2.7 new cases. The rate dipped temporarily but climbed to 2.7 by March 2024 (point B) and rebounded to around two by October 2024 (point C) after a summer decline.
Ongoing monitoring of PRRSV genetic diversity, including the emergent Lineage 1C.5 and other strains, is crucial for effective management of PRRSV. The emergence of a new, divergent Lineage 1C.5 clonally expanded clade in Iowa, followed by its spread to other states, highlights an outbreak that warrants close attention, particularly regarding its potential to become dominant nationwide. Genetic analysis revealing a clonal expansion within Lineage 1C.5 suggests heightened transmissibility, while lower median Ct values and a higher effective reproduction number emphasize the clade’s potential increased virulence and spread; but these features based on sequence analysis remain to be confirmed by experimental inoculation studies. These findings underscore the importance of continued surveillance to mitigate the impact of PRRSV outbreaks on swine health, particularly when new strains are emerging in the swine population.
Questions regarding the information contained in this article can be directed to Dr. Michael Zeller (mazeller@iastate.edu) at the ISU VDL.
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 mniederwerder@swinehealth.org or Dr. Lisa Becton at lbecton@swinehealth.org.