NPPC/SHIC PRRS Lineage 1C Minnesota Strain Update Meeting Summary

June 23, 2021 — 

During the 2021 World Pork Expo, an emergency PRRS meeting sponsored by NPPC and SHIC was held on June 10 to discuss the current situation related to the new PRRS Lineage 1C 1-4-4 variant. The objectives of the meeting were to continue to raise awareness of the current situation together with share information from monitoring programs, practitioners and producers in an attempt to better understand the magnitude of the outbreaks and work towards understanding how to decrease the rapid transmission of this virus. The agenda for the 2-hour meeting included four speakers whose presentations are summarized below.

1. Dr. Mariana Kikuti - Morrison Swine Health Monitoring Project Update (MSHMP), University of Minnesota
Within the MSHMP participant database, the new PRRS Lineage 1C variant had been detected early in 2020. A large number of cases (e.g. sequences) composed mainly of growing pig farms constituted the first wave of this outbreak in the fall/winter. A second wave of transmission began in April 2021. As of 5/22/21, 192 sequences originating from 167 sites (30 breeding herds, 101 growing pig sites, 36 unknown) from 14 MSHMP participating systems were identified. An estimated ~80K sows and ~300K growing pigs from MSHMP participants have been infected. However, these numbers are likely underestimating the overall situation in the U.S. A map highlighting the temporal and spatial distribution of these cases was shown in which most of the cases have been limited to Southern Minnesota and Northern Iowa. Current preliminary results of a case-control study for the Oct-Dec 2020 cases were shared with no associations alluding to a specific transmission route. Phylogenetic trees of the above-mentioned sequences at both ORF5 and whole genome level were shown. The same subclade structure was seen in both trees and these sequences grouped separately from any other PRRS virus seen historically. Limitations of both RFLP and lineage classifications in identifying this new variant were shown. Combining both RFLP and Lineage will increase the probability of correctly classifying this variant, but some cases might still be misclassified. The current best approach for identifying this variant is through pairwise nucleotide identity or through placing sequences into a phylogenetic tree against reference sequences of this variant.

2. Dr. Giovani Trevisan - Swine Disease Reporting System (SDRS), Iowa State University
Detection of PRRSV at the end of 2020 and April-May 2021 was higher than expected. When assessing the Ct values by month and comparing them with previous years, the mean Ct value for the wean-to-market pig age category was the lowest in the 2021 April-May time. The percentage of positivity rate in the wean-to-market category also increased above the expected level in the months of April-May. When examining ORF5 sequence data, RFLP changed over time with the 1-4-4 having increased detection during 2021, contributed mainly by the detection of the new emergent L1C variant strain. The initial detection of L1C variant strains dates of January 2020, and the epidemiological detection curve began showing signals of circulation, forming the first wave; since September 2020, a second and higher wave of detection started in April 2021, with most sequences coming from wean-to-market animals originating from nine different states (IA, MN, IL, IN, MI, MO, NE, SD, and WI).

3. Dr. Laura Bruner - Swine Vet Center, St. Peter, MN,
Given the current situation of multiple sow and growing pig herd outbreaks during the months of April-May 2021 with this virus there is a need to collaborate to better understand how this pathogen is currently being transmitted. To better characterize the situation and understand the magnitude of the outbreak and practitioner perceptions regarding the recent increase in cases, a survey was generated and shared with 22 veterinarians representing approximately 1.8M sows. A total of 15 (68% response rate) kindly responded. A total of 31 sow farms were confirmed positive between week 17 and 22 of 2021. The total number of sows, nursery and finish pig sites (and pigs) turning 1-4-4 positive was 35 (107K sows), 29 (185K sows) and 80 (337K sows), respectively. It is important to highlight that these numbers are underestimating the magnitude of the outbreak. Practitioners' felt that the virus could have entered through many routes but in order of importance the perceived reason was airborne, area disease pressure, farm biosecurity breach, trucking biosecurity breach, feed introduction, gilt introduction and other. With regards to events occurring in the month leading up to the break, practitioners identified grow-finish breaks and manure pumpingspreading as major events contributing to the break. Practitioners believe that the following areas of research with regards to this new variant should be prioritized: Aerosol capability, Air filter efficacy, Infectious dose, Efficacy of both "normal" PRRS protocols and disinfectants.

4. Dr. Derald Holtkamp, Rapid Response Corps/Outbreak Investigation, Iowa State University
During outbreak investigations you can learn important details regarding operational connections. These investigations look for hazards, that can lead to failures in the process that ultimately infect pigs. It seems that with this new virus the low Ct levels lead to contamination which can be part of a set of failures. In one particular outbreak investigation conducted in a sow farm located in a low dense region, the virus was 100% similar to a virus found in another sow farm within the company. The person doing the maintenance in this farm has a brother who does the maintenance of the other sow farm that had the same virus. They both live close to each other and their kids interacted closely by going to each other's house. During the farm visit, there was a towel hanging on the wrong side of the shower. These findings give an idea of the attention given to small details. Another connection in this investigation detected that both sow farms shared the truck for cull sow removal; however, this was conducted through a transfer station. The weaned truck trailer was another connection. Hazard analysis can be conducted prospectively and do not need to wait for an outbreak.