Reduction of Influenza a Virus Prevalence in Pigs at Weaning After Using Custom-Made Influenza Vaccines in the Breeding Herds of an Integrated Swine Farm System

Vaccination is a common influenza A virus (IAV) control strategy for pigs. Vaccine efficacy depends on strain cross-protection and effective vaccination program implementation. We evaluated a multi-faceted IAV vaccination strategy which included: a) monthly surveillance of pigs at weaning, b) selection of epidemiologically-relevant strains from farms under surveillance, c) updating IAV strains in custom-made vaccines, and d) seasonal mass vaccination with custom-made vaccines given to sows in 35 farrow-to-wean farms within an integrated swine farm system. Reduction of IAV in pigs from vaccinated sows was determined by monthly monitoring farms for 30 months by IAV rRT-PCR (PCR) testing of nasal wipes collected from litters of piglets at weaning. Hemagglutinin (HA) nucleotide and amino acid (AA) sequence homology of the circulating and vaccine strains was determined by pairwise alignment and AA comparison at antigenic sites. Of the 35 farms monitored, 28 (80%) tested positive at least once and 481 (5.75%) of 8,352 PCR tests were IAV positive. Complete HA sequences were obtained from 54 H1 (22 H1-δ_1B.2.1, 28 H1-γ_1A.3.3.3, and 4 H1-pdm_1A.3.3.2 clades) and 14 H3 (12 IV-A 3.1990.4.1 and 2 IV-B 3.1990.4.2 clades) circulating IAV strains. During the study, custom-made vaccines were updated three times (eight strains total) and administered to sows at five distinct time periods. The HA AA similarity between vaccine and circulating strains ranged from 95% to 99%; however, the 0 to 71% similarity at HA antigenic sites prompted the vaccine updates. Herd IAV prevalence decreased from 40% (14/35) to 2.9% (1/35) accompanied by a numerical reduction in IAV-positive samples post-vaccination. Our results support having a comprehensive approach to controlling influenza in swine herds that includes surveillance, vaccination, and careful program implementation to reduce IAV in pigs.