SwIAV antibody and swIAV prevalence in the different stable units
The results of the IAV antibody ELISA and the real-time RT PCR for IAV detection in gilts, first parity sows and piglets at the different stages of the production (quarantine in/out, mating, gestation and 1-week after farrowing) for the ten study herds are summarized in Table 1.
Among the ten herds included in the study, two herds had swIAV positive gilts just after arrival in the quarantine, whereas six herds had swIAV positive gilts at the end of the quarantine. The viral status in and out of the quarantine was not significantly correlated (p = 0.5). Most herds (9 of 10) received seropositive gilts in the quarantine, but the prevalence varied greatly between herds, from 15 to 95% seropositive gilts. At the end of the quarantine period all herds had seropositive gilts, with a prevalence varying from 20 to 100%.
In the mating unit, a low prevalence of swIAV positive gilts was found as four herds had 5% of the gilts testing positive at this stage.
The prevalence of swIAV antibody positive gilts/first parity sows of the gestation and farrowing unit ranged from 55 to100% and 40 to100%, respectively. In addition, in the farrowing unit, three herds had first parity sows testing positive for swIAV in nasal swabs and six of the ten herds had swIAV positive 1-week old litters in the farrowing unit. More litters from swIAV positive first parity sows were virus positive compared to litters from swIAV negative gilts (50% vs. 11%, p = 0.048), though the number of virus positive individual sows was rather low (n = 4). For the effect of the antibody status of gilts, there was no statistical significant difference in the number of virus positive piglets from antibody positive or antibody negative gilts (12 vs. 11%, p = 0.4).
Sow herd—swIAV vaccination
The prevalence of swIAV positive gilts/first parity sows and swIAV antibody positive gilts/first parity sows in relation to the application of swIAV vaccination in the sow herd are summarized in Fig. 2.
Among non-vaccinated herds, no swIAV was found among sows in the mating and farrowing unit, however, three of five herds had swIAV circulating among piglets in the farrowing unit with a prevalence of 10 to 35% (Table 1).
Among herds with a sow vaccination strategy for swIAV, four of five herds had virus positive sows in the mating unit, all with a prevalence of 5%. In the farrowing unit, three herds had virus positive sows with a prevalence of 5 to 10% and three herds (two related to the virus positive sows) had virus positive piglets with a prevalence from 5 to 45% (Table 1).
The prevalence of virus positive sows or piglets did not differ significantly between non-vaccinated and vaccinated herds (p > 0.9, Table 2).
The prevalence of seropositive first parity sows differed significantly between non-vaccinated and vaccinated herds in both the gestating unit (69% vs. 92%, p = 0.013) and farrowing unit (58% vs. 95%, p = 0.02). Also S/N values differed significantly between the swIAV antibody positive gilts/first parity sows of non-vaccinated and vaccinated herds in both the gestating (0.31 vs. 0.21, p = 0.03) and farrowing unit (0.33 vs. 0.20, p = 0.02), indicating significantly higher antibody levels in vaccinated gilts/first parity sows.
Quarantine—gilt swIAV vaccination and all-in/all-out management
Among all ten herds included, two herds included a primary (prime-boost) vaccination program for gilts within the quarantine (Table 3).
A comparison of the prevalence of swIAV positive- and swIAV antibody positive gilts in relation to the application of a primary vaccination (prime-boost) program for gilts within the quarantine is summarized in Fig. 2b.
At the end of the quarantine period a significant difference was found in the prevalence of seropositive gilts (52 vs 93%, p = 0.003) in herds that did not vaccinate compared to herds that vaccinated gilts, and a tending difference was also found in the prevalence of virus positive gilts (14% vs. 3%, p = 0.053) (Table 4).
A comparison of the prevalence of swIAV and swIAV antibodies in relation to having all-in/all-out (AIAO) management of the quarantine is presented in Fig. 2c. Having an AIAO management of the quarantine is defined by all new pigs coming into the quarantine at the same time and all pigs leaving the quarantine at the same time resulting in no continuous intake of gilts into the sow herd. Among the ten herds, five herds had quarantines with AIAO management (Table 5).
For herds having AIAO management a significant difference was found in the prevalence of both seropositive (81 vs. 39%, p < 0.0001) and swIAV positive (19 vs 4%, p = 0.002) gilts in the end of the quarantine period (Table 4).
Combining results for quarantine vaccination and the presence of AIAO management, five herds that neither vaccinated and nor had AIAO management of the quarantine, showed 18 (23%) virus positive gilts at the end of the quarantine period. In herds with either quarantine vaccination of gilts and no AIAO management or no vaccination of gilts and practice of AIAO management, 3% and 5% of the gilts were virus positive, respectively (Table 5). None of the ten herds had both quarantine vaccination of gilts and AIAO management.
A regression model with herds as fixed effect showed a significant lower risk of viral shedding by the end of the quarantine period with the use of swIAV vaccination or AIAO management of the quarantine (Table 6).
The results of the questionnaire and the check-list are presented in Table 3 and Additional file 3: Table S1. Table 3 provides an overview of the vaccination strategies applied in the vaccinated herds. In brief, it should be noted that only two of the influenza vaccinated herds, had a primary (prime-boost) vaccination in the quarantine, and all herds included gilts/first parity sows in their mass sow vaccination program. Moreover, all vaccinated herds applied several other vaccines at the same time as the influenza vaccine. In specific, Herd 10 was applying a modified live vaccine against porcine reproductive and respiratory syndrome virus (PRRSv) at the same time as the Respiporc FLU3 vaccine (Ceva Santé Animale, France). Additional file 3: Table S1 provides information on herd size and production systems as well as health status, quarantine location and -management and IAV vaccination status of the personnel. In brief, it should be noted that five of the herds had a continuous intake of gilts into the sow herd, and that only one herd had personnel (4 out of 7 workers) that was vaccinated against human seasonal influenza virus.
Lineages and sequencing
From six (four non-vaccinated and two vaccinated) of the nine swIAV positive herds it was possible to determine the HA and NA lineages circulating in the herds by sequencing. In the remaining three swIAV positive herds, the viral load was too low to obtain high quality sequences. The HA and NA sequences were compared to the sequences of the corresponding vaccine strains included in Respiporc FLU3  (Table 3). For the four herds where an hemagglutinin (HA) protein of the Eurasian avian H1 lineage (H1av) was identified a comparison was made to the corresponding H1av vaccine component of Respiporc FLU3. The comparison revealed major differences as the overall amino acid identity ranged between 89–92%, and several residues in both antigenic sites (AS) and the receptor binding site (RBS) were divergent (Table 7 and Additional file 4: Figure S1). One of the four herds was vaccinating with Respiporc FLU3 (Herd 10). The remaining vaccinated herd wherefrom it was possible to determine the lineage of the circulating strain, it was discovered that a non-matching vaccine was applied as the H1pdm09N1av strain was detected.
Herd 1 was a newly started herd with a new breeding stock. Interestingly, 30% of the gilts of this herd were positive for H1N1pdm09 at the end of the quarantine, thereby posing a high risk for swIAV introduction into the newly established sow herd, where no swIAV was documented at least in the gilts, first parity sows and piglets sampled in this study. It was therefore decided to investigate if swIAV were circulating within the sow herd 3 months later. Remarkably, these “follow-up” samples revealed that 9/12 pools obtained in the farrowing unit was positive for H1N1pdm09, including pigs from 1- to 4-week-of-age.
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