Swine influenza virus infection dynamics in two pig farms; results of a longitudinal assessment

Abstract

In order to assess the dynamics of influenza virus infection in pigs, serological and virological follow-ups were conducted in two whole batches of pigs from two different farms (F1 and F2), from 3 weeks of age until market age. Anti-swine influenza virus (SIV) antibodies (measured by ELISA and hemagglutination inhibition) and nasal virus shedding (measured by RRT-PCR and isolation in embryonated chicken eggs and MDCK cells) were carried out periodically. SIV isolates were subtyped and hemagglutinin and neuraminidase genes were partially sequenced and analyzed phylogenetically. In F1, four waves of viral circulation were detected, and globally, 62/121 pigs (51.2%) were positive by RRT-PCR at least once. All F1 isolates corresponded to H1N1 subtype although hemagglutination inhibition results also revealed the presence of antibodies against H3N2. The first viral wave took place in the presence of colostral-derived antibodies. Nine pigs were positive in two non-consecutive sampling weeks, with two of the animals being positive with the same isolate. Phylogenetic analyses showed that different H1N1 variants circulated in that farm. In F2, only one isolate, H1N2, was detected and all infections were concentrated in a very short period of time, as assumed for a classic influenza outbreak. These findings led us to propose that influenza virus infection in pigs might present different patterns, from an epidemic outbreak to an endemic form with different waves of infections with a lower incidence.

Figure 1

Seroprevalence and incidence of SIV in Farm 1. Antibodies against SIV were analyzed by ELISA (line) and nasal shedders were determined by RRT-PCR (bars) at each sampling time.

Figure 2

Phylogenetic tree of the HA1 and NA1 genes of SIV isolates from Farm 1. The accession numbers of sequence data of influenza virus were deposited in GenBank under the accession numbers [GenBank: JF960169, JF960172 - JF960174, JF960176, JF960177, JF960180 - JF960184, JF960187, JF960189, JF960190, JF960192, JF960193, JF960197, JF960199 - JF960208, JQ301920 - JQ301944]. The strains are indicated by the isolate name and between brackets by the animal number following by the age of animals in which the virus was isolated (in weeks). Strains given in red correspond to available isolates from pigs of 3 and 4 weeks of age. Strains given in blue correspond to available isolates from pigs of 7 weeks of age. Strains given in green correspond to available isolates from pigs of 13 and 15 weeks of age. Strains given in purple correspond to available isolates from pigs of 20 weeks of age. Abbreviations: cluster I, I; cluster II, II; cluster III, III; cluster IV, IV; cluster V, V; and cluster VI, VI.

Figure 3

Phylogenetic analysis for HA and NA of SIV isolates retrieved in Farm 1. The strains isolated in our study are highlighted in red. Unrooted bootstrapped neighbour-joining trees of nucleotide sequences of hemagglutinin and neuraminidase. Bootstrap values, calculated on 1000 replicated trees, are shown if ≥ 70 percent. Scale bars indicate substitutions per site. The accession numbers of sequence data are provided in Additional file 2: Table S2.

Figure 4

Distribution of viral shedders according to RRT-PCR results in Farm 1. Open separations between pens are represented as dashed lines; closed separations between pens are shown with solid lines. Arrows show movements of RRT-PCR positive pigs.

Figure 5

Seroprevalence and incidence of SIV in Farm 2. The techniques and symbols used are the same as those used in Figure 1.

Figure 6

Phylogenetic analysis for HA and NA of SIV isolates retrieved in Farm 2. Color scheme, rooting, and scale are the same as those used in Figure 3. The accession numbers of sequence data are provided in Additional file 2: Table S2.