Acute Influenza A virus outbreak in an enzootic infected sow herd: Impact on viral dynamics, genetic and antigenic variability and effect of maternally derived antibodies and vaccination

Abstract

Influenza A virus (IAV) is a highly contagious pathogen in pigs. Swine IAV (swIAV) infection causes respiratory disease and is thereby a challenge for animal health, animal welfare and the production economy. In Europe, the most widespread strategy for controlling swIAV is implementation of sow vaccination programs, to secure delivery of protective maternally derived antibodies (MDAs) to the newborn piglets. In this study we report a unique case, where a persistently swIAV (A/sw/Denmark/P5U4/2016(H1N1)) infected herd experienced an acute outbreak with a new swIAV subtype (A/sw/Denmark/HB4280U1/2017(H1N2)) and subsequently decided to implement a mass sow vaccination program. Clinical registrations, nasal swabs and blood samples were collected from four different batches of pigs before and after vaccination. Virus isolation, sequencing of the virus strain and hemagglutinin inhibition (HI) tests were performed on samples collected before and during the outbreak and after implementation of mass sow vaccination. After implementation of the sow mass vaccination, the time of infection was delayed and the viral load significantly decreased. An increased number of pigs, however, tested positive at two consecutive sampling times indicating prolonged shedding. In addition, a significantly smaller proportion of the 10–12 weeks old pigs were seropositive by the end of the study, indicating an impaired induction of antibodies against swIAV in the presence of MDAs. Sequencing of the herd strains revealed major differences in the hemagglutinin gene of the strain isolated before- and during the acute outbreak despite that, the two strains belonged to the same HA lineage. The HI tests confirmed a limited degree of cross-reaction between the two strains. Furthermore, the sequencing results of the hemagglutinin gene obtained before and after implementation of mass sow vaccination revealed an increased substitution rate and an increase in positively selected sites in the globular head of the hemagglutinin after vaccination.

Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses

“…The resulting tree, including information on sampling dates, was subsequently checked for the presence of a temporal signal (i.e., whether nucleotide changes accumulate proportionally to elapsed time) using the program TempEST [64]. Thereafter, the software package BEAST2 version 2.5.2 [65] was used to determine the substitution rate of each of the eight gene segments as previously described [66]. Briefly, the substitution model was specified to be HKY with gamma distributed rates over sites, with a strict clock model, and using tip dates (sampling dates).…”

Co-circulation of multiple influenza A variants in swine harboring genes from seasonal human and swine influenza viruses

“…This in turn results in very complex phylogenetic trees with a lot of clusters and subclusters, which disrupt the pectinate structure. Still, despite the lack of a clear pectinate like evolution, the H1av variants had clearly undergone positive selection on specific codons located in antigenic sites, which is known to alter the binding of neutralizing antibodies [48][49][50] . This further confirm our previous findings, that the herd immunity leads to significant antigenic drift in the globular head of the HA protein, as seen for human seasonal IAV 51 .…”

“…Subsequently, the alignments of each lineage were analyzed in the program BEAST2 version 2.5.2, where the model settings were as previously described 68 . Briefly, the HKY substitution model with gammadistributed rates over sites was chosen along with a strict clock model including tip dates.…”

“…The surface gene segments of the different lineages; H1pdm09, H1av, N1pdm, N1av, N2hu and N2sw were investigated for the presence of positive selection using the CODEML program of the PAML package as previously described 48 . Briefly, this was done by comparing the fits of CODEML's substitution models M1a and M2a (NSsites = 1 and 2).…”

A universal RT-qPCR assay for “One Health” detection of influenza A viruses

“…In addition, a more recently designed RT-qPCR which amplifies elsewhere within the MP-segment was validated [24] and featured successfully in subsequent AIV outbreaks and wild bird investigations [25][26][27][28], AIV in vivo studies [29,30] and SwIV field investigations [31][32][33][34]. The importance of appropriate test validation has been emphasised in a veterinary context [35], with an MP-segment RT-qPCR for generic detection of contemporary H1N1, H1N2 and H3N2 SwIV subtypes in European pigs having been also validated [36].…”