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

Reassortment incompetent live attenuated and replicon influenza vaccines provide improved protection against influenza in piglets

Swine influenza A viruses (swIAV) cause an economically important respiratory disease in modern pig production. Continuous virus transmission and antigenic drift are difficult to control in enzootically infected pig herds. Here, antibody-positive piglets from a herd enzootically infected with swIAV H1N2 (clade 1 A.3.3.2) were immunized using a homologous prime-boost vaccination strategy with novel live attenuated influenza virus (LAIV) based on a reassortment-incompetent bat influenza-swIAV chimera or a vesicular stomatitis virus-based replicon vaccine. Challenge infection of vaccinated piglets by exposure to H1N2 swIAV-infected unvaccinated seeder pigs showed that both LAIV and replicon vaccine markedly reduced virus replication in the upper and lower respiratory tract, respectively, compared to piglets immunized with commercial heterologous or autologous adjuvanted whole-inactivated virus vaccines. Our novel vaccines may aid in interrupting continuous IAV transmission chains in large enzootically infected pig herds, improve the health status of the animals, and reduce the risk of zoonotic swIAV transmission.

Detection and Characterization of Influenza A Virus Endemic Circulation in Suckling and Nursery Pigs Originating from Vaccinated Farms in the Same Production System

Inactivated influenza A virus (IAV) vaccines help reduce clinical disease in suckling piglets, although endemic infections still exist. The objective of this study was to evaluate the detection of IAV in suckling and nursery piglets from IAV-vaccinated sows from farms with endemic IAV infections. Eight nasal swab collections were obtained from 135 two-week-old suckling piglets from four farms every other week from March to September 2013. Oral fluid samples were collected from the same group of nursery piglets. IAV RNA was detected in 1.64% and 31.01% of individual nasal swabs and oral fluids, respectively. H1N2 was detected most often, with sporadic detection of H1N1 and H3N2. Whole-genome sequences of IAV isolated from suckling piglets revealed an H1 hemagglutinin (HA) from the 1B.2.2.2 clade and N2 neuraminidase (NA) from the 2002A clade. The internal gene constellation of the endemic H1N2 was TTTTPT with a pandemic lineage matrix. The HA gene had 97.59% and 97.52% nucleotide and amino acid identities, respectively, to the H1 1B.2.2.2 used in the farm-specific vaccine. A similar H1 1B.2.2.2 was detected in the downstream nursery. These data demonstrate the low frequency of IAV detection in suckling piglets and downstream nurseries from farms with endemic infections in spite of using farm-specific IAV vaccines in sows.

A neonatal piglet model reveals interactions between nasal microbiota and influenza A virus pathogenesis

While vaccination and therapeutics for prevention/treatment of influenza are available, new strategies are needed to combat influenza disease in susceptible populations, particularly young children and newborns. Host associated microbiota play an important role in modulating the virulence of numerous pathogens, including the influenza A virus. In this study, we examined microbiome-influenza interactions in a neonatal piglet model system. The nasal microbiome of newborn piglets was longitudinally sampled before and after intranasal infection with recombinant viruses expressing hemagglutinins (HAs) derived from distinct zoonotic H1 subtypes. We found that viruses expressing different parental HAs manifested unique patterns of pathogenicity, and varied impacts on microbial community diversity. Despite these virus specific differences, a consistent microbial signature of viral infection was detected. Our results indicate that influenza A virus infection associates with the restructuring of nasal microbiome and such shifts in microbial diversity may contribute to outcomes of viral infection in neonatal piglets.

Swine influenza A virus infection dynamics and evolution in intensive pig production systems

Swine influenza A virus (swIAV) is one of the main viral pathogens responsible for respiratory disease in farmed pigs. While outbreaks are often epidemic in nature, increasing reports suggest that continuous, endemic infection of herds is now common. The move towards larger herd sizes and increased intensification in the commercial pig industry may promote endemic infection; however, the impact that intensification has on swIAV infection dynamics and evolution is unclear. We carried out a longitudinal surveillance study for over 18 months on two enzootically infected, intensive, indoor, and multi-site pig production flows. Frequent sampling of all production stages using individual and group sampling methods was performed, followed by virological and immunological testing and whole-genome sequencing. We identified weaned pigs between 4 and 12-weeks old as the main reservoir of swIAV in the production flows, with continuous, year-round infection. Despite the continuous nature of viral circulation, infection levels were not uniform, with increasing exposure at the herd level associated with reduced viral prevalence followed by subsequent rebound infection. A single virus subtype was maintained on each farm for the entire duration of the study. Viral evolution was characterised by long periods of stasis punctuated by periods of rapid change coinciding with increasing exposure within the herd. An accumulation of mutations in the surface glycoproteins consistent with antigenic drift was observed, in addition to amino acid substitutions in the internal gene products as well as reassortment exchange of internal gene segments from newly introduced strains. These data demonstrate that long-term, continuous infection of herds with a single subtype is possible and document the evolutionary mechanisms utilised to achieve this.

Use of prototype side stream filtration system to control dust levels in a commercial swine farrowing building

Swine meat provides an essential global food source. Due to economies of scale, modern U.S. swine production primarily occurs indoors to maintain an optimal environment across the stages of swine production. Indoor concentrations of dust and contaminant gases in swine production buildings increase in the winter months due to reduced ventilation to optimal building temperature. In this study, an engineering control technology designed to recirculate the air in a swine farrowing room through a mobile air handling unit containing high-efficiency particulate filters was presented. A mobile solution could be easily deployed as an intervention method if an infectious disease outbreak occurs at a swine operation. The performance of this control technology was evaluated following deployment in a production farrowing barn for a period of 6 weeks during the winter in the Midwestern United States. Contaminant concentrations of inhalable dust, respirable dust, and carbon dioxide were measured in the room treated by the prototype system and compared to contaminant concentrations measured in an untreated "control" room. Over 6 weeks, the mean inhalable and respirable dust concentrations observed during the study period for the "treatment" room were 2.61 and 0.14 mg/m3, respectively, compared to 3.51 and 0.25 mg/m3, respectively, for the control room. The mobile recirculating ventilation system, operating at a flow rate of 45 m3/min (5 room air exchanges per hour), reduced the inhalable dust by 25% and respirable dust by 48% as measured with a real-time aerosol monitor, when compared to the control room. In addition, no concentration differences in carbon dioxide and relative humidity between the treatment and the control rooms were observed. Inhalable and respirable concentrations of dust were significantly reduced (p = 0.001), which demonstrates an essential improvement of the air quality that may prove beneficial to reduce the burden of disease among both workers and animals.

Seroprevalence of Swine Influenza A Virus (swIAV) Infections in Commercial Farrow-to-Finish Pig Farms in Greece

Swine influenza is a highly contagious respiratory disease caused by influenza A virus infection. Pigs play an important role in the overall epidemiology of influenza because of their ability to transmit influenza viruses of avian and human origin, which plays a potential role in the emergence of zoonotic strains with pandemic potential. The aim of our study was to assess the seroprevalence of Swine Influenza Viruses (swIAVs) in commercial pig farms in Greece. A total of 1416 blood samples were collected from breeding animals (gilts and sows) and pigs aged 3 weeks to market age from 40 different swIAV vaccinated and unvaccinated commercial farrow-to-finish pig farms. For the detection of anti-SIV antibodies, sera were analyzed using an indirect ELISA kit CIVTEST SUIS INFLUENZA®, Hipra (Amer, Spain). Of the total 1416 animals tested, 498 were seropositive, indicating that the virus circulates in both vaccinated (54% seroprevalence) and unvaccinated Greek pig farms (23% seroprevalence). In addition, maternally derived antibody (MDA) levels were lower in pigs at 4 and 7 weeks of age in unvaccinated farms than in vaccinated farms. In conclusion, our results underscore the importance of vaccination as an effective tool for the prevention of swIAV infections in commercial farrow-to-finish pig farms.

Evaluation of early single dose vaccination on swine influenza A virus transmission in piglets: From experimental data to mechanistic modelling

Swine influenza A virus (swIAV) is a major pathogen affecting pigs with a huge economic impact and potentially zoonotic. Epidemiological studies in endemically infected farms permitted to identify critical factors favoring on-farm persistence, among which maternally-derived antibodies (MDAs). Vaccination is commonly practiced in breeding herds and might be used for immunization of growing pigs at weaning. Althoughinterference between MDAs and vaccination was reported in young piglets, its impact on swIAV transmission was not yet quantified. To this aim, this study reports on a transmission experiment in piglets with or without MDAs, vaccinated with a single dose injection at four weeks of age, and challenged 17 days post-vaccination. To transpose small-scale experiments to real-life situation, estimated parameters were used in a simulation tool to assess their influence at the herd level. Based on a thorough follow-up of the infection chain during the experiment, the transmission of the swIAV challenge strain was highly dependent on the MDA status of the pigs when vaccinated. MDA-positive vaccinated animals showed a direct transmission rate 3.6-fold higher than the one obtained in vaccinated animals without MDAs, estimated to 1.2. Vaccination nevertheless reduced significantly the contribution of airborne transmission when compared with previous estimates obtained in unvaccinated animals. The integration of parameter estimates in a large-scale simulation model, representing a typical farrow-to-finish pig herd, evidenced an extended persistence of viral spread when vaccination of sows and single dose vaccination of piglets was hypothesized. When extinction was quasi-systematic at year 5 post-introduction in the absence of sow vaccination but with single dose early vaccination of piglets, the extinction probability fell down to 33% when batch-to-batch vaccination was implemented both in breeding herd and weaned piglets. These results shed light on a potential adverse effect of single dose vaccination in MDA-positive piglets, which might lead to longer persistence of the SwIAV at the herd level.

Evolution and Introductions of Influenza A Virus H1N1 in a Farrow-to-Finish Farm in Guatemala

Commercial swine farms provide unique systems for interspecies transmission of influenza A viruses (FLUAVs) at the animal-human interface. Bidirectional transmission of FLUAVs between pigs and humans plays a significant role in the generation of novel strains that become established in the new host population. Active FLUAV surveillance was conducted for 2 years on a commercial pig farm in Southern Guatemala with no history of FLUAV vaccination. Nasal swabs (n = 2,094) from fattening pigs (6 to 24 weeks old) with respiratory signs were collected weekly from May 2016 to February 2018. Swabs were screened for FLUAV by real-time reverse transcriptase PCR (RRT-PCR), and full virus genomes of FLUAV-positive swabs were sequenced by next-generation sequencing (NGS). FLUAV prevalence was 12.0% (95% confidence interval [CI], 10.6% to 13.4%) with two distinct periods of high infection. All samples were identified as FLUAVs of the H1N1 subtype within the H1 swine clade 1A.3.3.2 and whose ancestors are the human origin 2009 H1N1 influenza pandemic virus (H1N1 pdm09). Compared to the prototypic reference segment sequence, 10 amino acid signatures were observed on relevant antigenic sites on the hemagglutinin. The Guatemalan swine-origin FLUAVs show independent evolution from other H1N1 pdm09 FLUAVs circulating in Central America. The zoonotic risk of these viruses remains unknown but strongly calls for continued FLUAV surveillance in pigs in Guatemala. IMPORTANCE Despite increased surveillance efforts, the epidemiology of FLUAVs circulating in swine in Latin America remains understudied. For instance, the 2009 H1N1 influenza pandemic strain (H1N1 pdm09) emerged in Mexico, but its circulation remained undetected in pigs. In Central America, Guatemala is the country with the largest swine industry. We found a unique group of H1N1 pdm09 sequences that suggests independent evolution from similar viruses circulating in Central America. These viruses may represent the establishment of a novel genetic lineage with the potential to reassort with other cocirculating viruses and whose zoonotic risk remains to be determined.

A New Sampling Approach for the Detection of Swine Influenza a Virus on European Sow Farms

Simple Summary

Due to concerns in public health and its negative impact on the pig industry the need for Influenza A virus (IAV) surveillance is rising. The gold standard procedure for detecting IAV is to sample acutely diseased pigs. Endemic infections with unspecific clinical signs and low disease prevalence need new approaches. Our study aimed to evaluate a standardized sampling procedure for the detection of IAV in epidemically and endemically infected farms. We performed a cross-sectional study in 131 farms investigating three different age groups per farm in 12 European countries. The results of our investigation indicate that 10 nasal swabs each in suckling piglets, weaners and middle of nursery is a valuable tool for influenza detection and identification of subtypes. However, for farms with a lower prevalence than 15% it is advisable to either increase the number of nasal swabs in each age group or to use group sampling methods. Interestingly, different subtypes were found in different age groups. Thus, our study underlines that sampling of different age groups is mandatory to obtain a comprehensive overview on all circulating variants on farm. In addition, our results highlight that sampling strategies should also consider piglets without obvious clinical signs for IAV infection.

Abstract

Swine influenza A virus (swIAV), which plays a major role in the porcine respiratory disease complex (PRDC), is eliminated from the respiratory tract within 7–9 days after infection. Therefore, diagnosis is complicated in endemically infected swine herds presenting no obvious clinical signs. This study aimed to investigate the right time point for sampling to detect swIAV. A cross-sectional study was performed in 131 farms from 12 European countries. The sampling protocol included suckling piglets, weaners, and nursery pigs. In each age group, 10 nasal swabs were collected and further examined in pools of 5 for swIAV by Matrix rRT-PCR, followed by a multiplex RT-PCR to determine the influenza subtype. SwIAV was detected in 284 (37.9%) of the samples and on 103 (78.6%) farms. Despite the highest number of animals with clinical signs being found in the nursery, the weaners were significantly more often virus-positive compared to nursery pigs (p = 0.048). Overall, the swIAV detection rate did not significantly differ between diseased or non-diseased suckling and nursery piglets, respectively; however, diseased weaners had significantly more positive pools than the non-diseased animals. Interestingly, in 9 farms, different subtypes were detected in different age groups. Our findings indicate that to detect all circulating swIAV subtypes on a farm, different age groups should be sampled. Additionally, the sampling strategy should also aim to include non-diseased animals, especially in the suckling period.

The role of gilts in transmission dynamics of swine influenza virus and impacts of vaccination strategies and quarantine management

BACKGROUND

Along with an expanding global swine production, the commercial housing and management of swine herds, provide an optimal environment for constant circulation of swine influenza virus (swIAV), thereby challenging farmers and veterinarian in determining optimal control measures. The aim of this study was to investigate the role of gilts in the swIAV transmission dynamics, and to evaluate the impact of different control measures such as quarantine and gilt vaccination.

METHODS

The study was conducted as a cross-sectional study in ten Danish sow herds, including five swIAV vaccinated and five unvaccinated herds. Blood- and nasal swab samples of gilts, first parity sows and their piglets were collected at different stages in the production system (quarantine in/out, mating, gestation and farrowing) and analyzed for the presence of swIAV and swIAV antibodies. Associations between the detection of swIAV, seroprevalence, antibody levels, sow and gilt vaccination strategy and quarantine biosecurity were thereafter investigated to identify possible risk factors for swIAV introductions and persistence within the herds.

RESULTS

Nine of the ten herds of the study had swIAV circulation and swIAV was detected in the quarantine, mating- and farrowing unit. The prevalence of seropositive gilts and first parity sows was significantly higher in the vaccinated herds, but swIAV was still present in nasal swabs from both gilts, first parity sows and piglets in these herds. Quarantine gilt vaccination and all-in/all-out management resulted in a significant reduction of swIAV positive gilts at the end of the quarantine period.

CONCLUSION

The results underline that herd vaccination and/or quarantine facilities are crucial to avoid swIAV introductions into sow herds.

Impact of maternally derived immunity on immune responses elicited by piglet early vaccination against the most common pathogens involved in porcine respiratory disease complex

Background

Newborn piglets can trigger an elementary immune response, but the acquirement of specific antibodies and/or cellular immunity against pathogens before they get infected post-natally is paramount to preserve their health. This is especially important for the pathogens involved in porcine respiratory disease complex (PRDC) as they are widespread, fairly resistant at environment, and genetically variable; moreover, some of them can cause intrauterine/early life infections.

Main body

Piglet protection can be achieved by either passive transfer of maternal derived immunity (MDI) and/or actively through vaccination. However, vaccinating piglets in the presence of remaining MDI might interfere with vaccine efficacy. Hence, the purpose of this work is to critically review the putative interference that MDI may exert on vaccine efficacy against PRDC pathogens. This knowledge is crucial to design a proper vaccination schedule.

Conclusion

MDI transferred from sows to offspring could potentially interfere with the development of an active humoral immune response. However, no conclusive interference has been shown regarding performance parameters based on the existing published literature.

Evolution of influenza A virus in intensive and free-range swine farms in Spain

Swine harbor genetically diverse influenza A viruses (IAVs) with the capacity to host-switch to humans, causing global pandemics. Spain is the largest swine producer in Europe and has a mixed production system that includes 'white coat' pigs raised intensively in modern buildings and free-range Iberian pigs that interface differently with humans, wildlife, and other swine. Through active longitudinal IAV surveillance in nine Spanish provinces during 2015-9, we generated forty-seven complete or near-complete genome sequences from IAVs collected from swine in both systems. Genetically diverse IAVs were identified in intensively raised white pigs and free-range Iberian pigs, including new H3N1 reassortants. Both systems are dynamic environments for IAV evolution, but driven by different processes. IAVs in white pigs were genetically related to viruses found in swine raised intensively in other European countries, reflecting high rates of viral introduction following European trade routes. In contrast, IAVs in Iberian pigs have a genetic makeup shaped by frequent introductions of human IAVs, reflecting rearing practices with high rates of human contact. Transmission between white and Iberian pigs also occurred. In conclusion, Iberian swine with high rates of human contact harbor genetically diverse IAVs and potentially serve as intermediary hosts between white pigs and humans, presenting an understudied zoonotic risk that requires further investigation.

[Challenges in Influenza diagnostics in a swine herd - a case report]

In a gilt producing farm in Lower Austria, respiratory diseases occurred over the previous years in self-reared gilts after being introduced into the sow herd. In addition, fertility disorders in terms of late abortions and re-breeders were observed in the fall of 2019. Nasal swabs of 3 gilts with respiratory signs and fever were tested positive for influenza A virus (IAV) subtype H1avN1 by PCR. However, examination of serum samples from these animals at 2 different time points did not detect antibodies using the standard hemagglutination inhibition (HI) test of the laboratory. Examination of additional age groups likewise failed to detect H1avN1 antibody titers. In consequence to the extension of the diagnostic panel of the HI test by 7 additional H1avN1 test antigens, a clear seroconversion of the PCR positive sows against 2 different H1avN1 isolates could be measured. In addition, high antibody titers against these 2 H1avN1 strains were also detectable in the majority of the remaining age groups tested. Following the administration of the trivalent influenza vaccine, which has been approved throughout Europe, a significant improvement of the clinical presentation in the herd was achieved. The present case report illustrates that direct and indirect pathogen detection should be used in combination for targeted influenza diagnostics. In addition, it was shown that the continuous adaptation of test antigens to the isolates circulating in the field would be extremely crucial for the significance of the HI test.

Improving Current Knowledge on Seroprevalence and Genetic Characterization of Swine Influenza Virus in Croatian Pig Farms: A Retrospective Study

In a total of 1536 blood serum samples analysed by ELISA, antibodies for IAV nucleoprotein (NP) were detected in 30.3%. Results from HI show that the most common subtype of swIAV in the Croatian pig population was H1N1 (44.6%), followed by H3N2 (42.7%) and H1N2 (26.3%). Antibodies to at least one subtype were detected in 62.19% of blood serum samples. Detection of swIAV antigen was performed by IHC and detected in 8 of 28 lung samples collected post-mortem. The matrix (M) gene was detected in nine of one hundred and forty-two lung tissue samples and in seven of twenty-nine nasopharyngeal swabs. Phylogenetic analysis of amplified HA and NA gene fragments in Croatian isolates suggests the presence of swIAV H1avN1av.

Development of an antigen Enzyme-Linked AptaSorbent Assay (ELASA) for the detection of swine influenza virus in field samples

Influenza viruses are highly variable pathogens that infect a wide range of mammalian and avian species. According to the internal conserved proteins (nucleoprotein: NP, and matrix proteins: M), these viruses are classified into type A, B, C, and D. Influenza A virus in swine is of significant importance to the industry since it is responsible for endemic infections that lead to high economic loses derived from poor weight gain, reproductive disorders, and the role it plays in Porcine Respiratory Disease Complex (PRDC). To date, swine influenza virus (SIV) diagnosis continues to be based in complex and expensive technologies such as RT-qPCR. In this study, we aimed to improve actual tools by the implementation of aptamers as capture molecules. First, three different aptamers have been selected using as target the recombinant NP of Influenza A virus expressed in insect cells. Then, these molecules have been used for the development of an Enzyme-Linked AptaSorbent Assay (ELASA) in combination with specific monoclonal antibodies for Influenza A detection. A total of 171 field samples (nasal swabs) have been evaluated with the newly developed assay obtaining a 79.7% and 98.1% sensitivity and specificity respectively, using real time RT-PCR as standard assay. These results suggest that the assay is a promising method that could be used for Influenza A detection in analysis laboratories facilitating surveillance labours.

Seasonal Variation in Prevalence of Mycoplasma hyopneumoniae and Other Respiratory Pathogens in Peri-Weaned, Post-Weaned, and Fattening Pigs with Clinical Signs of Respiratory Diseases in Belgian and Dutch Pig Herds, Using a Tracheobronchial Swab Sampling Technique, and Their Associations with Local Weather Conditions

Besides Mycoplasma hyopneumoniae (M. hyopneumoniae), many other viruses and bacteria can concurrently be present in pigs. These pathogens can provoke clinical signs, known as porcine respiratory disease complex (PRDC). A sampling technique on live animals, namely tracheobronchial swab (TBS) sampling, was applied to detect different PRDC pathogens in pigs using PCR. The objective was to determine prevalence of different PRDC pathogens and their variations during different seasons, including correlations with local weather conditions. A total of 974 pig farms and 22,266 pigs were sampled using TBS over a 5-year period. TBS samples were analyzed using mPCR and results were categorized and analyzed according to the season of sampling and local weather data. In samples of peri-weaned and post-weaned piglets, influenza A virus in swine (IAV-S), porcine reproductive and respiratory syndrome virus-European strain (PRRSV1), and M. hyopneumoniae were found as predominant pathogens. In fattening pigs, M. hyopneumoniae, porcine circovirus type 2 (PCV-2) and PRRSV1 were predominant pathogens. Pathogen prevalence in post-weaned and finishing pigs was highest during winter, except for IAV-S and A. pleuropneumoniae, which were more prevalent during autumn. Associations between prevalence of several PRDC pathogens, i.e., M. hyopneumoniae, PCV-2 and PRRSV, and specific weather conditions could be demonstrated. In conclusion, the present study showed that many respiratory pathogens are present during the peri-weaning, post-weaning, and fattening periods, which may complicate the clinical picture of respiratory diseases. Interactions between PRDC pathogens and local weather conditions over the 5-year study period were demonstrated.

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

Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018. In total, 3800 submissions were received with a steady increase in swIAV-positive submissions, reaching 56% in 2018. Full-genome sequences were obtained from 129 swIAV-positive samples. Altogether, 17 different circulating genotypes were identified including six novel reassortants harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx (clade 1A.3.3.2) viruses. The results provide essential data for the control of swIAV in pigs and emphasize the importance of contemporary surveillance for discovering novel swIAV strains posing a potential threat to the human population.

Assessment of exposure to influenza A viruses in pigs between weaning and market age

Influenza A viruses (IAVs) are common causes of respiratory infection in pigs. The objective of this study was to characterize the circulation of IAVs between weaning and market age on the basis of development of antibody response and molecular epidemiology of detected viruses. Two batches of weaned pigs were followed in the nursery and finisher barns with a sample of 81 and 75 pigs. Nasal swabs and blood samples were collected from individual pigs for virological and serological analyses. A H3N2 subtype virus, of cluster IV, was detected in Study 1, with a maximum of 97.9% identity to HA gene of viruses previously isolated in Ontario. In Study 2, a H1N1 subtype virus, of 2009 H1N1 pandemic lineage, was detected, with a maximum of 97.8% identity to HA gene of viruses previously isolated in Ontario. On the basis of HA gene, it was observed that pigs were being detected with the same virus over time. The existence of antibody titers for IAV other than the isolated one confirmed that more than one subtype can circulate in the same population. In Study 1, pigs with higher numbers of IAV detection had lower serological titers for the same virus that was confirmed to circulate in the nursery (P < 0.01). Thorough knowledge of all endemic viral strains is fundamental for development of infection and disease control, particularly in complex production systems. This may include consideration of sampling and testing strategies which could detect circulation of all IAV variants, even if they have low prevalence.

Infection Dynamics of Swine Influenza Virus in a Danish Pig Herd Reveals Recurrent Infections with Different Variants of the H1N2 Swine Influenza A Virus Subtype

Influenza A virus (IAV) in swine, so-called swine influenza A virus (swIAV), causes respiratory illness in pigs around the globe. In Danish pig herds, a H1N2 subtype named H1N2dk is one of the main circulating swIAV. In this cohort study, the infection dynamic of swIAV was evaluated in a Danish pig herd by sampling and PCR testing of pigs from two weeks of age until slaughter at 22 weeks of age. In addition, next generation sequencing (NGS) was used to identify and characterize the complete genome of swIAV circulating in the herd, and to examine the antigenic variability in the antigenic sites of the virus hemagglutinin (HA) and neuraminidase (NA) proteins. Overall, 76.6% of the pigs became PCR positive for swIAV during the study, with the highest prevalence at four weeks of age. Detailed analysis of the virus sequences obtained showed that the majority of mutations occurred at antigenic sites in the HA and NA proteins of the virus. At least two different H1N2 variants were found to be circulating in the herd; one H1N2 variant was circulating at the sow and nursery sites, while another H1N2 variant was circulating at the finisher site. Furthermore, it was demonstrated that individual pigs had recurrent swIAV infections with the two different H1N2 variants, but re-infection with the same H1N2 variant was also observed. Better understandings of the epidemiology, genetic and antigenic diversity of swIAV may help to design better health interventions for the prevention and control of swIAV infections in the herds.

Diversity of influenza A viruses retrieved from respiratory disease outbreaks and subclinically infected herds in Spain (2017-2019)

The present study was aimed to assess the diversity of influenza A viruses (IAV) circulating in pig farms in the Iberian Peninsula. The study included two different situations: farms suffering respiratory disease outbreaks compatible with IAV (n = 211) and randomly selected farms without overt respiratory disease (n = 19). Initially, the presence of IAV and lineage determination was assessed by qRT‐PCR using nasal swabs. IAV was confirmed in 145 outbreaks (68.7%), mostly in nurseries (53/145; 36.5%). Subtyping by RT‐qPCR was possible in 94 of those cases being H1avN2hu (33.6%), H1avN1av (24.3%) and H1huN2hu (18.7%), the most common lineages. H3huN2hu and H1pdmN1pdm represented 7.5% and 6.5% of the cases, respectively. As for the randomly selected farms, 15/19 (78.9%) were positive for IAV. Again, the virus was mostly found in nurseries and H1avN2hu was the predominant lineage. Virus isolation in MDCK cells was attempted from positive cases. Sixty of the isolates were fully sequenced with Illumina MiSeq®. Within those 60 isolates, the most frequent genotypes had internal genes of avian origin, and these were D (19/60; 31.7%) and A (11/60; 18.3%), H1avN2hu and H1avN1av, respectively. In addition, seven previously unreported genotypes were identified. In two samples, more than one H or N were found and it was not possible to precisely establish their genotypes. A great diversity was observed in the phylogenetic analysis. Notably, four H3 sequences clustered with human isolates from 2004–05 (Malaysia and Denmark) that were considered uncommon in pigs. Overall, this study indicates that IAV is a very common agent in respiratory disease outbreaks in Spanish pig farms. The genetic diversity of this virus is continuously expanding with clear changes in the predominant subtypes and lineages in relatively short periods of time. The current genotyping scheme has to be enlarged to include the new genotypes that could be found in the future.

A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide

The global anxiety and a significant threat to public health due to the current COVID-19 pandemic reiterate the need for active surveillance for the zoonotic virus diseases of pandemic potential. Influenza virus due to its wide host range and zoonotic potential poses such a significant threat to public health. Swine serve as a “mixing vessel” for influenza virus reassortment and evolution which as a result may facilitate the emergence of new strains or subtypes of zoonotic potential. In this context, the currently available scientific data hold a high significance to unravel influenza virus epidemiology and evolution. With this objective, the current systematic review summarizes the original research articles and case reports of all the four types of influenza viruses reported in swine populations worldwide. A total of 281 articles were found eligible through screening of PubMed and Google Scholar databases and hence were included in this systematic review. The highest number of research articles (n = 107) were reported from Asia, followed by Americas (n = 97), Europe (n = 55), Africa (n = 18), and Australia (n = 4). The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were the most common influenza A virus subtypes reported in swine in most countries across the globe, however, few strains of influenza B, C, and D viruses were also reported in certain countries. Multiple reports of the avian influenza virus strains documented in the last two decades in swine in China, the United States, Canada, South Korea, Nigeria, and Egypt provided the evidence of interspecies transmission of influenza viruses from birds to swine. Inter-species transmission of equine influenza virus H3N8 from horse to swine in China expanded the genetic diversity of swine influenza viruses. Additionally, numerous reports of the double and triple-reassortant strains which emerged due to reassortments among avian, human, and swine strains within swine further increased the genetic diversity of swine influenza viruses. These findings are alarming hence active surveillance should be in place to prevent future influenza pandemics.

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

The degree of antigenic drift in swine influenza A viruses (swIAV) has historically been regarded as minimal compared to that of human influenza A virus strains. However, as surveillance activities on swIAV have increased, more isolates have been characterized, revealing a high level of genetic and antigenic differences even within the same swIAV lineage. The objective of this study was to investigate the level of genetic drift in one enzootically infected swine herd over one year. Nasal swabs were collected monthly from sows (n = 4) and piglets (n = 40) in the farrowing unit, and from weaners (n = 20) in the nursery. Virus from 1-4 animals were sequenced per month. Analyses of the sequences revealed that the hemagglutinin (HA) gene was the main target for genetic drift with a substitution rate of 7.6 × 10-3 substitutions/site/year and evidence of positive selection. The majority of the mutations occurred in the globular head of the HA protein and in antigenic sites. The phylogenetic tree of the HA sequences displayed a pectinate typology, where only a single lineage persists and forms the ancestor for subsequent lineages. This was most likely caused by repeated selection of a single immune-escape variant, which subsequently became the founder of the next wave of infections.

Reproductive performance of pandemic influenza A virus infected sow herds before and after implementation of a vaccine against the influenza A (H1N1)pdm09 virus

Background

Reproductive failure in sow herds due to infection with influenza A viruses has been described in the literature, but only a few studies have focused on the pathogenesis and the clinical signs of the infection. Case reports indicate an association between infections with influenza A viruses and reduced reproductive performance, although it has been difficult to experimentally reproduce the clinical outcome of poor reproductive performance. The aim of the present longitudinal field study was to compare the reproductive performance parameters before and after the implementation of vaccination against the influenza A (H1N1)pdm09 virus in sow herds infected with pandemic influenza A virus. Therefore, farm-specific data of 137 sow herds in Germany, including 60,153 sows, as well as the clinical presentation of the infection were surveyed via questionnaire. Furthermore, average performance parameters (return to oestrus rate, abortion rate, stillbirth rate, number of piglets born alive per litter, preweaning mortality rate and number of piglets weaned per sow per year) were recorded for 6 months before vaccination and 6 months after completion of primary vaccination.

Results

In 79.8% of the farms, the clinical presentation of the infection was characterised by a reduced reproductive performance. These findings were confirmed by analysis of the performance parameters, which revealed a significant decline in the return to oestrus rate (p < 0.001), abortion rate (p < 0.001) and preweaning mortality rate (p = 0.023) and a significant increase of the number in piglets born alive (p = 0.001) and piglets weaned per sow per year (p < 0.001) after immunisation. The stillbirth rate did not change significantly.

Conclusion

The present study represents the first attempt to demonstrate the association of influenza A virus infection, vaccination and the alteration in reproductive performance parameters, investigating a large number of cases. The results show that by vaccinating against the influenza A (H1N1)pdm09 virus, an improvement in reproductive performance can be achieved in sow herds infected with pandemic influenza A virus. Additionally, the large number of herds that were affected by poor reproductive performance after infection with the aforementioned virus confirms the assumption of an association between pandemic influenza A virus and reproductive losses.

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

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.

Limited impact of influenza A virus vaccination of piglets in an enzootic infected sow herd

Recent studies have questioned the effect of maternal derived antibodies (MDAs) to protect piglets against infection with influenza A virus (IAV). The lack of protection against IAV infections provided by MDAs has encouraged alternative vaccination strategies targeting young piglets in an attempt to stimulate an early antibody response. There is a lack of studies documenting the efficacy of piglet vaccination. In the present study, we monitored a group of vaccinated and non-vaccinated piglets in a Danish sow herd that initiated piglet vaccination with ¼ dose of an inactivated swine influenza vaccine at the time of castration (day 3-4). A total of 160 piglets from 11 sows were included and either vaccinated with 0.5 mL inactivated swine influenza vaccine or sham-vaccinated. From week 0 until week 6, all included piglets were clinically examined and nasal swapped once per week and weighed at weeks 0, 3 and 6. Blood samples were collected from sows at week 0 and from piglets at week 3. Vaccination of piglets had limited effect on clinical signs, body weight, antibody development and viral shedding, within the first 6 weeks of life. At least 50% of all pigs of each treatment group tested positive for IAV at week 2, and very early onset of IAV shedding was observed. In total, 18 pigs were IAV positive in nasal swabs for more than one consecutive sampling time indicating prolonged shedding and 14 pigs were IAV positive with negative samplings in between indicating re-infection with the same IAV strain.

Longitudinal field studies reveal early infection and persistence of influenza A virus in piglets despite the presence of maternally derived antibodies

A longitudinal study was performed in three Danish farrow to grower (30 kilos) herds over a 4-month period to investigate the dynamics and clinical impacts of influenza A virus (IAV) infections. In each herd, four batches consisting of four sows each with five ear-tagged piglets were included. Nasal swabs and/or blood were sampled from the sows and/or the piglets prior to farrowing and at weeks 1, 3, and 5 and at the end of the nursery period. Clinical examinations were performed at each sampling time. The sows and piglets were tested for IAV and IAV antibodies in nasal swabs and blood samples, respectively. The results revealed three enzootically infected herds, where the majority of the pigs were infected during the first 5 weeks after birth. Infected piglets of only 3 days of age were detected in the farrowing unit, where the sows were also shedding virus. In all herds, low to moderate numbers of infected pigs (ranging from 3.6 to 20.7%) were found to be virus positive in nasal swabs at two consecutive sampling times. Furthermore, clinical signs of respiratory disease were associated with IAV detection. The findings of this study documented that IAV can persist in herds and that piglets as young as 3 days can be infected despite the presence of maternally derived antibodies.

Effect of strain-specific maternally-derived antibodies on influenza A virus infection dynamics in nursery pigs

Reducing the number of influenza A virus (IAV) infected pigs at weaning is critical to minimize IAV spread to other farms. Sow vaccination is a common measure to reduce influenza levels at weaning. However, the impact of maternally-derived antibodies on IAV infection dynamics in growing pigs is poorly understood. We evaluated the effect of maternally-derived antibodies at weaning on IAV prevalence at weaning, time of influenza infection, number of weeks that pigs tested IAV positive, and estimated quantity of IAV in nursery pigs. We evaluated 301 pigs within 10 cohorts for their influenza serological (seroprevalence estimated by hemagglutination inhibition (HI) test) and virological (prevalence) status. Nasal swabs were collected weekly and pigs were bled 3 times throughout the nursery period. There was significant variability in influenza seroprevalence, HI titers and influenza prevalence after weaning. Increase in influenza seroprevalence at weaning was associated with low influenza prevalence at weaning and delayed time to IAV infection throughout the nursery. Piglets with IAV HI titers of 40 or higher at weaning were also less likely to test IAV positive at weaning, took longer to become infected, tested IAV RT-PCR positive for fewer weeks, and had higher IAV RT-PCR cycle threshold values compared to piglets with HI titers less than 40. Our findings suggest that sow vaccination or infection status that results in high levels of IAV strain-specific maternally-derived antibodies may help to reduce IAV circulation in both suckling and nursery pigs.

Computationally optimized broadly reactive vaccine based upon swine H1N1 influenza hemagglutinin sequences protects against both swine and human isolated viruses

Swine H1 influenza viruses were stable within pigs for nearly 70 years until in 1998 when a classical swine virus reassorted with avian and human influenza viruses to generate the novel triple reassortant H1N1 strain that eventually led to the 2009 influenza pandemic. Previously, our group demonstrated broad protection against a panel of human H1N1 viruses using HA antigens derived by the COBRA methodology. In this report, the effectiveness of COBRA HA antigens (SW1, SW2, SW3 and SW4), which were designed using only HA sequences from swine H1N1 and H1N2 isolates, were tested in BALB/c mice. The effectiveness of these vaccines were compared to HA sequences designed using both human and swine H1 HA sequences or human only sequences. SW2 and SW4 elicited antibodies that detected the pandemic-like virus, A/California/07/2009 (CA/09), had antibodies with HAI activity against almost all the classical swine influenza viruses isolated from 1973-2015 and all of the Eurasian viruses in our panel. However, sera collected from mice vaccinated with SW2 or SW4 had HAI activity against ~25% of the human seasonal-like influenza viruses isolated from 2009-2015. In contrast, the P1 COBRA HA vaccine (derived from both swine and human HA sequences) elicited antibodies that had HAI activity against both swine and human H1 viruses and protected against CA/09 challenge, but not a human seasonal-like swine H1N2 virus challenge. However, the SW1 vaccine protected against this challenge as well as the homologous vaccine. These results support the idea that a pan-swine-human H1 influenza virus vaccine is possible.

First demonstration of the circulation of a pneumovirus in French pigs by detection of anti-swine orthopneumovirus nucleoprotein antibodies

The presence of pneumoviruses in pigs is poorly documented. In this study, we used the published sequence of the nucleoprotein (N) of the recently identified Swine Orthopneumovirus (SOV) to express and purify SOV N as a recombinant protein in Escherichia coli. This protein was purified as nanorings and used to set up an enzyme-linked immunosorbent assay, which was used to analyse the presence of anti-pneumovirus N antibodies in swine sera. Sera collected from different pig farms in the West of France and from specific pathogen free piglets before colostrum uptake showed indirectly that a pneumovirus is circulating in pig populations with some variations between animals. Piglets before colostrum uptake were sero-negative for anti-pneumovirus antibodies while most of the other pigs showed positivity. Interestingly, in two farms presenting respiratory clinical signs and negative or under control for some common respiratory pathogens, pigs were detected positive for anti-pneumovirus antibodies. Globally, anti-pneumovirus N antibody concentrations were variable between and within farms. Further studies will aim to isolate the circulating virus and determine its potential pathogenicity. SOV could potentially become a new member of the porcine respiratory complex, important on its own or in association with other viral and bacterial micro-organisms.

Genetic and antigenic dynamics of influenza A viruses of swine on pig farms in Thailand

Surveillance studies of influenza A virus of swine (IAV-S) have accumulated information regarding IAVs-S circulating in Thailand, but how IAVs-S evolve within a farm remains unclear. In the present study, we isolated 82 A(H1N1)pdm09 and 87 H3N2 viruses from four farms from 2011 through 2017. We then phylogenetically and antigenically analyzed the isolates to elucidate their evolution within each farm. Phylogenetic analysis demonstrated multiple introductions of A(H1N1)pdm09 viruses that resembled epidemic A(H1N1)pdm09 strains in humans in Thailand, and they reassorted with H3N2 viruses as well as other A(H1N1)pdm09 viruses. Antigenic analysis revealed that the viruses had acquired antigenic diversity either by accumulating substitutions in the hemagglutinin protein or through the introduction of IAV-S strains with different antigenicity. Our results, obtained through continuous longitudinal surveillance, revealed that IAV-S can be maintained on a pig farm over several years through the generation of antigenic diversity due to the accumulation of mutations, introduction of new strains, and reassortment events.

Live attenuated influenza virus vaccine reduces virus shedding of newborn piglets in the presence of maternal antibody

Background

Influenza A virus in swine (IAV‐S) causes an acute respiratory disease of swine which results in great economic losses in pig production. Major control strategies include the use of killed vaccines (KV) in breeding females to confer passive immunity to their offspring. A bivalent H1N1 and H3N2 NS1‐truncated live attenuated IAV‐S vaccine have recently become available, which showed promising results in young pigs.

Objective

The aim of this study was to investigate the effect of an intranasal vaccination of newborn pigs with or without maternally derived antibodies (MDA) on virus shedding (via nasal swabs tested by virus isolation).

Methods

The study was performed as intratracheal challenge experiments with either a heterologous H1N2 or H3N2 viruses.

Results and conclusion

The results of this study showed a significant decrease in the incidence and duration of shedding viable virus for vaccinated newborn piglets with or without MDA, providing strong evidence that intranasal vaccination is overcoming passively acquired maternal immunity. This study indicates that intranasal vaccination with a truncated NS1 live attenuated IAV‐S vaccine of newborn piglets with maternal antibodies can be a valuable tool for reducing the prevalence of heterologous H1N2 and H3N2 IAV‐S in pig herds.

Coinfection modulates inflammatory responses, clinical outcome and pathogen load of H1N1 swine influenza virus and Haemophilus parasuis infections in pigs

BACKGROUND

Respiratory co-infections are important factor affecting the profitability of pigs production. Swine influenza virus (SIV) may predispose to secondary infection. Haemophilus parasuis (Hps) can be a primary pathogen or be associated with other pathogens such as SIV. To date, little is known about the effect of coinfection with SIV and Hps on the disease severity and inflammatory response and the role of Hps in the induction of pneumonia in the absence of other respiratory pathogens. In the study we investigated the influence of SIV and Hps coinfection on clinical course, inflammatory response, pathogens shedding and load at various time points following intranasal inoculation. The correlation between local concentration of cytokines and severity of disease as well as serum acute phase proteins (APP) concentration has been also studied.

RESULTS

All co-infected pigs had fever, while in single inoculated pigs fever was observed only in part of animals. Necropsy revealed lesions in the lungs all SIV-inoculated and co-inoculated pigs, while in Hps-single inoculated animals only 1 out of 11 pigs revealed gross lung lesions. The SIV shedding was the highest in co-inoculated pigs. There were no differences between Hps-single inoculated and co-inoculated groups with regard to Hps shedding. The significant increase in Hps titre in the lung has been found only in co-inoculated group. All APP increased after co-infection. In single-inoculated animals various kinetics of APP response has been observed. The lung concentrations of cytokines were induced mostly in SIV + Hps pigs in the apical and middle lobe. These results correlated well with localization of gross lung lesions.

CONCLUSIONS

The results revealed that SIV increased the severity of lung lesions and facilitated Hps (PIWetHps192/2015) replication in the porcine lung. Furthermore, Hps influenced the SIV nasal shedding. Enhanced Hps and SIV replication, together with stronger systemic and local inflammatory response contributed to a more severe clinical signs and stronger, earlier immune response in co-inoculated animals. We confirmed the previous evidence that single-Hps infection does not produce significant pneumonic lesions but it should be in mind that other strains of Hps may produce lesions different from that reported in the present study.

Influenza Herd-Level Prevalence and Seasonality in Breed-to-Wean Pig Farms in the Midwestern United States

Influenza is a costly disease for pig producers and understanding its epidemiology is critical to control it. In this study, we aimed to estimate the herd-level prevalence and seasonality of influenza in breed-to-wean pig farms, evaluate the correlation between influenza herd-level prevalence and meteorological conditions, and characterize influenza genetic diversity over time. A cohort of 34 breed-to-wean farms with monthly influenza status obtained over a 5-year period in piglets prior to wean was selected. A farm was considered positive in a given month if at least one oral fluid tested influenza positive by reverse transcriptase polymerase chain reaction. Influenza seasonality was assessed combining autoregressive integrated moving average (ARIMA) models with trigonometric functions as covariates. Meteorological conditions were gathered from local land-based weather stations, monthly aggregated and correlated with influenza herd-level prevalence. Influenza herd-level prevalence had a median of 28% with a range from 7 to 57% and followed a cyclical pattern with levels increasing during fall, peaking in both early winter (December) and late spring (May), and decreasing in summer. Influenza herd-level prevalence was correlated with mean outdoor air absolute humidity (AH) and temperature. Influenza genetic diversity was substantial over time with influenza isolates belonging to 10 distinct clades from which H1 delta 1 and H1 gamma 1 were the most common. Twenty-one percent of farms had three different clades co-circulating over time, 18% of farms had two clades, and 41% of farms had one clade. In summary, our study showed that influenza had a cyclical pattern explained in part by air AH and temperature changes over time, and highlighted the importance of active surveillance to identify high-risk periods when strategic control measures for influenza could be implemented.

Longitudinal study of influenza A virus circulation in a nursery swine barn

Commercial production of swine often involves raising animals in large groups through the use of multi-stage production systems. In such systems, pigs can experience different degrees of contact with animals of the same or different ages. Population size and degree of contact can greatly influence transmission of endemic pathogens, including influenza A virus (IAV). IAV can display high genetic variability, which can further complicate population-level patterns. Yet, the IAV transmission in large multi-site swine production systems has not been well studied. The objectives of this study were to describe the IAV circulation in a multi-source nursery facility and identify factors associated with infection in nursery pigs. Pigs from five sow herds were mixed in one all-in/all-out nursery barn, with 81 and 75 pigs included in two longitudinal studies. Virus isolation was performed in Madin-Darby canine kidney cells and serology was performed using hemagglutination inhibition assays. Risk factor analysis for virological positivity was conducted using logistic regression and stratified Cox’s regression for recurrent events. In Study 1, at ≈30 days post-weaning, 100% of pigs were positive, with 43.2% of pigs being positive recurrently over the entire study period. In study 2, 48% of pigs were positive at the peak of the outbreak, and 10.7% were positive recurrently over the entire study period. The results suggest that IAV can circulate during the nursery phase in an endemic pattern and that the likelihood of recurrent infections was associated in a non-linear way with the level of heterologous (within-subtype) maternal immunity (p < 0.05). High within-pen intracluster correlation coefficients (> 0.75) were also observed for the majority of sampling times suggesting that pen-level factors played a role in infection dynamics in this study.

Control of endemic swine flu persistence in farrow-to-finish pig farms: a stochastic metapopulation modeling assessment

Swine influenza viruses (swIAVs) are known to persist endemically in farrow-to-finish pig farms, leading to repeated swine flu outbreaks in successive batches of pigs at a similar age (mostly around 8 weeks of age). This persistence in European swine herds involves swIAVs from European lineages including H1_avN1, H1_huN2, H3N2, the 2009 H1N1 pandemic virus and their reassortants. The specific population dynamics of farrow-to-finish pig farms, the immune status of the animals at infection-time, the co-circulation of distinct subtypes leading to consecutive or concomitant infections have been evidenced as factors favouring swIAV persistence within herds. We developed a stochastic metapopulation model representing the co-circulation of two distinct swIAVs within a typical farrow-to-finish pig herd to evaluate the risk of reassortant viruses generation due to co-infection events. Control strategies related to herd management and/or vaccination schemes (batch-to-batch or mass vaccination of the sow herd and vaccination of growing pigs) were implemented to assess their relative efficacy regarding viral persistence. The overall probability of a co-infection event for France, possibly leading to reassortment, was evaluated to 16.8%. The export of consecutive piglets batches was identified as the most efficient measure facilitating swIAV infection fade-out. Although some vaccination schemes (batch-to-batch vaccination) had a beneficial effect in breeding sows by reducing the persistence of swIAVs within this subpopulation, none of vaccination strategies achieved swIAVs fade-out within the entire farrow-to-finish pig herd.

Epidemiological features of influenza circulation in swine populations: A systematic review and meta-analysis

Background

The emergence of the 2009 influenza pandemic virus with a swine origin stressed the importance of improving influenza surveillance in swine populations. The objectives of this systematic review and meta-analysis were to describe epidemiological features of swine influenza (SI) across the world and identify factors impacting swine influenza virus surveillance.

Methods

The systematic review followed the PRISMA guidelines. Articles published after 1990 containing data on SI on pig and herd-level seroprevalence, isolation and detection rates, and risk factors were included. Meta-regression analyses using seroprevalence and virological rates were performed.

Results

A total of 217 articles were included. Low avian influenza (AI) seroprevalence (means pig = 4.1%; herd = 15%) was found, showing that AIV do not readily establish themselves in swine while SIV seroprevalence was usually high across continents (influenza A means pig = 32.6–87.8%; herd = 29.3–100%). Higher pig density and number of pigs per farm were shown by the meta-regression analyses and/or the risk factor articles to be associated with higher SI seroprevalence. Lower seroprevalence levels were observed for countries with low-to-medium GDP. These results suggest that larger industrial farms could be more at risk of SIV circulation. Sampling swine with influenza-like illness (ILI) was positively associated with higher isolation rates; most studies in Europe, Latin and North America were targeting swine with ILI.

Conclusions

To improve understanding of SI epidemiology, standardization of the design and reporting of SI epidemiological studies is desirable. Performance of SI surveillance systems in low-to-medium GDP countries should be evaluated to rule out technical issues linked to lower observed SIV prevalence. Targeting certain swine age groups, farming systems and swine with ILI may improve the surveillance cost-effectiveness. However, focusing on pigs with ILI may bias virus detection against strains less virulent for swine but which may be important as pandemic threats.

Estimation of the transmission parameters for swine influenza and porcine reproductive and respiratory syndrome viruses in pigs from weaning to slaughter under natural conditions

In the present study, the transmission parameters of swine influenza virus (SIV) and porcine reproductive and respiratory virus (PRRSV) have been calculated using the basic reproductive rate (R) parameter in two commercial pig farms (F1 and F2). In order to do this, a serological (PRRSV genotype 1 and SIV) and virological (SIV) follow-up of a batch of animals was carried out weekly from 3 weeks of age until the age of slaughter on each farm. Results of the analysis for SIV and PRRSV showed different transmission profiles depending on the farm, the pathogen, and time of transmission. In F1, transmission of both viruses was detected throughout the sampling. The R_t (R for a given period of time) value for SIV ranged from 1.5 [0.9-2.3] to 3.6 [2.3-4.9] from farrowing to the beginning of the fattening period, and the R_t value for PRRSV was 3.3 [2.9-4.3] to 3.5 [2.8-4.1] from farrowing until the slaughter age. These results indicated that both viruses were transmitted enzootically in that farm for these periods of time. A different transmission pattern with a higher incidence was also observed during the fattening period in F1 (after 15 weeks of age) for SIV, coinciding with the entrance of a new subtype. In this case, R value for SIV reached 3.3 [1.65-4.9]. On the other hand, in F2, SIV and PRRSV seemed to be restricted to the fattening period. R reached a value of 6.4 [4.1-8.8] for SIV and 7.1 [3.5-10.6] for PRRSV. These findings suggest a different origin of the virus, as well as a more epidemic circulation, especially for SIV, where most of the new cases were observed in a one week period. In conclusion, the present study offers a reliable estimation of the range of R_t values for SIV and genotype 1 PRRSV transmission under field conditions, suggesting that enzootic circulations of both viruses are similar in terms of transmission, probably higher for PRRSV, but also that transmission of SIV is more efficient (or epidemic) than transmission of a genotype 1 PRRSV isolate in naïve animals given the new cases observed in only in F2.

Two years of surveillance of influenza a virus infection in a swine herd. Results of virological, serological and pathological studies

Swine farms provide a dynamic environment for the evolution of influenza A viruses (IAVs). The present report shows the results of a surveillance effort of IAV infection in one commercial swine farm in Argentina. Two cross-sectional serological and virological studies (n=480) were carried out in 2011 and 2012. Virus shedding was detected in nasal samples from pigs from ages 7, 21 and 42-days old. More than 90% of sows and gilts but less than 40% of 21-days old piglets had antibodies against IAV. In addition, IAV was detected in 8/17 nasal swabs and 10/15 lung samples taken from necropsied pigs. A subset of these samples was further processed for virus isolation resulting in 6 viruses of the H1N2 subtype (δ2 cluster). Pathological studies revealed an association between suppurative bronchopneumonia and necrotizing bronchiolitis with IAV positive samples. Statistical analyses showed that the degree of lesions in bronchi, bronchiole, and alveoli was higher in lungs positive to IAV. The results of this study depict the relevance of continuing long-term active surveillance of IAV in swine populations to establish IAV evolution relevant to swine and humans.

Using oral fluids samples for indirect influenza A virus surveillance in farmed UK pigs

Influenza A virus (IAV) is economically important in pig production and has broad public health implications. In Europe, active IAV surveillance includes demonstration of antigen in nasal swabs and/or demonstration of antibodies in serum (SER) samples; however, collecting appropriate numbers of individual pig samples can be costly and labour‐intensive. The objective of this study was to compare the probability of detecting IAV antibody positive populations using SER versus oral fluid (OF) samples. Paired pen samples, one OF and 5–14 SER samples, were collected cross‐sectional or longitudinally. A commercial nucleoprotein (NP)‐based blocking ELISA was used to test 244 OF and 1004 SER samples from 123 pens each containing 20–540 pigs located in 27 UK herds. Overall, the IAV antibody detection rate was higher in SER samples compared to OFs under the study conditions. Pig age had a significant effect on the probability of detecting positive pens. For 3–9‐week‐old pigs the probability of detecting IAV antibody positive samples in a pen with 95% confidence intervals was 40% (23–60) for OF and 61% (0.37–0.80) for SER (P = 0.04), for 10–14‐week‐old pigs it was 19% (8–40) for OF and 93% (0.71–0.99) for SER (P < 0.01), and for 18–20‐week‐old pigs it was 67% (41–85) for OF and 81% (0.63–0.91) for SER (P = 0.05). Collecting more than one OF sample in pens with more than 25 less than 18‐week‐old pigs should be further investigated in the future to elucidate the suitability of OF for IAV surveillance in herds with large pen sizes.

Effect of herd size on subclinical infection of swine in Vietnam with influenza A viruses

Background

Influenza A viruses of swine (IAV-S) cause acute and subclinical respiratory disease. To increase our understanding of the etiology of the subclinical form and thus help prevent the persistence of IAV-S in pig populations, we conducted active virologic surveillance in Vietnam, the second-largest pig-producing country in Asia, from February 2010 to December 2013.

Results

From a total of 7034 nasal swabs collected from clinically healthy pigs at 250 farms and 10 slaughterhouses, we isolated 172 IAV-S from swine at the weaning and early-fattening stages. The isolation rate of IAV-S was significantly higher among pigs aged 3 weeks to 4.5 months than in older and younger animals. IAV-S were isolated from 16 large, corporate farms and 6 family-operated farms from among the 250 farms evaluated. Multivariate logistic regression analysis revealed that “having more than 1,000 pigs” was the most influential risk factor for IAV-S positivity. Farms affected by reassortant IAV-S had significantly larger pig populations than did those where A(H1N1)pdm09 viruses were isolated, thus suggesting that large, corporate farms serve as sites of reassortment events.

Conclusions

We demonstrate the asymptomatic circulation of IAV-S in the Vietnamese pig population. Raising a large number of pigs on a farm has the strongest impact on the incidence of subclinical IAV-S infection. Given that only some of the corporate farms surveyed were IAV-S positive, further active monitoring is necessary to identify additional risk factors important in subclinical infection of pigs with IAV-S in Vietnam.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-016-0844-z) contains supplementary material, which is available to authorized users.

Maternally Derived Immunity Extends Swine Influenza A Virus Persistence within Farrow-to-Finish Pig Farms: Insights from a Stochastic Event-Driven Metapopulation Model

Swine Influenza A Viruses (swIAVs) have been shown to persist in farrow-to-finish pig herds with repeated outbreaks in successive batches, increasing the risk for respiratory disorders in affected animals and being a threat for public health. Although the general routes of swIAV transmission (i.e. direct contact and exposure to aerosols) were clearly identified, the transmission process between batches is still not fully understood. Maternally derived antibodies (MDAs) were stressed as a possible factor favoring within-herd swIAV persistence. However, the relationship between MDAs and the global spread among the different subpopulations in the herds is still lacking. The aim of this study was therefore to understand the mechanisms induced by MDAs in relation with swIAV spread and persistence in farrow-to-finish pig herds. A metapopulation model has been developed representing the population dynamics considering two subpopulations—breeding sows and growing pigs—managed according to batch-rearing system. This model was coupled with a swIAV-specific epidemiological model, accounting for partial passive immunity protection in neonatal piglets and an immunity boost in re-infected animals. Airborne transmission was included by a between-room transmission rate related to the current prevalence of shedding pigs. Maternally derived partial immunity in piglets was found to extend the duration of the epidemics within their batch, allowing for efficient between-batch transmission and resulting in longer swIAV persistence at the herd level. These results should be taken into account in the design of control programmes for the spread and persistence of swIAV in swine herds.

Detection of porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV) in oral fluid of pigs

Recently oral fluid has become a novel sample type for pathogen nucleic acid and antibody detection, as it is easy to obtain with non-invasive procedures. The objective of the study was to analyze porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV) circulation in growing pigs from three Polish production farms, using Real Time PCR and ELISA testing of oral fluid and serum. Oral fluids were collected every 2weeks, in the same 3-4 pens of pigs aged between 5 and 17weeks. Additionally, blood samples were collected every 4weeks from 4 pigs corresponding to the same pens as oral fluid and tested for the presence of PRRSV nucleic acid (pooled by 4) and antibodies. In farm A no PRRSV circulation was detected and only maternal antibodies were present. In farm B and farm C antibodies to PRRSV in serum and oral fluid were detected in most samples. In farm B PRRSV Type 1 was detected in 80.9% of oral fluid samples and in 58.3% of serum pools, and in farm C in 92.8% of oral fluid samples and 75% serum pools. Striking differences were observed between different pens in PRRSV detection patterns. In farms B and C ORF5 sequence analysis showed the presence of wild type strains which were about 84-85% identical to the modified live vaccine used. In all three farms two waves of IAV shedding with oral fluid were detected, in weaners and fatteners.

Maternally-derived antibodies do not prevent transmission of swine influenza A virus between pigs

A transmission experiment involving 5-week-old specific-pathogen-free (SPF) piglets, with (MDA(+)) or without maternally-derived antibodies (MDA(-)), was carried out to evaluate the impact of passive immunity on the transmission of a swine influenza A virus (swIAV). In each group (MDA(+)/MDA(-)), 2 seeders were placed with 4 piglets in direct contact and 5 in indirect contact (3 replicates per group). Serological kinetics (ELISA) and individual viral shedding (RT-PCR) were monitored for 28 days after infection. MDA waning was estimated using a nonlinear mixed-effects model and survival analysis. Differential transmission rates were estimated depending on the piglets' initial serological status and contact structure (direct contact with pen-mates or indirect airborne contact). The time to MDA waning was 71.3 [52.8-92.1] days on average. The airborne transmission rate was 1.41 [0.64-2.63] per day. The compared shedding pattern between groups showed that MDA(+) piglets had mainly a reduced susceptibility to infection compared to MDA(-) piglets. The resulting reproduction number estimated in MDA(+) piglets (5.8 [1.4-18.9]), although 3 times lower than in MDA(-) piglets (14.8 [6.4-27.1]), was significantly higher than 1. Such an efficient and extended spread of swIAV at the population scale in the presence of MDAs could contribute to swIAV persistence on farms, given the fact that the period when transmission is expected to be impacted by the presence of MDAs can last up to 10 weeks.

Influenza A virus infection of healthy piglets in an abattoir in Brazil: animal-human interface and risk for interspecies transmission

Asymptomatic influenza virus infections in pigs are frequent and the lack of measures for controlling viral spread facilitates the circulation of different virus strains between pigs. The goal of this study was to demonstrate the circulation of influenza A virus strains among asymptomatic piglets in an abattoir in Brazil and discuss the potential public health impacts. Tracheal samples (n = 330) were collected from asymptomatic animals by a veterinarian that also performed visual lung tissue examinations. No slaughtered animals presented with any noticeable macroscopic signs of influenza infection following examination of lung tissues. Samples were then analysed by reverse transcription-polymerase chain reaction that resulted in the identification of 30 (9%) influenza A positive samples. The presence of asymptomatic pig infections suggested that these animals could facilitate virus dissemination and act as a source of infection for the herd, thereby enabling the emergence of influenza outbreaks associated with significant economic losses. Furthermore, the continuous exposure of the farm and abattoir workers to the virus increases the risk for interspecies transmission. Monitoring measures of swine influenza virus infections and vaccination and monitoring of employees for influenza infection should also be considered. In addition regulatory agencies should consider the public health ramifications regarding the potential zoonotic viral transmission between humans and pigs.

The influence of experimental infection of gilts with swine H1N2 influenza A virus during the second month of gestation on the course of pregnancy, reproduction parameters and clinical status

Background

The course of swine influenza in pigs is reported to be similar to human influenza. Occasionally abortions and other reproduction disorders have been associated with influenza A virus (IAV) infection in pigs. Abortions may be a consequence of high fever, pro-inflammatory cytokines or transplacental transmission of the virus.

The role of IAV in the complications observed during pregnancy has been scanty and the true importance of this agent as a cause of reproductive problems in swine is not known. The aim was to determine the possible involvement of swine H1N2 IAV strain on reproductive disorders in pregnant gilts under experimental conditions.

Results

The gestation length was from 113 to 116 days, no abortion or any other reproduction disorders were noted. A PCR assay confirms the presence of IAV in the nasal swabs taken from inoculated gilts between 1 and 5 dpi. In the nasal swabs from control gilts and newborn piglets, no IAV genetic material was found. No viral RNA was detected in samples of blood taken from gilts and piglets, placentas, lungs and tracheas taken from piglets euthanized after delivery. The significant decrease in the number and percentage of lymphocytes without leukopenia was observed at 4 dpi in inoculated gilts. The percentage of granulocytes increased significantly at 4 dpi in inoculated pigs. The concentration of IL-6, IL-10 and TNF-α were higher in inoculated gilts, while IL-4 and IFN-γ were not detected in the serum of any of animals. The serum concentrations of C-reactive protein remained stable during study, while haptoglobin concentrations increased significantly after inoculation.

Conclusions

The results of the study indicate that infection of pregnant gilts with swine H1N2 IAV in the second month of pregnancy does not cause abortion and other reproduction disorders. No evidence for transplacental transmission of swine H1N2 IAV was found. However, due to subclinical course of influenza in the present experiment caution should be taken in extrapolating these results to the cases of acute influenza. The other limitation is IAV diversity. It cannot be excluded that other subtypes of IAV could be associated to reproduction failure in pigs.

Assessment of seasonality of influenza in swine using field submissions to a diagnostic laboratory in Ontario between 2007 and 2012

Background

Seasonality of any infectious disease is important for its control and monitoring. While influenza seasonality in people has been evaluated extensively, this question has not been studied well in swine populations.

Objective

The goal of this study was to investigate seasonality of influenza in swine, using diagnostic submissions to a diagnostic laboratory.

Methods

Two thousand seven hundred and eleven virological tests within 685 submissions and 5471 serological tests within 193 submissions in Ontario swine between 2007 and 2012 were included in the study and converted to total monthly number of virological and serological submissions, and the number of positive submissions. Data were analyzed by time-series decomposition, fixed-effect Poisson, random-effect Poisson regression with month as uncorrelated and correlated random effects.

Results

All approaches identified seasonality in virological submissions (P < 0·02) with peak in January and April, and a trough in July, but were not able to detect seasonality of influenza-positive virological submissions (P > 0·13). Seasonality of positive serological submissions was identified only if independence between months was assumed (P < 0·03). Almost 50% of serological submissions had evidence of exposure to H3N2 and H1N1.

Conclusions

Thus, this study identified evidence of seasonality in influenza-like disease in swine herds, but not in circulation of influenza virus. Evidence of seasonality in exposure to influenza was dependent on assumptions of between-month correlation. High exposure to H3N2 and H1N1 subtypes warrants more detailed investigation of within-herd influenza virus circulation. The study provides initial insight into seasonality of influenza in swine and should be followed with herd-level studies.

Phylogeny of Spanish swine influenza viruses isolated from respiratory disease outbreaks and evolution of swine influenza virus within an endemically infected farm

In the present study, outbreaks of respiratory disease were investigated for the presence of swine influenza virus (SIV). In 14 cases the circulating SIV strains were isolated, fully sequenced and compared with other known SIVs. The viruses causing the outbreaks belonged to the H1N1 (including human pandemic H1N1), H3N2 and H1N2 subtypes. In 11/14 cases the phylogenetic analyses indicated the occurrence of probable reassortment events. In the second part of the study, the genetic evolution of H1N1 SIV was assessed in a longitudinal study in closed groups of pigs over six months. Sequencing of the 22 isolates indicated co-circulation of two different variants for the same virus, as well as the emergence of SIV reassortants at certain time-points. These results indicate that reassortment events in SIV are common, and point towards the need for a better understanding of the epidemiology of SIV, particularly in endemic farms.

Kinetics of influenza A virus nucleoprotein antibody (IgM, IgA, and IgG) in serum and oral fluid specimens from pigs infected under experimental conditions

Indirect influenza A virus (IAV) nucleoprotein (NP) antibody ELISAs were used to compare the kinetics of the NP IgM, IgA, and IgG responses in serum and pen-based oral fluid samples collected from 82 pigs followed for 42 days post inoculation (DPI). Treatment categories included vaccination (0, 1) and inoculation (0, 1) with contemporary H1N1 or H3N2 isolates. Antibody ontogeny was markedly affected by vaccination status, but no significant differences were detected between H1N1 and H3N2 inoculated groups of the same vaccination status (0, 1) in IgM, IgA, or IgG responses. Therefore, these data were combined in subsequent analyses. The correlation between serum and oral fluid responses was evaluated using the pen-based oral fluid sample-to-positive (S/P) ratios versus the mean serum S/P ratios of pigs within the pen. IgM responses in serum and oral fluid were highly correlated in unvaccinated groups (r=0.810), as were serum and oral fluid IgG responses in both unvaccinated (r=0.839) and vaccinated (r=0.856) groups. In contrast, IgM responses were not correlated in vaccinated groups and the correlation between serum and oral fluid IgA was weak (r∼0.3), regardless of vaccination status. In general, vaccinated animals exhibited a suppressed IgM response and accelerated IgG response. The results from this study demonstrated that NP-specific IgM, IgA, and IgG antibody were detectable in serum and oral fluid and their ontogeny was influenced by vaccination status, the time course of the infection, and specimen type.

Dynamics of influenza A virus infections in permanently infected pig farms: evidence of recurrent infections, circulation of several swine influenza viruses and reassortment events

Concomitant infections by different influenza A virus subtypes within pig farms increase the risk of new reassortant virus emergence. The aims of this study were to characterize the epidemiology of recurrent swine influenza virus infections and identify their main determinants. A follow-up study was carried out in 3 selected farms known to be affected by repeated influenza infections. Three batches of pigs were followed within each farm from birth to slaughter through a representative sample of 40 piglets per batch. Piglets were monitored individually on a monthly basis for serology and clinical parameters. When a flu outbreak occurred, daily virological and clinical investigations were carried out for two weeks. Influenza outbreaks, confirmed by influenza A virus detection, were reported at least once in each batch. These outbreaks occurred at a constant age within farms and were correlated with an increased frequency of sneezing and coughing fits. H1N1 and H1N2 viruses from European enzootic subtypes and reassortants between viruses from these lineages were consecutively and sometimes simultaneously identified depending on the batch, suggesting virus co-circulations at the farm, batch and sometimes individual levels. The estimated reproduction ratio R of influenza outbreaks ranged between 2.5 [1.9-2.9] and 6.9 [4.1-10.5] according to the age at infection-time and serological status of infected piglets. Duration of shedding was influenced by the age at infection time, the serological status of the dam and mingling practices. An impaired humoral response was identified in piglets infected at a time when they still presented maternally-derived antibodies.