Influenza surveillance in pigs: balancing act between broad diagnostic coverage and specific virus characterization

Assessment of individual and population-based sampling for detection of influenza A virus RNA in breeding swine herds

Sample types currently used for Influenza A virus (IAV) surveillance in swine farms vary in sensitivity, convenience of collection, and herd representativeness. Family oral fluids are an effective population-based sample type for detecting porcine reproductive and respiratory syndrome virus (PRRSV) (ribonucleic acid) RNA by real-time reverse transcription-polymerase chain reaction (RT-rtPCR) in breeding herds. However, little is known about the efficacy of family oral fluids samples for detecting IAV RNA in these herds. This study compared the probability of IAV RNA detection among individual and population-based samples. A 3,500-sow breeding herd was sampled for matched sets (n = 57) of family oral fluids, udder wipes, sow nasal wipes, individual piglet nasal wipes, and drinker wipes, tested by RT-rtPCR for IAV RNA. Overall, 57.9 % (33/57) of family oral fluids, 49.1 % (28/57) of udder wipes, 28.1 % (16/57) of sow nasal wipes, 15.8 % (9/57) of drinker wipes, and 66.6 % (38/57) of individual piglet nasal wipes were positive. Family oral fluids showed a Kappa value of 0.81, indicating near-perfect agreement with individual piglet nasal wipes, while udder wipes had a substantial agreement (Kappa = 0.65). Other sample types showed fair agreement (Kappa < 0.28). These results validate family oral fluids as an efficient alternative population-based sample for IAV surveillance in breeding herds. The proportion of positive piglets within litters by room was 91 % in room A (20/22), 70 % in room B (17/24), and 9 % in room C (1/11). This study also highlights the importance of sampling different farrowing rooms within the same breeding herd to enhance IAV surveillance.

Influenza A virus shedding and reinfection during the post-weaning period in swine: longitudinal study of two nurseries

INTRODUCTION

Influenza A virus in swine (IAV-S) is common in the United States commercial swine population and has the potential for zoonotic transmission.

OBJECTIVE

To elucidate influenza shedding the domestic pig population, we evaluated two commercial swine farms in Illinois, United States, for 7 weeks. Farm 1 had a recent IAV-S outbreak. Farm 2 has had IAV-S circulating for several years.

METHODS

Forty post-weaning pigs on Farm 1 and 51 pigs from Farm 2 were individually monitored and sampled by nasal swabs for 7 weeks.

RESULTS

RT-PCR results over time showed most piglets shed in the first 2 weeks post weaning, with 91.2% shedding in week one, and 36.3% in week two. No difference in the number of pigs shedding was found between the two nurseries. Reinfection events did differ between the farms, with 30% of piglets on Farm 1 becoming reinfected, compared to 7.8% on Farm 2. In addition, whole genome sequencing of nasal swab samples from each farm showed identical viruses circulating between the initial infection and the reinfection periods. Sequencing also allowed for nucleic and amino acid mutation analysis in the circulating viruses, as well the identification of a potential reverse zoonosis event. We saw antigenic site mutations arising in some pigs and MxA resistance genes in almost all samples.

CONCLUSION

This study provided information on IAV-S circulation in nurseries to aid producers and veterinarians to screen appropriately for IAV-S, determine the duration of IAV-S shedding, and predict the occurrence of reinfection in the nursery period.

Effect of stabilizers on the detection of swine influenza A virus (swIAV) in spiked oral fluids over time

BACKGROUND

Aggregated samples such as oral fluids (OFs) display an animal friendly and time and cost-efficient sample type for swine Influenza A virus (swIAV) monitoring. However, further molecular and biological characterization of swIAV is of particular significance. The reportedly inferior suitability of aggregated samples for subtyping of swIAV presents a major drawback compared to nasal swabs, still considered the most appropriate sample type for this purpose (Garrido-Mantilla et al. BMC Vet Res 15(1):61, 2019). In addition, the viral load in the original sample, storage conditions and characteristics of different swIAV strains might further compromise the eligibility of aggregated samples for molecular detection and subtyping. Therefore, the present study aimed to evaluate the suitability of stabilizing media to minimize the degradation of viral RNA and thus increase the detection and subtyping rate of swIAV by RT-qPCR in spiked OFs under different conditions (virus strain, storage temperature and viral load in the original sample) over a time span of 14 days.

RESULTS

The use of stabilizing media in spiked OFs resulted in a significant higher probability to detect swIAV RNA compared to OFs without stabilizers (OR = 46.1, p < 0.001). In addition, swIAV degradation over time was significantly reduced in samples suspended with stabilizer (OR = 5.80, p < 0.001), in samples stored at 4 °C (OR = 2.53, p < 0.001) and in samples spiked with the avian derived H1N2 subtype (OR = 2.26, p < 0.01). No significant differences in swIAV RNA detection and degradation of swIAV RNA in spiked OFs over time were observed between the three different stabilizing media.

CONCLUSION

Addition of stabilizers and storage of samples under cooled conditions significantly improved detection and subtyping of swIAV in spiked OFs.

Mechanistic Models of Influenza Transmission in Commercial Swine Populations: A Systematic Review

Influenza in commercial swine populations leads to reduced gain in fattening pigs and reproductive issues in sows. This literature review aims to analyze the contributions of mathematical modeling in understanding influenza transmission and control among domestic swine. Twenty-two full-text research articles from seven databases were reviewed, categorized into swine-only (n = 13), swine-avian (n = 3), and swine-human models (n = 6). Strains of influenza models were limited to H1N1 (n = 7) and H3N2 (n = 1), with many studies generalizing the disease as influenza A. Half of the studies (n = 14) considered at least one control strategy, with vaccination being the primary investigated strategy. Vaccination was shown to reduce disease prevalence in single animal cohorts. With a continuous flow of new susceptible animals, such as in farrow-to-finish farms, it was shown that influenza became endemic despite vaccination strategies such as mass or batch-to-batch vaccination. Human vaccination was shown to be effective at mitigating human-to-human influenza transmission and to reduce spillover events from pigs. Current control strategies cannot stop influenza in livestock or prevent viral reassortment in swine, so mechanistic models are crucial for developing and testing new biosecurity measures to prevent future swine pandemics.