Shortening Duration of Swine Exhibitions to Reduce Risk for Zoonotic Transmission of Influenza A Virus

Estimating the risk of zoonotic transmission of swine influenza A variant during agricultural fairs in the United States: a mathematical modeling

Introduction

Agricultural fairs offer a unique interface between humans and swine. We investigate the transmissibility of influenza A variant from pigs to humans using epidemiological data from a 2011 zoonotic outbreak of an influenza H3N2 variant during an agricultural county fair in Pennsylvania.

Methods

We developed a mathematical model for the transmission of a swine influenza pathogen among pigs and humans at an agricultural fair. We fitted our model to the outbreak data to estimate zoonotic transmissibility. We considered nine data-driven scenarios of swine-to-swine basic reproductive number (R0) and the number of infected pigs at the start of the fair, and we simulated the zoonotic outbreak dynamics.

Results

We estimated the probability of swine-to-human H3N2v transmission per minute of swine contact for which our model best fitted the data. The probability of transmission of H3N2v per minute of contact with swine among club members was estimated to vary from 0.029 (95% confidence interval (CI): 0.028-0.030), when R0 = 2 with 1 initially infected pig, to 0.00099 (0.00095-0.00102), when R0 = 6 with 5 initially infected pigs. For attendees, we showed that the probability equals 0.0168 (95% CI: 0.0167-0.0169), when R0 = 2 with 1 initially infected pig, and 0.00371 (95% CI: 0.00368-0.00373), when R0 = 2 with 5 initially infected pigs. For all scenarios, we estimated H3N2v infection prevalence among club members and attendees to average 12 and 0.7%, respectively.

Discussion

These results show that the transmission risk may vary substantially between club members and attendees and with the underlying disease transmission among pigs. Although fair attendees may have a small transmissibility risk, annual fair attendees represent a large population likely to experience zoonotic events and facilitate the emergence of a potential pandemic influenza variant.

Evolution of influenza A viruses in exhibition swine and transmission to humans, 2013-2015

AIMS

Swine are a mixing vessel for the emergence of novel reassortant influenza A viruses (IAV). Interspecies transmission of swine-origin IAV poses a public health and pandemic risk. In the United States, the majority of zoonotic IAV transmission events have occurred in association with swine exposure at agricultural fairs. Accordingly, this human-animal interface necessitates mitigation strategies informed by understanding of interspecies transmission mechanisms in exhibition swine. Likewise, the diversity of IAV in swine can be a source for novel reassortant or mutated viruses that pose a risk to both swine and human health.

METHODS AND RESULTS

In an effort to better understand those risks, here we investigated the epidemiology of IAV in exhibition swine and subsequent transmission to humans by performing phylogenetic analyses using full genome sequences from 272 IAV isolates collected from exhibition swine and 23 A(H3N2)v viruses from human hosts during 2013-2015. Sixty-seven fairs (24.2%) had at least one pig test positive for IAV with an overall estimated prevalence of 8.9% (95% CI: 8.3-9.6, Clopper-Pearson). Of the 19 genotypes found in swine, 5 were also identified in humans. There was a positive correlation between the number of human cases of a genotype and its prevalence in exhibition swine. Additionally, we demonstrated that A(H3N2)v viruses clustered tightly with exhibition swine viruses that were prevalent in the same year.

CONCLUSIONS

These data indicate that multiple genotypes of swine-lineage IAV have infected humans, and highly prevalent IAV genotypes in exhibition swine during a given year are also the strains detected most frequently in human cases of variant IAV. Continued surveillance and rapid characterization of IAVs in exhibition swine can facilitate timely phenotypic evaluation and matching of candidate vaccine strains to those viruses present at the human-animal interface which are most likely to spillover into humans.

Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections

Patterns of within-host influenza A virus (IAV) diversity and evolution have been described in natural human infections, but these patterns remain poorly characterized in non-human hosts. Elucidating these dynamics is important to better understand IAV biology and the evolutionary processes that govern spillover into humans. Here, we sampled an IAV outbreak in pigs during a week-long county fair to characterize viral diversity and evolution in this important reservoir host. Nasal wipes were collected on a daily basis from all pigs present at the fair, yielding up to 421 samples per day. Subtyping of PCR-positive samples revealed the co-circulation of H1N1 and H3N2 subtype swine IAVs. PCR-positive samples with robust Ct values were deep-sequenced, yielding 506 sequenced samples from a total of 253 pigs. Based on higher-depth re-sequenced data from a subset of these initially sequenced samples (260 samples from 168 pigs), we characterized patterns of within-host IAV genetic diversity and evolution. We find that IAV genetic diversity in single-subtype infected pigs is low, with the majority of intrahost Single Nucleotide Variants (iSNVs) present at frequencies of <10%. The ratio of the number of nonsynonymous to the number of synonymous iSNVs is significantly lower than under the neutral expectation, indicating that purifying selection shapes patterns of within-host viral diversity in swine. The dynamic turnover of iSNVs and their pronounced frequency changes further indicate that genetic drift also plays an important role in shaping IAV populations within pigs. Taken together, our results highlight similarities in patterns of IAV genetic diversity and evolution between humans and swine, including the role of stochastic processes in shaping within-host IAV dynamics.

African Swine Fever: A Review of Current Disease Management Strategies and Risks Associated with Exhibition Swine in the United States

African swine fever is a high-consequence foreign animal disease endemic to sub-Saharan Africa and the island of Sardinia. The U.S. is the world's third largest pork producer, and ASF introduction would severely disrupt the pork supply chain, emphasizing the need to protect market access for U.S. proteins. However, niche producers raising swine intended for exhibition may not follow stringent biosecurity protocols, and livestock show circuits may promote untracked animal movement across the country, potentially exacerbating virus' spread in the event of ASF incursion into the U.S. Youth membership in state or national swine organizations offers a route for outreach and educational activities to enhance foreign animal disease preparedness, and adult presence at swine exhibitions allows a wide variety of programming for all ages to better serve all levels of understanding.

Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections

Patterns of within-host influenza A virus (IAV) diversity and evolution have been described in natural human infections, but these patterns remain poorly characterized in non-human hosts. Elucidating these dynamics is important to better understand IAV biology and the evolutionary processes that govern spillover into humans. Here, we sampled an IAV outbreak in pigs during a week-long county fair to characterize viral diversity and evolution in this important reservoir host. Nasal wipes were collected on a daily basis from all pigs present at the fair, yielding up to 421 samples per day. Subtyping of PCR-positive samples revealed the co-circulation of H1N1 and H3N2 subtype IAVs. PCR-positive samples with robust Ct values were deep-sequenced, yielding 506 sequenced samples from a total of 253 pigs. Based on higher-depth re-sequenced data from a subset of these initially sequenced samples (260 samples from 168 pigs), we characterized patterns of within-host IAV genetic diversity and evolution. We find that IAV genetic diversity in single-subtype infected pigs is low, with the majority of intra-host single nucleotide variants (iSNVs) present at frequencies of <10%. The ratio of the number of nonsynonymous to the number of synonymous iSNVs is significantly lower than under the neutral expectation, indicating that purifying selection shapes patterns of within-host viral diversity in swine. The dynamic turnover of iSNVs and their pronounced frequency changes further indicate that genetic drift also plays an important role in shaping IAV populations within pigs. Taken together, our results highlight similarities in patterns of IAV genetic diversity and evolution between humans and swine, including the role of stochastic processes in shaping within-host IAV dynamics.