Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Encinas P

PROVIDER: S-EPMC8754697 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:The last influenza pandemic in 2009 emerged from swine and surveillance of swine influenza is important for pandemic preparedness. Movement of swine during husbandry, trade or marketing for slaughter provide opportunities for transfer and genetic reassortment of swine influenza viruses. Over 90% of the swine slaughtered at the central swine abattoir in Hong Kong are imported from farms located in multiple provinces in mainland China. There is opportunity for virus cross-infection during this transport and slaughter process. Of the 26,980 swabs collected in the slaughterhouse in Hong Kong from 5 January 2012 to 15 December 2016, we analysed sequence data on influenza A (H3N2) virus isolates (n = 174) in conjunction with date of sampling and originating farm. Molecular epidemiology provided evidence of virus cross-infection between swine originating from different farms during transport. The findings are also suggestive of a virus lineage persisting in a swine farm for over 2 years, although the lack of information on management practices at farm-level means that alternative explanations cannot be excluded. We used virus serology and isolation data from 4226 pairs of linked serum and swabs collected from the same pig at slaughter from swine originating from Guangdong Province to compare the force of infection (FOI) during transport and within farms. The mean weekly FOI during transport was λt = 0.0286 (95% CI = 0.0211-0.0391) while the weekly FOI in farms was λf = 0.0089 (95% CI = 0.0084-0.0095), assuming a possible exposure duration in farm of 28 weeks, suggesting increased FOI during the transport process. Pigs sourced from farms with high seroprevalence were found to be a significant risk factor (adjusted OR = 2.24, p value = .015) for infection of imported pigs during transport by multivariable logistic regression analysis, whereas pigs with HAI titre of ≥1:40 were associated with a substantial reduction in infection risk by 67% (p value = 0.012). Transport may increase virus cross-infection rates and provide opportunities for virus reassortment potentially increasing zoonotic risk to those involved in the transportation and slaughtering processes.

Dataset Information

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets