College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, USA.
Transbound Emerg Dis. 2021 Jan;68(1):62-75. doi: 10.1111/tbed.13529. Epub 2020 Mar 18.
Suckling piglets play an important role at maintaining influenza A virus (IAV) infections in breeding herds and disseminating them to other farms at weaning. However, the role they play at weaning to support and promote genetic variability of IAV is not fully understood. The objective here was to evaluate the genetic diversity of IAV in pigs at weaning in farms located in the Midwestern USA. Nasal swabs (n = 9,090) collected from piglets in breed-to-wean farms (n = 52) over a six-month period across seasons were evaluated for the presence of IAV. Nasal swabs (n = 391) from 23 IAV-positive farms were whole-genome sequenced. Multiple lineages of HA (n = 7) and NA (n = 3) were identified in 96% (22/23) and 61% (237/391) of the investigated farms and individual piglets, respectively. Co-circulation of multiple types of functional HA and NA was identified in most (83%) farms. Whole IAV genomes were completed for 126 individual piglet samples and 25 distinct and 23 mixed genotypes were identified, highlighting significant genetic variability of IAV in piglets. Co-circulation of IAV in the farms and co-infection of individual piglets at weaning was observed at multiple time points over the investigation period and appears to be common in the investigated farms. Statistically significant genetic variability was estimated within and between farms by AMOVA, and varying levels of diversity between farms were detected using the Shannon-Weiner Index. Results reported here demonstrate previously unreported levels of molecular complexity and genetic variability among IAV at the farm and piglet levels at weaning. Movement of such piglets infected at weaning may result in emergence of new strains and maintenance of endemic IAV infection in the US swine herds. Results presented here highlight the need for developing and implementing novel, effective strategies to prevent or control the introduction and transmission of IAV within and between farms in the country.
仔猪在维持种猪群中的甲型流感病毒（IAV）感染以及在断奶时将其传播到其他农场方面发挥着重要作用。然而，它们在断奶时支持和促进 IAV 遗传多样性的作用尚未完全了解。本研究旨在评估美国中西部断奶仔猪中 IAV 的遗传多样性。在跨越季节的六个月期间，从种猪到断奶的农场（n=52）的仔猪中采集鼻拭子（n=9090），评估IAV 的存在情况。从 23 个 IAV 阳性农场的 391 个鼻拭子中进行了全基因组测序。在 96%（22/23）和 61%（237/391）的调查农场和个体仔猪中分别鉴定出了多种 HA（n=7）和 NA（n=3）的谱系。在大多数（83%）农场中发现了多种功能 HA 和 NA 的共同循环。对 126 个个体仔猪样本和 25 个不同和 23 个混合基因型的完整 IAV 基因组进行了完成，突出了仔猪中 IAV 的遗传多样性。在调查期间的多个时间点观察到农场中 IAV 的共同循环以及个体仔猪的共同感染，这在调查农场中似乎很常见。AMOVA 估计了农场内和农场间的遗传变异，使用香农-威纳指数检测到了农场间的多样性差异。本研究结果显示了在农场和仔猪水平上，IAV 的分子复杂性和遗传多样性达到了前所未有的水平。在断奶时感染的仔猪的迁移可能导致新菌株的出现，并维持美国猪群中的地方性 IAV 感染。本研究结果强调了需要制定和实施新的、有效的策略，以防止或控制该国农场内和农场间 IAV 的引入和传播。
