Data Sheet 1_Influenza A virus shedding and reinfection during the post-weaning period in swine: longitudinal study of two nurseries.docx

IntroductionInfluenza A virus in swine (IAV-S) is common in the United States commercial swine population and has the potential for zoonotic transmission.ObjectiveTo 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.MethodsForty post-weaning pigs on Farm 1 and 51 pigs from Farm 2 were individually monitored and sampled by nasal swabs for 7 weeks.ResultsRT-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.ConclusionThis 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.

引言猪流感病毒A型（IAV-S）在美国的商业猪群中普遍存在，并具有潜在的动物源性传播风险。研究目的为阐明家猪群体中的流感排毒情况，本研究对美国伊利诺伊州的两家商业猪场进行了为期7周的评估。农场1近期发生了IAV-S疫情，而农场2已有数年IAV-S的持续流行。研究方法对农场1的40头断奶后猪和农场2的51头猪进行了个体监测和采样，采样方式为鼻腔拭子。研究结果显示，随着时间的推移，RT-PCR检测结果表明，大部分猪仔在断奶后的前两周内排毒，其中第一周有91.2%的猪仔排毒，第二周有36.3%的猪仔排毒。在两个猪舍中，排毒猪的数量没有发现差异。在两个农场中，再感染事件有所不同，农场1的30%的猪仔发生了再感染，而农场2为7.8%。此外，对每个农场鼻腔拭子样本的全基因组测序显示，在初次感染和再感染期间存在相同的病毒株。测序还允许对循环病毒进行核酸和氨基酸突变分析，以及识别潜在的逆向动物源性传播事件。我们发现部分猪仔出现了抗原位点突变，几乎所有样本中均检测到MxA耐药基因。结论本研究提供了关于猪流感病毒A型在猪舍中循环的信息，以帮助养殖户和兽医适当筛查IAV-S，确定IAV-S的排毒持续时间，并预测猪舍期间的再感染发生。