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A型流感病毒（Influenza A virus in swine, IAV-S）在美国商业猪群中广泛流行，且具备引发人畜共患传播的潜在风险。
研究目的：为阐明家猪群体中的流感排毒规律，我们于美国伊利诺伊州的两家商业猪场开展了为期7周的监测研究。其中猪场1近期暴发过IAV-S疫情，猪场2则已持续数年存在IAV-S的循环传播。
研究方法：本研究对猪场1的40头断奶仔猪与猪场2的51头生猪进行个体监测，通过鼻拭子采样完成检测，采样周期共计7周。
研究结果：随时间推移的RT-PCR检测结果显示，绝大多数仔猪在断奶后前2周出现病毒排毒：第1周排毒率达91.2%，第2周为36.3%。两家保育猪场的排毒猪只数量无显著差异。但再次感染事件的发生率在两家猪场间存在明显差异：猪场1中有30%的仔猪发生再次感染，而猪场2的该比例仅为7.8%。此外，对两家猪场鼻拭子样本的全基因组测序结果表明，初次感染与再次感染周期内流行的病毒基因组完全一致。测序分析还实现了对流行病毒的核酸与氨基酸突变特征解析，并识别出一起潜在的反向人畜共患事件。研究团队观察到部分猪只出现了抗原位点突变，且几乎所有样本中均检出MxA耐药基因。
研究结论：本研究阐明了保育猪群中IAV-S的流行特征，可为养殖生产者与兽医合理开展IAV-S筛查、确定病毒排毒时长以及预测保育阶段再次感染的发生提供科学依据。