Transmission pair characteristics.

Transmission bottlenecks are defined by the number of unique virions or genotypes that establish an infection, and they restrict viral diversity that passes from one infected host to another. Previous work identified a tight transmission bottleneck for seasonal influenza A virus (IAV) based on analysis of 43 household pairs, largely from a single A(H3N2) predominant season. While many viral and host factors are known to influence IAV transmission in households, their impact on the transmission bottleneck is not clear. Nasal swabs were collected daily from IAV infected individuals enrolled in two case-ascertained U.S. household transmission studies, FluTES (2017/2018–2019/2020 seasons) and RVTN (2021/2022 season). Viruses were sequenced in duplicate, and intrahost single nucleotide variants (iSNV) were identified at a 0·5% frequency threshold using a benchmarked pipeline with >99·99% specificity for mutations present in both replicates. Transmission pairs were defined based on co-residence, test date, and genetic distance. For each possible transmission pair, the bottleneck was estimated using a beta binomial and a clonal mutation model. We sequenced 567 samples from 319 individuals and 102 households in duplicate. Based on epidemiologic linkage and a sequence-based cut-off, we defined 59 transmission pairs for the beta binomial model and 56 transmission pairs for the clonal mutation model. Across all pairs, we identified a transmission bottleneck of 1 both using the beta-binomial model (CI 1, 1) and the clonal mutation model (CI: 1.00, 1.22). In our cohort, influenza season, subtype, and host factors (influenza vaccination status, sex, and age) did not alter the transmission bottleneck. IAV is subject to a tight genetic bottleneck during transmission, which limits onward propagation of newly arising nucleotide variants. Tight bottlenecks appear to be intrinsic to the transmission process, as host and viral factors within households do not affect its size.

传播瓶颈（transmission bottleneck）指能够建立感染的独特病毒粒子或基因型的数量，其可限制病毒多样性从受感染宿主向另一宿主的传递。既往研究通过对43组家庭配对样本的分析，在以A(H3N2)亚型为主导的单一流行季中，证实季节性甲型流感病毒（influenza A virus, IAV）存在严格的传播瓶颈。尽管已知诸多病毒与宿主因素可影响家庭环境中IAV的传播，但这些因素对传播瓶颈的具体影响尚不明确。本研究纳入两项经病例确认的美国家庭传播研究——FluTES（2017/2018~2019/2020流行季）与RVTN（2021/2022流行季），每日采集IAV感染者的鼻拭子样本。病毒样本均进行双份测序；采用经过验证的分析流程，以0.5%的频率阈值鉴定宿主内单核苷酸变异（intrahost single nucleotide variants, iSNV），该流程对两份重复样本中共存突变的检测特异性高于99.99%。传播配对样本基于共同居住情况、检测日期与遗传距离进行界定。针对每一组潜在传播配对，分别采用β二项式模型与克隆突变模型对传播瓶颈进行估算。本研究对来自102个家庭、319名个体的567份样本进行了双份测序。基于流行病学关联与序列截断值，本研究为β二项式模型界定了59组传播配对，为克隆突变模型界定了56组传播配对。对所有配对样本分析后发现，采用β二项式模型（置信区间CI：1, 1）与克隆突变模型（CI：1.00, 1.22）均得到传播瓶颈数值为1的结果。在本研究队列中，流感流行季、病毒亚型以及宿主因素（流感疫苗接种状态、性别与年龄）均未对传播瓶颈产生影响。IAV在传播过程中存在严格的遗传瓶颈，这会限制新出现的核苷酸变异的后续传播。由于家庭环境中的宿主与病毒因素均不会改变传播瓶颈的大小，因此严格的传播瓶颈似乎是病毒传播过程的固有属性。