Abstract Seasonal human influenza viruses continually change antigenically to escape from neutralizing antibodies. It remains unclear how genetic variation in the intrahost virus population and selection at the level of individual hosts translates to the fast-paced evolution observed at the global level because emerging intrahost antigenic variants are rarely detected. We tracked intrahost variants in the hemagglutinin and neuraminidase surface proteins using longitudinally collected samples from 52 patients infected by A/H3N2 influenza virus, mostly young children, who received oseltamivir treatment. We identified emerging putative antigenic variants and oseltamivir-resistant variants, most of which remained detectable in samples collected at subsequent days, and identified variants that emerged intrahost immediately prior to increases in global rates. In contrast to most putative antigenic variants, oseltamivir-resistant variants rapidly increased to high frequencies in the virus population. Importantly, the majority of putative antigenic variants and oseltamivir-resistant variants were first detectable four or more days after onset of symptoms or start of treatment, respectively. Our observations demonstrate that de novo variants emerge, and may be positively selected, during the course of infection. Additionally, based on the 4–7 days post-treatment delay in emergence of oseltamivir-resistant variants in six out of the eight individuals with such variants, we find that limiting sample collection for routine surveillance and diagnostic testing to early timepoints after onset of symptoms can potentially preclude detection of emerging, positively selected variants.

中文翻译：

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需要纵向取样以最大限度地检测宿主内 A/H3N2 病毒变种

摘要 季节性人类流感病毒不断地改变抗原性以逃避中和抗体。目前尚不清楚宿主内病毒种群的遗传变异和个体宿主水平的选择如何转化为在全球水平观察到的快节奏进化，因为很少检测到新出现的宿主内抗原变异。我们使用纵向收集的 52 名 A/H3N2 流感病毒感染患者的样本追踪宿主内血凝素和神经氨酸酶表面蛋白的变异，这些患者主要是接受奥司他韦治疗的幼儿。我们确定了新出现的假定抗原变体和奥司他韦耐药变体，其中大部分在随后几天收集的样本中仍可检测到，并确定了在全球比率增加之前立即出现在宿主内的变体。与大多数假定的抗原变体相比，奥司他韦耐药变体在病毒群体中迅速增加到高频率。重要的是，大多数假定的抗原变异体和奥司他韦耐药变异体分别在症状出现或治疗开始后四天或更长时间首次可检测到。我们的观察表明，在感染过程中会出现新变体，并且可能会被积极选择。此外，基于治疗后 4-7 天延迟出现奥司他韦耐药变异的 8 名个体中有 6 名具有此类变异，