College of Veterinary Medicine, South China Agricultural University, Guangzhou.
Shantou University Medical College, Guangzhou, China.
J Infect Dis. 2018 May 5;217(11):1699-1707. doi: 10.1093/infdis/jiy082.
Avian influenza A virus H7N9 has caused 5 epidemic waves of human infections in China since 2013. Avian influenza A viruses may face strong selection to adapt to novel conditions when establishing themselves in humans. In this study, we sought to determine whether adaptive evolution had occurred in human-isolated H7N9 viruses.
We evaluated all available genomes of H7N9 avian influenza A virus. Maximum likelihood trees were separately reconstructed for all 8 genes. Signals of positive selection and convergent evolution were then detected on branches that lead to changes in host tropism (from avian to human).
We found that 3 genes had significant signals of positive selection (all of them P < .05). In addition, we detected 34 sites having significant signals for parallel evolution in 8 genes (all of them P < .05), including 7 well-known sites (Q591K, E627K, and D701N in PB2 gene; R156K, V202A, and L244Q in HA; and R289K in NA) that play roles in crossing species barriers for avian influenza A viruses.
Our study suggests that, during infection in humans, H7N9 viruses have undergone adaptive evolution to adapt to their new host environment and that the sites where parallel evolution occurred might play roles in crossing species barriers and respond to the new selection pressures arising from their new host environments.
自 2013 年以来，甲型 H7N9 禽流感病毒已在中国引发了 5 波人类感染疫情。当禽流感病毒在人类中建立自己的种群时，它们可能会面临强烈的选择，以适应新的环境。在本研究中，我们试图确定人类分离的 H7N9 病毒是否发生了适应性进化。
我们评估了所有可用的 H7N9 禽流感病毒基因组。分别为所有 8 个基因重建最大似然树。然后在导致宿主嗜性（从禽类到人类）改变的分支上检测到正选择和趋同进化的信号。
我们发现 3 个基因有显著的正选择信号（均 P <.05）。此外，我们在 8 个基因中检测到 34 个具有平行进化显著信号的位点（均 P <.05），包括 7 个众所周知的位点（PB2 基因中的 Q591K、E627K 和 D701N；HA 中的 R156K、V202A 和 L244Q；以及 NA 中的 R289K），这些位点在禽流感病毒跨越物种屏障方面发挥作用。
我们的研究表明，在人类感染期间，H7N9 病毒经历了适应性进化，以适应其新的宿主环境，而平行进化发生的位点可能在跨越物种屏障和应对新的选择压力方面发挥作用，这些选择压力来自它们的新宿主环境。
