Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
Bach Mai Hospital, Hanoi, Vietnam.
mSphere. 2021 Jan 6;6(1):e01043-20. doi: 10.1128/mSphere.01043-20.
The influenza A(H1N1)pdm09 virus emerged in April 2009 with an unusual incidence of severe disease and mortality, and currently circulates as a seasonal influenza virus. Previous studies using consensus viral genome sequencing data have overlooked the viral genomic and phenotypic diversity. Next-generation sequencing (NGS) may instead be used to characterize viral populations in an unbiased manner and to measure within-host genetic diversity. In this study, we used NGS analysis to investigate the within-host genetic diversity of influenza A(H1N1)pdm09 virus in the upper and lower respiratory samples from nine patients who were admitted to the intensive care unit (ICU). A total of 47 amino acid substitution positions were found to differ between the upper and lower respiratory tract samples from all patients. However, the D222G/N substitution in hemagglutinin (HA) protein was the only amino acid substitution common to multiple patients. Furthermore, the substitution was detected only in the six samples from the lower respiratory tract. Therefore, it is important to investigate influenza A(H1N1)pdm09 virus populations using multiple paired samples from the upper and lower respiratory tract to avoid overlooking potentially important substitutions, especially in patients with severe disease. The D222G/N substitution in the hemagglutinin (HA) protein of influenza A(H1N1)pdm09 virus has been reported to be associated with disease severity and mortality in numerous previous studies. In the present study, 75% of lower respiratory samples contained heterogeneous influenza populations that carried different amino acids at position 222 of the HA protein, whereas all upper respiratory samples only contained the wild-type 222D. These results suggest the influenza A(H1N1)pdm09 virus has diversified inside the host owing to differences in tissue specificity. In this study, the within-host genetic diversity of influenza A(H1N1)pdm09 virus was investigated for the first time using next-generation sequencing analysis of the viral whole-genome in samples extracted from the upper and lower respiratory tracts of patients with severe disease.
甲型 H1N1 流感病毒于 2009 年 4 月出现，其疾病严重程度和死亡率异常，目前作为季节性流感病毒传播。以前使用共识病毒基因组测序数据的研究忽略了病毒基因组和表型多样性。下一代测序（NGS）可用于以无偏倚的方式对病毒群体进行特征描述，并测量宿主内遗传多样性。在这项研究中，我们使用 NGS 分析来研究从 9 名入住重症监护病房（ICU）的患者的上呼吸道和下呼吸道样本中甲型 H1N1 流感病毒的宿主内遗传多样性。总共发现所有患者的上呼吸道和下呼吸道样本之间有 47 个氨基酸取代位置不同。然而，血凝素（HA）蛋白中的 D222G/N 取代是多个患者共同的唯一氨基酸取代。此外，该取代仅在来自下呼吸道的 6 个样本中检测到。因此，使用来自上呼吸道和下呼吸道的多个配对样本来研究甲型 H1N1 流感病毒群体非常重要，以避免忽略潜在的重要取代，尤其是在患有严重疾病的患者中。在许多先前的研究中，已报道甲型 H1N1 流感病毒血凝素（HA）蛋白中的 D222G/N 取代与疾病严重程度和死亡率有关。在本研究中，75%的下呼吸道样本含有异质性流感群体，其 HA 蛋白第 222 位携带不同的氨基酸，而所有上呼吸道样本仅含有野生型 222D。这些结果表明，由于组织特异性的差异，甲型 H1N1 流感病毒在宿主内发生了多样化。在这项研究中，首次使用来自重症患者上呼吸道和下呼吸道样本的病毒全基因组的下一代测序分析来研究甲型 H1N1 流感病毒的宿主内遗传多样性。
