BACKGROUND Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences. RESULTS We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes. CONCLUSION This is the first genomic characterization of HMPV genomes from African patients.

中文翻译：

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来自肯尼亚和赞比亚的人类偏肺病毒株的全基因组测序和系统发育分析。


背景人类偏肺病毒（HMPV）是幼儿急性呼吸道疾病的重要原因。全基因组测序可以更好地识别传播事件和爆发，而这对于亚基因组序列来说并不总是可行。结果我们报告了一种基于 2 反应扩增子的下一代测序方法，可直接从临床样本中确定代表三个亚组（A2、B1 和 B2）的 5 种 HMPV 毒株的完整基因组序列。除了报告来自非洲的五种新的 HMPV 基因组之外，我们还检查了公开可用的 HMPV 基因组的遗传多样性和序列模式。我们发现HMPV A组和B组的总体核苷酸序列同一性分别为71.3%和80%，HMPV组间SH和G表面蛋白基因在氨基酸水平上的多样性更大，并且多个亚组在各个国家共同传播。 HMPV 组之间的序列比较显示，由于终止密码子位置的变化，G 蛋白长度（219 至 241 个氨基酸）存在差异。全基因组系统发育分析显示除 F 和 M2 基因外，与各个基因序列集一致。结论 这是非洲患者 HMPV 基因组的首次基因组表征。