The genomic epidemiology of influenza B virus (IBV) remains understudied in Africa despite significance to design of effective local and global control strategies We undertook surveillance throughout 2016 in coastal Kenya, recruiting individuals presenting with acute respiratory illness at nine outpatient health facilities (any age) or admitted to the Kilifi County Hospital (<5 years old) Whole genomes were sequenced for a selected 111 positives;94 (84 7%) of B/Victoria lineage and 17 (15 3%) of B/Yamagata lineage Inter-lineage reassortment was detected in ten viruses;nine with B/Yamagata backbone but B/Victoria NA and NP segments and one with a B/Victoria backbone but B/Yamagata PB2, PB1, PA, and MP segments Five phylogenomic clusters were identified among the sequenced viruses;(i), pure B/Victoria clade 1A (n = 93, 83 8%), (ii), reassortant B/Victoria clade 1A (n = 1, 0 9%), (iii), pure B/Yamagata clade 2 (n = 2, 1 8%), (iv), pure B/Yamagata clade 3 (n = 6, 5 4%), and (v), reassortant B/Yamagata clade 3 (n = 9, 8 1%) Using divergence dates and clustering patterns in the presence of global background sequences, we counted up to twenty-nine independent IBV strain introductions into the study area (∼900 km2) in 2016 Local viruses, including the reassortant B/Yamagata strains, clustered closely with viruses from neighbouring Tanzania and Uganda Our study demonstrated that genomic analysis provides a clearer picture of locally circulating IBV diversity The high number of IBV introductions highlights the challenge in controlling local influenza epidemics by targeted approaches, for example, sub-population vaccination or patient quarantine The finding of divergent IBV strains co-circulating within a single season emphasises why broad immunity vaccines are the most ideal for influenza control in Kenya

中文翻译：

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通过对单个季节采样的毒株进行基因组分析揭示了肯尼亚沿海乙型流感病毒的流行病学和进化动态


尽管 B 型流感病毒 (IBV) 的基因组流行病学对于设计有效的本地和全球控制策略具有重要意义，但在非洲仍然没有得到充分研究。 2016 年我们在肯尼亚沿海地区进行了监测，在 9 个门诊医疗机构（任何年龄）招募了患有急性呼吸道疾病的个体或住进基利菲县医院（<5 岁） 对选定的 111 个阳性样本进行全基因组测序；94 个（84±7%）B/Victoria 谱系和 17 个（15±3%）B/Yamagata 谱系 谱系间重配在 10 种病毒中检测到；9 种具有 B/Yamagata 主干，但 B/Victoria NA 和 NP 片段，一种具有 B/Victoria 主干，但 B/Yamagata PB2、PB1、PA 和 MP 片段 在测序病毒中鉴定出 5 个系统发育簇；(i)，纯 B/Victoria 进化枝 1A (n = 93, 83 8%)，(ii)，重配 B/Victoria 进化枝 1A (n = 1, 0 9%)，(iii)，纯 B/Yamagata 进化枝2 (n = 2, 1 8%)，(iv)，纯 B/Yamagata 进化枝 3 (n = 6, 5 4%)，和 (v)，重配 B/Yamagata 进化枝 3 (n = 9, 8 1%) ) 在全球背景序列存在的情况下，利用分歧日期和聚类模式，我们计算出 2016 年有多达 29 个独立的 IBV 毒株引入研究区域（∼900 km2） 本地病毒，包括重配 B/Yamagata 毒株，紧密聚类我们的研究表明，基因组分析可以更清楚地了解当地传播的IBV多样性 大量IBV的引入凸显了通过有针对性的方法（例如亚群疫苗接种或患者隔离）控制当地流感流行的挑战不同 IBV 毒株在一个季节内共同传播的发现强调了为什么广泛免疫疫苗是最理想的选择肯尼亚的流感控制