Multi-species co-circulation of adenoviruses identified by next generation sequencing during an outbreak in coastal Kenya in 2023

ARNOLD W. LAMBISIA, Martin Mutunga, Esther N. Katama, Charles N Agoti, Charlotte J. Houldcroft
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Abstract

Background Although seven human adenovirus (HAdV) species are known to exist, only F (types 40 and 41) and G, are identified as diarrhoeal disease agents. The role of other HAdV species in diarrhoeal disease remains unclear and data of their prevalence is limited. We describe HAdV species and types in hospitalised children with diarrhoea in coastal Kenya. Methods 329 stool samples collected between June 2022 and August 2023 from children aged <13-years were screened for HAdV using quantitative polymerase chain reaction (qPCR). Positive HAdV cases were genotyped by adenovirus primers from the RespiCoV panel by amplification, next generation sequencing followed by phylogenetic analysis. Results 65 samples (20%) tested HadV positive from which five HAdV species were identified. Other than HAdV F, other species included A, B, C and D; these were detected as either mono-detections or coinfections. Six HAdV F identified by NGS had been missed by our q PCR typing method. This appeared to be as a result of a 133-nucleotide deletion in the long fiber protein which abrogated a primer and probe binding site. Based on VESIKARI scores grading of diarrhoeal disease severity, 93% of the HAdV cases presented with severe disease. One child with an HAdV F infection died. Conclusion Our study shows the enormous diversity and clinical characteristics of HAdV species in children with diarrhoea in coastal Kenya. These data offers an opportunity to improve current diagnostic assays, increase knowledge of HAdV in Africa for control of outbreaks in the future.
在 2023 年肯尼亚沿海疫情爆发期间,通过新一代测序确定了腺病毒的多物种共同流行情况
背景虽然已知有七种人类腺病毒(HAdV),但只有 F 型(40 和 41 型)和 G 型被确定为腹泻病原体。其他 HAdV 种类在腹泻病中的作用仍不清楚,有关其流行情况的数据也很有限。我们描述了肯尼亚沿海地区住院腹泻儿童中的 HAdV 种类和类型。方法 使用定量聚合酶链反应(qPCR)对 2022 年 6 月至 2023 年 8 月间收集的 329 份 13 岁儿童粪便样本进行了 HAdV 筛查。对HAdV阳性病例使用RespiCoV面板中的腺病毒引物进行基因分型扩增、下一代测序,然后进行系统发育分析。结果65个样本(20%)检测出HadV阳性,从中鉴定出5种HAdV。除 HAdV F 外,其他病原体包括 A、B、C 和 D;这些病原体均为单种或混合感染。我们的 q PCR 分型方法漏掉了通过 NGS 鉴定出的六种 HAdV F。这似乎是由于长纤维蛋白中的 133 个核苷酸缺失导致引物和探针结合位点失效。根据腹泻病严重程度的 VESIKARI 评分,93% 的 HAdV 病例病情严重。一名感染 HAdV F 的儿童死亡。结论我们的研究表明,肯尼亚沿海地区腹泻儿童中的 HAdV 种类繁多,临床特征各异。这些数据为改进目前的诊断方法、增加对非洲 HAdV 的了解、控制未来的疫情爆发提供了机会。
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