Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme.
School of Health and Human Sciences, Pwani University, Kilifi, Kenya.
J Infect Dis. 2018 May 5;217(11):1728-1739. doi: 10.1093/infdis/jiy098.
Human coronavirus NL63 (HCoV-NL63) is a globally endemic pathogen causing mild and severe respiratory tract infections with reinfections occurring repeatedly throughout a lifetime.
Nasal samples were collected in coastal Kenya through community-based and hospital-based surveillance. HCoV-NL63 was detected with multiplex real-time reverse transcription PCR, and positive samples were targeted for nucleotide sequencing of the spike (S) protein. Additionally, paired samples from 25 individuals with evidence of repeat HCoV-NL63 infection were selected for whole-genome virus sequencing.
HCoV-NL63 was detected in 1.3% (75/5573) of child pneumonia admissions. Two HCoV-NL63 genotypes circulated in Kilifi between 2008 and 2014. Full genome sequences formed a monophyletic clade closely related to contemporary HCoV-NL63 from other global locations. An unexpected pattern of repeat infections was observed with some individuals showing higher viral titers during their second infection. Similar patterns for 2 other endemic coronaviruses, HCoV-229E and HCoV-OC43, were observed. Repeat infections by HCoV-NL63 were not accompanied by detectable genotype switching.
In this coastal Kenya setting, HCoV-NL63 exhibited low prevalence in hospital pediatric pneumonia admissions. Clade persistence with low genetic diversity suggest limited immune selection, and absence of detectable clade switching in reinfections indicates initial exposure was insufficient to elicit a protective immune response.
人冠状病毒 NL63（HCoV-NL63）是一种在全球流行的病原体，可引起轻度和重度呼吸道感染，一生中会反复发生再感染。
在肯尼亚沿海地区通过社区和医院监测收集鼻样本。使用多重实时逆转录 PCR 检测 HCoV-NL63，对阳性样本进行刺突（S）蛋白的核苷酸测序。此外，选择 25 名有重复 HCoV-NL63 感染证据的个体的配对样本进行全基因组病毒测序。
HCoV-NL63 在 1.3%（75/5573）的儿童肺炎入院病例中被检测到。2008 年至 2014 年间，在基利菲有两种 HCoV-NL63 基因型循环。全基因组序列形成一个单系分支，与来自其他全球地点的当代 HCoV-NL63 密切相关。观察到重复感染的意外模式，一些个体在第二次感染时显示出更高的病毒滴度。其他两种地方性冠状病毒 HCoV-229E 和 HCoV-OC43 也观察到类似的模式。HCoV-NL63 的重复感染不伴有可检测的基因型转换。
在肯尼亚沿海地区，HCoV-NL63 在医院儿科肺炎入院病例中表现出低流行率。分支持续存在且遗传多样性低表明免疫选择有限，再感染中未检测到可检测的分支转换表明初始暴露不足以引起保护性免疫反应。
