Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
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DOI：
10.1038/s41598-019-46509-w
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发表时间：
2019-07-11
影响因子：
4.6
通讯作者：
Nokes, D. James
中科院分区：
文献类型：
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作者：
Agoti, Charles N.;Phan, My V. T.;Nokes, D. James
婴儿（1 岁以下）最有可能罹患危及生命的呼吸道合胞病毒 (RSV) 疾病。仅靠 RSV 流行病学数据不足以确定家庭中谁从谁那里获得感染 (WAIFW)。我们调查了感染者内部和感染者之间的 RSV 基因组变异，并评估了其在追踪家庭传播方面的潜在效用。在肯尼亚沿海的整个 RSV 季节中，无论症状状况如何，每 3-4 天都会从 20 个家庭的成员收集鼻拭子，并筛查 RSV 核酸。使用下一代测序为 51.1% 的阳性样本 (191/374) 生成 > 90% RSV 全长基因组。在家庭感染爆发期间观察到的单核苷酸多态性 (SNP) 范围为 0-21（中位数：3），而在单宿主感染事件期间观察到的 SNP 范围为 0-17（中位数：1）。仅使用病毒基因组数据的分辨率不足以完全重建家庭内的传播链。对于有明确指示病例的家庭，最有可能的婴儿感染源是幼儿（1 岁至 < 3 岁）或学龄儿童（6 岁至 < 12 岁）同住者。然而，为了最好地解决家庭内的 WAIFW，我们建议对 RSV 基因组和流行病学数据进行综合分析。
Infants (under 1-year-old) are at most risk of life threatening respiratory syncytial virus (RSV) disease. RSV epidemiological data alone has been insufficient in defining who acquires infection from whom (WAIFW) within households. We investigated RSV genomic variation within and between infected individuals and assessed its potential utility in tracking transmission in households. Over an entire single RSV season in coastal Kenya, nasal swabs were collected from members of 20 households every 3-4 days regardless of symptom status and screened for RSV nucleic acid. Next generation sequencing was used to generate > 90% RSV full-length genomes for 51.1% of positive samples (191/374). Single nucleotide polymorphisms (SNPs) observed during household infection outbreaks ranged from 0-21 (median: 3) while SNPs observed during single-host infection episodes ranged from 0-17 (median: 1). Using the viral genomic data alone there was insufficient resolution to fully reconstruct withinhousehold transmission chains. For households with clear index cases, the most likely source of infant infection was via a toddler (aged 1 to < 3 years-old) or school-aged (aged 6 to < 12 years-old) cooccupant. However, for best resolution of WAIFW within households, we suggest an integrated analysis of RSV genomic and epidemiological data.