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家庭中呼吸道合胞病毒感染的基因组分析及其在推断谁感染婴儿中的作用。

Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.

机构信息

Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Epidemiology and Demography Department, Kilifi, Kenya.

Pwani University, School of Health and Human Sciences, Kilifi, Kenya.

出版信息

Sci Rep. 2019 Jul 11;9(1):10076. doi: 10.1038/s41598-019-46509-w.

DOI:10.1038/s41598-019-46509-w
PMID:31296922
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6624209/
Abstract

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 within-household 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) co-occupant. However, for best resolution of WAIFW within households, we suggest an integrated analysis of RSV genomic and epidemiological data.

摘要

婴儿（1 岁以下）是最有生命危险的呼吸道合胞病毒（RSV）疾病的高危人群。仅基于 RSV 流行病学数据不足以确定家庭内谁从谁那里获得感染（WAIFW）。我们研究了感染个体内部和之间的 RSV 基因组变异，并评估了其在家庭传播追踪中的潜在用途。在肯尼亚沿海地区整个 RSV 单一季节期间，无论症状状态如何，每隔 3-4 天都会从 20 个家庭的成员中采集鼻拭子，并对 RSV 核酸进行筛查。使用下一代测序技术，对 374 个阳性样本中的 51.1%（191 个）生成了>90%的 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）范围从 0-21（中位数：3），而在单个宿主感染期间观察到的 SNP 范围从 0-17（中位数：1）。仅使用病毒基因组数据，无法完全重建家庭内的传播链。对于有明确索引病例的家庭，婴儿感染的最可能来源是幼儿（1 至<3 岁）或学龄儿童（6 至<12 岁）同居者。然而，为了更好地确定家庭内的 WAIFW，我们建议对 RSV 基因组和流行病学数据进行综合分析。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/2e2050f1caec/41598_2019_46509_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/ed0af4f14c7c/41598_2019_46509_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/9b7427fd27b8/41598_2019_46509_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/2e2050f1caec/41598_2019_46509_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/ed0af4f14c7c/41598_2019_46509_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/2517c4e6933a/41598_2019_46509_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/fc036665f1ea/41598_2019_46509_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/6a5d0426c668/41598_2019_46509_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/df6918ccc260/41598_2019_46509_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/681c1a3f2ac6/41598_2019_46509_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/9b7427fd27b8/41598_2019_46509_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fc7f/6624209/2e2050f1caec/41598_2019_46509_Fig8_HTML.jpg

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