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.
Highlights
Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
Over the six-month period (December 2009 – June 2010), a total of 7,695 nasopharyngeal-flocked swabs (NPS) were collected from the 20 HHs, 415 (5.4%) of which were determined to be respiratory syncytial virus (RSV) real-time RT-PCR positive (cycle threshold (Ct) value of
Samples were processed for WGS21 with successful amplification and assembly of RSV contigs of >1000 nucleotides length in 246 samples (65.7%)
Summary
Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant. 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. 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). For best resolution of WAIFW within households, we suggest an integrated analysis of RSV genomic and epidemiological data. Respiratory syncytial virus (RSV) is a leading viral cause of bronchiolitis and pneumonia during infancy[1]. Global estimates in 2015 indicated that RSV causes ~33.1 million episodes of acute lower respiratory tract illness annually, ~3.2 million of which lead to hospital admissions and ~60,000 deaths in hospitalized children aged under 5
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