Title :

Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis.

Abstract :

Detailed information on the source, spread and evolution of respiratory syncytial
virus (RSV) during seasonal community outbreaks remains sparse. Molecular
analyses of attachment (G) gene sequences from hospitalized cases suggest that
multiple genotypes and variants co-circulate during epidemics and that RSV
persistence over successive seasons is characterized by replacement and multiple 
new introductions of variants. No studies have defined the patterns of
introduction, spread and evolution of RSV at the local community and household
level. We present a whole genome sequence analysis of 131 RSV group A viruses
collected during 6-month household-based RSV infection surveillance in Coastal
Kenya, 2010 within an area of 12 km(2). RSV infections were identified by regular
symptom-independent screening of all household members twice weekly. Phylogenetic
analysis revealed that the RSV A viruses in nine households were closely related 
to genotype GA2 and fell within a single branch of the global phylogeny. Genomic 
analysis allowed the detection of household-specific variation in seven
households. For comparison, using only G gene analysis, household-specific
variation was found only in one of the nine households. Nucleotide changes were
observed both intra-host (viruses identified from same individual in follow-up
sampling) and inter-host (viruses identified from different household members)
and these coupled with sampling dates enabled a partial reconstruction of the
within household transmission chains. The genomic evolutionary rate for the
household dataset was estimated as 2.307 × 10 (-) (3) (95% highest posterior
density: 0.935-4.165× 10 (-) (3)) substitutions/site/year. We conclude that (i)
at the household level, most RSV infections arise from the introduction of a
single virus variant followed by accumulation of household specific variation and
(ii) analysis of complete virus genomes is crucial to better understand viral
transmission in the community. A key question arising is whether prevention of
RSV introduction or spread within the household by vaccinating key transmitting
household members would lead to a reduced onward community-wide transmission.

Authors :

Agoti, C.N., Munywoki, P.K., Phan, M.V.T., Otieno, J.R., Kamau, E., Bett, A., Kombe, I., Githinji,
G., Medley, G.F., Cane, P.A., Kellam, P., Cotten, M., Nokes, D.J.

PubMed link :

Journals :

Virus Evol. 2017