Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing.
Bottom Line: The analysis of RSV full genomes, compared to subgenomic regions, provided more precise estimates of the RSV sequence changes and revealed important patterns of RSV genomic variation and global movement.The new RSV genomic sequences and the novel sequencing method reported here provide important data for understanding RSV transmission and vaccine development.Given the complex interplay between RSV A and RSV B infections, the existence of local RSV B evolution is an important factor in vaccine deployment.
Affiliation: KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.Show MeSH
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Mentions: Two sets of reverse transcription and PCR primers were selected from all available RSVA and RSVB genomic sequence data based on frequency, location, and predicted PCR function (see Table 1 for further details). The general pattern of primer sites and the locations of primer targets in RSVA and RSVB genomes are shown in Fig. 1A. Actual PCR results are shown in Fig. 1B for RSVA and RSVB samples, with PCR products of the expected size obtained for all 6 amplicons. These primers were used as part of a deep-sequencing process for RSV combining the full cDNA preparation and genome amplification, deep sequencing with Illumina MiSeq, and de novo assembly (Fig. 1C) to generate 27 complete or nearly complete genomes (11 group A and 16 group B; median length, 14,990 nt; range, 14,666 to 15,232 nt). An additional number of samples yielded RSV contigs of >5,000 nt in length, and these were also retained for further analysis. A summary of the genomic sequences in this study is provided in Table 2.
Affiliation: KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.