Science and Technology Production
Congress
Authorship
Date
2014
Publishing House and Editing Place
Organizing Committee of the RSV2014 Symposium
Summary
Information provided by the agent in
SIGEVA
This work describes the structure of HRSV viral populations that infected patients who suffered acute lower respiratory infection (LRI) and those who suffered prolonged LRI or reinfection between outbreaks from 2011 to 2013. The genetic variation and evolutionary dynamics of the G gene ectodomain were analyzed at intrapatient variation level by clonal Sanger sequencing (CSS) and next generation sequencing (NGS).Viral variants were reconstructed by aligning NGS data sets with reference strains u...
This work describes the structure of HRSV viral populations that infected patients who suffered acute lower respiratory infection (LRI) and those who suffered prolonged LRI or reinfection between outbreaks from 2011 to 2013. The genetic variation and evolutionary dynamics of the G gene ectodomain were analyzed at intrapatient variation level by clonal Sanger sequencing (CSS) and next generation sequencing (NGS).Viral variants were reconstructed by aligning NGS data sets with reference strains using QuRe and Bowtie2. Calculation of average diversity (Pi) measured as p-distances and bayesian phylogenetic analyses were performed to analyze the viral population dynamics within samples and to determine associations between local and global circulating HRSV strains (MEGA v6 and MrBayes). The average depth of coverage for the NGS data sets ranged from 1000X to 20000X, while for the CSS was 60X, showing the potential ability of the NGS to analyze viral population structures. Between the analyzed patients, two presented a strong immunosuppression, and as a consequence viral variants within the first and the second samples were clustered together with their direct sequences and with each other in a closely related genetic clade. The maximum Pi between variants was very low (0.38%; SE0.10%), suggesting a prolonged shedding. Another patient harbored in his first sample only viral variants associated with the HRSV strain with a 72-nt duplication that emerged in 2011, his second sample (9 days apart) harbored two variants and in his third sample (50 days apart from the first sample) there were at least four types of variants associated with the ones of his previous samples and wit8ih local circulating strains, suggesting a prolonged shedding and reinfections probably due to many hospitalizations. The maximum Pi value was 3.96% (SE0.43%). Another patient suffered the first LRI in the 2011-outbreak and the second one in the 2012-outbreak, and viral variants found between them were completely different, thus suggesting a reinfection. Conclusions about how HRSV encounters and surmounts different immune environments are derived from this study, showing that these patients, in different natural conditions of infection, might act as genetic reservoirs that could provide in turn molecular plasticity to HRSV.
Show more
Show less
Key Words
CLONAL SANGER SEQUENCINGNGSINTRAPATIENT VARIATIONHRSV