Determination of Seasonal Influenza Intrahost Viral Diversity as a Function of Host Immune Status

Abstract

Abstract Background Seasonal influenza viruses evolve predominately via antigenic drift, the slow accumulations of genetic mutations leading to changes in key antigenic sites. Due to the accumulation of antigenic changes, influenza vaccines must be updated each year and, even then, can suffer from limited efficacy due to strain mismatch. Despite high levels of genetic diversity seen across the population, most studies show that intrahost viral diversity in humans following natural infection is limited. It is unclear where the population-level diversity in influenza virus originates. Previous studies have shown that host characteristics, such as pre-existing immunity, may affect the intrahost viral evolution during a single infection. As very young children have limited immunologic memory, we hypothesize these infections may serve as a source of viral diversity. Methods In this study, we characterize influenza genetic diversity in the pediatric population as a function of age and vaccine status. We use next generation sequencing to assess intrahost influenza virus diversity in 200 clinical isolates generated during the 2017-2018 flu season from children between 6 months and 18 years of age. We quantify intrahost diversity as the number and frequency of mutations of influenza virus present within each clinical isolate. The clinical samples were obtained from left over influenza-positive nasopharyngeal swabs from the Children's Hospital of Philadelphia Infectious Disease Diagnostics Laboratory. We stratify these isolates by host subject age and vaccine status (with respect to that season's influenza vaccine). Results The isolates sequenced thus far fall within the 6B.1A, 6B.1A.1, and 6B.1A.5b clades for H1N1 and 3C.2a.1, 3C.2a2, and 3C.3a1 clades for H3N2, as expected. Thus far, there does not appear to be a significant relationship between the number of variants detected and either the age or vaccine status of the subject for either H3N2 or H1N1, though this may change as additional isolates are sequenced. Conclusions Through ongoing studies, we evaluate how host age and vaccination status influences intrahost viral diversity. Using clinical metadata, we investigate the association between viral diversity and the duration of symptoms and disease severity. By identifying a reservoir of influenza diversity, we will be better able to evaluate influenza strains for inclusion in the seasonal vaccine.