Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses

Abstract

While influenza virus diversity and antigenic drift have been well characterized on a global scale, the factors that influence the virus’ rapid evolution within and between human hosts are less clear. Given the modest effectiveness of seasonal vaccination, vaccine-induced antibody responses could serve as a potent selective pressure for novel influenza variants at the individual or community level. We used next generation sequencing of patient-derived viruses from a randomized, placebo-controlled trial of vaccine efficacy to characterize the diversity of influenza A virus and to define the impact of vaccine-induced immunity on within-host populations. Importantly, this study design allowed us to isolate the impact of vaccination while still studying natural infection. We used pre-season hemagglutination inhibition and neuraminidase inhibition titers to quantify vaccine-induced immunity directly and to assess its impact on intrahost populations. We identified 166 cases of H3N2 influenza over 3 seasons and 5119 person-years. We obtained whole genome sequence data for 119 samples and used a stringent and empirically validated analysis pipeline to identify intrahost single nucleotide variants at ≥1% frequency. Phylogenetic analysis of consensus hemagglutinin and neuraminidase sequences showed no stratification by pre-season HAI and NAI titer, respectively. In our study population, we found that the vast majority of intrahost single nucleotide variants were rare and that very few were found in more than one individual. Most samples had fewer than 15 single nucleotide variants across the entire genome, and the level of diversity did not significantly vary with day of sampling, vaccination status, or pre-season antibody titer. Contrary to what has been suggested in experimental systems, our data indicate that seasonal influenza vaccination has little impact on intrahost diversity in natural infection and that vaccine-induced immunity may be only a minor contributor to antigenic drift at local scales.

Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing

“…The new data and previously published sequences are available on nextstrain to facilitate real-time tracking and further study of EV-D68 evolution and spread. Intrapatient variability was mostly low and dominated by rare synonymous substitutions, consistent with deep sequencing studies on in-fluenza virus infections (Debbink et al, 2017). However, three patients showed evidence of dual infections.…”

Asynchrony between virus diversity and antibody selection limits influenza virus evolution

“…1A–D, G–H, Fig. 4B–C)(Debbink et al, 2017; Dinis et al, 2016; McCrone et al, 2018; Leonard et al, 2016). The combination of mucosal sIgA protection and a realistically timed antibody recall response explains how there can exist immune protection against reinfection – and thus a population level selective advantage for new antigenic variants – without observable within-host antigenic selection in typical infections of experienced hosts.…”

“…We downloaded processed variant frequencies and subject metadata from the two NGS studies of immunocompetent human subjects naturally infected with A/H3N2 with known vaccination status (Debbink et al, 2017; McCrone et al, 2018) from the study Github repositories and journal websites. We independently verified that reported antigenic site and antigenic ridge amino acid substitutions were correctly indicated, determined the number of subjects with no NGS-detectable antigenic amino acid substitutions, and produced figures from the aggregated data.…”

“…Surprisingly, new antigenic variants are rarely observed in human seasonal influenza virus infections, even in recently infected or vaccinated hosts (Debbink et al, 2017; Dinis et al, 2016; McCrone et al, 2018; Leonard et al, 2016; Han, Maurer-Stroh, & Russell, 2019; Valesano et al, 2019) (Fig. 1A,B).…”

“…( A, B ) meta-analysis of A/H3N2 viruses from next-generation sequencing studies of naturally infected individuals (Debbink et al, 2017; McCrone et al, 2018). ( A ) Number of infections leading to substitutions in classically defined antigenic sites in HA (Wiley, Wilson, & Skehel, 1981) and in the antigenic ridge (Koel et al, 2013) regardless of within-host frequency.…”