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 withinhost 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. Author summaryInfluenza is a significant global health problem. Vaccination is the best way to prevent influenza virus infection, and seasonal influenza vaccines are considered for reformulation each year in order to keep up with the virus' evolution. Despite these efforts, vaccine recipients often develop an immune response that does not protect from infection. Given the current recommendation that all people over 6 months of age get vaccinated, it is important to understand how vaccination itself may impact viral evolution during natural human infection. We studied how vaccination may alter viral evolution within individuals, as each person harbors many highly-related influenza variants that differ in their ability to escape the immune response. We compared groups of people in a vaccine trial to determine the impact that vaccination has on viral diversity and variant selection within individuals. We did not detect significant differences in the number of variants detected or in the prevalence of mutations that co...

Linking influenza virus evolution within and between human hosts

“…We calculated rates of within-host influenza evolution from deep-sequencing data in three published studies that together represented 308 acute H3N2 influenza infections (Figure 3, Figure S3) (Debbink et al, 2017;Dinis et al, 2016;. We estimated evolutionary rates separately for synonymous, nonsynonymous, and stop-codon (nonsense) mutations in each patient and each viral gene, and we averaged the rates estimated for each patient to calculate a single rate of evolution for each gene and mutation type.…”

“…We downloaded raw sequencing data from the NCBI SRA database for Bioprojects PRJNA344659 (Debbink et al, 2017), PRJNA412631 (McCrone et al, 2018), and PRJNA364676 (Xue et al, 2017). We obtained sequencing data for (Dinis et al, 2016) by personal communication.…”

“…Several recent studies have used deep sequencing to identify within-host mutations in hundreds of clinical influenza infections (Debbink et al, 2017;Dinis et al, 2016;. However, it remains unclear what role these within-host mutations play in the global evolution of influenza virus.…”

“…However, it remains unclear what role these within-host mutations play in the global evolution of influenza virus. The same within-host mutations are only rarely observed in different individuals, and mutations that reach detectable frequencies at the global scale are not notably more common than other mutations within hosts (Debbink et al, 2017;. Specifically, although influenza virus displays rapid antigenic evolution on the global scale, antigenic variants are present at low frequencies within hosts (Dinis et al, 2016;.…”

“…Individual withinhost mutations are challenging to track on a global scale, but by comparing large numbers of genetic variants identified within and between hosts, we can infer the evolutionary forces that act on different classes of mutations. We analyze within-host viral variation in 308 acute influenza infections from three deep-sequencing datasets (Debbink et al, 2017;Dinis et al, 2016;, and we calculate rates of evolution within and between hosts to determine how selection and genetic drift shape viral evolution. Synonymous mutations accumulate at similar rates within and between hosts, but nonsynonymous mutations are less prevalent globally than they are within hosts across most of the influenza genome.…”