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. 2018 May 3;7:e35962. doi: 10.7554/eLife.35962

Figure 2. Within-host dynamics of IAV.

(A) Histogram of within-host iSNV frequency in 249 high quality samples. Bin width is 0.05 beginning at 0.02. As in Figure 1, mutations were classified as nonsynonymous (blue) if they were nonsynonymous in any known influenza reading frame. Synonymous mutations are gold. (B) The within-host frequency of nonsynonymous mutations in HA stratified by whether or not they are in known antigenic sites (p=0.46 Wilcoxon rank sum). (C) The global frequency of putative antigenic minority iSNV identified in our cohort that have circulated at frequencies above 5% globally since their time of collection. Each variant is labeled according the H3 numbering scheme. The dashed line indicates when samples were collected. Frequency traces are faded prior to the collection date. (D) Timing of sample collection for 43 paired longitudinal samples relative to day of symptom onset. Of the 49 total, 43 pairs had minority iSNV present in either sample. (E) The change in frequency over time for minority iSNV identified for the paired samples in (A). Nonsynonymous and synonymous iSNV are plotted separately. Mutations are colored according to whether they were detected in both isolates (blue), detected only the first isolate (red), or detected only in the second isolate (yellow). The threshold of detection was 2%. The arrows indicate mutations in known antigenic sites.

Figure 2—source data 1. The frequency and class (nonsynonymous/synonymous) of identified iSNV.
elife-35962-fig2-data1.csv (30.8KB, csv)
DOI: 10.7554/eLife.35962.014
Figure 2—source data 2. Meta data for nonsynonymous iSNV found in HA.
elife-35962-fig2-data2.csv (3KB, csv)
DOI: 10.7554/eLife.35962.015
Figure 2—source data 3. Frequency and meta data for antigenic iSNV that were also identified at the global level.
elife-35962-fig2-data3.csv (50.2KB, csv)
DOI: 10.7554/eLife.35962.016
Figure 2—source data 4. Sampling day for within-host sample pairs.
elife-35962-fig2-data4.csv (1.4KB, csv)
DOI: 10.7554/eLife.35962.017
Figure 2—source data 5. Frequencies of mutations identified in longitudinal sample pairs.
elife-35962-fig2-data5.csv (7.5KB, csv)
DOI: 10.7554/eLife.35962.018

Figure 2.

Figure 2—figure supplement 1. (A) Reproducibility of iSNV identification for paired samples acquired on the same day.

Figure 2—figure supplement 1.

The x-axis represents iSNV frequencies found in the home-acquired nasal swab. The y-axis represents iSNV frequencies found the clinic-acquired combined throat and nasal swab. Dashed line is a one to one expectation. (B) Frequency of all minority iSNV as determined from replicate RT-PCR and sequencing libraries (see Materials and methods). Data are stratified by viral load of original samples. Note that samples with viral loads > 105 were not run in duplicate and those with viral loads < 103 were not used in the study. Dashed line is a one to one expectation.