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

Figure 1. Within-host diversity of IAV populations.

(A) Boxplots (median, 25th and 75th percentiles, whiskers extend to most extreme point within median ±1.5 x IQR) of the number of viral genomes per microliter transport media stratified by day post symptom onset. Notches represent the approximate 95% confidence interval of the median. (B) Boxplots (median, 25th and 75th percentiles, whiskers extend to most extreme point within median ±1.5 x IQR) of the number of iSNV in 249 high quality samples stratified by day post symptom onset. (C) The number of iSNV in each isolate stratified by vaccination status. The red lines indicate the median. (D) Location of all identified iSNV in the influenza A genome. Mutations are colored nonsynonymous (blue) and synonymous (gold) relative to that sample’s consensus sequence. Mutations are considered nonsynonymous if they are nonsynonymous in any known influenza open reading frame. Triangles signify mutations that were found in more than one individual in a given season.

Figure 1—source data 1. Titers and day of sampling for all samples processed from the cohort.
elife-35962-fig1-data1.csv (16.1KB, csv)
DOI: 10.7554/eLife.35962.008
Figure 1—source data 2. The number of iSNV and day of sampling for samples that qualified for iSNV identification.
elife-35962-fig1-data2.csv (2.4KB, csv)
DOI: 10.7554/eLife.35962.009
Figure 1—source data 3. The number of iSNV and vaccination status for samples that qualified for iSNV identification.
elife-35962-fig1-data3.csv (2.4KB, csv)
DOI: 10.7554/eLife.35962.010
Figure 1—source data 4. Location and frequency of iSNV identified in each individual.
(The highest quality sample was used when two where available).
elife-35962-fig1-data4.csv (44.7KB, csv)
DOI: 10.7554/eLife.35962.011

Figure 1.

Figure 1—figure supplement 1. Sequence coverage for all samples.

Figure 1—figure supplement 1.

For each sample, the sliding window mean coverage was calculated using a window size of 200 and a step of 100. The distributions of these means are plotted as box plots (median, 25th and 75th percentiles, whiskers extend to most extreme point within median ±1.5 x IQR) where the y-axis represents the read depth and the x-axis indicates the position of the window in a concatenated IAV genome.
Figure 1—figure supplement 2. Approximate maximum likelihood trees of the concatenated coding sequences for high quality H1N1 samples.

Figure 1—figure supplement 2.

The branches are colored by season; the tip identifiers are colored by household. Arrows with numbers indicate consensus and putative minor haplotypes for samples with greater than 10 iSNV. Trees were made using FastTree (Price et al., 2010). ‘Caledonia’ refers to A/New Caledonia/20/1999(H1N1). ‘H1N1’ refers to sequence from a plasmid clone derived from a clinical sample corresponding to A/California/07/2009.
Figure 1—figure supplement 3. Approximate maximum likelihood trees of the concatenated coding sequences for high quality H3N2 samples.

Figure 1—figure supplement 3.

The branches are colored by season; the tip identifiers are colored by household. Arrows with numbers indicate consensus and putative minor haplotypes for samples with greater than 10 iSNV. Trees were made using FastTree (Price et al., 2010). ‘Wisconsin_2005’ refers to A/Wisconsin/67/2005(H3N2). ‘Perth’, ‘Victoria’, and ‘HK’ refer to sequences from plasmid clones derived from clinical samples corresponding to A/Perth/16/2009, A/Victoria/361/2011, A/Hong Kong/4801/2014, respectively.
Figure 1—figure supplement 4. The effect of titer on the number of iSNV identified.

Figure 1—figure supplement 4.

(A) The number of iSNV identified in an isolate (y-axis) plotted against the titer (x-axis, genomes/μl transport media).