Box plots summarizing the number of intra-host single-nucleotide variants (iSNVs; median, interquartile range [IQR], and whiskers extending within median ±1.5 × IQR) identified in samples with …
Black line plots the mean coverage for a sliding window of 50 base pairs (stepsize = 25 base pairs). The interquartile range is shaded in dark pink while the full range is denoted in light pink. (A) …
Each circle represents a nucleotide variant site (with frequency estimated between 0.02 and 0.98) found in reads attributed to at least two different amplicons (at least 100× coverage for each …
Tip names are given in the format: ‘Patient ID_Days since symptom onset_putative consensus or minority sequence.’ The tree is rooted to the A/Brisbane/10/2007 virus (H3N2_Bris07; EPI_ISL_103644). …
Tip names are given in the format: ‘Patient ID_Days since symptom onset_putative consensus or minority sequence.’ The tree is rooted to the A/California/04/2009 virus (H1N1pdm09_Cali09; …
Time is measured by number of days since symptom onset. Each point represents a patient included in this study who was treated with oseltamivir (Supplementary file 4).
Top panel shows the evolutionary rate of individual gene segments over all timepoints () while the bottom panel depicts the genome-wide evolutionary rate () for each day since symptom onset. All …
All rates are stratified by substitution type (synonymous – blue; nonsynonymous – red; stop codon – gray). Wilcoxon signed-rank tests were performed to assess if the paired synonymous and …
All rates are stratified by substitution type (synonymous – blue; nonsynonymous – red; stop codon – gray). Wilcoxon signed-rank test was not performed here due to the low number of samples collected …
Each plotted line is the linearly regressed line to the evolutionary rates computed for each A/H3N2-infected individual. Based on our findings, we expect that synonymous rates correlate negatively …
Variants that could potentially be PCR artifacts were removed (i.e., those found under the 75th percentile [6.3%] of frequency range of variants located in overlapping amplicons but were only …
(A) A/H3N2 and (B) A/H1N1pdm09 virus specimens, sorted by frequency bins of 5% and substitution type (synonymous – blue; nonsynonymous – red; stop-codon – gray).
(A) Breakdown of intra-host single-nucleotide variants (iSNVs) identified in seasonal A/H3N2 virus samples. The top panels plot the nucleotide positions where iSNVs were found in at least two …
Top panel shows the number of subjects where nonsynonymous variants were found in the respective protein site. Different canonical antigenic sites of the HA protein are colored (HA numbering based …
Top panel shows the number of subjects where nonsynonymous variants were found in the respective protein site. Bottom panel plots selected as well as parallel amino acid mutations found in multiple …
Top panel shows the number of subjects where nonsynonymous variants were found in the respective protein site. Bottom panel plots selected as well as parallel amino acid mutations found in multiple …
Top panel shows the number of subjects where nonsynonymous variants were found in the respective protein site. Bottom panel plots selected as well as parallel amino acid mutations found in multiple …
Top panel shows the number of subjects where nonsynonymous variants were found in the respective protein site. Different canonical antigenic sites of the HA protein are colored (HA numbering based …
Top panel shows the number of subjects where nonsynonymous variants were found in the respective protein site. Bottom panel plots selected as well as parallel amino acid mutations found in multiple …
Top panel shows the number of subjects where nonsynonymous variants were found in the respective protein site. Bottom panel plots selected as well as parallel amino acid mutations found in multiple …
All A/H3N2 virus samples collected from all patients with site coverage above the 100× are included. The distributions were compared to that of neighboring sites, ±10 nucleotide positions adjacent …
Amino acid sites with potentially linked epistatic amino acid variants as tabulated in Table 1 are separately colored, with their corresponding positions annotated on the monomeric structure.
We assumed that synonymous mutations are neutral for all simulations. (A) Neutral expectation where all nonsynonymous mutations are neutral (). We tested our hypotheses where the majority of …
Blue line with markers denotes the population size computed from the model. When virions, we assumed that remained constant at 107 (pink dashed line) to reduce computational costs of …
Box plots summarizing the statistic (intra-host single-nucleotide variants [iSNVs]; median, interquartile range [IQR], and whiskers extending within median ±1.5 × IQR) computed for samples with …
The mean and standard deviation (SD) values reported are based on the results of five distinct simulations. Variants with mean kcal/mol are deemed to be stabilizing while destabilizing mutants …
(kcal/mol) | ||
---|---|---|
Variants | Mean | SD |
G384R | −3.84 | 0.06 |
M426I | 2.61 | 0.05 |
G384R,M426I | −0.42 | 0.06 |
G102R | 4.87 | 0.00 |
G384R,G102R | 0.76 | 0.09 |
A493T | 11.96 | 0.30 |
G384R,A493T | 5.56 | 0.19 |
V197I | −3.11 | 0.02 |
S353Y | −1.97 | 0.68 |
V197I,S353Y | −4.48 | 0.14 |
Parameter | Meaning | Value (units) | Source |
---|---|---|---|
- | Number of hours per replicative generation | 6 hr | Assumption |
Average number of virions produced by an infected cell | 100 virions | Frensing et al., 2016 | |
Initial target cell population size | 4 × 108 virions | Hadjichrysanthou et al., 2016 | |
Per capita decay rate | Two per-generation | Assumption | |
Within-host basic reproduction number | 5 | Hadjichrysanthou et al., 2016 | |
µ | Per-site, per-generation mutation rate | 3 × 10−5 per-site, per-generation | McCrone et al., 2020 |
Mean number of nonsynonymous (NS), synonymous (S), and stop codon (Stop) variants per sample for each gene segment as well as the corresponding NS/S ratio.
Potentially linked nonsynonymous variants in within-host A/H1N1pdm09 and A/H3N2 virus samples.
Sample names are given in the format of 'Patient ID_Days since symptom onset.' Both linkage disequilibrium () and the normalized measures are tabulated alongside the inferred maximum-likelihood haplotype frequencies ( and are the haplotype frequencies with variant i or ii only while is the frequency of haplotypes encoding both variants).
A/H3N2 segment-specific primers.
Patients metadata (provided as an Excel file).
Acknowledgment table of reference sequences downloaded from GISAID.