Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Clinical Samples
2.3. RNA Extraction, Viral Load Determination, and Full-Genome Amplification
2.4. Illumina Sequencing
2.5. Bioinformatic Analysis
2.6. Statistical Analysis
2.7. Accession Numbers
3. Results
3.1. Sequencing Efficacy
3.2. Distribution of Consensus Variants According to Clades, Severity, or Vaccination
3.3. Diversity and Quasispecies Analysis
4. Discussion
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Patient Characteristics | Mild Outcome | Severe Outcome | ||
---|---|---|---|---|
Baseline Demographics | Number of patients (% of total) | 97 (55%) | 79 (45%) | |
Age in median years (range) | 34 (0–91) | 73 (1–97) | ||
Sex | Male | 48 | 36 | |
Female | 48 | 43 | ||
Origin | Lyon University Hospitals | 6 | 65 | |
Surveillance network | 91 | 14 | ||
Sample Characteristics | Sample type | NPA | 2 | 6 |
NS | 95 | 49 | ||
TBA | 0 | 13 | ||
BAL | 0 | 11 | ||
Median time since onset of symptoms, days (range) | 1 (0–5) | 3 (0–8) | ||
Viral load—median cycle threshold (range) | 19.7 (14.9–30) | 23.3 (17–35.3) | ||
Clinical Characteristics | Vaccinated against Influenza for the current season | 21 | 7 | |
Severe outcome risk factor * | 17 | 65 | ||
Main severity component | Respiratory | - | 70 | |
Neurological | 5 | |||
Multiple organ failure | 4 |
(a) | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PB2 | PB1 | PA | HA1 | HA2 | NP | |||||||||||||
255 | 480 | 52 | 614 | 565 | 121 | 131 | 142 | 144 | 171 | 262 | 77 | 150 | 450 | 472 | ||||
Significant p < | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 0.05 | 0.05 | 0.01 | 0.05 | 0.05 | 0.05 | 0.01 | 0.01 | 0.05 | 0.05 | |||
Consensus | V | V | R | E | V | N | T | R | S | K | S | V | E | G | A | |||
Variants | I | I | W/K | D | M | K | K | G/K | K/R | N | N/I | I | G | S/N | T | |||
Severe cases | - | - | - | - | - | N | T | R | - | - | - | - | - | - | - | |||
Vaccinated cases | V | V | W/K | D | M | N | - | - | S | K | S | V | E | G | A | |||
NA | M1 | M2 | NS1 | NS2 | ||||||||||||||
93 | 140 | 149 | 161 | 263 | 339 | 468 | 147 | 23 | 99 | 146 | 196 | 224 | 67 | |||||
Significant p < | 0.05 | 0.01 0.005 | 0.001 0.001 | 0.05 | 1 × 10−4 | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 1 × 10−4 0.001 | 0.05 | 0.05 | ||||
Consensus | G | I | V | N | V | N | H | V | S | S | L | K | R | E | ||||
Variants | D | L | A | S | V | D | L/P | M | N | T | S | E | S/K | A/K | ||||
Severe cases | - | I | A | - | I | - | - | - | S | - | - | E | R | E | ||||
Vaccinated cases | G | I | A | N | - | N | H | M | - | S | L | E | - | - |
(b) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
NS1 | NS1 | |||||||||
Mild | K196 | 196E | Total | Severe | K196 | 196E | Total | |||
NA | V263 | 64 | 13 | 77 | NA | V263 | 32 | 9 | 41 | |
263I | 2 | 8 | 10 | 263I | 0 | 27 | 27 | |||
Total | 66 | 21 | 87 | Total | 32 | 36 | 68 |
Segment | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | ||||
Mild/Severe | Threshold | 1 | n | 62/47 | 6/9 | 58/46 | 74/56 | 61/45 | 64/49 | 82/68 | 60/46 |
Mean | 1.88/2.38 | 2.33/2.55 | 2.03/3.46 | 0.99/1.54 | 2.75/2.73 | 1.64/2.24 | 0.41/0.65 | 0.42/0.59 | |||
p | 0.17 | 0.81 | <0.001 | <0.005 | 0.88 | 0.03 | 0.53 | 0.17 | |||
5 | n | 80/69 | 53/38 | 80/67 | 85/69 | 81/65 | 83/68 | 91/73 | 83/68 | ||
Mean | 1.68/1.95 | 0.83/1.05 | 1.71/2.84 | 0.93/1.43 | 2.40/2.23 | 1.64/2.07 | 0.41/0.60 | 0.42/0.54 | |||
p | 0.40 | 0.26 | <0.001 | <0.005 | 0.73 | 0.27 | 0.75 | 0.25 | |||
Not Vaccinated/Vaccinated | Threshold | 1 | n | 45/23 | 5/3 | 44/22 | 56/26 | 46/22 | 51/23 | 65/26 | 45/19 |
Mean | 2.22/1.78 | 3.4/1.3 | 2.84/2.13 | 1.20/0.77 | 3.22/2.27 | 1.84/1.47 | 0.51/0.35 | 0.44/0.47 | |||
p | 0.57 | 0.36 | 0.49 | 0.33 | 0.05 | 0.49 | 0.76 | 0.58 | |||
5 | n | 62/26 | 37/17 | 62/26 | 67/27 | 63/26 | 65/27 | 69/27 | 65/25 | ||
Mean | 1.85/1.69 | 1.14/0.53 | 2.23/2.00 | 1.18/0.74 | 2.68/2.15 | 1.75/1.63 | 0.51/0.33 | 0.45/0.52 | |||
p | 0.76 | 0.26 | 0.89 | 0.28 | 0.30 | 0.77 | 0.62 | 0.47 |
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Simon, B.; Pichon, M.; Valette, M.; Burfin, G.; Richard, M.; Lina, B.; Josset, L. Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season. Viruses 2019, 11, 108. https://doi.org/10.3390/v11020108
Simon B, Pichon M, Valette M, Burfin G, Richard M, Lina B, Josset L. Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season. Viruses. 2019; 11(2):108. https://doi.org/10.3390/v11020108
Chicago/Turabian StyleSimon, Bruno, Maxime Pichon, Martine Valette, Gwendolyne Burfin, Mathilde Richard, Bruno Lina, and Laurence Josset. 2019. "Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season" Viruses 11, no. 2: 108. https://doi.org/10.3390/v11020108
APA StyleSimon, B., Pichon, M., Valette, M., Burfin, G., Richard, M., Lina, B., & Josset, L. (2019). Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season. Viruses, 11(2), 108. https://doi.org/10.3390/v11020108