Table 1. Description of samples positive for chikungunya and dengue virus by real-time reverse transcription-PCR with corresponding Illumina mapping data, United Kingdom, 2017a (n = 26 samples).
Sample | Ct value | Estimated genome copy number in the sample (/mL) | Sample type | Total reads (R1 + R2)b |
% reads mapping to reference viral genome | % 20x coverage | % 10x coverage | Reference virusc | Reference size (nts) |
---|---|---|---|---|---|---|---|---|---|
CHIKV 1 | 14.72 | 2.12E + 10 | Plasma | 1,113,560 | 78.32 | 99.59 | 99.72 | CHIKV | 11,826 |
CHIKV 2 | 20.06 | 5.49E + 08 | Serum | 1,278,624 | 98.48 | 99.14 | 99.47 | CHIKV | 11,826 |
CHIKV 3 | 21.41 | 2.18E + 08 | Plasma | 1,391,258 | 95.23 | 98.86 | 99.37 | CHIKV | 11,826 |
CHIKV 4 | 22.74 | 8.76E + 07 | Plasma | 888,968 | 19.16 | 97.08 | 97.32 | CHIKV | 11,826 |
CHIKV 5 | 23.77 | 4.33E + 07 | Plasma | 1,357,606 | 97.13 | 99.16 | 99.58 | CHIKV | 11,826 |
CHIKV 6 | 25.4 | 1.42E + 07 | Serum | 3,236,848 | 34.88 | 97.80 | 98.40 | CHIKV | 11,826 |
CHIKV 7 | 25.76 | 1.11E + 07 | Plasma | 3,748,070 | 72.77 | 99.04 | 99.56 | CHIKV | 11,826 |
CHIKV 8 | 28.17 | 2.13E + 06 | Plasma | 1,499,952 | 28.41 | 98.69 | 99.00 | CHIKV | 11,826 |
CHIKV 9 | 30.08 | 5.76E + 05 | Serum | 1,035,026 | 6.66 | 95.98 | 98.22 | CHIKV | 11,826 |
CHIKV 10 | 30.37 | 4.72E + 05 | Serum | 1,575,222 | 16.84 | 97.39 | 98.01 | CHIKV | 11,826 |
CHIKV 11 | 30.66 | 3.87E + 05 | Serum | 1,143,054 | 13.52 | 95.36 | 96.96 | CHIKV | 11,826 |
CHIKV 12 | 30.95 | 3.17E + 05 | Serum | 1,507,380 | 10.93 | 96.11 | 96.52 | CHIKV | 11,826 |
CHIKV 13 | 32.2 | 1.35E + 05 | Serum | 1,323,920 | 5.03 | 88.47 | 89.38 | CHIKV | 11,826 |
CHIKV 14 | 32.57 | 1.05E + 05 | Serum | 1,479,404 | 21.72 | 96.32 | 96.93 | CHIKV | 11,826 |
DENV 1 | 16.29 | 4.21E + 09 | Plasma | 439,292 | 93.44 | 99.51 | 99.58 | DENV 1 | 10,735 |
DENV 2 | 16.85 | 2.83E + 09 | Serum | 513,472 | 92.56 | 99.40 | 99.58 | DENV 1 | 10,735 |
DENV 3 | 17.67 | 1.58E + 09 | Plasma | 738,814 | 92.53 | 99.58 | 99.58 | DENV 2 | 10,723 |
DENV 4 | 18.20 | 1.09E + 09 | Serum | 477,368 | 93.97 | 98.73 | 99.12 | DENV 2 | 10,723 |
DENV 5 | 19.73 | 3.67E + 08 | Serum | 915554 | 89.65 | 99.14 | 99.40 | DENV 2 | 10,723 |
DENV 6 | 21.22 | 3.61E + 07 | Serum | 3,587,926 | 83.87 | 99.68 | 99.69 | DENV 4 | 10,649 |
DENV 7 | 23.76 | 2.11E + 07 | Serum | 4,146,678 | 2.17 | 86.99 | 89.13 | DENV 1 | 10,735 |
DENV 8 | 24.8 | 1.01E + 07 | Serum | 777,264 | 69.23 | 99.56 | 99.58 | DENV 3 | 10,707 |
DENV 9 | 25.28 | 7.17E + 06 | Plasma | 787,728 | 26.97 | 98.77 | 98.81 | DENV 2 | 10,723 |
DENV 10 | 26.98 | 2.15E + 06 | Serum | 596,240 | 6.58 | 93.47 | 93.97 | DENV 3 | 10,707 |
DENV 11 | 28.69 | 6.39E + 05 | Serum | 1,034,698 | 3.73 | 94.44 | 94.70 | DENV 1 | 10,735 |
DENV 12 | 31.29 | 1.01E + 05 | Serum | 1,374,766 | 0.47 | 71.46 | 77.76 | DENV 1 | 10,735 |
CHIKV: chikungunya virus; Ct: cycle threshold; DENV: dengue virus.
a The Illumina mapping data presented in the table were obtained in 2017 on samples that had been collected and found positive for chikungunya or dengue virus by real-time reverse transcription-PCR in 2016.
b ‘R1 + R2’ indicates paired-end sequencing.
c For DENV the serotype is also indicated.