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. 2018 Dec 13;23(50):1800228. doi: 10.2807/1560-7917.ES.2018.23.50.1800228

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.

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