Table 3. Summary of Nanopore mapping data on chikungunya and dengue virus positive samples by real-time reverse transcription-PCR, United Kingdom, 2017a (n = 8 samples).
| Sample | Ct value | Total reads |
% reads mapping to appropriate viral sequence | % 20x coverage |
20x genome length (nt) |
% 10x coverage | Referenceb | Reference size (nt) | Max de novo contig (nt) |
|---|---|---|---|---|---|---|---|---|---|
| CHIKV 1 | 14.7 | 267,171 | 65.1 | 98.57 | 11,658 | 99.2 | CHIKV | 11,826 | 5,263 |
| CHIKV 3 | 21.4 | 1,891,028 | 85.1 | 99.76 | 11,798 | 99.9 | CHIKV | 11,826 | 10,793 |
| CHIKV 4 | 22.7 | 216,493 | 11.6 | 94.11 | 11,130 | 97.2 | CHIKV | 11,826 | 4,256 |
| CHIKV 9 | 30.08 | 3,481,358 | 4.08 | 100 | 11,826 | 100 | CHIKV | 11,826 | 9,860 |
| DENV 1 | 16.3 | 284,622 | 71.3 | 99.9 | 10,719 | 99.9 | DENV 1 | 10,735 | 8,281 |
| DENV 2 | 16.9 | 203,700 | 72.1 | 99.6 | 10,692 | 99.6 | DENV 1 | 10,735 | 10,157 |
| DENV 6 | 21.2 | 1,377,721 | 71.1 | 99.9 | 10,634 | 99.9 | DENV 4 | 10,649 | 7,877 |
| DENV 11 | 28.7 | 1,111,566 | 2.9 | 95.3 | 10,226 | 96.3 | DENV 1 | 10,735 | 4,699 |
CHIKV: chikungunya virus; Ct: cycle threshold; DENV: dengue virus.
a The Nanopore 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 For DENV the serotype is also indicated.