Volume 21, Number 1—January 2015
Research
Protocol for Metagenomic Virus Detection in Clinical Specimens1
Claudia Kohl
, Annika Brinkmann, Piotr W. Dabrowski, Aleksandar Radonić, Andreas Nitsche, and Andreas Kurth
, Annika Brinkmann, Piotr W. Dabrowski, Aleksandar Radonić, Andreas Nitsche, and Andreas Kurth
Table 5
Output of next-generation sequencing for development of a protocol for metagenomic virus detection in infectious disease settings*
| Name | No. original reads | No. remaining reads† | Minimum, maximum (mean) read length), nt† | Sendai virus | Vaccinia virus | Influenza virus, A/ PR8/1934 | Reovirus, T3/Bat/G/342/08 | No. nonviral reads |
|---|---|---|---|---|---|---|---|---|
| Chicken RNA library | 1,636,344 | 1,076,582 | 100, 464 (240) | 46 | 7 | 0 | 0 | 999,947 |
| Chicken DNA library | 1,332,908 | 808,516 | 100, 463 (248) | 0 | 1,343 | 0 | 0 | 998,657 |
| Chicken random library | 1,347,059 | 576,467 | 100, 460 (199) | 3 | 510 | 0 | 0 | 999,486 |
| Chicken TUViD-VM protocol | 2,021,403 | 969,236 | 100, 455 (220) | 60,408 | 224 | 4,934 | 0 | 934,434 |
| Marmoset RNA library | 2,859,201 | 1,555,567 | 100, 464 (223) | 6 | NA | NA | NA | 999,994 |
| Marmoset DNA library | 2,856,326 | 1,711,121 | 100, 464 (246) | 0 | NA | NA | NA | 1,000,000 |
| Marmoset random library | 598,451 | 355,443 | 100, 464 (200) | 11 | NA | NA | NA | 999,989 |
| Marmoset TUViD-VM protocol | 1,007,051 | 640,088 | 100, 460 (223) | 446,813 | NA | NA | NA | 553,186 |
*Standardization value for all procedures was 1,000,000. TUViD-VM, tissue-based universal virus detection for viral metagenomics; NA, not applicable.
†After length filtering of 100–1,000 nt.
1Preliminary results of this study were presented at the Biodefense and Emerging Infectious Diseases Meeting, January 29, 2014, Washington DC, USA.
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