Table 1.
Binning of probes into specific pathogen signature probe sets
| Pathogen | Family | Genome size (nt) | Total tiling probes | Top 20% AES* (a) | GC content filter (b) | Human genome filter (c) | No. of filtered probes left (d = a - (b + c)) | No. of predicted cross-hybridizing probes (HD ≤ 4 and MCM ≥ 18) (e) | No. of probes in pathogen r-signature (d + e) | |
| 1 | LCMV | Arenaviridae | 10,056 | 1,283 | 348 | 2 | 8 | 338 | 0 | 338 |
| 2 | Hantaan | Bunyaviridae | 6,533 | 834 | 156 | 5 | 5 | 146 | 6 | 152 |
| 3 | Sin Nombre | Bunyaviridae | 6,562 | 837 | 182 | 1 | 2 | 179 | 6 | 185 |
| 4 | 229E | Coronaviridae | 27,317 | 3,495 | 494 | 11 | 11 | 472 | 0 | 472 |
| 5 | OC43 | Coronaviridae | 30,738 | 3,937 | 634 | 15 | 22 | 597 | 3 | 600 |
| 6 | SARS | Coronaviridae | 29,711 | 3,805 | 575 | 8 | 2 | 565 | 1 | 566 |
| 7 | Dengue serotype 1 | Flaviviridae | 10,717 | 1,370 | 230 | 2 | 8 | 220 | 8 | 228 |
| 8 | Dengue serotype 2 | Flaviviridae | 10,722 | 1,370 | 241 | 0 | 9 | 232 | 11 | 243 |
| 9 | Dengue serotype 3 | Flaviviridae | 10,707 | 1,370 | 230 | 0 | 4 | 226 | 13 | 239 |
| 10 | Dengue serotype 4 | Flaviviridae | 10,649 | 1,361 | 229 | 1 | 7 | 221 | 3 | 224 |
| 11 | Japanese encephalitis | Flaviviridae | 10,976 | 1,404 | 310 | 3 | 2 | 305 | 12 | 317 |
| 12 | West Nile | Flaviviridae | 10,962 | 1,401 | 320 | 2 | 2 | 316 | 9 | 325 |
| 13 | Yellow fever | Flaviviridae | 10,862 | 1,389 | 255 | 2 | 3 | 250 | 2 | 252 |
| 14 | Hepatitis B | Hepadnaviridae | 3,215 | 409 | 147 | 14 | 0 | 133 | 0 | 133 |
| 15 | Influenza A† | Orthomyxoviridae | 12,561 | 1,582 | 510 | 1 | 15 | 494 | 0 | 494 |
| 16 | Influenza B | Orthomyxoviridae | 14,452 | 1,822 | 665 | 5 | 18 | 642 | 2 | 644 |
| 17 | Human papillomavirus type 10 | Papillomaviridae | 7,919 | 1,011 | 287 | 16 | 9 | 262 | 0 | 262 |
| 18 | hMPV | Paramyxoviridae | 13,335 | 1,705 | 322 | 44 | 17 | 261 | 0 | 261 |
| 19 | Newcastle disease | Paramyxoviridae | 15,186 | 1,943 | 329 | 0 | 2 | 327 | 3 | 330 |
| 20 | Nipah | Paramyxoviridae | 18,246 | 2,335 | 389 | 12 | 5 | 372 | 0 | 372 |
| 21 | Parainfluenza 1 | Paramyxoviridae | 15,600 | 1,995 | 330 | 8 | 13 | 309 | 2 | 311 |
| 22 | Parainfluenza 2 | Paramyxoviridae | 15,646 | 2,002 | 333 | 10 | 2 | 321 | 0 | 321 |
| 23 | Parainfluenza 3 | Paramyxoviridae | 15,462 | 1,979 | 409 | 28 | 23 | 358 | 3 | 361 |
| 24 | RSV B | Paramyxoviridae | 15,225 | 1,948 | 383 | 28 | 4 | 351 | 4 | 355 |
| 25 | Echovirus 1 | Picornaviridae | 7,397 | 945 | 238 | 1 | 10 | 227 | 22 | 249 |
| 26 | Enterovirus A | Picornaviridae | 7,413 | 946 | 193 | 3 | 0 | 190 | 8 | 198 |
| 27 | Enterovirus B | Picornaviridae | 7,389 | 944 | 179 | 0 | 4 | 175 | 22 | 197 |
| 28 | Enterovirus C | Picornaviridae | 7,401 | 945 | 183 | 0 | 0 | 183 | 4 | 187 |
| 29 | Enterovirus D | Picornaviridae | 7,390 | 944 | 155 | 0 | 3 | 152 | 8 | 160 |
| 30 | Foot and mouth disease | Picornaviridae | 8,115 | 1,036 | 194 | 14 | 3 | 177 | 0 | 177 |
| 31 | Hepatitis A | Picornaviridae | 7,478 | 955 | 163 | 1 | 6 | 156 | 0 | 156 |
| 32 | Rhinovirus A (type 89) | Picornaviridae | 7,152 | 913 | 191 | 6 | 6 | 179 | 1 | 180 |
| 33 | Rhinovirus B | Picornaviridae | 7,212 | 920 | 197 | 2 | 2 | 193 | 0 | 193 |
| 34 | HIV 1 | Retroviridae | 9,181 | 1,174 | 191 | 4 | 0 | 187 | 0 | 187 |
| 35 | Rubella | Togaviridae | 9,755 | 1,246 | 117 | 65 | 0 | 52 | 0 | 52 |
| Total | 419,242 | 53,555 | 9768 | 9921 |
*AES scores for all tiling probes were ranked together and only those probes in the top 20th percentile were retained. †Segment 7 of Influenza A was omitted during probe design.