Table 1.
NGS data for samples sequenced ± enrichment with HIV xGen.
| Specimen ID | Country | Group or M subtype | Viral Load | Input copy no. | Library type | Total reads | HIV reads | % HIV reads | Genome coverage% | Avg. coverage depth | Std. Dev. |
|---|---|---|---|---|---|---|---|---|---|---|---|
| O-LA34 | Cameroon | HIV-1 O | 8.06 | 8019 | *HIV-SMART | 1,336,488 | 50,865 | 3.80 | 100 | 986 | 589 |
| – | – | – | – | 20667 | SSIII-xGen | 1,477,954 | 1,436,992 | 97.23 | 100 | 14,576 | 11,026 |
| N-LA28 | Cameroon | HIV-1 N | 7.61 | nt | *HIV-SMART | 1,564,286 | 155,741 | 10.00 | 100 | 3,422 | 1,604 |
| – | – | – | – | 7333 | SSIII-xGen | 2,033,250 | 2,020,867 | 99.39 | 100 | 22,538 | 17,020 |
| 2A-LA38 | Senegal | HIV-2A | 6.95 | *Ovation single cell | 3,029,490 | 40,402 | 1.33 | 100 | 573.43 | 445.55 | |
| – | – | – | – | 28355 | SSIII | 37,384 | 152 | 0.41 | 72 | 2 | 2 |
| – | – | – | – | – | SSIII-xGen | 342,284 | 331,623 | 96.89 | 100 | 3,400 | 3,344 |
| C-8119636 | South Africa | HIV-1 C | 5.62 | 8870 | *HIV-SMART | 5,446,060 | 367,224 | 6.74 | 99 | 6,481 | 4,483 |
| – | – | – | – | 85260 | SSIII | 586,936 | 15800 | 2.69 | 98 | 156 | 196 |
| – | – | – | – | – | SSIII-xGen | 400,458 | 393,350 | 98.23 | 100 | 4,042 | 5,648 |
| 02-421-10 | Cameroon | HIV-1 CRF02 | 4.48 | 643 | *HIV-SMART | 1,418,404 | 42,153 | 2.97 | 61 | 1,201 | 1,127 |
| – | – | – | – | 6177 | SSIII | 412,134 | 80 | 0.02 | 37 | 1 | 1 |
| – | – | – | – | – | SSIII-xGen | 9,776 | 7,131 | 72.94 | 82 | 78 | 231 |
| PBS1342† | DRC | HIV-1 URF | 4.59 | 3830 | HIV-SMART | 662,360 | 3,511 | 0.53 | 86 | 19 | 94 |
| – | – | – | – | – | HIV-SMART-xGen | 691,384 | 669,074 | 96.77 | 95 | 8,673 | 14,978 |
| – | – | – | – | – | SSIII | 3,432,778 | 1,095 | 0.03 | 99 | 11 | 8 |
| – | – | – | – | – | SSIII-xGen | 786,548 | 747,840 | 95.07 | 97 | 8,746 | 13,219 |
| PBS1191 | DRC | HIV-1 G | 3.86 | 1426 | HIV-SMART | 411,612 | 2,067 | 0.50 | 51 | 7 | 94 |
| – | – | – | – | – | HIV-SMART-xGen | 2,156,988 | 1,504,919 | 69.77 | 100 | 17,823 | 21,968 |
| – | – | – | – | – | SSIII | 1,276,656 | 306 | 0.02 | 45 | 2 | 4 |
| – | – | – | – | – | SSIII-xGen | 3,968,286 | 3,313,601 | 83.50 | 96 | 36,912 | 126,521 |
| PBS888 | DRC | HIV-1 A | 3.47 | 581 | HIV-SMART | 1,037,832 | 208 | 0.02 | 56 | 2 | 4 |
| – | – | – | – | – | HIV-SMART-xGen | 2,172,982 | 1,880,055 | 86.52 | 100 | 25,171 | 53,285 |
| – | – | – | – | – | SSIII | 4,532,554 | 257 | 0.01 | 54 | 2 | 2 |
| – | – | – | – | – | SSIII-xGen | 1,699,092 | 925,860 | 54.49 | 96 | 10,689 | 23,552 |
| 70641 | DRC | HIV-1 A1 | 5.78 | HIV-SMART | 1,361,655 | 51,646 | 3.79 | 99 | 947 | 1,385 | |
| – | – | – | – | HIV-SMART-xGen | 9,759,614 | 9,158,341 | 93.84 | 100 | 193,337 | 648,377 | |
| PBS5635† | DRC | HIV-1 D | 5.31 | HIV-SMART | 1,255,489 | 12,653 | 1.01 | 95 | 259 | 320 | |
| – | – | – | – | HIV-SMART-xGen | 574,273 | 522,043 | 90.91 | 99 | 12,321 | 30,529 | |
| P406 | DRC | HIV-1 G | 5.21 | HIV-SMART | 2,206,004 | 4,676 | 0.20 | 98 | 76 | 98 | |
| – | – | – | – | HIV-SMART-xGen | 1,238,978 | 629,912 | 50.84 | 100 | 14,903 | 40,689 | |
| PBS1189‡ | DRC | HIV-1 F1 | 4.98 | HIV-SMART | 1,978,086 | 2,260 | 0.11 | 82 | 41 | 76 | |
| – | – | – | – | HIV-SMART-xGen | 522,902 | 463,644 | 88.67 | 86 | 9,236 | 41,558 | |
| 50† | DRC | HIV-1 A1 basal | 4.96 | HIV-SMART | 1,662,501 | 1,731 | 0.10 | 83 | 29 | 38 | |
| – | – | – | – | HIV-SMART-xGen | 237,883 | 218,072 | 91.67 | 83 | 4,899 | 15,280 | |
| 87-2580† | DRC | HIV-1 G | 4.85 | HIV-SMART | 2,200,708 | 5,741 | 0.26 | 96 | 112 | 167 | |
| – | – | – | – | HIV-SMART-xGen | 529,218 | 221,335 | 41.82 | 96 | 5,088 | 10,026 | |
| PBS6126 | DRC | HIV-1 A1 | 4.67 | HIV-SMART | 149,709 | 115 | 0.08 | 79 | 2.6 | 2.4 | |
| – | – | – | – | HIV-SMART-xGen | 28,606 | 11,644 | 40.70 | 100 | 4,034 | 276 | |
| 2049‡ | DRC | HIV-1 CRF37 basal | 4.31 | HIV-SMART | 2,720,263 | 1,677 | 0.06 | 73 | 33 | 46 | |
| – | – | – | – | HIV-SMART-xGen | 10,689,440 | 9,321,568 | 87.20 | 90 | 201,793 | 340,069 | |
| PBS0724‡ | DRC | HIV-1A1 | 4.02 | HIV-SMART | 107,044 | 1 | 0.00 | 2 | 0.02 | 0.16 | |
| – | – | – | – | HIV-SMART-xGen | 2,010,039 | 1,061,113 | 52.79 | 100 | 21,120 | 38,865 | |
| PBS1195 | DRC | HIV-1 A2 | 3.77 | HIV-SMART | 605,867 | 51 | 0.01 | 54 | 1.2 | 1.4 | |
| – | – | – | – | HIV-SMART-xGen | 85,628 | 45,233 | 52.83 | 100 | 1,039 | 1,847 | |
| 2106 | DRC | HIV-1 A1 | 3.76 | HIV-SMART | 1,664,855 | 598 | 0.04 | 80 | 13 | 14 | |
| – | – | – | – | HIV-SMART-xGen | 1,355,794 | 1,054,751 | 77.80 | 100 | 24,313 | 57,096 | |
| P4039 | DRC | HIV-1 A1 | 3.58 | HIV-SMART | 419,163 | 132 | 0.03 | 71 | 2.8 | 3 | |
| – | – | – | – | HIV-SMART-xGen | 398,324 | 228,302 | 57.32 | 100 | 5,084 | 6,066 | |
| P3844 | DRC | HIV-1 K | 4.67 | HIV-SMART | 37,076 | 7 | 0.02 | 8 | 1.27 | 0.59 | |
| – | – | – | – | HIV-SMART-xGen | 1,883,032 | 992,447 | 52.7 | 97 | 23,300 | 57,444 |
*
Previously published data reported in Berg et al. (2016).
†
Genome completed (100%) with Sanger.
‡
Genome coverage increased with Sanger but still incomplete.