Table 2.
Transmission variants and subtypes in protocol C individuals.
| PCID | Coded ID | Sample date | EDI | VL | Transmission variants | Sequence type | Subtype by NFLG | Subtype by pol |
|---|---|---|---|---|---|---|---|---|
| 175,019 | R49M | 30-Mar-05 | 10 | 3,000,000 | Single | TF | A1 | A1 |
| 175,042 | R463F | 9-Mar-07 | 10 | 152,000,000 | Single | TF | A1 | A1 |
| 175,079 | R3103M | 19-Sep-08 | 13 | 750,001 | Single | TF | A1 | A1 |
| 175,089 | R3584M | 15-Dec-09 | 13 | 223,440 | Single | TF | A1C | A1 |
| 175,005 | R53F | 16-Jun-05 | 14 | 2,090,040 | Single | TF | A1 | A1 |
| 175,062 | R1135M | 11-Feb-08 | 14 | 1,256,940 | Single | TF | A1 | A1 |
| 175,065 | R269M | 24-Mar-08 | 14 | 31,700,000 | Single | Con | A1 | A1 |
| 175,072 | R3137M | 28-May-08 | 14 | 9,061,540 | Single | Con | C | C |
| 175,053 | R254F | 8-Aug-07 | 15 | 1,876,000 | Single | TF | A1C | C |
| 175,090 | R3469F | 15-Apr-10 | 15 | 2,920,000 | >2 | TF(P1) | A1 | A1 |
| 175,093 | R2302M | 9-Jul-10 | 15 | 3,760,000 | Single | TF | A1 | A1 |
| 175,094 | R3843F | 14-Oct-10 | 16 | 4,400,000 | Single | TF | A1 | A1 |
| 175,059 | R977F | 14-Dec-07 | 17 | 7,290,000 | Single | TF | A1 | A1 |
| 175,038 | R880F | 12-Jan-07 | 21 | 730,000 | Single | TF | A1 | A1 |
| 175,097 | R3894M | 18-Mar-11 | 23 | 6,934,997 | Single | TF | CD | CD |
| 175,092 | R3671F | 8-Jun-10 | 25 | 3,940,000 | Single | NA | A1 | A1 |
| 175,074 | R873F | 24-Jul-08 | 37 | 219,920 | 2 | TF(P1) | A1 | A1 |
| 175,071 | R1077F | 12-Jun-08 | 41 | 4,702,444 | 3 | TF(P2) | A1 | A1 |
| 175,008 | R50M | 25-May-05 | 45 | 117,608 | >2 | NA | C | C |
| 175,020 | R57F | 12-Oct-05 | 46 | 134,472 | >2 | NA | A1 | A1 |
| 175,014 | R59M | 21-Oct-05 | 46 | 806,290 | Single | TF | A1 | A1 |
| 175,017 | R44M | 3-May-05 | 49 | 123,560 | Single | TF | A1C | A1 |
| 175,011 | R63M | 14-Dec-05 | 50 | 184,270 | Single | Con | A1C | A1C |
| 175,012 | R40F | 31-Mar-05 | 53 | 1,398,004 | Single | TF | A1C | A1 |
| 175,027 | R72M | 10-Aug-06 | 67 | 425,000 | >2 | NA | A1 | A1 |
| 175,010 | R65M | 27-Jan-06 | 73 | 148,220 | Single | TF | A1 | A1 |
PCID, protocol C identification number of the participant; Coded ID, coded identification number used in two previous publications (Haaland et al., 2009; Yue et al., 2015); Sample date, date of sample collection; EDI, time since estimated date of infection; VL, viral load of sample; Transmission variants, number of genetic variants transmitted from partner; Sequence type, sequence defined as TF: transmitted founder virus sequence amplicon identical to consensus identified in NFLG amplicons; (P1), (P2): TF sequence identified in subpopulation 1 or 2 of multiple variants, Con: consensus sequence of NFLG amplicons: Subtype by NFLG: subtype as deduced from the NFLG sequence, Subtype by pol: Subtype defined previously from pol gene sequencing.