Table 1.
Viral genome nucleotide diversity at the first visit in acute infection
| Group and subjecta | Time postonset of symptomsb | Fiebig stagec | Genome sequence length (no. of nt)d | Mean no. of InSites/genomee | Mean pairwise genetic distance (range)f | Mean HD (range)g | Mean InSites HD (range)h |
|---|---|---|---|---|---|---|---|
| Transmission pairs | |||||||
| T1-PIC58368i | ∼10 yr | VI | |||||
| R1- PIC87014i | 8 days | I | 9,217 | 0.1 | 0.17 (0.08–0.27) | 14.98 (6–25) | 0 |
| T2-PIC88403 | 14 days | V | 9,104 | 0.2 | 0.33 (0.17–0.48) | 28.09 (6–25) | 0.71 (0–2) |
| R2-PIC38051 | 3 days | I | 9,107 | 0.22 | 0.29 (0.19–0.37) | 25.28 (17–32) | 0.39 (0–1) |
| T3-PIC51550 | ∼9 yr | VI | |||||
| R3-PIC38417 | 25 days | V | 9,030 | 0.7 | 0.44 (0.27–0.68) | 40.07 (24–63) | 2.78 (0–5) |
| T4-PIC55751 | 18 daysj | Vj | 9,147 | 0.3 | 0.31 (0.17–0.45) | 27.67 (15–41) | 1.07 (0–3) |
| R4-PIC11286 | 13 days | V | 9,098 | 18.6 | 0.72 (0.15–1.49) | 67.38 (13–40) | 47.51 (0–110) |
| Variant 1 (n = 7) | 0.32 (0.14–0.52) | 28.76 (13–43) | |||||
| Variant 2 (n = 3) | 0.76 (0.57–0.96)k | 67.33 (51–84) | |||||
| Seroconverters | |||||||
| S1-PIC71101 | 7 days | I | 9,096 | 0.3 | 0.36 (0.22–0.51) | 31.44 (20–41) | 0.36 (0–1) |
| S2-PIC83747 | 6 days | I | 9,110 | 0.1 | 0.3 (0.14–0.39) | 26.53 (13–36) | 0.36 (0–1) |
| S3-PIC90770 | 3 days | I | 9,057 | 0.4 | 0.39 (0.21–0.57) | 34.51 (19–52) | 1.07 (0–3) |
Transmission pairs consist of the transmitting (T) and recipient (R) partners; seroconverters S1 to S3 are subjects without identified transmitting partners. PIC identification numbers are given.
Time postonset of clinical symptoms of primary HIV infection at visit 1.
Fiebig stages (I to V) within acute infection were defined according to reference 17. Stage VI corresponds to chronic infection of open-ended duration.
Total nucleotide (nt) length of nearly full-length genome sequence alignment.
Mean number of phylogenetically informative sites (InSites) per genome sequence at visit 1 (phylogenetically informative sites are sites at which a mutation is present in at least two sequences in the individual's data set).
Mean pairwise diversity (HKY substitution model corrected) for visit 1 genome sequences.
Mean Hamming distance for visit 1 genome sequences (all nucleotide sites).
Hamming distance for genome phylogenetically informative sites only.
Sequences from these subjects were described in reference 41.
Subject T4, although enrolled during primary infection, was infected for ∼9 years prior to transmission to R4.
Recombination among variants resulted in higher diversity for this variant population.