Diversity analysis of full-length HIV-1 genomes derived from patients with primary infection
| Number of transmitted viruses | ||||||||||||||||
| Subject | Fiebig stage | Total number of HIV-1 genomes | Maximum nt length of viral genome analyzed | Minimum nt length of viral genome analyzed | Number of genomes analyzeda | Nucleotide sequence diversity (mean %) | Nucleotide sequence diversity (range %) | Max HD | Poisson estimated days since MRCAb | Lambdac | Goodness of fit p-value | HD fit to Poisson | Star phylogeny | Deviation from star phylogeny | env-only analysisd | Full-length genome analysis |
| WITO4160 | II | 18 | 9,027 | 7,698 | 14 | 0.04 | 0–0.09 | 8 | 17 (12, 22) | 3.57 | 0.923 | Yes | Yes | 1 | 1 | |
| SUMA0874 | II | 6 | 9,033 | 9,020 | 6 | 0.03 | 0.01–0.04 | 4 | 11 (7, 15) | 2.33 | 0.546 | Yes | Yes | 1 | 1 | |
| WEAU0575 | II | 9 | 9,028 | 9,022 | 9 | 0.03 | 0–0.08 | 7 | 14 (8, 21) | 3.06 | 0.49 | Yes | No | Early stochastic | 1 | 1 |
| TRJO4551 | II | 7 | 9,051 | 9,046 | 7 | 0.06 | 0.03–0.07 | 7 | 20 (14, 26) | 4.29 | 0.836 | Yes | Yes | 1 | 1 | |
| 04013226-2 | II | 9 | 9,068 | 9,038 | 8 | 0.08 | 0.04–0.11 | 10 | 33 (28, 38) | 7.04 | 0.269 | Yes | No | Early stochastic | 1 | 1 |
| 04013396-0 | IV | 5 | 9,049 | 9,048 | 4 | 0.03 | 0–0.06 | 5 | 12 (7, 17) | 2.5 | 0.704 | Yes | Yes | 1 | 1 | |
| CH40 (700010040) | II | 26e | 3,593 | 2,977 | 26 | 0.04 | 0–0.11 | 4 | 16 (12, 21) | 1.372 | 0.251 | Yes | Yes | 1 | 1 | |
| CH40 (700010040) | V | 9 | 8,990 | 8,989 | 9 | 0.05 | 0.01–0.1 | 9 | 21 (14, 28) | 4.44 | 0.46 | Yes | No | CTL selection | 1 | 1 |
| CH58 (700010058) | III | 7 | 9,027 | 8,717 | 7 | 0.06 | 0.02–0.1 | 9 | 24 (14, 33) | 5.05 | 0.941 | Yes | No | Early stochastic | 1 | 1 |
| CH77 (700010077) | II | 23e | 2,785 | 2,785 | 23 | 0.05 | 0–0.14 | 4 | 20 (13,26) | 1.3 | 0.449 | Yes | Yes | 1 | 1 | |
| CH77 (700010077) | V | 8 | 9,048 | 9,037 | 8 | 0.06 | 0.02–0.13 | 12 | 27 (16, 37) | 5.75 | 0.46 | Yes | No | CTL selection | 1 | 1 |
| ZM246F | II | 10 | 8,978 | 8,977 | 10 | 0.04 | 0–0.09 | 8 | 17 (10, 24) | 3.56 | 0.88 | Yes | No | Early stochastic | 1 | 1 |
| ZM249M | IV | 7 | 9,054 | 8,735 | 7 | 0.03 | 0.01–0.06 | 5 | 15 (9, 20) | 3.1 | 0.671 | Yes | Yes | 1 | 1 | |
| ZM247F | II | 13 | 9,040 | 7,957 | 12 | 1.19 | 0.01–2.46 | 220 | 493 (314, 673) | 106.197 | 0 | No | No | Two strains | 2 | 2 |
| ZM247F lng 1f | II | 9 | 9,040 | 7,957 | 8 | 0.05 | 0.01–0.09 | 8 | 21 (14, 28) | 4.5 | 0.967 | Yes | Yes | 1 | 1 | |
| ZM247F lng 2f | II | 4 | 9,034 | 9,033 | 4 | 0.05 | 0.02–0.08 | 7 | 21 (14, 28) | 4.5 | 0.939 | Yes | Yes | 1 | 1 | |
| Number of transmitted viruses | ||||||||||||||||
| Subject | Fiebig stage | Total number of HIV-1 genomes | Maximum nt length of viral genome analyzed | Minimum nt length of viral genome analyzed | Number of genomes analyzeda | Nucleotide sequence diversity (mean %) | Nucleotide sequence diversity (range %) | Max HD | Poisson estimated days since MRCAb | Lambdac | Goodness of fit p-value | HD fit to Poisson | Star phylogeny | Deviation from star phylogeny | env-only analysisd | Full-length genome analysis |
| WITO4160 | II | 18 | 9,027 | 7,698 | 14 | 0.04 | 0–0.09 | 8 | 17 (12, 22) | 3.57 | 0.923 | Yes | Yes | 1 | 1 | |
| SUMA0874 | II | 6 | 9,033 | 9,020 | 6 | 0.03 | 0.01–0.04 | 4 | 11 (7, 15) | 2.33 | 0.546 | Yes | Yes | 1 | 1 | |
| WEAU0575 | II | 9 | 9,028 | 9,022 | 9 | 0.03 | 0–0.08 | 7 | 14 (8, 21) | 3.06 | 0.49 | Yes | No | Early stochastic | 1 | 1 |
| TRJO4551 | II | 7 | 9,051 | 9,046 | 7 | 0.06 | 0.03–0.07 | 7 | 20 (14, 26) | 4.29 | 0.836 | Yes | Yes | 1 | 1 | |
| 04013226-2 | II | 9 | 9,068 | 9,038 | 8 | 0.08 | 0.04–0.11 | 10 | 33 (28, 38) | 7.04 | 0.269 | Yes | No | Early stochastic | 1 | 1 |
| 04013396-0 | IV | 5 | 9,049 | 9,048 | 4 | 0.03 | 0–0.06 | 5 | 12 (7, 17) | 2.5 | 0.704 | Yes | Yes | 1 | 1 | |
| CH40 (700010040) | II | 26e | 3,593 | 2,977 | 26 | 0.04 | 0–0.11 | 4 | 16 (12, 21) | 1.372 | 0.251 | Yes | Yes | 1 | 1 | |
| CH40 (700010040) | V | 9 | 8,990 | 8,989 | 9 | 0.05 | 0.01–0.1 | 9 | 21 (14, 28) | 4.44 | 0.46 | Yes | No | CTL selection | 1 | 1 |
| CH58 (700010058) | III | 7 | 9,027 | 8,717 | 7 | 0.06 | 0.02–0.1 | 9 | 24 (14, 33) | 5.05 | 0.941 | Yes | No | Early stochastic | 1 | 1 |
| CH77 (700010077) | II | 23e | 2,785 | 2,785 | 23 | 0.05 | 0–0.14 | 4 | 20 (13,26) | 1.3 | 0.449 | Yes | Yes | 1 | 1 | |
| CH77 (700010077) | V | 8 | 9,048 | 9,037 | 8 | 0.06 | 0.02–0.13 | 12 | 27 (16, 37) | 5.75 | 0.46 | Yes | No | CTL selection | 1 | 1 |
| ZM246F | II | 10 | 8,978 | 8,977 | 10 | 0.04 | 0–0.09 | 8 | 17 (10, 24) | 3.56 | 0.88 | Yes | No | Early stochastic | 1 | 1 |
| ZM249M | IV | 7 | 9,054 | 8,735 | 7 | 0.03 | 0.01–0.06 | 5 | 15 (9, 20) | 3.1 | 0.671 | Yes | Yes | 1 | 1 | |
| ZM247F | II | 13 | 9,040 | 7,957 | 12 | 1.19 | 0.01–2.46 | 220 | 493 (314, 673) | 106.197 | 0 | No | No | Two strains | 2 | 2 |
| ZM247F lng 1f | II | 9 | 9,040 | 7,957 | 8 | 0.05 | 0.01–0.09 | 8 | 21 (14, 28) | 4.5 | 0.967 | Yes | Yes | 1 | 1 | |
| ZM247F lng 2f | II | 4 | 9,034 | 9,033 | 4 | 0.05 | 0.02–0.08 | 7 | 21 (14, 28) | 4.5 | 0.939 | Yes | Yes | 1 | 1 | |
Genomes with multiple APOBEC G-to-A hypermutations or large deletions were excluded from model analysis.
Predicted minimum number of days needed to achieve observed within-patient diversity.
Mean of best fitting Poisson distribution. Lambda is the free parameter that defines a Poisson.
Env-only analyses were previously reported (unpublished data) (11, 12).
SGA sequences representing 3′ half subgenomic fragments from the screening sample.
lng 1= lineage 1; lng 2= lineage 2.