Table II.

Diversity analysis of full-length HIV-1 genomes derived from patients with primary infection

Number of transmitted viruses
SubjectFiebig stageTotal number of HIV-1 genomesMaximum nt length of viral genome analyzedMinimum nt length of viral genome analyzedNumber of genomes analyzedaNucleotide sequence diversity (mean %)Nucleotide sequence diversity (range %)Max HDPoisson estimated days since MRCAbLambdacGoodness of fit p-valueHD fit to PoissonStar phylogenyDeviation from star phylogenyenv-only analysisdFull-length genome analysis
WITO4160II189,0277,698140.040–0.09817 (12, 22)3.570.923YesYes11
SUMA0874II69,0339,02060.030.01–0.04411 (7, 15)2.330.546YesYes11
WEAU0575II99,0289,02290.030–0.08714 (8, 21)3.060.49YesNoEarly stochastic11
TRJO4551II79,0519,04670.060.03–0.07720 (14, 26)4.290.836YesYes11
04013226-2II99,0689,03880.080.04–0.111033 (28, 38)7.040.269YesNoEarly stochastic11
04013396-0IV59,0499,04840.030–0.06512 (7, 17)2.50.704YesYes11
CH40 (700010040)II26e3,5932,977260.040–0.11416 (12, 21)1.3720.251YesYes11
CH40 (700010040)V98,9908,98990.050.01–0.1921 (14, 28)4.440.46YesNoCTL selection11
CH58 (700010058)III79,0278,71770.060.02–0.1924 (14, 33)5.050.941YesNoEarly stochastic11
CH77 (700010077)II23e2,7852,785230.050–0.14420 (13,26)1.30.449YesYes11
CH77 (700010077)V89,0489,03780.060.02–0.131227 (16, 37)5.750.46YesNoCTL selection11
ZM246FII108,9788,977100.040–0.09817 (10, 24)3.560.88YesNoEarly stochastic11
ZM249MIV79,0548,73570.030.01–0.06515 (9, 20)3.10.671YesYes11
ZM247FII139,0407,957121.190.01–2.46220493 (314, 673)106.1970NoNoTwo strains22
ZM247F lng 1fII99,0407,95780.050.01–0.09821 (14, 28)4.50.967YesYes11
ZM247F lng 2fII49,0349,03340.050.02–0.08721 (14, 28)4.50.939YesYes11
  • a Genomes with multiple APOBEC G-to-A hypermutations or large deletions were excluded from model analysis.

  • b Predicted minimum number of days needed to achieve observed within-patient diversity.

  • c Mean of best fitting Poisson distribution. Lambda is the free parameter that defines a Poisson.

  • d Env-only analyses were previously reported (unpublished data) (11, 12).

  • e SGA sequences representing 3′ half subgenomic fragments from the screening sample.

  • f lng 1= lineage 1; lng 2= lineage 2.