TABLE 3.

Diversity of SGA-direct sequence-derived complete env genes in subjects with primary HIV-1 infections

SubjectFiebig stageDate sample collected (mo/day/yr)No. of SGA env ampliconsNucleotide sequence lengthNucleotide sequence diversityAmino acid sequence diversityTime to MRCAa (days)Viral complexityNo. of variants transmitted
MeanRangeMeanRange
ZM184FV07/10/03262604-26210.130.00-0.310.330.00-0.8043Homogeneous1
ZM214MVI07/02/03352544-25680.450.00-1.100.930.00-2.00231Heterogeneousb>1
ZM215FVI10/19/02322502-25804.260.00-7.387.320.00-13.41,869Heterogeneous≥4
ZM246FII01/14/032725320.050.00-0.200.100.00-0.3626Homogeneous1
VI04/04/03142531-25320.310.16-0.400.580.24-0.95107
ZM247FII10/28/03252583-25951.120.00-2.741.780.00-4.40788cHeterogeneous2
III11/01/03192592-25950.560.00-2.700.900.00-4.29774
ZM249MIV08/05/03242562-25630.070.00-0.270.160.00-0.8231Homogeneous1
V08/12/032525620.050.00-0.160.140.00-0.4716
ZM178FVI01/18/03262560-26130.410.00-0.670.990.00-1.85112Homogeneous1
ZM180MV07/20/02242588-25600.230.04-0.390.470.00-1.0671Homogeneous1
ZM206FVI07/13/02352538-25600.250.04-0.470.610.00-1.2973Homogeneous1
ZM229MVI10/19/02292526-25922.280.04-5.824.080.00-10.31,502Heterogeneous≥4
ZM231FV12/17/02482513-25450.130.00-0.430.320.00-1.3073Homogeneous1
ZM235FV12/20/02282244-25650.160.00-0.390.340.00-0.8254Homogeneous1
  • a The time to the MRCA was estimated by using the average branch length to root of midpoint-rooted neighbor-joining trees (inferred after excluding gaps and with Kimura's two-parameter correction) assuming a rate of 1.7 × 10−5 substitutions per site per day (estimated from the extent of env sequence divergence in subject ZM246F).

  • b The number of transmitted variants could not be determined.

  • c The time to the MRCA for sequences within each of the two discrete transmitted virus lineages in subject ZM247F was estimated to be between 10 and 31 days.