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Table 3 Mean nucleotide distances within the gag gene over time in blood and seminal plasma

From: HIV-1 sequence evolution in vivo after superinfection with three viral strains

  B1 strain B2 strain Subtype AE
Year Tamura-Neia Synb Nonsync Tamura-Neia Synb Nonsync Tamura-Neia Synb Nonsync
2001 blood 0.008 ± 0.001 0.011 ± 0.004 0.006 ± 0.001 - - - - - -
2002 blood 0.007 ± 0.001 0.012 ± 0.003 0.005 ± 0.001 0.009 ± 0.002 0.022 ± 0.006 0.005 ± 0.001 - - -
2003d blood - - - - - - 0.003 ± 0.001 0.002 ± 0.002 0.003 ± 0.001
2004 blood 0.022 ± 0.004 0.071 ± 0.012 0.006 ± 0.002 0.008 ± 0.002 0.008 ± 0.004 0.008 ± 0.002 0.004 ± 0.002 0.006 ± 0.006 0.003 ± 0.002
2005 blood 0.021 ± 0.003 0.051 ± 0.009 0.010 ± 0.002 0.025 ± 0.005 0.060 ± 0.014 0.011 ± 0.003 -e - -
2004 semen 0.008 ± 0.002 0.011 ± 0.003 0.006 ± 0.002 0.002 ± 0.001 0.006 ± 0.004 0.001 ± 0.001 -e - -
2005 semen 0.007 ± 0.002 0.017 ± 0.005 0.003 ± 0.001 0.008 ± 0.002 0.007 ± 0.004 0.008 ± 0.002 -e - -
  1. a: Tamura-Nei distance with gamma-parameter α = 0.25. Standard errors were estimated by the bootstrap method with 500 bootstrap replicates each.
  2. b and c: Nei-Gojobori method, p-distance, syn= synonymous, nonsyn= nonsynonymous
  3. d Nucleotide differences of strains B1 and B2 were not calculated in 2003, because only B1/B2 or B/AE recombinant sequences were retrieved.
  4. e Nucleotide distances were not calculated for subtype AE in 2005 (blood plasma), 2004 and 2005 (seminal plasma) as no AE fragments were amplified by the generic primers from these samples.