Retrovirology

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-Nei^a	Syn^b	Nonsyn^c	Tamura-Nei^a	Syn^b	Nonsyn^c	Tamura-Nei^a	Syn^b	Nonsyn^c
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	-	-	-
2003^d 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	-	-

^a: Tamura-Nei distance with gamma-parameter α = 0.25. Standard errors were estimated by the bootstrap method with 500 bootstrap replicates each.
^b and ^c: Nei-Gojobori method, p-distance, syn= synonymous, nonsyn= nonsynonymous
^d Nucleotide differences of strains B1 and B2 were not calculated in 2003, because only B1/B2 or B/AE recombinant sequences were retrieved.
^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.

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