Retrovirology

Table 4 Mean nucleotide distances within env-V3 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	0.010 ± 0.002	0.011 ± 0.003	0.008 ± 0.002	-	-	-	-	-	-
2002 blood	0.017 ± 0.004	0.014 ± 0.005	0.012 ± 0.003	0.006 ± 0.002	0.010 ± 0.004	0.004 ± 0.002	-	-	-
2004 blood	0.012 ± 0.004	0.012 ± 0.007	0.010 ± 0.004	0.005 ± 0.003	0.000 ± 0.000	0.006 ± 0.003	0.009 ± 0.002	0.010 ± 0.002	0.008 ± 0.002
2005 blood	0.028 ± 0.009	0.050 ± 0.021	0.015 ± 0.006	0.022 ± 0.006	0.040 ± 0.014	0.014 ± 0.004	0.010 ± 0.003	0.021 ± 0.003	0.005 ± 0.002
2004 semen	0.009 ± 0.004	0.017 ± 0.012	0.006 ± 0.003	0.008 ± 0.003	0.013 ± 0.009	0.005 ± 0.002	-^d	-	-
2005 semen	-^d	-	-	0.010 ± 0.003	0.017 ± 0.010	0.006 ± 0.002	-^d	-	-

^a: Tamura-Nei distance with gamma-parameter α = 0.38. Standard errors were estimated by the bootstrap method with 500 bootstrap replicates each.
^b and ^c Nei-Gojobori distance method, p-distance, syn = synonymous, nonsyn= nonsynonymous.
^d Nucleotide distances were not calculated for strain B1 in 2005 (seminal plasma) and subtype AE in 2004 (seminal plasma) and 2005 (seminal plasma) as the generic primers did not amplify B1 or AE fragments from these samples, and the products generated with specific primers were too short to conduct evolution studies.

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