The Use of Bioinformatics for Studying HIV Evolutionary and Epidemiological History in South America

Table 1

Coalescent estimates of epidemic growth rate of HIV-1 clades in South America.

Subtype	Demographic model	Molecular clock	Gene	Growth rate(year^−1)	Reference
B	Exponential growth	Strict	pol (PR)	0.23; (0.20–0.26)	[105]
			pol (RT)	0.35; (0.31–0.40)
			pol (PR/RT)	0.4; (0.2–0.7)	[106]
	Logistic growth	Strict	env (C2-V3)	0.54; (0.32–0.78)	[87]
			pol (PR-RT)	0.56; (0.35–0.80)
F1	Logistic growth	Strict	env (C2-V3)	0.61; (0.40–0.86)	[87]
			pol (PR-RT)	0.59; (0.31–0.92)
C	Exponential growth	Strict	pol (PR)	0.77; (0.62–0.93)	[105]
			pol (RT)	0.63; (0.51–0.75)
			pol (PR/RT)	0.7; (0.3–1.0)	[106]
	Logistic growth	Strict	env (C2-V3)	0.77; (0.45–1.14)	[111]
			pol (RT)	0.70; (0.41–1.00)
		Relaxed	env (C2-V3)	0.87; (0.50–1.29)
			pol (RT)	0.81; (0.40–1.26)
CRF12_BF	Logistic growth	Relaxed	vpu	2.24; (0.21–4.56)	[95]
		Strict	pol (PR-RT)	1.08; (0.79–1.44)	[96]
		Relaxed		1.22; (0.85–1.64)
CRF28_BF/CRF29_BF	Logistic growth	Relaxed	pol (PR-RT)	1.18; (0.64–1.38)	[97]
			gag	1.20; (0.59–1.47)
CRF31_BC	Logistic growth	Strict	pol (RT)	1.26; (0.61–2.10)	[111]
		Relaxed		1.27; (0.44–2.26)
CRF38_BF	Logistic growth	Strict	pol (PR-RT)	0.83; (0.31–1.81)	[96]
		Relaxed		0.92; (0.41–1.75)