Follow-up Study of Intrahost HIV Type 2 Variability Reveals Discontinuous Evolution of C2V3 Sequences

Esteves, Aida; Piedade, João; Santos, C. A. F.; Venenno, Teresa; Canas-Ferreira, Wanda F.; Parreira, Ricardo

doi:10.1089/088922201750063179

Cited by 5 publications

(2 citation statements)

References 8 publications

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“…Heterochronous HIV-1 group O env data were obtained from the two available intrapatient evolution studies [33,36]. For HIV-2, we analyzed env clones from two serially sampled patients [66]; the sequence “C9/1997” from patient C was excluded from the analysis because it has been identified previously as a recombinant [67]. In addition, we inferred substitution rates from population sequences sampled at different time points in four separate patients [68].…”

Section: Methodsmentioning

confidence: 99%

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

et al. 2007

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Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood and has been attributed to host genetics, host immune responses, co-infection, viral genetics, and adaptation. Here, we develop a new “relaxed-clock” phylogenetic method to estimate absolute rates of synonymous and nonsynonymous substitution through time. We identify an unexpected association between the synonymous substitution rate of HIV and disease progression parameters. Since immune activation is the major determinant of HIV disease progression, we propose that this process can also determine viral generation times, by creating favourable conditions for HIV replication. These conclusions may apply more generally to HIV evolution, since we also observed an overall low synonymous substitution rate for HIV-2, which is known to be less pathogenic than HIV-1 and capable of tempering the detrimental effects of immune activation. Humoral immune responses, on the other hand, are the major determinant of nonsynonymous rate changes through time in the envelope gene, and our relaxed-clock estimates support a decrease in selective pressure as a consequence of immune system collapse.

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Section: Methodsmentioning

confidence: 99%

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

et al. 2007

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“…Prospective [29][30][31] and cross-sectional [32] studies examining intrapatient evolution of HIV-2 have been limited. For the present study, we examined the intrapatient HIV-2 evolution of env C2V3C3 in 8 individuals from Dakar, Senegal, over the course of ∼10 years per subject.…”

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confidence: 99%

Long‐Term Intrapatient Viral Evolution during HIV‐2 Infection

et al. 2007

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Background. Disease progression and transmission of human immunodeficiency virus (HIV) type 2 are attenuated, compared with HIV-1, which is consistent with the lower plasma viral loads observed in HIV-2 infection. Although numerous studies have characterized the intrapatient evolution of viral sequences during HIV-1 infection, prospective studies examining intrapatient evolution during HIV-2 infection have been limited.Methods. We examined viral sequence evolution in the C2V3C3 region of the viral env gene in 8 HIV-2-infected individuals from Dakar, Senegal, over the course of approximately 10 years. To compare results with HIV-1 infection, we reanalyzed data from our previous study that prospectively examined intrapatient viral evolution in HIV-1-infected individuals from the same population.Results. HIV-2 sequences from early and late time points were phylogenetically intermixed for all subjects. No distinct trends were observed in terms of increases or decreases in fragment size or the number of N-linked glycosylation sites, and ratios of synonymous substitutions per synonymous site to nonsynonymous substitutions per nonsynonymous site suggested selection to be neutral or negative. In homologous env C2V3 sequences, rates of viral divergence and diversification were slower in individuals infected with HIV-2 than in those infected with HIV-1.Conclusions. Viral evolution occurs slowly in HIV-2 infection, which is consistent with the slow disease progression of HIV-2 and supports the notion that viral evolution may be a relevant correlate for disease progression.

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Chapter 9 HIV Induced AIDS and Related Cancers

Cadogan

Dalgleish

2008

Advances in Cancer Research

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Follow-up Study of Intrahost HIV Type 2 Variability Reveals Discontinuous Evolution of C2V3 Sequences

Cited by 5 publications

References 8 publications

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

Long‐Term Intrapatient Viral Evolution during HIV‐2 Infection

Chapter 9 HIV Induced AIDS and Related Cancers

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