Carbon-Mangels, Miriam (2014)
Intra-host HIV-1 evolution and the co-receptor switch.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Kurzbeschreibung (Abstract)

The course of an infection with the human immunodeficiency virus type 1 (HIV-1) is characterised by three phases: primary infection, chronic infection and acquired immunodeficiency syndrome (AIDS). These stages are defined based on levels of the number of CD4-positive T-helper cells (CD4+). This characteristic three-staged classification is also reflected in the course of the viral divergence and in the emergence of viral diversity.

It is known that the V3 loop, a region encoded in the HIV envelope gene, is important for T cell infection. The CD4 receptor of the cells is used as primary receptor for viral cell entry, and the CCR5 or CXCR4 are the most important co-receptors that are necessary for cell entry. In about half of all patients, HIV switches from CCR5 towards CXCR4 usage during the late stage of infection, which hints at the onset of AIDS. Since the co-receptor tropism is determined by the V3 loop sequence, an understanding of the mechanisms of its evolution and of the circumstances leading to the co-receptor switch is of high interest. In the first part of the present work, we analysed longitudinal patient data, comprising information on CD4+ cell count, viral load, medication, coinfections and V3 loop sequences. We examined the correlations among the clinical and evolutionary data as well as the co-receptor usage over time, guided by different questions: Is the course of disease one-directional? Can successful drug therapy influence co-receptor usage? What are the genetic differences between CCR5- and CXCR4-tropic viruses?

Due to the weak statistical support of our data, we only found few indications that successful HAART therapy influences the course of disease and the direction of the coreceptor switch. We hypothesise that successful therapy can pause or roll back the course of infection, enabling the CD4+ cells to recover to high levels of immune pressure. A suppression of the viral load further can displace X4-tropic viral variants in the viral population in favour of R5-tropic variants.

In the second part of this work, we derived a fitness function to approximate the replication capacity of R5 and X4-tropic viruses. Based on a set of V3 loop sequences gathered from the Los Alamos HIV data base, the fitness function is composed of two components: the main fitness term describes the amino acid preferences found in the R5 and the X4 consensus sequence, and the additional epistatic term describes the effects of double mutations. While the impact of the main and epistatic fitness contribution can be influenced by a weighting parameter, an additional parameter controls the importance of available CCR5 and CXCR4 positive target cells. The fitness function enabled us to observe the differences of the underlying R5 and X4 fitness landscapes.

A comparison of the sequence data set showed that the R5-tropic viral sequences were highly conserved, in contrast to the X4 sequences. Network analyses confirmed the higher sequence variability of the X4 sequences, which we found to be distributed over a larger sequence space. Interestingly, our analyses revealed that the most weakly conserved sequence positions of the X4 data set were very sensible to mutations. Upon an alteration of the most weakly conserved nt positions, the X4 sequences showed an increased probability to acquire stop condons and to loose their replicative capacity.

The last part of the work describes an in silico approach of the V3 loop evolution based on the R5 and X4 fitness function. Simulations enable us to mimic the sequence evolution in silico, and to monitor the course of the viral diversity and divergence as well as the mean fitness of the simulated viral population over time. First results indicated that our simulation is able to imitate the evolutionary course of the viral diversity and divergence of an HIV infection. In our simulations, the sequence evolution followed a chemically sensible course. Amino acids that differed from the favoured chemical properties were first replaced by amino acids belonging to the favourable chemical class and finally converged into the dominant amino acid in the specific sequence position. The present project was designed to prepare the ground for deeper insights into the evolutionary dynamics of the HIV V3 loop. Our work enabled us to gain broader knowledge of the properties of R5- and X4-tropic viral sequences.

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