The Impact of Genetic Diversity on HIV-1 Molecular Epidemiology and Antiviral Drug Resistance

Abstract

HIV-1 is a retrovirus that jumped from chimpanzees and/or gorillas to hu mans in the first half of the twentieth century. After its transmission to humans, it acquired a high amount of genetic diversity, due to high r ates of mutation and recombination. Until now, nine subtypes (A, B, C, D , F, G H, J and K) and 43 Circulating Recombinant Forms (CRFs) have been described. Furthermore, several Unique Recombinant Forms (URFs) are con tinuously generated when different subtypes recombine. To understand the impact of HIV-1 genetic diversity on its molecular epidemiology, evolut ionary dynamics and response to antiretrovirals, we used bioinformatics methods combining phylogenetic analysis, population genetics, statistica l and data mining approaches. Understanding the molecular epidemiology of HIV-1 and its changes along time is crucial to better monitor the pandemic and to develop efficient vaccines and antiretrovirals. In Chapter 2 of this thesis, we describe t he molecular epidemiology of HIV-1 in Angola, a country geographically c lose to Democratic Republic of Congo (DRC), currently known as the origi n of the pandemic. In our sample of Angolan patients, we found an enormo us amount of genetic diversity, including a high number of recombinant f orms, only comparable to its neighboring country DRC. In Chapter 3, we d escribe the molecular epidemiology of HIV-1 in Europe in patients newly diagnosed in 2002-2003. We found a large amount of non-B subtypes (33%), which seem to be mainly infecting immigrants, heterosexuals and women. Our studies indicate that non-B subtypes seem still to be restrained to certain risk groups and to patients originated from continents other tha n Europe, suggesting their continuous import in Europe. The origin and evolutionary history of HIV-1 subtypes is still a largely debated issue. In Chapter 4, we studied the origin of subtype G and CRF 02_AG and found that subtype G is in fact a recombinant, which may be at least partly originating from CRF02_AG, thus inversing the role of par ent and recombinant . Our study brings new striking data, especially b ecause until now the origin of HIV-1 subtypes was thought to be due to f ounder and sampling effects. Our new data indicates that recombination o ccurred already early on in the epidemic and is affecting also the so-ca lled pure subtypes. In Chapter 5, we analyze the evolutionary rate of different subtypes and CRFs. Our results suggest that the evolutionary rate is subtype-depende nt and that it can be attributed not only to host immune pressure measur ed in the nonsynonymous substitution rate, but also to the replicative f itness of the subtypes/CRFs measured in the synonymous substitution rate . Our results suggest that the different HIV-1 subtypes or CRFs have ind eed different biological properties, some of which may explain the diffe rences in the epidemics of these subtypes/CRFs. In the last part of this thesis we evaluate the effect of all these epid emic and genetic differences on HIV-1 antiretroviral therapy. This issue has been widely studied in the last few years. However, in this thesis we develop new approaches for the study of therapy response. We consider each subtype as an individual and compare each subtype to its own wild- type, unlike previous studies, which have considered subtype B as the gl obal wild-type of all subtypes. In Chapter 6, we investigate the baselin e susceptibility of subtypes C, F, G and CRF02_AG to protease inhibitors . We found differences in baseline susceptibility of different subtypes that become more evident if we group our sequences according to certain polymorphisms in protease instead of grouping it by subtypes, suggesting it is the actual genetic background that makes the difference, and not some other characteristic of the subtypes. In Chapter 7, we analyze the effect on therapy response of 89I/V mutations, which is different among the different subtypes. We find that the mutation is indeed associated w ith PI treatment, but only in several non-B subtypes, including subtype G, that have 89M as wild-type sequence, as opposed to 89L as wild-type i n other subtypes. Its phenotypic effect is only measurable when combined with the L90M mutation. These mutations are further studied in Chapter 8 in the context of the comparison of the interpretation of genotypic an d phenotypic data of subtypes B and G. Interestingly, the combination of M89I/L90M in subtype G has a phenotypic effect on susceptibility to nel finavir comparable to the L90M only as major mutation in subtype B. This argues that failing nelfinavir results in similar phenotypic effects in subtype B compared to subtype G, but for this effect, 2 mutations are n eeded in subtype G, while only one mutation is needed in subtype B. In conclusion, the epidemics of HIV-1 and the genetic differences among the resulting subtypes and CRFs result in different biological propertie s and play a role in resistance development towards antiviral treatment. This raises questions on how such differences should be implemented in drug resistance interpretation systems that have traditionally been buil t on information from subtype B.status: publishe