t is well known that HIV-1 presents a unique degree of genetic diversity. HIV-1 strains are classified in 3 groups, 9 different pure subtypes, 51 Circulating Recombinant Forms (CRFs) and several Unique Recombinant Forms (URFs)
While on one hand high rates of mutation and recombination of HIV-1 pose serious problems in the study of HIV-1 evolutionary history and on the development of an efficient vaccine, on the other hand allow studying high rates of evolution of HIV-1 strains in the short term as in no other organism. HIV-1 can therefore be used as an evolutionary model to develop methods that can later be adapted to other organisms.
Furthermore, the enormous amount of sequences available in public databases, offer the possibility to study this genetic diversity in detail.
We have several parallel projects that study the molecular epidemiology of HIV-1 in large (ex: comparison between different subtypes) and short scale (ex: transmission chains within the same subtype in the same city).
In a large scale, we are investigating the molecular epidemiology of HIV-1 in Europe in general and specifically in Estonia, Slovenia and in Portugal. We have also been involved in collaborations that investigated the molecular epidemiology of HIV-1 in African countries such as Sao Tome e Principe, Mozambique and Angola. Furthermore, we are interested in the impact of HIV-1 genetic diversity on the evolution of the virus, as for example in response to immune selective pressure or in development of resistance to antiretrovirals.
In a shorter scale, we are interested in the development of methods for detection of superinfection, transmission chains and detection of transmission of drug resistance to antiretrovirals.
Transmitted drug resistance (TDR) is substantial and results in the recommendation to test for TDR in all drug naïve patients. In Europe, newly diagnosed patients with TDR represent about 10% of all cases. While resistance to protease inhibitors (PIs) and Nucleoside Reverse Transcriptase Inhibitors (NRTIs) is predicted to stabilize, resistance to Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) can increase by more than 30%. Given that NNRTIs are included in first line regimens in most cases, this is a worrying finding. In our studies, we are using databases of genomic sequences to develop methods, based on phylodynamic approaches. to detect and analyse cases of TDR.
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