Molecular Epidemiology of Human Immunodeficiency Virus (HIV)
Code
21220
Academic unit
NOVA Medical School | Faculdade de Ciências Médicas
Department
Medical Virology
Credits
6
Teacher in charge
Prof. Doutor Ricardo Manuel Soares Parreira
Teaching language
Portuguese
Objectives
1. Understanding of the biological nature of the mechanisms involved in generation of genetic diversity in HIV and its consequences in terms of performance of diagnostic and viral load follow up testing, and therapeutic possibilities.
2. Recognition of how the genetic features of HIV may be used as epidemiological markers to follow up viral spread in space and time.
3. Demonstration of basic skills regarding de execution of experimental protocols used for assessment of the genetic diversity of circulating viral strains, and the critical analysis of the obtained results.
4. Use of different algorithms for interpretation of genetic polymorphisms in the protease (PR) and reverse transcriptase (RT) genes, and analysis of the results in terms of viral drugsusceptibility/therapeutic failure.
5. Acquisition of basic skills in phylogenetic reconstruction, aiming at the genetic analysis of viral genomes and the identification of viral recombinants.
Prerequisites
n/a
Subject matter
1. Genetic variability and molecular epidemiology of the human immunodeficiency vírus (VIH).
2. Follow up of the HIV infection and anti-retroviral drug susceptibility testing (genotypic and phenotypic tests).
3. Automated search of genetic polymorphisms in the protease and reverse-transcriptase viral sequences, associated with therapeutic failure using antiretroviral drugs.
4. Assessment of HIV genetic diversity by using HMA (Heteroduplex Mobility Assay).
5. Preparation of proviral DNA from dry blood samples spotted onto FTA® cards, and its amplification by nesterPCR.
6. Molecular cloning of amplified PCR fragments (including ligation to a plasmid vector, preparation of Escherichia coli competent cells and their transformation, and plasmid DNA extraction and analysis).
7. HIV1 genomic sequence analysis using multiple molecular phylogenetic techniques, including phylogenetic tree building and bootscanning.
Bibliography
1. Hemelaar, J. (2012). The origin and diversity of the HIV1 pandemic. Trends Mol Med. 18(3), 18292.
2. Tebit, D.M., & Arts, E.J. (2011). Tracking a century of global expansion and evolution of HIV to drive
understanding and to combat disease. Lancet Infect Dis. 11(1), 4556.
3. Taylor, B.S., Sobieszczyk, M.E., McCutchan, F.E., & Hammer, S.M. (2008). The challenge of HIV1
Subtype diversity. N Engl J Med. 358(15), 1590602.
4. Skar, H., Hedskog, C., & Albert, J. (2011). HIV1 evolution in relation to molecular epidemiology and
antiretroviral resistance. Ann N Y Acad Sci., 1230, 10818.
5. Paraskevis, D., Paredes, R., Poljak, M., Schmit, J.C., Soriano, V., Walter, H., Sönnerborg, A.; & European HIV Drug Resistance Guidelines Panel (2011). European recommendations for the clinical use of HIV drug resistance testing: 2011 update. AIDS Rev., 13(2), 77108.
Teaching method
Laboratory classes will be carried out in a BLS1 (biosafety laboratory with basic biosafety contention) setting, while those based on bioinformatic analyses of viral sequences will be carried out in a computer room, with individual dedicated computers, running freeware software.
Evaluation method
The evaluation procedure includes 3 components: class performance (10% of the final grade), formal written exam (50% of the final grade), and seminar presentation and discussion (40% of the final grade).