BioAfrica - Introduction to HIV Sequencing and Phylogenetic Analysis Program .

Action for Building Capacity (ABC) Fogarty Workshops:
Introduction to HIV Sequencing and Phylogenetic Analysis.

9 to 13 of February 2004, Durban, South Africa.

Workshop Director: Professor Sharon Cassol

Workshop Organizers: Karen Bishop and Donnie McGrath

Sponsors:Fogarty ABC Training program, Africa Centre for Health and Population Studies ABC program, Tufts-New England
Medical Center, The Nelson R Mandela School of Medicine, and the Wellcome Trust.

Workshop Program:

Day 1 (9 of February): Introductory lecture on HIV sequencing;

Methods lecture on RNA extraction from plasma, tissue and Breast Milk.

RNA isolation

RT reaction

Day 2 (10 of February): Lecture on principles of RT and PCR

Methods lecture on practical aspects of PCR

Set up PCR reaction; agarose gel electrophoresis.

Day 3 (11 of February): Lecture on Sequencing

Methods lecture on practical aspects of sequencing

Purify PCR products; quantitation; Set-up sequencing reaction; purify sequencing products

Day 4 (12 of February): Methods lecture on set up of the ABI 3100 genetic analyser

Demonstration on setting up the ABI 3100 and loading samples.

Bioinformatics Lecture I (Introduction to bioinformatics)

Bioinformatics Pratical Lecture I (Electropherogram Editing).

Day 5 (13 of February): HIV Sequence Analysis

Bioinformatics Pratical Lecture II (Sequence Alignment).

Bioinformatics Pratical Lecture III (HIV Subtyping).

Bioinformatics Pratical Lecture III (Protein Analysis).

Workshop Lectures:

Sharon Cassol, PhD (Professor at the Molecular Virology and Bioinformatics unit at Africa Centre, Nelson Mandela School of Medicine, South Africa)

Denis York, PhD (Professor at the Virology department at the Nelson Mandela School of Medicine, South Africa)

Tulio de Oliveira, (Researcher Scientist at the Molecular Virology and Bioinformatics unit at Africa Centre, Nelson Mandela School of Medicine, South Africa)

Michelle Gordon, (Researcher Scientist at the Molecular Virology and Bioinformatics unit at Africa Centre, Nelson Mandela School of Medicine, South Africa)

Natalie Graham (Researcher Scientist at the Molecular Virology and Bioinformatics unit at Africa Centre, Nelson Mandela School of Medicine, South Africa)

Ryan Doherty (Master student at the Molecular Virology and Bioinformatics unit at Africa Centre, Nelson Mandela School of Medicine, South Africa)

Bioinformatics and Computer System Support:

Patrick Charls, CCA (System Administrator at the Southern African Medical Research Council (MRC), Durban, South Africa)

Sponsors:

Fogarty ABC Training program:

Tufts-New England
Medical Center

Africa Centre for Health and Population Studies ABC program

The Nelson R Mandela School of Medicine

The Wellcome Trust

The BioAfrica web site is maintained by: Dr. Tulio de Oliveira,