HIV-1-Genetics-Africans

Genetic Diversity of Strains of HIV-1 circulating in African Populations

Background

• HIV is categorized into HIV type 1 (HIV-1) and HIV type 2 (HIV-2) on the basis of differences in the viral antigens and genetic characteristics (Seitz, 2016). HIV-1 is more virulent and the major cause for the global AIDS pandemic (MA et al., 2017) while HIV-2 is less virulent and less common.
• The existence of genetic variation in HIV-1 is caused by the error-prone reverse transcriptase enzyme, recombination events during replication of the virus, HIV-1 rapid turnover in the body and immune system selective pressures (Désiré et al., 2018).
• HIV-1 genetic variability is the major obstacle in the treatment of HIV and development of effective drugs. This variability occurs rapidly with some variants believed to be more virulent and resistant to different antiretroviral drugs. It is therefore pertinent to establish the genetic diversity of HIV-1.

Prerequisites, software and installations

• Involves the retrieval, from NCBI and Los Alamos databases, of HIV full sequences from different African countries.

• Download Miniconda for your specific OS to your home directory

Linux: wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

Mac: curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

• Run:

bash Miniconda3-latest-Linux-x86_64.sh

bash Miniconda3-latest-MacOSX-x86_64.sh

• Install the following packages

conda install -c bioconda mafft

conda install -c bioconda iqtree

conda install -c bioconda figtree

conda install -c bioconda aliview

Genetic diversity Workflow

People/ Team

Hesborn Obura, Bioscience Research Center,Pwani University, P.O. Box 195-80108, Kilifi, Kenya

Clement Mlay, Bioscience Research Center,Pwani University, P.O. Box 195-80108, Kilifi, Kenya

Lindani Moyo, National University of Science and Technology, Zimbabwe & Stellenbosch University, South Africa

Kauthar Mwanamkuu Omar, Pwani University, Kilifi, Kenya, P.O. Box 195-80108, Kilifi, Kenya

Wilson Mudaki, Bioscience Research Center,Pwani University, P.O. Box 195-80108, Kilifi, Kenya

Erick Masunge Sinza, Tanzania Human Genetics Organization, P.O. Box 65001, Dar es Salaam, Tanzania

Gladys Rotich, International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100 Nairobi, Kenya

Brenda Muthoni Kamau, Pwani University, Kilifi Kenya, P.O. Box 195-80108, Kilifi, Kenya

Brenda Muthoni Karumbo, KEMRI Wellcome Trust Research Programme, Kilifi, Kenya