Molecular Epidemiology of HIV-1 in African Countries: A Comprehensive Overview

Abstract

The human immunodeficiency virus type 1 (HIV-1) originated in non-human primates in West-central Africa and continues to be a major global public health issue, having claimed almost 33 million lives so far. In Africa, it is estimated that more than 20 million people are living with HIV/Acquired Immunodeficiency Syndrome (AIDS) and that more than 730,000 new HIV-1 infections still occur each year, likely due to low access to testing. The high genetic variability of HIV-1, due to a fast replication cycle and high mutation rate, may cause the generation of many viral variants in a single infected patient during a single day. Therefore, the active monitoring and characterization of the HIV-1 subtypes and recombinant forms circulating through African countries poses a significant challenge to more specific diagnoses, treatments, care, and intervention strategies. In this review, a concise characterization of all the subtypes and recombinant forms circulating in Africa is presented to highlight the magnitude of the HIV-1 threat among the African countries and to understand virus genetic diversity and dispersion dynamics better.

Keywords: Africa; HIV-1; circulating recombinant form (CRF); recombinant; subtypes.

Figure 1

Schematic representation of the evolutionary relationships of human immunodeficiency virus type 1 (HIV-1) groups, subtypes, sub-subtypes, and recombinant forms. “U” for untyped. Worldwide proportions of HIV-1: subtype C (46.6%), B (12.1%), A (10.3%), G (4.6%), D (2.7%), F, H, J, K (together 0.9%), circulating Recombinant Forms (CRFs) 16.7%, unique Recombinant Forms (URFs) 6.1%. N, O, and P groups are extremely rare.

Figure 2

Pattern of the currently dominant genotypes in Africa, 1990–2020. Map of Africa showing the predominant subtypes and/or recombinant forms in the five geographic regions: Northern (Algeria, Egypt, Libya, Morocco, Sudan, *South Sudan, Tunisia), Western (Benin, Burkina Faso, Cabo Verde, Côte d’Ivoire, Gambia, Ghana, Guinea, Guinea-Bissau, Liberia, Mali, Mauritania, Niger, Nigeria, Senegal, Sierra Leone, Togo) Central (Angola, Cameroon, Central African Republic, Chad, the Democratic Republic of the Congo, Equatorial Guinea, Gabon, Burundi, Rwanda), Eastern (Djibouti, Eritrea, Ethiopia, Kenya, Madagascar, Malawi, Mauritius, Mayotte, Mozambique, Réunion, Seychelles, Somalia, Uganda, United Republic of Tanzania, Zambia, Zimbabwe), Southern (Botswana, Saint Helena, eSwatini, Lesotho, Namibia, South Africa). African macro regions are colored according to the dominant genotype. (*) South Sudan was included in Northern Africa.

Figure 3

The geographic distribution of HIV-1 subtypes, CRFs, and URFs, 2015–2020. The colors representing the different HIV-1 subtypes and recombinants are indicated in the legend.

Figure 4

Percentage of the cumulative occurrence for each subtype over the 1990–2020 period. HIV-1 subtypes, CRFs, and URFs in 1990–1999, 2000–2009, 2010–2014, 2015–2020. Subtypes O, F2, N, and CFRs 22_01_A1 and 10_CD are present in the Los Alamos HIV-1 database from 1992, 1993, 1995, 1996, and 1997, respectively. (*) from 1992, (“) from 1993, (°) from 1995, (’’’) from 1996, (^) from 1997.

Figure 5

Distribution of HIV-1 subtypes, CRFs, and URFs in 1990–1999, 2000–2009, 2010–2020. Proportion of each subtype relative to the others at the continental level is represented. The colors representing the different HIV-1 subtypes and recombinants are indicated in the legend on the right-hand side of the figure. (*) from 1992, (“) from 1993, (°) from 1995, (’’’) from 1996, (^) from 1997.