HIV-1 genetic diversity and transmitted drug resistance mutations among patients from the North, Central and South regions of Angola

Abstract

Background: Angola presents a very complex HIV-1 epidemic characterized by the co-circulation of several HIV-1 group M subtypes, intersubtype recombinants and unclassified (U) variants. The viral diversity outside the major metropolitan regions (Luanda and Cabinda) and the prevalence of transmitted drug resistance mutations (DRM) since the introduction of HAART in 2004, however, has been barely studied.

Methods: One hundred and one individuals from the Central (n = 44), North (n = 35), and South (n = 22) regions of Angola were diagnosed as HIV-1 positive and had their blood collected between 2008 and 2010, at one of the National Referral Centers for HIV diagnosis, the Kifangondo Medical Center, located in the border between the Luanda and Bengo provinces. Angolan samples were genotyped based on phylogenetic and bootscanning analyses of the pol (PR/RT) gene and their drug resistance profile was analyzed.

Results: Among the 101 samples analyzed, 51% clustered within a pure group M subtype, 42% were classified as intersubtype recombinants, and 7% were denoted as U. We observed an important variation in the prevalence of different HIV-1 genetic variants among country regions, with high frequency of subtype F1 in the North (20%), intersubtype recombinants in the Central (42%), and subtype C in the South (45%). Statistically significant difference in HIV-1 clade distribution was only observed in subtype C prevalence between North vs South (p = 0.0005) and Central vs South (p = 0.0012) regions. DRM to NRTI and/or NNRTI were detected in 16.3% of patients analyzed.

Conclusions: These results demonstrate a heterogeneous distribution of HIV-1 genetic variants across different regions in Angola and also revealed an unexpected high frequency of DRM to RT inhibitors in patients that have reported no antiretroviral usage, which may decrease the efficiency of the standard first-line antiretroviral regimens currently used in the country.

Figure 1. Detailed distribution of HIV-1 variants found in the Angolan population.

a) Frequency of “pure” subtypes, inter-subtype recombinants and unclassified (U) sequences within the 101 HIV-1 group M Angolan samples analyzed. b) Frequency of Circulating Recombinants Forms (CRFs) and Unique Recombinant Forms (URFs) within the 42 inter-subtype recombinants samples described above.

Figure 2. ML tree of the pol (PR/RT) region of Angolan viruses (black circles) classified as “pure” subtypes, CRFs-like, or the putative new recombinant_UH.

Reference sequences from all HIV-1 subtypes and CRFs 02_AG, 18_cpx, 25_cpx and 45_cpx were also included. aLRT values are only shown at key notes. The scale represents number of substitutions per site. A representative bootscanning plot and the proposed schematic structure of recombinant_UH strains are shown. The dashed line indicates the cut-off of 70%.

Figure 3. Schematic drawing showing breakpoint pattern at the pol (PR/RT) region of the HIV-1 URFs found in Angola.

Breakpoint positions were obtained using bootscanning and phylogenetic analyses. The pol gene is colored according to the subtype as shown in the figure legend. The fragments not analyzed are represented in white.

Figure 4. B. ML tree of the pol (PR/RT) region of Angolan sequences classified as U (black circles) plus reference sequences from all HIV-1 subtypes.

aLRT values are only shown at key notes. The scale represents number of substitutions per site. Bootscanning plots of Angolan U strains are shown. Only one representative bootscanning plot is shown for the phylogenetically related Angolan U sequences ANG58, ANG61 and ANG69. The dashed line indicates the cut-off of 70%.

Figure 5. Map of Angola showing the frequency of HIV-1 genetic variants across different country regions (Central, North and South).

Provinces where patients included in the present study were from are indicated: Luanda, Bengo, Cuanza Norte and Cuanza Sul provinces of the Central region (red stars); Cabinda, Zaire and Uíge provinces of the North region (blue stars); and Benguela, Huíla and Namíbe provinces of the South region (black stars). Kifangondo is indicated with a black and blue star. Statistically significant difference in HIV-1 clade distribution was observed in subtype C prevalence between North vs South (p = 0.0005) and Central vs South (p = 0.0012) regions.