Phylogenetic evidence of extensive spatial mixing of diverse HIV-1 group M lineages within Cameroon but not between its neighbours

Abstract

From the perspective of developing relevant interventions for treating HIV and controlling its spread, it is particularly important to comprehensively understand the underlying diversity of the virus, especially in countries where the virus has been present and evolving since the cross-species transmission event that triggered the global pandemic. Here, we generate and phylogenetically analyse sequences derived from the gag-protease (2010 bp; n = 115), partial integrase (345 bp; n = 36), and nef (719 bp; n = 321) genes of HIV-1 group M (HIV-1M) isolates sampled between 2000 and 2022 from two cosmopolitan cities and 40 remote villages of Cameroon. While 52.4% of all sequenced viruses belonged to circulating recombinant form (CRF) 02_AG (CRF02_AG), the remainder were highly diverse, collectively representing seven subtypes and sub-subtypes, eight CRFs, and 36 highly divergent lineages that fall outside the established HIV-1M classification. Additionally, in 77 samples for which at least two genes were typed, 31% of the studied viruses apparently had fragments from viruses belonging to different clades. Furthermore, we found that the distribution of HIV-1M populations is similar between different regions of Cameroon. In contrast, HIV-1M demographics in Cameroon differ significantly from those in its neighbouring countries in the Congo Basin (CB). In phylogenetic trees, viral sequences cluster according to the countries where they were sampled, suggesting that while there are minimal geographical or social barriers to viral dissemination throughout Cameroon, there is strongly impeded dispersal of HIV-1M lineages between Cameroon and other locations of the CB. This suggests that the apparent stability of highly diverse Cameroonian HIV-1M populations may be attributable to the extensive mixing of human populations within the country and the concomitant trans-national movements of major lineages with very similar degrees of fitness; coupled with the relatively infrequent inter-national transmission of these lineages from neighbouring countries in the CB.

Keywords: Cameroon; HIV-1 group M (HIV-1M); evolution; phylogenetic; viral diversity.

Figure 1.

Map of the equatorial rain forest regions of Cameroon illustrating the sites where samples were collected: red circles represent city sampling sites; green circles represent remote villages sampling sites; and blue stars represent the sites where HIV-1 group M (M), group N (N), group O (O), and group P (P) reservoirs were identified.

Figure 2.

Distribution of HIV-1 group M subtypes and recombinants in Cameroon: the TreeMap represents the 395 viruses from the three studied genes, gag-prot, nef, and integrase. The genetic composition of the IGRs is shown in the table; N represents the number of subtypes and CRFs, n represents the number of sequenced viruses, and f represents the frequency of each IGR.

Figure 3.

Distributions of HIV-1 group M subtypes and recombinants in Cameroon according to sampling locations: distribution of subtypes and CRFs in (a) cities and within (b) rural areas. N represents the number of subtypes and CRFs and n represents the number of sequenced viruses.

Figure 4.

Geographic distribution of subtypes and recombinants among HIV-1 group M subtypes and recombinants sampled in Cameroon and its neighbouring countries (Central African Republic or CAF, Equatorial Guinea or GNQ, Gabon or GAB, and Republic of Congo or COG).

Figure 5.

MCC trees of the HIV-1 group M CRF02_AG sequences of different genes of sequences sampled from different regions of Cameroon: the best-performing clock and demographic models were a relaxed clock Skygrid model for the nef dataset and a relaxed clock exponential growth rate model for both the gag-prot and pol datasets. (a) nef gene, (b) gag-prot gene, and (c) integrase gene. The trees are temporally scaled such that distances between points represent 10 years (a and c) and 20 years (b) of evolution for these new Cameroonian sequences. As the legend indicates, each specific region is represented by a unique colour. Turquoise = centre; blue = city; purple = East; and brickred = South. Sequences from different regions are often clustered with sequences from other regions.

Figure 6.

MCC trees inferred from protease sequences depicting the relationship between the epidemic in Cameroon and its neighbours in the CB: the best-performing clock and demographic models were relaxed clock exponential growth for both the prot_CRF02_AG and prot_CRF11_cpx datasets and strict clock exponential growth for the prot_G. (a) HIV-1 group M CRF02_AG sequences sampled from Cameroon, GNQ, and GAB; (b) HIV-1 group M CRF11_cpx from Cameroon and CAF; and (c) HIV-1 group M subtype G from Cameroon and the Congo Republic (COG). The trees are temporally scaled such that distances between points represent 10 years (a) and 50 years (b and c) of evolution for these sequences. Each country is represented by a unique colour and shape. Yellow circle = Cameroon; green diamond = GNQ; grey square = GAB, blue triangle = CAF; and inverted red triangle = Congo Republic.