Molecular epidemiology, evolution and transmission dynamics of HIV-1 in Ghana, West Africa

Reconstructing the origins and transmission of the HIV epidemic in Ghana has, since the first diagnosis in 1986, yet to be reported. This study described the transmission clusters of HIV in the Ghanaian setting using a maximum-likelihood tree via the IQTree approach. Using 71 newly described full-length Ghanaian HIV-1 sequences, we performed molecular phylodynamic analysis to determine major drivers of HIV transmission in Ghana, a West African population where the HIV-1 CRF02_AG recombinant is prevalent. However, to reconstruct the origin of the most predominant subtype CRF02_AG, we combined 48 CRF02_AG sequences in our dataset with 140 full-length CRF02_AG sequences downloaded from the Los Alamos National Laboratory HIV database and utilized the ancestral trait reconstruction model in BEAST v.1.10.5 to reconstruct an MCC tree, summarized in TreeAnnotator and visualized with treeio package in R. Phylogeographic reconstruction to estimate the earliest introduction of HIV-1 showed that Cameroon and Nigeria were the sources of nine major introductions, with a time to most recent common ancestor (tMRCA) of 1964.2. Most intra-country transmission occurred from Greater Accra to other major regions. This is the first study to combine full-length HIV-1 genomic sequences with patient metadata to estimate the population dynamics and reconstruct the introduction of the predominant HIV-1 CRF02_AG in Ghana. This study illuminates our understanding of HIV transmission dynamics in Ghana and underscores the utility of combining demographic and molecular data in prospectively tracking HIV transmission to inform targeted public health interventions.