Patterns of HIV infection among native and refugee Afghans

Abstract

The current study was conducted to explore the origins of the HIV epidemics among the Afghan refugees in Pakistan and the native Afghans in Afghanistan. Phylogenetic analysis of HIV gag gene from 40 samples showed diverse HIV variants, originating from a number of countries. Intermixing of diverse HIV variants among Afghans may give rise to seeding of infections with rare HIV strains which may pose serious challenges for the treatment and control of infection.

HIV-1 Subtype A Gag Variability and Epitope Evolution

“…We also found that the majority of sequences from Afghanistan and Pakistan (year group 2005–10), grouped together in a single monophyletic cluster (Figure 1, green highlight). Clustering of Afghan and Pakistani sequences reflects the close relationship between the subtype A epidemic in the two countries, as evident from our previously published data [4], [26]. The HIV strains in Afghan refugees and Pakistani HIV-infected communities share phylogenetic relationship most likely because the routes of transmission of infection are the same between Pakistani patients and the Afghan refugees residing in Pakistan [4], [26].…”

“…To confirm whether genetic variability observations in the preceding analysis were also reflected in a population-specific manner, we analysed HIV-1 subtype A gag variability and gag epitope data from the Kenyan, Pakistani, and Afghan cohorts that we have been studying for the past five years [4], [8], [9], [24], [25]. Sequences from these three cohorts are predominantly found in 2005–2010 year-group.…”

“…The decrease observed in viral effective population size after 2004, combined with an increase in gag gene and epitope variability from 2005 onwards might be reflective of subtype A strains in populations with immunogenetic backgrounds that may increase the amount of immunological escape mutations while negatively affecting viral replication fitness [29]. For instance, it may be an indication of the introduction of subtype A viruses in populations having a predominance of protective alleles, such as HLA B*51 [30], as observed in the Afghan and Pakistani populations we studied [4], [5], [24], [25], where HLA data was available. The observed variability in the gag gene, as well as in the epitope pattern, could be driven, in part, by the varying HLA backdrops the viruses encountered as the HIV epidemic travelled through different populations.…”

“…These sequences were downloaded from the HIV Los Alamos National Laboratory (LANL) Database (http://www.hiv.lanl.gov/). Out of these 1,893, a total of 94 sequences (19 Kenyan, 60 Pakistani and 15 Afghan) were from our previously studied cohorts [4], [8]–[10]. (Accession numbers: Kenyan cohort sequences : GU245698, GU245706, GU245710, GU245712, GU245713-15, GU245720, GU245726-27, GU245734, GU245736-37, GU245742-43, GU245748-50, GU245758.…”

“…In subsequent years, as subtype A viruses were disseminated globally, sequences from different parts of world were made available in the LANL database. In the past few decades, HIV-1 subtype A has established itself in certain regions of the world including Kenya, Uganda, Japan, Azerbaijan, Belgium, Botswana, Belarus, Congo, and recently, Afghanistan and Pakistan (http://www.hiv.lanl.gov/) [4], [5]. Analysis of the evolutionary patterns of a virus in the context of its host populations sheds light on the selection pressures on viruses that are associated with specific host immune milieus [6], [7].…”