Identification of recombination hotspots in HIV-1 genome is animportant tool that can be used to predict evolution of the virus and to inform the design of an antiviral drug that avoids targeting the recombination hotspots (e.g. Gao, 2009). Depending on the different selective pressures acting on different genomic regions, recombination can facilitate the accumulation of mutations and accelerate the emergence of resistance to therapies, dissociate favorable combinations of mutations or contribute to emergence of multi-drug resistance bycombining multiple drug resistance mutations in a single recombinant product. The latter is mostly a problem in low- to middle-income countries as multiple subtypes tend to co-circulate in these countries (e.g. Rajaram et al, 2007). For example, under conditions of fast spreading of the virus, such as in standing social intravenous drug user networks, the chances of super-infection, and thus recombination, are greater than that of other transmission modes, suggesting that such epidemics may have a higher rate of virus recombination (Berry et al,2009). We hypothesize that differences in socioeconomic status between countries likely to influence difference in recombination rate of HIV-1 genes that are under strong purifying selection pressure (e.g. Pol gene), which in turn can influence the levels of nucleotide diversity of the virus. In this project we have examined and contrasted the correlationcoefficients between recombination rate and nucleotide diversity of recombination hotspots in Pol gene for low-income and high-income countries. Our study shows that there is a significant difference in recombination events and thus nucleotide diversity in HIV-1 pol gene accounting to socioeconomic status.
Dr. Helen Piontkivska