PRH coordinated the study and carried out data analysis and MLA. All authors read and approved the final manuscript.”
“Background

Human Immunodeficiency Virus (HIV), the virus responsible for Acquired Immunodeficiency Syndrome (AIDS), is one of the major causes of death around the world today. There were 2.1 million AIDS related deaths and 2.5 million new infections in 2007 alone with over 33.2 million people living with HIV-1 infection (AIDS epidemic update 2007, UNAIDS). Although the use of the Highly Active Anti-Retroviral Therapy (HAART) has significantly reduced the mortality Ruxolitinib and morbidity of HIV patients by chronically suppressing HIV-1 replication, we are far from finding a cure [1, 2]. Moreover, drug regimens not only come with many drawbacks such as increased malignancies, insulin resistance, glucose intolerance and diabetes mellitus [3, 4]. Other challenges to HAART efficiency are development of latency and drug resistance as viruses mutate and escape from the drug

action [5–8]. Despite isolated stories about cures for HIV infection [9] and a recent modest success in a clinical vaccine learn more trial [10, 11], a vaccine that can give total protection and a drug that can give complete cure remain to be designed [12, 13]. Immune response to the HIV infection consists of a combination of both humoral and cellular immunity [14, 15]. Furthermore, different immune responses can target the same regions of viral peptides. For example, V3-loop peptides of the Env gene can be presented by both class I and class II major histocompatibility complex (MHC) molecules and can be recognized by both Cytotoxic T-Lymphocytes (CTLs) and T-Helper cells oxyclozanide (Th), as well as by neutralizing antibodies (Ab) (e.g., [16–18]). Likewise, a highly conserved

region in the Gag gene (287-309 amino acid residues in p24) has been shown to interact with CTL, as well as B and T-Helper cells [19]. This, in turn, implies that escape changes driven by the selection pressure from one type of the host immune response can also lead to escape from a different immune mechanism (e.g., [20]). Recently, epitope vaccines (vaccines that contain synthetic peptides representing epitopes from pathogens) against HIV as well as other viruses such as Influenza have been suggested as a new strategy to avoid the viral escape from the host immune system as well as to counteract development of resistance against drugs [21–24]. While recognition of epitopes by the host immune system and mounting of immune response against pathogen is important in controlling and prevention of infections [25], mutations in the epitope regions can help pathogens to evade recognition by immune receptors and lead to subsequent escape of host immune system [26–28]. Selection by the immune system that promotes amino acid sequence diversification at viral epitopes has been shown to play a significant role in the evolution of different viruses, including HIV-1, SIV, Hepatitis C virus, and the Influenza A virus (e.g.