**3. Immune reconstitution during chronic HAART**

Despite the successful suppression of viral replication, some clients on HAART might fail to recover immune cells (immune reconstitution). It is estimated that half of HIV infected individuals on HAART might fail to reconstitute their CD4+ T cell counts to levels above 500 cells/μL. Additionally, up to 16% might fail to achieve a CD4+ T cell counts greater than 200 cells/μL, even with long term therapy of HAART [83]. There are factors determining rates of immune reconstitution including older age [84], lower baseline CD4+ T cell counts prior to HAART [85], and co-infection with hepatitis C virus (HCV) and TB [86, 87].

### **3.1 HAART is the most effective strategy for successful immune reconstitution**

Initiation of HAART in early stages of HIV infection is associated with not detectable viral load suggesting effective inhibition of viral replication [88, 89]. During treatment initiation (during the first 4 months of HIV infection), there is lower recovery of immune cells due to a narrow restorative time. It is explained that starting HAART initiates both the rate and extent of CD4+ T cells reconstitution [90].

While treating HIV infected individuals, combining cytokine, IL-7 therapy, prevents apoptosis of T cells and is required for naive T-cell survival. This increases CD4+ T cell counts among clients on treatment [91]. The T cells remain capable of responding to antigenic stimuli and produce cytokines after polyclonal and specific antigenic stimulation. Then repopulation appears to extend cells from thymus to effector sites of the immune system [92, 93].

## **4. HIV drug resistance**

Detecting HIV drug resistance is one of the major limiting factors in the successful treatment of HIV infection [94]. This includes genotypic and phenotypic assays. The genotypic detection is performed by matching results with lists of frequently updated HIV mutations that are known to confer drug resistance which are relatively inexpensive. However, it can only identify documented HIV mutations and may not detect new mutations that arise in a particular HIV variant. Although it is not easy to predict the actual degree of drug resistance, phenotypic testing yields

drug susceptibility of a particular HIV variant. It provides information on the sensitivity of a particular HIV variant in comparison to a control isolate with full drug sensitivity. Moreover, there is inconsistency in interpreting the detected decrease in viral drug sensitivity into actual decreases in clinical sensitivity. Hence, it needs to have large-scale clinical trials for a correlation might be made between changes in phenotypic sensitivity and actual drug resistance [95].

Investigators have assessed the effectiveness of HIV drug resistance testing in improving clinical response to pharmacotherapy, like the GART [96], the VIRADAPT [97] and the ARGENTA [98]. They reported that individuals whose drug selection was based on genotypic resistance testing had significantly lower viral loads than patients who did not receive resistance testing prior to starting therapy. This reflects reduced morbidity and mortality [97].

Several factors related to the life cycle and replication of HIV are key contributors toward the rapid and widespread emergence of resistance. Initially, the reverse transcriptase enzyme is highly prone to errors during the process of reverse transcription. Hence it makes errors in each HIV genome per round of replication process which enhances its mutation for every 2000 nucleotide bases [99]. In addition to these base substitutions, insertions can occur. The especial scenario of HIV drug resistance mechanism is also due to high rate of replication. When untreated, plasma HIV RNA levels range from 103 to 105 copies/ml or sometimes greater than 106 copies/ml in acute infection [100].

The HIV virus continues to infect new cells at a very high rate to maintain the infection to a stationary state. Additionally, increased rate of errors in the reverse transcription yields new variants with drug resistance. Some HIV variants manifest drug resistance due to intrinsic factors. Hence, antiretroviral resistance can still occur even during successful therapy of HIV infection [101].
