Prognostic value of virological and immunological responses after 6 months of antiretroviral treatment in adults with HIV-1 infection in sub-Saharan Africa.

BACKGROUND: HIV RNA monitoring is not available in most antiretroviral treatment (ART) programs in sub-Saharan Africa; switch to second-line therapy is mostly guided by clinical/immunological criteria. This may lead to unnecessary disease progression and drug resistance accumulation. We investigated the prognostic value of virological and immunological status 6 months after ART initiation with respect to death, loss to follow-up, and treatment switch. METHODS: We considered treatment-naive HIV-1-infected patients, starting ART with available 6-month visit and subsequent follow-up, enrolled in a prospective cohort comprising 5 ART sites in 3 sub-Saharan countries. Outcome measures included the time from 6-month visit to death for all causes, loss to follow-up, and switch to second line. RESULTS: Of 2539 patients, 62% were females, their median pre-ART CD4 count was 215 cells per microliter, median HIV RNA 4.6 Log10 copies per milliliter, 30% were on WHO stage 3/4. At 6 months, 85% had HIV RNA <1000 copies per milliliter. During 3112 person-years follow-up after the 6-month visit, 91 patients died. Death was predicted by 6-month HIV RNA ≥10,000 copies per milliliter, adherence, and 6-month CD4 <200 cells per microliter. The 2-year estimated probability of surviving ranged from 0.69 (with 6-month HIV RNA ≥10,000 and CD4 <200) to 0.95 (with HIV RNA <1000 and CD4 ≥200). Loss to follow-up (1.95 per 100 person-years follow-up) was predicted by the 6-month HIV RNA >10,000 copies per milliliter and adherence but not by CD4. Switch to second line (6.94 per 100 person-years follow-up) was predicted by 6-month HIV RNA and CD4. CONCLUSIONS: In patients starting ART in sub-Saharan Africa, 6-month HIV RNA independently predicts subsequent survival, retention to care, and switch to second-line therapy. This measure warrants further evaluation as specific time point monitoring option.

Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen.

Direct population sequencing and reverse hybridization (line probe assay [LiPA])-based methods are the most common methods for detecting hepatitis B virus (HBV) drug resistance mutations, although only mutations present in viral quasispecies with a prevalence of > or =20% can be detected by sequencing, and only known mutations are detected by LiPA. Massively parallel ultradeep pyrosequencing (UDPS; GS FLX platform) was used to analyze HBV quasispecies in reverse transcriptase (RT) and hepatitis B S antigen (HBsAg) from five drug-naive patients and eight drug-resistant patients. Eight primer pairs were used to obtain partially overlapping amplicons, covering the RT gene from codons 1 to 288 and the complete overlapping HBsAg sequence. A 1% mutation frequency was selected as the cutoff based on an error rate estimated on plasmid DNA. This technology enabled simultaneous analysis of between 2,852 and 18,016 clonally amplified fragments from each patient. The results indicate that UDPS has a relative sensitivity much higher than both direct sequencing and LiPA. In addition, the UDPS results are quantitative, allowing establishment of the relative frequency of both known mutations and novel substitutions. Some of the detected RT substitutions led to changes also in HBsAg. On the whole, genotype D presented a higher heterogeneity than genotype A. Considering the high quantity of information that can be provided by a single test from one patient, the short turnaround time, the information on substitution frequency, and the detection of rare variants, there are strong advantages conferred by UDPS, and the new method could play a relevant role in the clinical management of HBV infection and therapy.