Sequence ambiguity determined from routine pol sequencing is a reliable tool for real-time surveillance of HIV incidence trends.

This study explores the utility of SA defined as a proportion of ambiguous nucleotides detected in baseline pol sequences as a tool for routine real-time surveillance of HIV incidence trends at a national level. A total of 353 partial HIV-1 pol sequences obtained from persons diagnosed with HIV infection in Slovenia from 2000 to 2012 were studied, and SA was reported as a percentage of ambiguous base calls. Patients were characterized as recently infected by examining anti-HIV serological patterns and/or using commercial HIV-1 incidence assays (BED and/or LAg-Avidity assay). A mean SA of 0.29%, 0.14%, and 0.19% was observed for infections classified as recent by BED, LAg, or anti-HIV serological results, respectively. Welch's t-test showed a significant difference in the SA of recent versus long-standing infections (p < 0.001). CD4+ T-cell counts ≤250 cells/mm3 significantly correlated with higher SA (p < 0.001), whereas the homo/bisexual transmission route significantly correlated with lower SA (p = 0.005). When the LAg-assay was used as an indicator of recent infection, a receiver operating characteristic curve with the largest area under the curve (0.896) was observed for SA (sensitivity and specificity of 79%), indicating the best correlation of the data. A reliable estimation of the trends of HIV incident infection could be inferred from measuring SA irrespective of the cutoff used; however, in Slovenia it seems that lower cutoffs are more appropriate...
Source: Infection, Genetics and Evolution - Category: Genetics & Stem Cells Authors: Tags: Infect Genet Evol Source Type: research