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

Autori
Lunar, Maja ; Židovec Lepej, Snježana ; Poljak, Mario

Izvornik
Infection, genetics and evolution (1567-1348) 69 (2019); 146-152

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
HIV-1 ; Incidence ; Mixed base calls ; Sequence ambiguity ; Surveillance

Sažetak
Identifying individuals recently infected with HIV has been of great significance for close monitoring of HIV epidemic dynamics. Low HIV sequence ambiguity (SA) has been described as a promising marker of recent infection in previous studies. 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. Our data suggest that SA could be used as a real-time surveillance tool for close monitoring of HIV incidence trends, especially in countries where baseline HIV resistance genotyping is performed routinely, rendering this approach cost-effective.

Izvorni jezik
Engleski

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