Sequence ambiguity determined from routine pol sequencing is a reliable tool for real-time surveillance of HIV incidence trends.
Infect Genet Evol
; 69: 146-152, 2019 04.
Article
em En
| MEDLINE
| ID: mdl-30682549
ABSTRACT
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 (pâ¯<â¯0.001). CD4+ T-cell counts ≤250 cells/mm3 significantly correlated with higher SA (pâ¯<â¯0.001), whereas the homo/bisexual transmission route significantly correlated with lower SA (pâ¯=â¯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.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Variação Genética
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Infecções por HIV
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HIV-1
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Produtos do Gene pol do Vírus da Imunodeficiência Humana
Tipo de estudo:
Incidence_studies
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Prognostic_studies
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Risk_factors_studies
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Screening_studies
Limite:
Female
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Humans
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Male
País/Região como assunto:
Europa
Idioma:
En
Ano de publicação:
2019
Tipo de documento:
Article