Molecular Characterization of Ambiguous Mutations in HIV-1 Polymerase Gene: Implications for Monitoring HIV Infection Status and Drug Resistance

Du-Ping Zheng,Joshua R Devos,Margarida Rodrigues,Chunfu Yang,Duc B Nguyen,Ebi Bile,Karidia Diallo,John N Nkengasong

doi:10.1371/journal.pone.0077649

Abstract

Detection of recent HIV infections is a prerequisite for reliable estimations of transmitted HIV drug resistance (t-HIVDR) and incidence. However, accurately identifying recent HIV infection is challenging due partially to the limitations of current serological tests. Ambiguous nucleotides are newly emerged mutations in quasispecies, and accumulate by time of viral infection. We utilized ambiguous mutations to establish a measurement for detecting recent HIV infection and monitoring early HIVDR development. Ambiguous nucleotides were extracted from HIV-1 pol-gene sequences in the datasets of recent (HIVDR threshold surveys [HIVDR-TS] in 7 countries; n=416) and established infections (1 HIVDR monitoring survey at baseline; n=271). An ambiguous mutation index of 2.04×10-3 nts/site was detected in HIV-1 recent infections which is equivalent to the HIV-1 substitution rate (2×10-3 nts/site/year) reported before. However, significantly higher index (14.41×10-3 nts/site) was revealed with established infections. Using this substitution rate, 75.2% subjects in HIVDR-TS with the exception of the Vietnam dataset and 3.3% those in HIVDR-baseline were classified as recent infection within one year. We also calculated mutation scores at amino acid level at HIVDR sites based on ambiguous or fitted mutations. The overall mutation scores caused by ambiguous mutations increased (0.54×10-23.48×10-2/DR-site) whereas those caused by fitted mutations remained stable (7.50-7.89×10-2/DR-site) in both recent and established infections, indicating that t-HIVDR exists in drug-naïve populations regardless of infection status in which new HIVDR continues to emerge. Our findings suggest that characterization of ambiguous mutations in HIV may serve as an additional tool to differentiate recent from established infections and to monitor HIVDR emergence.

Highlights

With over 8.2 million HIV-infected patients on antiretroviral therapy (ART) in low- and middle-income countries at the end of 2011, emergence and transmission of HIV drug resistance (HIVDR) are ongoing public health challenges in the battle against HIV/AIDS [1,2,3,4,5,6]
To assess the transmitted HIVDR (t-HIVDR) in resource-limited countries, the World Health Organization (WHO) recommends conducting HIVDR threshold survey (HIVDR-TS) in recently HIV-infected populations enrolled by using WHO criteria [11,12]
Ambiguous mutations were extracted from 8 datasets of a total of 687 sequences (Table 1) and were used for statistical descriptive and significant analyses (Figure 1)

Summary

Introduction

With over 8.2 million HIV-infected patients on antiretroviral therapy (ART) in low- and middle-income countries at the end of 2011, emergence and transmission of HIV drug resistance (HIVDR) are ongoing public health challenges in the battle against HIV/AIDS [1,2,3,4,5,6]. To assess the t-HIVDR in resource-limited countries, the World Health Organization (WHO) recommends conducting HIVDR threshold survey (HIVDR-TS) in recently HIV-infected populations enrolled by using WHO criteria [11,12]. Estimate of HIV incidence requires recent infections that are determined by using serological assays with crosssectional HIV-positive samples at population level [13,14,15]. Studies have indicated that these assays overestimated HIV incidences due to false classification of recent infections in certain populations and lack of validated

Methods

Results

Conclusion