Xiaoyan Bai, Hongwei Zhang, Wei Shao, Lan Li, Zheng Zeng and Hao Wu
Objective: To distinguish HIV-1 recent infection (≤ 300 days) from long-term HIV-1 infection (>300 days) in China men who had sex with men (MSM) population. We analyzed the change over time in the proportion of ambiguous nucleotides in patient plasma sequences. We hypothesized that this method could be used to determine recent infections.
Methods: HIV-1 sequences and clinical data of MSM were collected from June 2007 to September 2010. All the sequences were obtained by single genome amplification and sequencing. HIV-ambi-count was used to calculate the proportion of ambiguous nucleotides, and the optimal cut-off values to identify recent infection were established using receiver operator characteristic analysis (ROC).
Results: A total of 188 sequences from 150 patients were collected (38 patients were sampled twice at different time points), consisting of 118 sequences of subtype CRF01_AE and 70 sequences of subtype B. The optimal cut-off values for determination of early HIV-1 infection in subtypes CRF01_AE and B were 0.31% and 0.347%, respectively. The sensitivity, specificity, positive and negative predictive values were 76.5%, 55%, 89.3% and 32.4% for subtype CRF01-AE (P=0.005), 80.6%, 62.5%, 94.3% and 29.4% for subtype B (P=0.017), respectively. The area under the ROC curve (AUCROC) was 0.652 (95% CI, 0.520-0.783, P=0.03) and 0.75 (95% CI, 0.622-0.878, P=0.022) for subtype CRF01-AE and B, respectively.
Conclusions: The proportion of ambiguous nucleotides may be a good marker to distinguish recent infection from long-term HIV-1 infection with high positive predictive value in the China MSM population.
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