Evaluation of sequence ambiguities of the HIV-1 pol gene as a method to identify recent HIV-1 infection in transmitted drug resistance surveys
Evaluation of sequence ambiguities of the HIV-1 pol gene as a method to identify recent HIV-1 infection in transmitted drug resistance surveys
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DOI：
10.1016/j.meegid.2013.03.050
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发表时间：
2013-08-01
影响因子：
3.2
通讯作者：
Jordan, Michael R.
中科院分区：
文献类型：
--
作者：
Andersson, Emmi;Shao, Wei;Jordan, Michael R.
确定人群中最近的艾滋病毒感染是一项公共卫生优先事项，以便在人群一级准确估计艾滋病毒发病率和传播的耐药性。通过对未感染艾滋病毒的人进行前瞻性随访来确定艾滋病毒发病率是具有挑战性的，而血清学检测具有重要的局限性。受感染宿主内的艾滋病毒多样性随着感染时间的延长而增加。我们探索了一种简单的生物信息学方法来评估病毒多样性，方法是确定来自HIV-1蛋白酶和逆转录酶标准基因分型的序列中模糊碱基调用的百分比。对来自瑞典、越南和埃塞俄比亚的691名最近感染(1岁)的人的序列进行了歧义分析。与以前的研究一致，近期和慢性感染HIV-1B亚型和非B亚型感染的个体的序列之间的歧义碱基比例有显著差异(p<；0.0001)。在我们的分析中，截止到
Identification of recent HIV infection within populations is a public health priority for accurate estimation of HIV incidence rates and transmitted drug resistance at population level. Determining HIV incidence rates by prospective follow-up of HIV-uninfected individuals is challenging and serological assays have important limitations. HIV diversity within an infected host increases with duration of infection. We explore a simple bioinformatics approach to assess viral diversity by determining the percentage of ambiguous base calls in sequences derived from standard genotyping of HIV-1 protease and reverse transcriptase. Sequences from 691 recently infected (1 year) individuals from Sweden, Vietnam and Ethiopia were analyzed for ambiguity. A significant difference (p < 0.0001) in the proportion of ambiguous bases was observed between sequences from individuals with recent and chronic infection in both HIV-1 subtype B and non-B infection, consistent with previous studies. In our analysis, a cutoff of