Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity
Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity
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DOI：
10.1097/01.aids.0000237368.64488.ae
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发表时间：
2006-07-13
期刊：
影响因子：
3.8
通讯作者：
Pillay, Deenan
中科院分区：
文献类型：
--
作者：
Gifford, Robert;de Oliveira, Tulio;Pillay, Deenan
背景：常规使用的耐药检测提供了丰富的HIV-1序列数据来源。然而，目前尚不清楚这些序列的标准基因分型在描述HIV-1遗传变异和检测新的遗传变异和流行病学趋势方面的可靠性。目的：比较常用基因分型方案中HIV-1耐药测试序列与参考菌株的分配。在三种标准基因分型方案中比较了10537个耐药测试序列的亚型分配，占英国所有报告感染病例的约五分之一。不一致的基因分型的方法，或未分配的至少一种方法，序列进行了检查，重组的证据，使用滑动窗口为基础的approaches.Results：虽然跨方法的协议是高亚型B，C和H，它通常是低得多（< 50%）的其他亚型。方法之间的不一致通常涉及密切相关但流行病学上不同的群体或涉及很大比例（类似于12%）的分歧序列，其中分析揭示了重组的广泛证据和异常重组形式的显着多样性。随着病毒株频繁的远距离转移和病毒株之间广泛的重组，HIV-1内的遗传和流行病学关系正变得越来越复杂。目前的亚型分配方法在鉴定新的遗传变异和区分流行病学上不同的菌株的能力方面各不相同。从耐药性测试数据中获取有意义的流行病学信息需要对所用方法有严格的理解，以便了解错误和错误分类的可能来源。(c)2006年利平科特威廉姆斯&威尔金斯。
Background: The routine use of drug resistance testing provides an abundant source of HIV-1 sequence data. However, it is not clear how reliable standard genotyping of these sequences is for describing HIV-1 genetic variation and for detecting novel genetic variants and epidemiological trends.Objectives: To compare assignment of HIV-1 resistance test sequences to reference strains across commonly used genotyping protocols.Methods: Subtype assignments were compared across three standard genotyping protocols for 10 537 resistance test sequences, representing approximately one-fifth of all reported infections in the United Kingdom. Sequences that were inconsistently genotyped across methods, or that were unassigned by at least one method, were examined for evidence of recombination using sliding-window-based approaches.Results: Although agreement across methods was high for subtypes B, C and H, it was generally much lower (< 50%) for other subtypes. Disagreement between methods typically involved closely related, but epidemiologically distinct, groups or involved a significant proportion (similar to 12%) of divergent sequences in which analysis revealed widespread evidence of recombination and a remarkable diversity of unusual recombinant forms.Conclusions: With frequent long-distance transfer of viral strains and widespread recombination between them, genetic and epidemiological relationships within HIV-1 are becoming increasingly complex. Current methods of subtype assignment vary in their ability to identify novel genetic variants and to distinguish epidemiologically distinct strains. Capturing meaningful epidemiological information from resistance test data will require a critical understanding of the methodologies used in order to appreciate the possible sources of error and misclassification. (c) 2006 Lippincott Williams & Wilkins.