A High-throughput Strategy to Identify HIV Intra-subtype Recombinant Sequences

描述(由申请人提供)：亚型内重组是HIV-1(人类免疫缺陷病毒1型)应用的一种有效策略，以产生非凡的病毒多样性，有助于患者内部的准物种和耐药性。在这里，我们提出了一种新的方法来检测HIV-1亚型内重组，以填补跟踪疾病进展和传播过程中HIV基因变化的必要性和缺乏亚型内分析方法之间的差距。由于更大的序列相似性，亚型内重组比亚型间重组更难检测到。因此，在检测亚型内重组时，不仅在HIV病例中，而且在其他生物体中，都应该考虑能够反映一个亚型内全谱多样性的适当的序列阵列。在这方面，我们假设这些序列在测序的片段中存在得更丰富，但在测序的全基因组序列中存在较少，而后者被广泛用于任何类型的HIV重组研究。我们的理论基础来自我们之前的研究，在我们的研究中，我们成功地识别了HIV-1 J亚型中的亚型。我们的发现是基于测序的片段，而不是完整的基因组序列。我们认为，所有已发表的序列片段都包含了很大程度的序列多样性，这在许多方面的研究中都被我们忽视了，包括病毒分子进化和分子流行病学研究。该项目的目标是(1)识别每个HIV-1亚型中具有代表性的亚型序列；以及(2)实现一个高通量的检测病毒亚型内重组的方案。我们的研究将为合理和定量评估HIV-1亚型内重组体的流行率提供基础，这对于跟踪动态和复杂的HIV流行以及设计改进的抗病毒疗法和疫苗至关重要。最后但并非最不重要的一点是，我们提出的研究策略也适用于其他病毒的重组研究。

DESCRIPTION (provided by applicant): Intra-subtype recombination is an efficient strategy applied by HIV-1 (human immunodeficiency virus type 1) to generate extraordinary virus diversity that contributes to intra-patient quasi-species and drug resistance. Here we propose a novel methodology to detect HIV-1 intra-subtype recombination to fill the gap between the necessity of tracking HIV genetic changes along disease progression and transmission and lack of intra-subtype analysis methodologies. Due to greater sequence similarity, intra-subtype recombination is harder to detect than inter-subtype recombination. Therefore the detection of intra- subtype recombination, not only in the HIV case but also in other organisms, should consider appropriate array of sequences that can reflect a full spectrum of diversity within a subtype. In this regard, we hypothesize that these sequences have existed more abundantly in sequenced fragments but are less present in sequenced complete genome sequences, while the latter are widely used in any kind of HIV recombination studies. Our rationale derives from our previous study, in which we successfully identified sub-subtypes within HIV-1 subtype J. Our findings were based on sequenced fragments rather than complete genome sequences. We believe that the repertoire of all published sequence fragments contains a great degree of sequence diversity that we have overlooked in many aspects of studies, including viral molecular evolution and molecular epidemiology studies. The objective of this project is to (1) identify sub-subtype representative sequences within each HIV-1 subtype; and (2) implement a high-throughput scheme for detection of viral intra-subtype recombination. Our proposed study will provide a basis for a rational and quantitative evaluation of the prevalence of HIV-1 intra-subtype recombinants, which is critical for tracking the dynamic and complex HIV epidemic and designing improved antiviral therapies and vaccines. Last but not the least, our proposed research strategy can also be applied to the recombination study in other viruses.