Geno2pheno:HIV-1 和 HEV 亚型的重组检测

M. Pirkl, Joachim Büch, Georg Friedrich, Michael Böhm, Dan Turner, Olaf Degen, Rolf Kaiser, Thomas Lengauer
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引用次数: 0

摘要

即使对 HIV-1 进行了三十年的抗逆转录病毒治疗,治疗失败仍是一个持续的挑战。如果病毒变种是亚型重组,情况更是如此。因此,改进对重组亚型的诊断有助于选择治疗方法。我们正在使用以前发表的计算方法 recco 的新实施方案来检测已知亚型的从头重组,独立于已知的循环重组型(CRFs)。我们根据突变调用和可能的重组断点,检测病毒参考序列多重比对中的最佳路径。我们使用一个调整参数来选择突变调用或断点。除了新型重组外,我们集成在 geno2pheno 网络服务 https://geno2pheno.org 中的工具 g2p-recco 还能在只给出带有断点的相关亚型的完整共识参考序列(不含 CRF)的情况下,成功检测出已知的重组事件。此外,该工具还可应用于其他病毒,如戊型肝炎病毒(HEV)。通过这种方法,我们还可以检测到 HEV 中几种以前未知的重组。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Geno2pheno: Recombination detection for HIV-1 and HEV subtypes
Even after three decades of antiretroviral therapy for HIV-1, therapy failure is a continual challenge. This is especially so, if the viral variant is a recombinant of subtypes. Thus, improved diagnosis of recombined subtypes can help with the selection of therapy. We are using a new implementation of the previously published computational method recco to detect de novo recombination of known subtypes, independent of and in addition to known circulating recombinant forms (CRFs). We detect an optimal path in a multiple alignment of viral reference sequences based on mutation calls and probable breakpoints for recombination. A tuning parameter is used to favor either mutation calls or breakpoints. Besides novel recombinants, our tool g2p-recco integrated in the geno2pheno web-service https://geno2pheno.org can successfully detect known recombinant events given only the full consensus references (without CRFs) of the involved subtypes with breakpoints. In addition, the tool can be applied to other viruses, i.e hepatitis E virus (HEV). In this fashion, we could also detect several previously unknown recombinations in HEV.
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