Genetic analysis of a UNAIDS HIV type 1 from Brazil revealed an unexpected recombination pattern.
Genetic analysis of a UNAIDS HIV type 1 from Brazil revealed an unexpected recombination pattern.
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对来自巴西的联合国艾滋病规划署 1 型艾滋病毒的基因分析揭示了一种意想不到的重组模式。
DOI：
10.1089/aid.2010.0105
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发表时间：
2010
影响因子：
1.5
通讯作者：
Ristic,Natalia
中科院分区：
文献类型：
--
作者：
Chin,MarioPS;Ristic,Natalia
编辑：世界卫生组织（世卫组织）艾滋病毒分离和鉴定网络（现称为联合国艾滋病规划署）由世卫组织全球艾滋病规划建立，目的是系统地分离和鉴定来自世界不同地区的艾滋病毒毒株，并获取有助于开发艾滋病毒疫苗的信息和试剂。1,2实验室网络从世卫组织在巴西、卢旺达、泰国和乌干达资助的疫苗评价点收集标本。这个集合包含大量不同重组模式的亚型间重组。3,4通过该网络在巴西收集的HIV-1序列中，我们在引导扫描分析中发现了具有冲突重组模式的重组菌株序列。所讨论的分离物是92BR023，它是从巴西Proto Alegre的一名无症状异性恋男性中分离出来的。2先前对92BR023分离物进行了基因分型，并报道了从病毒基因组中获得的6个序列。2-6序列片段包括gag中覆盖859-1587和1407-2131核苷酸位置的两个重叠区域（HXB2编号），3,5在pol中覆盖2265-3440和4230-5064的两个重叠区域，4,6在env中覆盖7032-7310和7050-7400的两个重叠序列（图1）。7根据基因分型数据显示，该分离物为B/C亚型重组物，具有C亚型gag、C亚型pol和B亚型env。然而，当我们通过引导扫描分析从洛斯阿拉莫斯HIV序列数据库获得的92BR023序列时，观察到更复杂的重组模式，其中一个序列似乎产生了相互矛盾的结果。在引导扫描分析（SimPlot版本3.5）。1)， 8我们以来自巴西的HIV-1亚型B和亚型C为参照，以来自其他地区的HIV-1亚型a和亚型K为外群。9比较92BR023 gag内的两个序列，覆盖基质（MA）和衣壳（CA）基因的片段属于C亚型，而由CA和核衣壳（NC）组成的部分属于B亚型（图1）。这与先前报道的92BR023具有C亚型gag不一致。gag基因可能存在重组断点，但在这两个片段的181-nt重叠序列中，有12个不匹配。0.066（12/181）的遗传距离与B亚型和C亚型之间的遗传距离相似，提示HIV-1序列可能存在错误。
Editor: The World Health Organization (WHO) Network for HIV Isolation and Characterization (now named UNAIDS) was established by the WHO Global Programme on AIDS to systematically isolate and characterize HIV strains from different parts of the world, and to obtain information and reagents that would facilitate HIV vaccine development. 1, 2 The laboratory network collected specimens from WHO-sponsored vaccine evaluation sites in Brazil, Rwanda, Thailand, and Uganda. This collection contains a significant number of intersubtype recombinants with diverse recombination patterns. 3, 4 Among the sequences of HIV-1 collected in Brazil by this network, we identified the sequences of a recombinant strain that have conflicting recombination patterns in bootscanning analysis.The isolate in question is 92BR023, which was isolated from an asymptomatic heterosexual male from Proto Alegre, Brazil. 2 The 92BR023 isolate was genotyped previously, and six sequences derived from the viral genome have been reported. 2–6 The sequence fragments included two overlapping regions in gag covering nucleotide positions 859–1587 and 1407–2131 (HXB2 numbering), 3, 5 two regions in pol spanning positions 2265–3440 and 4230–5064, 4, 6 and two overlapping sequences in env covering 7032–7310 and 7050–7400 (Fig. 1). 7 Based on the genotyping data, it was shown that this isolate is a B/C intersubtype recombinant with a subtype C gag, a subtype C pol, and a subtype B env. When we analyzed these sequences of 92BR023 obtained from the Los Alamos HIV Sequence Database by bootscanning, however, a more complex recombination pattern was observed and one of the sequences appeared to generate conflicting results. In the bootscanning analysis (SimPlot version 3.5. 1), 8 we used a subtype B and a subtype C HIV-1 from Brazil as references, and a subtype A and a subtype K virus from other regions as the outgroup. 9 Comparing the two sequences within the gag of 92BR023, the fragment covering the matrix (MA) and capsid (CA) genes belong to subtype C, whereas the part consisting of CA and nucleocapsid (NC) is subtype B (Fig. 1). This is not consistent with previous reports indicating that 92BR023 has a subtype C gag. It is possible that a recombination breakpoint is present in the gag gene, but out of the 181-nt overlapping sequences of the two fragments, there were 12 mismatches. The genetic distance of 0.066 (12/181) is similar to the genetic distance between subtypes B and C gag, suggesting that there might be errors in the HIV-1 sequences.