Although the first HIV circulating recombinant form (CRF01_AE) is the predominant strain in many Asian countries, it is uncommonly found in the Congo Basin from where it first originated. To fill the gap in the evolutionary history of this important strain, we sequenced near complete genomes from HIV samples with subgenomic CRF01_AE regions collected in Cameroon and the Democratic Republic of the Congo from 2001 to 2006. HIV genomes were generated from N = 13 plasma specimens by next-generation sequencing of metagenomic libraries prepared with spiked primers targeting HIV, followed by Sanger gap-filling. Genome sequences were aligned to reference strains, including Asian and African CRF01_AE sequences, and evaluated by phylogenetic and recombinant analysis to identify four CRF01_AE strains from Cameroon. We also identified two CRF02, one CRF27, and six unique recombinant form genomes (01|A1|G, 01|02|F|U, F|G|01, A1|D|01, F|G|01, and A1|G|01). Phylogenetic analysis, including the four new African CRF01_AE genomes, placed these samples as a bridge between basal Central African Republic CRF01_AE strains and all Asian, European, and American CRF01_AE strains. Molecular dating confirmed previous estimates indicating that the most recent common CRF01_AE ancestor emerged in the early 1970s (1968–1970) and spread beyond Africa around 1980 to Asia. The new sequences and analysis presented in this study expand the molecular history of the CRF01_AE clade, and are illustrated in an interactive Next Strain phylogenetic tree, map, and timeline at (https://nextstrain.org/community/EduanWilkinson/hiv-1_crf01).

中文翻译：

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刚果盆地的新基因组扩展了CRF01_AE起源和传播的历史。

尽管第一个HIV循环重组体（CRF01_AE）是许多亚洲国家的主要毒株，但在它最初起源的刚果盆地中却很少见。为了填补这一重要菌株的进化史的差距，我们测序从附近的HIV样本与在喀麦隆和刚果民主共和国从2001年到2006年HIV基因组收集的亚基因组CRF01_AE地区完整的基因组中，从产生ñ 通过用针对HIV的加标引物制备的宏基因组库的下一代测序，获得13个血浆标本，然后进行Sanger缺口填补。将基因组序列与参考菌株（包括亚洲和非洲的CRF01_AE序列）进行比对，并通过系统发育和重组分析进行评估，以鉴定来自喀麦隆的四种CRF01_AE菌株。我们还鉴定了两个CRF02，一个CRF27和六个独特的重组形式基因组（01 | A1 | G，01 | 02 | F | U，F | G | 01，A1 | D | 01，F | G | 01和A1 | G | 01）。系统发育分析，包括四个新的非洲CRF01_AE基因组，将这些样品作为中非共和国基础CRF01_AE菌株与所有亚洲，欧洲和美国CRF01_AE菌株之间的桥梁。分子测年证实了先前的估计，表明最近的共同CRF01_AE祖先出现在1970年代初（1968-1970年），并在1980年代左右从非洲传播到了亚洲。这项研究中提出的新序列和分析扩展了CRF01_AE进化枝的分子历史，并在（Next：//train.nextstrain.org/community/EduanWilkinson/hiv-1_crf01）的交互式Next Strain系统发育树，地图和时间轴中进行了说明。 ）。