Data_Sheet_4_Identification of a HIV-1 circulating BF1 recombinant form (CRF75_BF1) of Brazilian origin that also circulates in Southwestern Europe.PDF

IntroductionThe high recombinogenic potential of HIV-1 has resulted in the generation of countless unique recombinant forms (URFs) and around 120 reported circulating recombinant forms (CRFs). Here we identify through analyses of near full-length genomes (NFLG) a new HIV-1 CRF derived from subtypes B and F1.
MethodsHIV-1 protease-reverse transcriptase (Pr-RT) sequences were obtained by RT-PCR amplification from plasma RNA. Near full-length genome sequences were obtained after amplification by RT-PCR in 5 overlapping fragments. Phylogenetic sequence analyses were performed via maximum likelihood. Mosaic structures were analyzed by bootscanning and phylogenetic analyses of genome segments. Temporal end geographic estimations of clade emergence were performed with a Bayesian coalescent method.
ResultsThrough phylogenetic analyses of HIV-1 Pr-RT sequences obtained by us from samples collected in Spain and downloaded from databases, we identified a BF1 recombinant cluster segregating from previously reported CRFs comprising 52 viruses, most from Brazil (n = 26), Spain (n = 11), and Italy (n = 9). The analyses of NFLG genomes of 4 viruses of the cluster, 2 from Spain and 2 from Italy, allowed to identify a new CRF, designated CRF75_BF1, which exhibits a complex mosaic structure with 20 breakpoints. All 4 patients harboring CRF75_BF1 viruses studied by us had CD4+ T-cell lymphocyte counts below 220/mm3 less than one year after diagnosis, a proportion significantly higher (p = 0.0074) than the 29% found in other patients studied in Spain by us during the same period. The origin of the clade comprising CRF75_BF1 and related viruses was estimated around 1984 in Brazil, with subsequent introduction of CRF75_BF1 in Italy around 1992, and migration from Italy to Spain around 1999.
ConclusionA new HIV-1 CRF, designated CRF75_BF1, has been identified. CRF75_BF1 is the 6th CRF of South American origin initially identified in Western Europe, reflecting the increasing relationship of South American and European HIV-1 epidemics. The finding of low CD4+ T-cell lymphocyte counts early after diagnosis in patients harboring CRF75_BF1 viruses warrants further investigation on the virulence of this variant.

**引言**
HIV-1具有极高的重组潜能，已衍生出不计其数的独特重组型（Unique Recombinant Forms, URFs），且已报道的循环重组型（Circulating Recombinant Forms, CRFs）约有120种。本研究通过近全长基因组（near full-length genomes, NFLG）分析，鉴定出一种源自B亚型和F1亚型的新型HIV-1循环重组型。

**方法**
本研究通过逆转录聚合酶链式反应（reverse transcription-polymerase chain reaction, RT-PCR）从血浆RNA中扩增得到HIV-1蛋白酶-逆转录酶（protease-reverse transcriptase, Pr-RT）序列。通过RT-PCR分5个重叠片段扩增，获得近全长基因组序列。采用最大似然法（maximum likelihood）进行系统发育序列分析。通过自助扫描法（bootscanning）以及基因组片段的系统发育分析，对嵌合结构进行解析。采用贝叶斯合并模型法（Bayesian coalescent method）对进化枝出现的时间与地理起源进行推断。

**结果**
本研究对西班牙采集并从数据库下载的HIV-1 Pr-RT序列进行系统发育分析，鉴定出一个与此前报道的CRFs相区分的BF1重组进化枝，共包含52株病毒，其中多数来自巴西（n=26）、西班牙（n=11）和意大利（n=9）。对该进化枝中4株病毒的NFLG基因组进行分析（其中2株来自西班牙，2株来自意大利），鉴定出一种新型CRF，命名为CRF75_BF1，该重组型具有包含20个重组断点的复杂嵌合结构。本研究中所有携带CRF75_BF1病毒的患者，在确诊后一年内的CD4+T淋巴细胞计数均低于220/mm³，这一比例显著高于同期西班牙其他患者的29%（p=0.0074）。包含CRF75_BF1及其相关病毒的进化枝起源时间约为1984年，地点为巴西；CRF75_BF1随后于1992年左右传入意大利，并于1999年左右从意大利迁移至西班牙。

**结论**
本研究鉴定出一种新型HIV-1循环重组型，命名为CRF75_BF1。CRF75_BF1是第6种最初在西欧被鉴定的南美起源CRF，反映出南美与欧洲HIV-1流行株之间的联系日益紧密。携带CRF75_BF1病毒的患者在确诊早期即出现低CD4+T淋巴细胞计数的现象，提示需对该毒株的毒力开展进一步研究。