Sierra María, Thomson Michael M, Posada David, Pérez Lissette, Aragonés Carlos, González Zoila, Pérez Jorge, Casado Gema, Nájera Rafael
Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
J Acquir Immune Defic Syndr. 2007 Jun 1;45(2):151-60. doi: 10.1097/QAI.0b013e318046ea47.
BG intersubtype recombinants represented 11.6% of HIV-1 isolates in a recent survey in Cuba based on pol sequences, most of them forming a single clade further subdivided into 3 subclades. Here, we analyze 8 near full-length genomes and 1 gag-pol sequence from epidemiologically unlinked Cuban BG recombinants from these 3 subclades (3 from each). Near full-length sequences were also obtained from 3 subtype G and 2 subtype B Cuban viruses. Phylogenetic relationships were estimated via maximum likelihood, and mosaic structures of the recombinants were inferred with the bootscanning, MaxChi, Genconv, and GARD methods. For the near full-length genomes, all recombinants formed a strongly supported clade further subdivided into the same subclades previously defined in pol. Mosaic structures were identical within each subclade and different among subclades, although 5 breakpoints were coincident among all recombinants. Individual phylogenetic trees for nonrecombinant fragments (concatenated B and G subtype segments) indicated a common ancestry for the parental viruses and their relationships to local subtype B and G strains. These results allow us to identify 3 new BG intersubtype circulating recombinant forms in Cuba derived from a common recombinant ancestor, which originated from B and G subtype parental strains circulating in Cuba.
在古巴最近一项基于pol序列的调查中，BG亚型重组体占HIV-1分离株的11.6%，其中大多数形成一个单一进化枝，该进化枝进一步细分为3个亚进化枝。在此，我们分析了来自这3个亚进化枝（每个亚进化枝3个）的8个近全长基因组和1个来自古巴BG重组体的gag-pol序列，这些重组体在流行病学上无关联。还从3株G亚型和2株B亚型古巴病毒中获得了近全长序列。通过最大似然法估计系统发育关系，并使用bootscanning、MaxChi、Genconv和GARD方法推断重组体的镶嵌结构。对于近全长基因组，所有重组体形成一个得到有力支持的进化枝，该进化枝进一步细分为先前在pol中定义的相同亚进化枝。每个亚进化枝内的镶嵌结构相同，亚进化枝之间不同，尽管所有重组体中有5个断点是一致的。非重组片段（串联的B和G亚型片段）的个体系统发育树表明亲本病毒有共同的祖先，以及它们与当地B和G亚型毒株的关系。这些结果使我们能够在古巴识别出3种新的BG亚型间循环重组形式，它们源自一个共同的重组祖先，该祖先起源于在古巴流行的B和G亚型亲本毒株。
