Kousiappa Ioanna, Van De Vijver David A M C, Kostrikis Leondios G
Department of Biological Sciences, University of Cyprus , 1678 Nicosia, Cyprus.
AIDS Res Hum Retroviruses. 2009 Aug;25(8):727-40. doi: 10.1089/aid.2008.0239.
The molecular epidemiology of HIV-1 infection was previously studied in Cyprus but the degree of HIV-1 diversity has remained indefinable. The main objective of the present study is to examine HIV-1 strains isolated from 77 HIV-1-infected individuals representing 38% of the known infected population in Cyprus in the period 1986 to 2006. DNA of the near full-length genome encoding gag, pol, vif, vpr, vpu, tat, rev, env, and 5'-end of nef was amplified by nested PCR/RT-PCR from all HIV-1 seropositives and sequenced using a newly designed assay. Detailed phylogenetic and bootscanning analyses were performed to determine phylogenetic associations and subtype assignments. Phylogenetic analyses of the obtained viral sequences indicated that subtype B was the dominant subtype (61%), followed by subtype A (23.3%), subtype C (5.2%), CRF02_AG (3.9%), and subtype D, CRF01_AE, and CRF04_cpx (1.3% each). Two HIV-1 isolates (2.6%), originating from the Democratic Republic of Congo (DRC), were not classified in any pure (sub)subtype or circulating recombinant form (CRF). Complete phylogenetic and bootscanning analyses revealed that one of these isolates had a new, unique recombinant pattern, comprising segments of subtypes D and G, and is distinct from any other CRFs or URFs reported so far. Detailed analyses of the sequence of the second isolate, which could not be classified, reveal that it is close to subtype K reference sequences but clusters near the root of the clade. At least two epidemiologically unrelated HIV-1 seropositives with an HIV-1 variant similar to this isolate are required to designate this variant as a novel HIV-1 subtype or subsubtype of subtype K. Analogous to results of the earlier epidemiological studies, these data exhibit the extensive heterogeneity of HIV-1 infection in Cyprus, which is being fueled by a continuous entry of new strains from other countries, creating an evolving and polyphyletic infection.
此前曾对塞浦路斯的HIV-1感染分子流行病学进行过研究，但HIV-1的多样性程度仍不明确。本研究的主要目的是检测从77名HIV-1感染者中分离出的HIV-1毒株，这些感染者占1986年至2006年期间塞浦路斯已知感染人群的38%。通过巢式PCR/RT-PCR从所有HIV-1血清阳性者中扩增编码gag、pol、vif、vpr、vpu、tat、rev、env和nef 5'端的近全长基因组DNA，并使用新设计的检测方法进行测序。进行了详细的系统发育和靴带扫描分析，以确定系统发育关联和亚型归属。对获得的病毒序列进行的系统发育分析表明，B亚型是主要亚型（61%），其次是A亚型（23.3%）、C亚型（5.2%）、CRF02_AG（3.9%），以及D亚型、CRF01_AE和CRF04_cpx（各占1.3%）。来自刚果民主共和国的两株HIV-1分离株（2.6%）未被归类为任何纯（亚）亚型或循环重组形式（CRF）。完整的系统发育和靴带扫描分析显示，其中一株分离株具有一种新的独特重组模式，包含D亚型和G亚型的片段，与迄今报道的任何其他CRF或URF都不同。对第二株无法归类的分离株序列进行的详细分析表明，它与K亚型参考序列相近，但聚集在进化枝根部附近。至少需要两个在流行病学上无关的HIV-1血清阳性者，其HIV-1变异株与该分离株相似，才能将该变异株指定为K亚型的新型HIV-1亚型或亚亚型。与早期流行病学研究结果类似，这些数据显示了塞浦路斯HIV-1感染的广泛异质性，新毒株从其他国家不断传入加剧了这种异质性，形成了一种不断演变的多系感染。
