Recombination in feline immunodeficiency virus from feral and companion domestic cats.
Recombination in feline immunodeficiency virus from feral and companion domestic cats.
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DOI：
10.1186/1743-422x-5-76
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发表时间：
2008-06-17
期刊：
影响因子：
4.8
通讯作者：
Rodrigo, Allen G.
中科院分区：
文献类型：
--
作者：
Hayward, Jessica J.;Rodrigo, Allen G.
逆转录病毒的变性是一种相对常见的现象。我们研究重组猫免疫缺陷病毒从自然感染的新西兰家猫（猫卡图斯）的gag，pol和env基因的测序区域。基因内重组的发生率是最高的env，重组的证据在6.4%（n = 156）的所有猫。在gag（n = 48）和pol（n = 91）基因中的每一个中鉴定出进一步的重组体。通过比较不同基因的系统发育树发现了不一致的情况，表明基因间重组。使用Shimodaira-Hasegawa检验发现其中3个（7.7%，n = 39）不一致性存在显著差异。令人惊讶的是，我们从gag和pol基因的同源性表明，没有新西兰序列组与参考亚型C序列内的亚型成对距离。事实上，我们发现一个和两个不同的未知亚型组的gag和pol，分别。这些观察结果使我们推测，这些新西兰FIV毒株在A亚型亲本毒株和未定义的未知亚型毒株之间经历了几次重组事件，类似于HIV-1“E亚型”假设的进化历史。终点稀释测序用于确认推定的重组体和未知亚型组的共有序列，为这些序列的真实性提供证据。终点稀释测序也导致env基因中双重感染事件的鉴定。此外，建立了pol基因中相同亚型的变体之间的宿主内重组事件。这是第一个已知的例子，自然发生重组的猫感染的亲本菌株。在新西兰自然感染的家猫中发现了FIV在gag、pol和env区的基因内重组和复杂的基因间重组的证据，在所有三个基因区都鉴定出了未知亚型的毒株。这些结果对新西兰目前FIV疫苗的使用具有影响。
Recombination is a relatively common phenomenon in retroviruses. We investigated recombination in Feline Immunodeficiency Virus from naturally-infected New Zealand domestic cats (Felis catus) by sequencing regions of the gag, pol and env genes. The occurrence of intragenic recombination was highest in env, with evidence of recombination in 6.4% (n = 156) of all cats. A further recombinant was identified in each of the gag (n = 48) and pol (n = 91) genes. Comparisons of phylogenetic trees across genes identified cases of incongruence, indicating intergenic recombination. Three (7.7%, n = 39) of these incongruencies were found to be significantly different using the Shimodaira-Hasegawa test. Surprisingly, our phylogenies from the gag and pol genes showed that no New Zealand sequences group with reference subtype C sequences within intrasubtype pairwise distances. Indeed, we find one and two distinct unknown subtype groups in gag and pol, respectively. These observations cause us to speculate that these New Zealand FIV strains have undergone several recombination events between subtype A parent strains and undefined unknown subtype strains, similar to the evolutionary history hypothesised for HIV-1 "subtype E". Endpoint dilution sequencing was used to confirm the consensus sequences of the putative recombinants and unknown subtype groups, providing evidence for the authenticity of these sequences. Endpoint dilution sequencing also resulted in the identification of a dual infection event in the env gene. In addition, an intrahost recombination event between variants of the same subtype in the pol gene was established. This is the first known example of naturally-occurring recombination in a cat with infection of the parent strains. Evidence of intragenic recombination in the gag, pol and env regions, and complex intergenic recombination, of FIV from naturally-infected domestic cats in New Zealand was found. Strains of unknown subtype were identified in all three gene regions. These results have implications for the use of the current FIV vaccine in New Zealand.