Enteric Viruses Department, National Institute of Virology, Pune, India.
Virus Res. 2010 Feb;147(2):242-6. doi: 10.1016/j.virusres.2009.11.007. Epub 2009 Nov 24.
The phenomenon of recombination has been widely described among noroviruses (NoVs) in the past few years. In a NoV surveillance study conducted in western India, 3 novel and 3 known combinations of RNA-dependent RNA polymerase (RdRp) and capsid genes were identified in genogroup (G) II NoV strains. The present study pertains to the characterization of three novel intergenotype NoV GII recombinant strains. RT-PCRs were carried out for the amplification of nearly complete RdRp and complete capsid genes spanning ORF1/2 overlap of three strains followed by sequencing of the amplicons. The recombination event was confirmed by phylogenetic analysis using Bayesian MCMC approach, SimPlot analysis and Maximum chi(2) method. Three novel intergenotype (GII) recombinations of GII.b/GII.18, GII.1/GII.12 and GII.3/GII.13 specificities were identified respectively in the strains PC03, PC24 and PC25 for the first time. The breakpoint in the novel recombinants was placed in the vicinity of the 20 bp ORF1/2 overlap, a common hotspot known to exist in NoV recombinants. The capsid genes of all of the 3 recombinants were closely related to their counter parts in reference strains however, a high degree of variation emerged in the polymerase genes especially of PC24 and PC25 in comparison to the reference strains.
在过去的几年中,重组现象在诺如病毒(NoV)中得到了广泛描述。在印度西部进行的一项 NoV 监测研究中,在基因型(G)II NoV 株中发现了 3 种新的和 3 种已知的 RNA 依赖性 RNA 聚合酶(RdRp)和衣壳基因组合。本研究涉及对三种新型种间 NoV GII 重组株的特征描述。进行 RT-PCR 以扩增三个菌株的近乎完整的 RdRp 和完整的衣壳基因,跨越 ORF1/2 重叠区,然后对扩增子进行测序。通过贝叶斯 MCMC 方法、SimPlot 分析和最大 chi(2)方法的系统发育分析确认了重组事件。首次在菌株 PC03、PC24 和 PC25 中分别鉴定出三种新型种间(GII)重组 GII.b/GII.18、GII.1/GII.12 和 GII.3/GII.13 特异性。新重组体的断点位于 20 个碱基 ORF1/2 重叠区附近,这是 NoV 重组体中已知的共同热点。所有 3 个重组体的衣壳基因与其参考株的对应基因密切相关,但与参考株相比,聚合酶基因,尤其是 PC24 和 PC25 的基因高度变异。