Microarray analysis of evolution of RNA viruses: Evidence of circulation of virulent highly divergent vaccine-derived polioviruses
Microarray analysis of evolution of RNA viruses: Evidence of circulation of virulent highly divergent vaccine-derived polioviruses
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DOI：
10.1073/pnas.1633511100
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发表时间：
2003-08-05
影响因子：
11.1
通讯作者：
Chumakov, K
中科院分区：
文献类型：
--
作者：
Cherkasova, E;Laassri, M;Chumakov, K
提出了两种基于病毒探针与寡核苷酸微阵列杂交的方法，用于快速分析RNA病毒微进化过程中的遗传变异。病毒重组的微阵列分析以及重测序和异质性分析的微阵列能够生成疫苗衍生脊髓灰质炎病毒（VDPVs）的即时遗传图谱，并揭示其进化差异的程度。与基于cDNA测序和限制性片段长度多态性的传统方法不同，微阵列方法更适合分析异质群体和不同菌株的混合物。微阵列杂交谱对少量不同突变的累积存在非常敏感，包括那些无法通过测序揭示的突变，这使得该方法对病毒种群中核苷酸序列多样性谱的表征非常有用。通过使用这些方法，我们鉴定了从健康人分离的3型VDPV，而传统的筛查方法没有检测到。脊髓灰质炎毒株的突变谱与在人群中循环100年的情况一致，并且在转基因小鼠中具有高毒力，这证实了尽管免疫水平很高，但VDPV仍能在社区中持续存在。所提出的异质病毒群体精细基因分型的方法也可用于研究病毒、细菌和高等生物基因的遗传变化的各种其他应用。
Two approaches based on hybridization of viral probes with oligonucleotide microarrays were developed for rapid analysis of genetic variations during microevolution of RNA viruses. Microarray analysis of viral recombination and microarray for resequencing and heterogeneity analysis were able to generate instant genetic maps of vaccine-derived polioviruses (VDPVs) and reveal the degree of their evolutionary divergence. Unlike conventional methods based on cDNA sequencing and restriction fragment length polymorphism, the microarray approaches are better suited for analysis of heterogeneous populations and mixtures of different strains. The microarray hybridization profile is very sensitive to the cumulative presence of small quantities of different mutations, including those that cannot be revealed by sequencing, making this approach useful for characterization of profiles of nucleotide sequence diversity in viral populations. By using these methods, we identified a type-3 VDPV isolated from a healthy person and missed by conventional methods of screening. The mutational profile of the polio strain was consistent with > 1 yr of circulation in human population and was highly virulent in transgenic mice, confirming the ability of VDPV to persist in communities despite high levels of immunity. The proposed methods for fine genotyping of heterogeneous viral populations can also have utility for a variety of other applications in studies of genetic changes in viruses, bacteria, and genes of higher organisms.