Bioinformatics analysis of SARS coronavirus genome polymorphism.
Bioinformatics analysis of SARS coronavirus genome polymorphism.
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DOI：
10.1186/1471-2105-5-65
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发表时间：
2004-05-25
影响因子：
3
通讯作者：
Beljanski MV
中科院分区：
文献类型：
--
作者：
Pavlovic-Lazetic GM;Mitic NS;Beljanski MV
我们已经比较了38个SARS-CoV全基因组分离株。主要目的有两个：第一，分析和比较核苷酸序列，确定单核苷酸多态(SNP)、插入和缺失的位置；第二，根据序列相似性对它们进行分组，最终指向SARS-CoV分离株的系统发育。这种比较是基于基因组的多态，如插入或缺失以及SNPs的数量和位置。给出了所有38个分离株的核苷酸结构。根据SNPs的插入、缺失和差异，所有分离株的数据集被定性地划分为三个组，每个组都有自己的亚组。这些是A组有“常规”分离株(除了5‘和3’端没有插入/缺失)，B组有“长插入”的分离物，C组有“许多个体”的插入和缺失。与其他菌株相比，SNPs平均数量最少的菌株已被确定(TWh)。还给出了每组或亚组的SNPs、插入和缺失的密度分布，以及所有菌株的累积密度分布，以及TWh的基因图谱。由于单个SNP可能是随机发生的，因此与多个SNP(出现在两个或更多个分离物中)相对应的位置被识别和呈现。这一结果修正了以前的一些类似类型的结果。还识别了由多个SNPs引起的氨基酸变化(对于注释的序列，以及对于未注释的序列的预设的氨基酸变化)。给出了每个组或亚组中分离株的确切SNP位置。最后，用CLUSTALW程序绘制了SARS-CoV分离株的系统发育树，与以往的定性分类具有很高的一致性。SARS冠状病毒分离株的比较研究为基因组多态、指示毒株差异和变异进化提供了重要信息。它可能有助于开发有效的治疗方法。
We have compared 38 isolates of the SARS-CoV complete genome. The main goal was twofold: first, to analyze and compare nucleotide sequences and to identify positions of single nucleotide polymorphism (SNP), insertions and deletions, and second, to group them according to sequence similarity, eventually pointing to phylogeny of SARS-CoV isolates. The comparison is based on genome polymorphism such as insertions or deletions and the number and positions of SNPs. The nucleotide structure of all 38 isolates is presented. Based on insertions and deletions and dissimilarity due to SNPs, the dataset of all the isolates has been qualitatively classified into three groups each having their own subgroups. These are the A-group with "regular" isolates (no insertions / deletions except for 5' and 3' ends), the B-group of isolates with "long insertions", and the C-group of isolates with "many individual" insertions and deletions. The isolate with the smallest average number of SNPs, compared to other isolates, has been identified (TWH). The density distribution of SNPs, insertions and deletions for each group or subgroup, as well as cumulatively for all the isolates is also presented, along with the gene map for TWH. Since individual SNPs may have occurred at random, positions corresponding to multiple SNPs (occurring in two or more isolates) are identified and presented. This result revises some previous results of a similar type. Amino acid changes caused by multiple SNPs are also identified (for the annotated sequences, as well as presupposed amino acid changes for non-annotated ones). Exact SNP positions for the isolates in each group or subgroup are presented. Finally, a phylogenetic tree for the SARS-CoV isolates has been produced using the CLUSTALW program, showing high compatibility with former qualitative classification. The comparative study of SARS-CoV isolates provides essential information for genome polymorphism, indication of strain differences and variants evolution. It may help with the development of effective treatment.
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DOI：
10.1016/s0140-6736(03)13414-9
发表时间：
2003-05-24
期刊：
Lancet (London, England)
影响因子：
--
作者：
Ruan YJ;Wei CL;Ee AL;Vega VB;Thoreau H;Su ST;Chia JM;Ng P;Chiu KP;Lim L;Zhang T;Peng CK;Lin EO;Lee NM;Yee SL;Ng LF;Chee RE;Stanton LW;Long PM;Liu ET
通讯作者：
Liu ET
影响因子：
--
作者：
Qin, E;Zhu, QY;Yang, HM
通讯作者：
Yang, HM
影响因子：
3.2
作者：
Zeng, FY;Chan, CWM;Leung, FC
通讯作者：
Leung, FC
影响因子：
56.9
作者：
Marra, MA;Jones, SJM;Roper, RL
通讯作者：
Roper, RL
影响因子：
3.8
作者：
Thiel, V;Ivanov, KA;Ziebuhr, J
通讯作者：
Ziebuhr, J