A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae.
A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae.
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DOI：
10.1007/s00705-003-0162-1
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发表时间：
2003-11
影响因子：
2.7
通讯作者：
Enjuanes L
中科院分区：
文献类型：
--
作者：
González JM;Gomez-Puertas P;Cavanagh D;Gorbalenya AE;Enjuanes L
冠状病毒科包括冠状病毒属和轮状病毒属，是冠状病毒目的一部分，该目还包括另外两个科，动脉病毒科和轮状病毒科。根据遗传和血清学关系，1、2和3组以前被认为是冠状病毒属。本文对冠状病毒科的S蛋白(S)、膜蛋白(E)、膜蛋白(M)和核蛋白(N)结构蛋白以及两个最保守的复制酶结构域--依赖核糖核酸聚合酶(RdRp)和核糖核酸解旋酶(HEL)进行了比较序列分析，旨在修订冠状病毒科的分类学。冠状病毒属结构蛋白和复制酶蛋白的配对比较结果是一致的，并产生了以不连续簇分布的序列同一性百分比。组间两两配对的分数在最低百分位数处形成一个单独的簇。在冠状病毒外没有发现N和E蛋白的同源物，在圆环病毒中仅发现了S和M蛋白的(非常远的)同源物。组内序列保守性更高，尽管对于一些配对，特别是来自最多样化的组1的配对，得分与组间比较的得分接近甚至重叠。使用邻接加入算法对六种蛋白质进行的系统发育分析证实了三个冠状病毒组。RdRp和HEL结构域的比较序列分析被扩展到包括动脉病毒和冠状病毒同源物。冠状病毒属和环状病毒属序列之间的配对得分(22-25%和21-25%)与科间配对比较的值范围(12-22%和17-25%)非常接近或重叠，但远低于冠状病毒属内的配对比较得出的值(63-71%和59-67%)。系统发育分析证实，轮状病毒和冠状病毒在很大程度上是分开的，这与已建立的NidVirus家族之间的距离相当。根据这些得分与几个多属病毒科(如短冠冠状病毒科)的不同等级的分析结果进行比较，建议修订冠状病毒科的分类。我们建议将冠状病毒和轮状病毒属重新定义为冠状病毒科内的两个亚科或新冠病毒科内的两个亚科，并将目前的三个非正式冠状病毒群转换为冠状病毒科内的三个属。
The Coronaviridae family, comprising the Coronavirus and Torovirus genera, is part of the Nidovirales order that also includes two other families, Arteriviridae and Roniviridae. Based on genetic and serological relationships, groups 1, 2 and 3 were previously recognized in the Coronavirus genus. In this report we present results of comparative sequence analysis of the spike (S), envelope (E), membrane (M), and nucleoprotein (N) structural proteins, and the two most conserved replicase domains, putative RNA-dependent RNA polymerase (RdRp) and RNA helicase (HEL), aimed at a revision of the Coronaviridae taxonomy. The results of pairwise comparisons involving structural and replicase proteins of the Coronavirus genus were consistent and produced percentages of sequence identities that were distributed in discontinuous clusters. Inter-group pairwise scores formed a single cluster in the lowest percentile. No homologs of the N and E proteins have been found outside coronaviruses, and the only (very) distant homologs of S and M proteins were identified in toroviruses. Intragroup sequence conservation was higher, although for some pairs, especially those from the most diverse group 1, scores were close or even overlapped with those from the intergroup comparisons. Phylogenetic analysis of six proteins using a neighbor-joining algorithm confirmed three coronavirus groups. Comparative sequence analysis of RdRp and HEL domains were extended to include arterivirus and ronivirus homologs. The pairwise scores between sequences of the genera Coronavirus and Torovirus (22–25% and 21–25%) were found to be very close to or overlapped with the value ranges (12 to 22% and 17 to 25%) obtained for interfamily pairwise comparisons, but were much smaller than values derived from pairwise comparisons within the Coronavirus genus (63–71% and 59–67%). Phylogenetic analysis confirmed toroviruses and coronaviruses to be separated by a large distance that is comparable to those between established nidovirus families. Based on comparison of these scores with those derived from analysis of separate ranks of several multi-genera virus families, like the Picornaviridae, a revision of the Coronaviridae taxonomy is proposed. We suggest the Coronavirus and Torovirus genera to be re-defined as two subfamilies within the Coronavirdae or two families within Nidovirales, and the current three informal coronavirus groups to be converted into three genera within the Coronaviridae.
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影响因子：
14.9
作者：
Gorbalenya AE;Koonin EV;Donchenko AP;Blinov VM
通讯作者：
Blinov VM
影响因子：
3.7
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Den Boon JA;Snijder EJ;Locker JK;Horzinek MC;Rottier PJ
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Rottier PJ
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Gorbalenya, AE
影响因子：
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作者：
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通讯作者：
deGroot, RJ
影响因子：
6.8
作者：
GORBALENYA, AE;KOONIN, EV
通讯作者：
KOONIN, EV