Robertson Nancy L, Côté Fabien, Paré Christine, Leblanc Eric, Bergeron Michel G, Leclerc Denis
USDA, ARS, Subarctic Agricultural Research Service Unit, Arctic Plant Germplasm Introduction and Research Project, 533 E. Fireweed Avenue, Palmer, AK 99645, USA.
Virus Genes. 2007 Dec;35(3):807-14. doi: 10.1007/s11262-007-0139-3. Epub 2007 Jul 26.
The complete genome sequence of Nootka lupine vein-clearing virus (NLVCV) was determined to be 4,172 nucleotides in length containing four open reading frames (ORFs) with a similar genetic organization of virus species in the genus Carmovirus, family Tombusviridae. The order and gene product size, starting from the 5'-proximal ORF consisted of: (1) polymerase/replicase gene, ORF1 (p27) and ORF1RT (readthrough) (p87), (2) movement proteins ORF2 (p7) and ORF3 (p9), and, (3) the 3'-proximal coat protein ORF4, (p37). The genomic 5'- and 3'-proximal termini contained a short (59 nt) and a relatively longer 405 nt untranslated region, respectively. The longer replicase gene product contained the GDD motif common to RNA-dependent RNA polymerases. Phylogenetically, NLVCV formed a subgroup with the following four carmoviruses when separately comparing the amino acids of the coat protein or replicase protein: Angelonia flower break virus (AnFBV), Carnation mottle virus (CarMV), Pelargonium flower break virus (PFBV), and Saguaro cactus virus (SgCV). Whole genome nucleotide analysis (percent identities) among the carmoviruses with NLVCV suggested a similar pattern. The species demarcation criteria in the genus Carmovirus for the amino acid sequence identity of the polymerase (<52%) and coat (<41%) protein genes restricted NLVCV as a distinct species, and instead, placed it as a tentative strain of CarMV, PFBV, or SgCV when both the polymerase and CP were used as the determining factors. In contrast, the species criteria that included different host ranges with no overlap and lack of serology relatedness between NLVCV and the carmoviruses, suggested that NLVCV was a distinct species. The relatively low cutoff percentages allowed for the polymerase and CP genes to dictate the inclusion/exclusion of a distinct carmovirus species should be reevaluated. Therefore, at this time we have concluded that NLVCV should be classified as a tentative new species in the genus Carmovirus, family Tombusviridae.
努特卡羽扇豆脉明病毒（NLVCV）的全基因组序列被确定为4172个核苷酸长，包含四个开放阅读框（ORF），其基因组织与番茄病毒科番茄病毒属的病毒种类相似。从5'近端ORF开始的顺序和基因产物大小包括：（1）聚合酶/复制酶基因，ORF1（p27）和ORF1RT（通读）（p87），（2）运动蛋白ORF2（p7）和ORF3（p9），以及（3）3'近端衣壳蛋白ORF4（p37）。基因组5'和3'近端末端分别包含一个短的（59 nt）和一个相对较长的405 nt非翻译区。较长的复制酶基因产物包含RNA依赖性RNA聚合酶共有的GDD基序。在系统发育上，当分别比较衣壳蛋白或复制酶蛋白的氨基酸时，NLVCV与以下四种番茄病毒形成一个亚组：安吉利花碎色病毒（AnFBV）、香石竹斑驳病毒（CarMV）、天竺葵花碎色病毒（PFBV）和萨瓜罗仙人掌病毒（SgCV）。番茄病毒与NLVCV之间的全基因组核苷酸分析（百分比同一性）显示出相似的模式。番茄病毒属中关于聚合酶（<52%）和衣壳（<41%）蛋白基因氨基酸序列同一性的物种划分标准将NLVCV限制为一个独特的物种，相反，当同时使用聚合酶和CP作为决定因素时，它被归为CarMV、PFBV或SgCV的暂定株。相比之下，包括不同宿主范围且无重叠以及NLVCV与番茄病毒之间缺乏血清学相关性的物种标准表明NLVCV是一个独特的物种。应该重新评估用于决定是否将一种独特的番茄病毒纳入或排除的聚合酶和CP基因的相对较低的截止百分比。因此，此时我们得出结论，NLVCV应被归类为番茄病毒科番茄病毒属的一个暂定新物种。
