Choi S A, Ryu K H
Plant Virus GenBank, Division of Environmental and Life Sciences, Seoul Women's University, Seoul, Republic of Korea.
Arch Virol. 2003 Oct;148(10):1943-55. doi: 10.1007/s00705-003-0155-0.
The complete genomic nucleotide sequence and genome structure of Lily symptomless virus (LSV), a lily-infecting carlavirus, have been obtained. The genome of the Korean strain of LSV, LSV-Kr, was 8394 nucleotides long and contained six open reading frames (ORFs) coding for proteins of Mr 220 kDa (1948 aa), 25 kDa (228 aa), 12 kDa (106 aa), 7 kDa (64 aa), 32 kDa (291 aa) and 16 kDa (140 aa) from the 5' to 3' end, respectively, which is typical of carlaviruses. Genetic heterogeneity was observed in the ORF1 gene. A total of 221 of 5,847 nucleotides (nt) were heterologous in the ORF1 of replicase; 162 nt portions were silent and 59 nt resulted in amino acid changes. This heterogeneity indicates that the LSV-infecting lily plants contained a genetically heterogeneous population of LSV (quasispecies). Overall similarities to those of other carlaviruses for the six ORFs of LSV were from 76.1% to 31.6% and from 87.3% to 13.7%, at nucleotide and amino acid levels, respectively. The ORF1 replicase gene of LSV shares 40.9% to 56.8% and 48.9% and 58.6% identities with that of 5 other carlaviruses at the amino acid and nucleotide levels, respectively. LSV was closest to Blueberry scorch virus (BlScV) in this ORF, among the carlaviruses for which sequence information is available. The three triple gene blocks (ORF2-4), ORF5 (coat protein) and 3'-proximal 16 kDa ORF6 genes were further analyzed, and phylogenetic trees for the coding regions indicate that the LSV was the most closely related to Kalanchoe latent virus and BlScV. This is the first report of the complete nucleotide sequence and genome structure of LSV.
已获得侵染百合的香石竹潜隐病毒（LSV）的全基因组核苷酸序列及基因组结构。LSV韩国分离株（LSV-Kr）的基因组长度为8394个核苷酸，包含6个开放阅读框（ORF），从5'端到3'端分别编码分子量为220 kDa（1948个氨基酸）、25 kDa（228个氨基酸）、12 kDa（106个氨基酸）、7 kDa（64个氨基酸）、32 kDa（291个氨基酸）和16 kDa（140个氨基酸）的蛋白质，这是香石竹潜隐病毒属病毒的典型特征。在ORF1基因中观察到遗传异质性。在复制酶的ORF1中共有5847个核苷酸（nt）中的221个是异源的；162个nt部分是沉默的，59个nt导致氨基酸变化。这种异质性表明侵染百合的LSV植物含有遗传异质的LSV群体（准种）。LSV的6个ORF与其他香石竹潜隐病毒属病毒在核苷酸和氨基酸水平上的总体相似性分别为76.1%至31.6%和87.3%至13.7%。LSV的ORF1复制酶基因与其他5种香石竹潜隐病毒属病毒在氨基酸和核苷酸水平上的同一性分别为40.9%至56.8%和48.9%至58.6%。在有序列信息的香石竹潜隐病毒属病毒中，LSV在该ORF中与蓝莓焦枯病毒（BlScV）关系最为密切。对三个三联基因块（ORF2 - 4）、ORF5（外壳蛋白）和3'端附近的16 kDa ORF6基因进行了进一步分析，编码区的系统发育树表明LSV与长寿花潜隐病毒和BlScV关系最为密切。这是关于LSV全核苷酸序列和基因组结构的首次报道。
