严重急性呼吸综合征冠状病毒株HKU - 39849（HK - 39）的全基因组序列。

The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39).

作者信息

Zeng F Y, Chan C W M, Chan M N, Chen J D, Chow K Y C, Hon C C, Hui K H, Li J, Li V Y Y, Wang C Y, Wang P Y, Guan Y, Zheng B, Poon L L M, Chan K H, Yuen K Y, Peiris J S M, Leung F C

机构信息

Department of Zoology, University of Hong Kong, Hong Kong, SAR China.

出版信息

Exp Biol Med (Maywood). 2003 Jul;228(7):866-73. doi: 10.1177/15353702-0322807-13.

DOI:10.1177/15353702-0322807-13

PMID:12876307

Abstract

The complete genomic nucleotide sequence (29.7kb) of a Hong Kong severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) strain HK-39 is determined. Phylogenetic analysis of the genomic sequence reveals it to be a distinct member of the Coronaviridae family. 5' RACE assay confirms the presence of at least six subgenomic transcripts all containing the predicted intergenic sequences. Five open reading frames (ORFs), namely ORF1a, 1b, S, M, and N, are found to be homologues to other CoV members, and three more unknown ORFs (X1, X2, and X3) are unparalleled in all other known CoV species. Optimal alignment and computer analysis of the homologous ORFs has predicted the characteristic structural and functional domains on the putative genes. The overall nucleotides conservation of the homologous ORFs is low (<5%) compared with other known CoVs, implying that HK-39 is a newly emergent SARS-CoV phylogenetically distant from other known members. SimPlot analysis supports this finding, and also suggests that this novel virus is not a product of a recent recombinant from any of the known characterized CoVs. Together, these results confirm that HK-39 is a novel and distinct member of the Coronaviridae family, with unknown origin. The completion of the genomic sequence of the virus will assist in tracing its origin.

摘要

测定了一株香港严重急性呼吸综合征（SARS）冠状病毒（SARS-CoV）HK-39株的完整基因组核苷酸序列（29.7kb）。对该基因组序列的系统发育分析表明，它是冠状病毒科一个独特的成员。5' RACE分析证实至少存在六个亚基因组转录本，它们均含有预测的基因间序列。发现五个开放阅读框（ORF），即ORF1a、1b、S、M和N，与其他冠状病毒成员同源，另外三个未知的ORF（X1、X2和X3）在所有其他已知的冠状病毒种类中均未出现过。对同源ORF进行的最佳比对和计算机分析预测了推定基因上的特征性结构和功能域。与其他已知的冠状病毒相比，同源ORF的总体核苷酸保守性较低（<5%），这意味着HK-39是一种新出现的SARS-CoV，在系统发育上与其他已知成员相距较远。SimPlot分析支持这一发现，并且还表明这种新型病毒不是任何已知特征冠状病毒最近重组的产物。这些结果共同证实，HK-39是冠状病毒科一个新的独特成员，其起源未知。该病毒基因组序列的完成将有助于追踪其起源。