title: The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39).
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.
authors.affiliation: Department of Zoology, University of Hong Kong, Hong Kong, SAR China.
authors.forename: F Y
authors.initials: FY
authors.lastname: Zeng
authors.forename: C W M
authors.initials: CW
authors.lastname: Chan
authors.forename: M N
authors.initials: MN
authors.lastname: Chan
authors.forename: J D
authors.initials: JD
authors.lastname: Chen
authors.forename: K Y C
authors.initials: KY
authors.lastname: Chow
authors.forename: C C
authors.initials: CC
authors.lastname: Hon
authors.forename: K H
authors.initials: KH
authors.lastname: Hui
authors.forename: J
authors.initials: J
authors.lastname: Li
authors.forename: V Y Y
authors.initials: VY
authors.lastname: Li
authors.forename: C Y
authors.initials: CY
authors.lastname: Wang
authors.forename: P Y
authors.initials: PY
authors.lastname: Wang
authors.forename: Y
authors.initials: Y
authors.lastname: Guan
authors.forename: B
authors.initials: B
authors.lastname: Zheng
authors.forename: L L M
authors.initials: LL
authors.lastname: Poon
authors.forename: K H
authors.initials: KH
authors.lastname: Chan
authors.forename: K Y
authors.initials: KY
authors.lastname: Yuen
authors.forename: J S M
authors.initials: JS
authors.lastname: Peiris
authors.forename: F C
authors.initials: FC
authors.lastname: Leung
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D020121:5' Untranslated Regions / Q000235:genetics; D000595:Amino Acid Sequence; D001483:Base Sequence; D017124:Conserved Sequence; D018076:DNA, Complementary / Q000235:genetics; D016679:Genome, Viral; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D016366:Open Reading Frames; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D045473:Severe acute respiratory syndrome-related coronavirus / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D045169:Severe Acute Respiratory Syndrome / Q000821:virology; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D018076:DNA, Complementary; D012367:RNA, Viral; D014764:Viral Proteins