title: Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia.
abstract: Despite extensive laboratory investigations in patients with respiratory tract infections, no microbiological cause can be identified in a significant proportion of patients. In the past 3 years, several novel respiratory viruses, including human metapneumovirus, severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and human coronavirus NL63, were discovered. Here we report the discovery of another novel coronavirus, coronavirus HKU1 (CoV-HKU1), from a 71-year-old man with pneumonia who had just returned from Shenzhen, China. Quantitative reverse transcription-PCR showed that the amount of CoV-HKU1 RNA was 8.5 to 9.6 x 10(6) copies per ml in his nasopharyngeal aspirates (NPAs) during the first week of the illness and dropped progressively to undetectable levels in subsequent weeks. He developed increasing serum levels of specific antibodies against the recombinant nucleocapsid protein of CoV-HKU1, with immunoglobulin M (IgM) titers of 1:20, 1:40, and 1:80 and IgG titers of <1:1,000, 1:2,000, and 1:8,000 in the first, second and fourth weeks of the illness, respectively. Isolation of the virus by using various cell lines, mixed neuron-glia culture, and intracerebral inoculation of suckling mice was unsuccessful. The complete genome sequence of CoV-HKU1 is a 29,926-nucleotide, polyadenylated RNA, with G+C content of 32%, the lowest among all known coronaviruses with available genome sequence. Phylogenetic analysis reveals that CoV-HKU1 is a new group 2 coronavirus. Screening of 400 NPAs, negative for SARS-CoV, from patients with respiratory illness during the SARS period identified the presence of CoV-HKU1 RNA in an additional specimen, with a viral load of 1.13 x 10(6) copies per ml, from a 35-year-old woman with pneumonia. Our data support the existence of a novel group 2 coronavirus associated with pneumonia in humans.
authors.affiliation: Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong.
authors.forename: Patrick C Y
authors.initials: PC
authors.lastname: Woo
authors.forename: Susanna K P
authors.initials: SK
authors.lastname: Lau
authors.forename: Chung-ming
authors.initials: CM
authors.lastname: Chu
authors.forename: Kwok-hung
authors.initials: KH
authors.lastname: Chan
authors.forename: Hoi-wah
authors.initials: HW
authors.lastname: Tsoi
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.forename: Beatrice H L
authors.initials: BH
authors.lastname: Wong
authors.forename: Rosana W S
authors.initials: RW
authors.lastname: Poon
authors.forename: James J
authors.initials: JJ
authors.lastname: Cai
authors.forename: Wei-kwang
authors.initials: WK
authors.lastname: Luk
authors.forename: Leo L M
authors.initials: LL
authors.lastname: Poon
authors.forename: Samson S Y
authors.initials: SS
authors.lastname: Wong
authors.forename: Yi
authors.initials: Y
authors.lastname: Guan
authors.forename: J S Malik
authors.initials: JS
authors.lastname: Peiris
authors.forename: Kwok-yung
authors.initials: KY
authors.lastname: Yuen
mesh_terms: D000368:Aged; D000595:Amino Acid Sequence; D001483:Base Sequence; D015153:Blotting, Western; D017934:Coronavirus / Q000145:classification / Q000235:genetics*; D004797:Enzyme-Linked Immunosorbent Assay; D015751:Genes, pol; D016679:Genome, Viral; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009305:Nasopharynx / Q000821:virology; D016366:Open Reading Frames; D010802:Phylogeny; D011024:Pneumonia, Viral / Q000821:virology*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA