title: Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus.
abstract: A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient's sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events.
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Matthew
authors.initials: M
authors.lastname: Cotten
authors.forename: Tommy T
authors.initials: TT
authors.lastname: Lam
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Watson
authors.forename: Anne L
authors.initials: AL
authors.lastname: Palser
authors.forename: Velislava
authors.initials: V
authors.lastname: Petrova
authors.forename: Paul
authors.initials: P
authors.lastname: Grant
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.forename: Yi
authors.initials: Y
authors.lastname: Guan
authors.forename: Deenan
authors.initials: D
authors.lastname: Pillay
authors.forename: Paul
authors.initials: P
authors.lastname: Kellam
authors.forename: Eleni
authors.initials: E
authors.lastname: Nastouli
mesh_terms: D000818:Animals; D001483:Base Sequence; D002685:Chiroptera / Q000821:virology; D017934:Coronavirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D018352:Coronavirus Infections / Q000175:diagnosis* / Q000821:virology; D017931:DNA Primers; D018076:DNA, Complementary / Q000235:genetics; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007597:Jordan; D008969:Molecular Sequence Data; D010802:Phylogeny; D011780:Qatar; D012367:RNA, Viral / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012529:Saudi Arabia
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D012367:RNA, Viral
keywords: computer-aided design; coronavirus infections; disease transmission; evolution; high-throughput nucleotide sequencing; infectious; molecular; respiratory tract infections; viruses; zoonoses