Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus

Matthew Cotten, Tommy T Lam, Simon J Watson, Anne L Palser, Velislava Petrova, Paul Grant, Oliver G Pybus, Andrew Rambaut, Yi Guan, Deenan Pillay, Paul Kellam, Eleni Nastouli

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish
Pages (from-to)736-742B
JournalEmerging Infectious Diseases
Issue number5
Publication statusPublished - May 2013


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