Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus

Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus

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

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.

2013

evolution, Respiratory tract infections, disease transmission, Molecular, Infectious, coronavirus infections

DOI: 10.3201/eid1905.130057

Emerging Infectious Diseases

Centers for Disease Control and Prevention

Infectious and parasitic diseases, Medicine