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 publication

DOI

10.3201/eid1905.130057

Type

Journal article

Journal

Emerging infectious diseases

Publication Date

05/2013

Volume

19

Pages

736 - 42B

Addresses

Wellcome Trust Sanger Institute, Hinxton, UK.

Keywords

Animals, Chiroptera, Humans, Coronavirus, Coronavirus Infections, DNA, Complementary, RNA, Viral, DNA Primers, Reverse Transcriptase Polymerase Chain Reaction, Phylogeny, Base Sequence, Genome, Viral, Molecular Sequence Data, Jordan, Qatar, Saudi Arabia, High-Throughput Nucleotide Sequencing