Analysis of the metagenomic assembled #genome of #MERS-CoV and Alpha-CoV from #Camelus dromedarius in #Saudi Arabia
Abstract Background Dromedary camels are known carriers of Middle East respiratory syndrome coronavirus (MERS-CoV). This study aimed to identify respiratory RNA viruses circulating in the nasal cavities of camels that could potentially cause disease in humans. Methods Shotgun metagenomic paired-end sequencing was performed on four pools of nasal swabs collected from 40 camels originating from Sudan and Djibouti, using the MiSeq platform. Results Alphacoronavirus 229E was commonly detected in the camel pools. MERS-CoV was found in both pools from Sudan and one from Djibouti . Camel parainfluenza virus 3 (PIV3) was detected in the male camel pool from Sudan . Furthermore, near-complete (99.9 %) metagenomic assembled genomes (MAGs) of alphacoronavirus 229E (SIAU MAG01) and MERS-CoV (SIAU MAG02) were retrieved from the female camel pool from Sudan . Another MAG of alphacoronavirus 229E (SIAU MAG03) was recovered from a male camel pool imported from Sudan . In the phylogenetic analysis, SIA...