title: Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants.
abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging human pathogen related to SARS virus. In vitro studies indicate this virus may have a broad host range suggesting an increased pandemic potential. Genetic and epidemiological evidence indicate camels serve as a reservoir for MERS virus but the mechanism of cross species transmission is unclear and many questions remain regarding the susceptibility of humans to infection. Deep sequencing data was obtained from the nasal samples of three camels that had been experimentally infected with a human MERS-CoV isolate. A majority of the genome was covered and average coverage was greater than 12,000x depth. Although only 5 mutations were detected in the consensus sequences, 473 intrahost single nucleotide variants were identified. Many of these variants were present at high frequencies and could potentially influence viral phenotype and the sensitivity of detection assays that target these regions for primer or probe binding.
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, California, United States of America.
authors.forename: Monica K
authors.initials: MK
authors.lastname: Borucki
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, California, United States of America.
authors.forename: Victoria
authors.initials: V
authors.lastname: Lao
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, California, United States of America.
authors.forename: Mona
authors.initials: M
authors.lastname: Hwang
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, California, United States of America.
authors.forename: Shea
authors.initials: S
authors.lastname: Gardner
authors.affiliation: Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Danielle
authors.initials: D
authors.lastname: Adney
authors.affiliation: National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America.
authors.forename: Vincent
authors.initials: V
authors.lastname: Munster
authors.affiliation: Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Richard
authors.initials: R
authors.lastname: Bowen
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, California, United States of America.
authors.forename: Jonathan E
authors.initials: JE
authors.lastname: Allen
mesh_terms: D000818:Animals; D002162:Camelus; D002522:Chlorocebus aethiops; D018352:Coronavirus Infections / Q000235:genetics* / Q000635:transmission*; D006801:Humans; D065207:Middle East Respiratory Syndrome Coronavirus / Q000235:genetics* / Q000472:pathogenicity*; D009154:Mutation; D014709:Vero Cells