title: The recent ancestry of Middle East respiratory syndrome coronavirus in Korea has been shaped by recombination.
abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe cases of human respiratory disease. Since 2012, the victims have mainly come from the Middle East countries or sporadically from some other geographical regions seeded by the travelers who visited the Middle East. Such an introduction through travelling led to the emergence of a MERS-CoV outbreak in Korea in May 2015, which caused more than 140 confirmed human cases in less than a month. Using 70 complete genome sequences of MERS-CoV isolates, including the most recent sequences for the Korean and Chinese isolates, we reconstructed the phylogenetic relationships of the complete genome and the individual protein coding regions. The Korean MERS-CoV strain clustered in the previously established Hafr-Al-Batin-1_2013 clade together with two Saudi Arabian and one Chinese strain sampled in 2015. Although these four strains remained monophyletic in the entire protein-coding region, this clade showed different phylogenetic relationships across the genome, indicating a shared unique recombination pattern that is different from previously reported putative recombination strains. Our findings suggest that the recent ancestor of the Korean and its related MERS-CoV strains is characterized by unique mosaic genome pattern that is different from other putative recombinants.
authors.affiliation: Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.
authors.forename: Jin Il
authors.initials: JI
authors.lastname: Kim
authors.affiliation: Division of Respiratory Viruses.
authors.forename: You-Jin
authors.initials: YJ
authors.lastname: Kim
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven 3000, Belgium.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.affiliation: Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.
authors.forename: Ilseob
authors.initials: I
authors.lastname: Lee
authors.affiliation: Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.
authors.forename: Sehee
authors.initials: S
authors.lastname: Park
authors.affiliation: Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.
authors.forename: Joon-Yong
authors.initials: JY
authors.lastname: Bae
authors.affiliation: Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.
authors.forename: Donghwan
authors.initials: D
authors.lastname: Kim
authors.affiliation: Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.
authors.forename: Hyejin
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.
authors.forename: Seok-Il
authors.initials: SI
authors.lastname: Jang
authors.affiliation: Division of Respiratory Viruses.
authors.forename: Jeong-Sun
authors.initials: JS
authors.lastname: Yang
authors.affiliation: Division of Respiratory Viruses.
authors.forename: Hak
authors.initials: H
authors.lastname: Kim
authors.affiliation: Division of Biosafety Evaluation and Control.
authors.forename: Dae-Won
authors.initials: DW
authors.lastname: Kim
authors.affiliation: Division of Respiratory Viruses.
authors.forename: Jeong-Gu
authors.initials: JG
authors.lastname: Nam
authors.affiliation: Division of Respiratory Viruses.
authors.forename: Sung Soon
authors.initials: SS
authors.lastname: Kim
authors.affiliation: Division of Influenza Virus, Center for Infectious Diseases.
authors.forename: Kisoon
authors.initials: K
authors.lastname: Kim
authors.affiliation: Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea.|The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea.
authors.forename: Jae
authors.initials: J
authors.lastname: Myun Lee
authors.affiliation: Laboratory Science Division, International Vaccine Institute, Seoul 151-742, Republic of Korea.|The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea.
authors.forename: Man Ki
authors.initials: MK
authors.lastname: Song
authors.affiliation: College of Pharmacy, Korea University, Sejong 339-700, Republic of Korea.|The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea.
authors.forename: Daesub
authors.initials: D
authors.lastname: Song
authors.affiliation: Division of Life &Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea.|The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea.
authors.forename: Jun
authors.initials: J
authors.lastname: Chang
authors.affiliation: ATGen, Seongnam 463-400, Republic of Korea.|The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea.
authors.forename: Kee-Jong
authors.initials: KJ
authors.lastname: Hong
authors.affiliation: Department of Biological Science, Sungkyunkwan University, Suwon 440-746, Republic of Korea.|The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea.
authors.forename: Yong-Soo
authors.initials: YS
authors.lastname: Bae
authors.affiliation: Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.
authors.forename: Jin-Won
authors.initials: JW
authors.lastname: Song
authors.affiliation: Korea National Institute of Health, Osong 361-951, Republic of Korea.
authors.forename: Joo-Shil
authors.initials: JS
authors.lastname: Lee
authors.affiliation: Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.|The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea.
authors.forename: Man-Seong
authors.initials: MS
authors.lastname: Park
mesh_terms: D018352:Coronavirus Infections / Q000453:epidemiology* / Q000821:virology*; D019143:Evolution, Molecular; D016679:Genome, Viral; D006801:Humans; D065207:Middle East Respiratory Syndrome Coronavirus / Q000145:classification* / Q000235:genetics*; D016366:Open Reading Frames; D010802:Phylogeny; D011995:Recombination, Genetic; D056910:Republic of Korea / Q000453:epidemiology