@article{e965736ce01544b68b04a4d5ef64ecd9,
title = "The phylogeography of MERS-CoV in hospital outbreak-associated cases compared to sporadic cases in Saudi Arabia",
abstract = "This study compared the phylogeography of MERS-CoV between hospital outbreak-associated cases and sporadic cases in Saudi Arabia. We collected complete genome sequences from human samples in Saudi Arabia and data on the multiple risk factors of human MERS-CoV in Saudi Arabia reported from 2012 to 2018. By matching each sequence to human cases, we identified isolates as hospital outbreak-associated cases or sporadic cases. We used Bayesian phylogenetic methods including temporal, discrete trait analysis and phylogeography to uncover transmission routes of MERS-CoV isolates between hospital outbreaks and sporadic cases. Of the 120 sequences collected between 19 June 2012 and 23 January 2017, there were 64 isolates from hospital outbreak-associated cases and 56 from sporadic cases. Overall, MERS-CoV is fast evolving at 7.43 × 10-4 substitutions per site per year. Isolates from hospital outbreaks showed unusually fast evolutionary speed in a shorter time-frame than sporadic cases. Multiple introductions of different MERS-CoV strains occurred in three separate hospital outbreaks. MERS-CoV appears to be mutating in humans. The impact of mutations on viruses transmissibility in humans is unknown.",
keywords = "Epidemiology, Hospital outbreaks, MERS-CoV, Nosocomial, Phylogenetics, Phylogeography",
author = "Xin Chen and Adam, {Dillon Charles} and Chughtai, {Abrar Ahmad} and Sacha Stelzer-Braid and Matthew Scotch and MacIntyre, {Chandini Raina}",
note = "Funding Information: Funding: This research was funded by the Australian National Health & Medical Research Council (NHMRC), Centres of Research Excellence, Integrated systems for epidemic response, Grant APP1107393. D.C.A. was supported by the Australian Government Research Training Program Scholarship. D.C.A. and C.R.M. are also supported by an NHMRC Postgraduate Scholarship (grant number 1169037) and NHMRC Principal Research Fellowship (grant number 1137582) respectively. MS was supported by the National Library of Medicine of the National Institutes of Health under Award Number R01LM012080. Funding Information: Acknowledgments: We would like to acknowledge the funding provided by the Australian NHMRC, Centres of Research Excellence, Integrated systems for epidemic response, Grant APP1107393, and the support for DCA through an Australian Government Research Training Program Scholarship. DCA and CRM are also supported by an NHMRC Postgraduate Scholarship (grant number 1169037) and NHMRC Principal Research Fellowship (grant number 1137582) respectively. MS is supported by the National Library of Medicine of the National Institutes of Health under Award Number R01LM012080. Publisher Copyright: {\textcopyright} 2020 by the authors.",
year = "2020",
month = may,
doi = "10.3390/v12050540",
language = "English (US)",
volume = "12",
journal = "Viruses",
issn = "1999-4915",
publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",
number = "5",
}