The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia
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 20...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-05-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/12/5/540 |
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| author | Xin Chen Dillon Charles Adam Abrar Ahmad Chughtai Sacha Stelzer-Braid Matthew Scotch Chandini Raina MacIntyre |
| author_facet | Xin Chen Dillon Charles Adam Abrar Ahmad Chughtai Sacha Stelzer-Braid Matthew Scotch Chandini Raina MacIntyre |
| author_sort | Xin Chen |
| collection | DOAJ |
| description | 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<sup>−4</sup> 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. |
| first_indexed | 2024-03-10T19:50:30Z |
| format | Article |
| id | doaj.art-52cae0e494e742478a129740182a559d |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T19:50:30Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-52cae0e494e742478a129740182a559d2023-11-20T00:25:10ZengMDPI AGViruses1999-49152020-05-0112554010.3390/v12050540The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi ArabiaXin Chen0Dillon Charles Adam1Abrar Ahmad Chughtai2Sacha Stelzer-Braid3Matthew Scotch4Chandini Raina MacIntyre5Biosecurity Research Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, AustraliaBiosecurity Research Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, AustraliaSchool of Public Health and Community Medicine, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, AustraliaSchool of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, AustraliaBiodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USABiosecurity Research Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, AustraliaThis 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<sup>−4</sup> 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.https://www.mdpi.com/1999-4915/12/5/540MERS-CoVphylogeneticsphylogeographyepidemiologyhospital outbreaksnosocomial |
| spellingShingle | Xin Chen Dillon Charles Adam Abrar Ahmad Chughtai Sacha Stelzer-Braid Matthew Scotch Chandini Raina MacIntyre The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia Viruses MERS-CoV phylogenetics phylogeography epidemiology hospital outbreaks nosocomial |
| title | The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia |
| title_full | The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia |
| title_fullStr | The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia |
| title_full_unstemmed | The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia |
| title_short | The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia |
| title_sort | phylogeography of mers cov in hospital outbreak associated cases compared to sporadic cases in saudi arabia |
| topic | MERS-CoV phylogenetics phylogeography epidemiology hospital outbreaks nosocomial |
| url | https://www.mdpi.com/1999-4915/12/5/540 |
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