Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone
We generated genome sequences from 218 cases of Ebola virus disease (EVD) in Sierra Leone (SLE) during 2014–2015 to complement available datasets, particularly by including cases from a period of low sequence coverage during peak transmission of Ebola virus (EBOV) in the highly-affected We...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-01-01
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| Series: | Viruses |
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| Online Access: | http://www.mdpi.com/1999-4915/11/1/71 |
| _version_ | 1819296229287264256 |
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| author | Petrus Jansen van Vuren Jason T. Ladner Antoinette A. Grobbelaar Michael R. Wiley Sean Lovett Mushal Allam Arshad Ismail Chantel le Roux Jacqueline Weyer Naazneen Moolla Nadia Storm Joe Kgaladi Mariano Sanchez-Lockhart Ousman Conteh Gustavo Palacios Janusz T. Paweska |
| author_facet | Petrus Jansen van Vuren Jason T. Ladner Antoinette A. Grobbelaar Michael R. Wiley Sean Lovett Mushal Allam Arshad Ismail Chantel le Roux Jacqueline Weyer Naazneen Moolla Nadia Storm Joe Kgaladi Mariano Sanchez-Lockhart Ousman Conteh Gustavo Palacios Janusz T. Paweska |
| author_sort | Petrus Jansen van Vuren |
| collection | DOAJ |
| description | We generated genome sequences from 218 cases of Ebola virus disease (EVD) in Sierra Leone (SLE) during 2014–2015 to complement available datasets, particularly by including cases from a period of low sequence coverage during peak transmission of Ebola virus (EBOV) in the highly-affected Western Area division of SLE. The combined dataset was utilized to produce phylogenetic and phylodynamic inferences, to study sink–source dynamics and virus dispersal from highly-populated transmission hotspots. We identified four districts in SLE where EBOV was introduced and transmission occurred without onward exportation to other districts. We also identified six districts that substantially contributed to the dispersal of the virus and prolonged the EVD outbreak: five of these served as major hubs, with lots of movement in and out, and one acted primarily as a source, exporting the virus to other areas of the country. Positive correlations between case numbers, inter-district transition events, and district population sizes reaffirm that population size was a driver of EBOV transmission dynamics in SLE. The data presented here confirm the role of urban hubs in virus dispersal and of a delayed laboratory response in the expansion and perpetuation of the EVD outbreak in SLE. |
| first_indexed | 2024-12-24T04:54:47Z |
| format | Article |
| id | doaj.art-35eae22cc1a74af29c843d2dcc682656 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-24T04:54:47Z |
| publishDate | 2019-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-35eae22cc1a74af29c843d2dcc6826562022-12-21T17:14:25ZengMDPI AGViruses1999-49152019-01-011117110.3390/v11010071v11010071Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra LeonePetrus Jansen van Vuren0Jason T. Ladner1Antoinette A. Grobbelaar2Michael R. Wiley3Sean Lovett4Mushal Allam5Arshad Ismail6Chantel le Roux7Jacqueline Weyer8Naazneen Moolla9Nadia Storm10Joe Kgaladi11Mariano Sanchez-Lockhart12Ousman Conteh13Gustavo Palacios14Janusz T. Paweska15Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South AfricaCenter for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD 21702, USACentre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South AfricaCenter for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD 21702, USACenter for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD 21702, USASequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South AfricaSequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South AfricaCentre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South AfricaCentre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South AfricaCentre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South AfricaCentre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South AfricaCentre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South AfricaCenter for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD 21702, USAMinistry of Health and Sanitation, Freetown 47235, Sierra LeoneCenter for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD 21702, USACentre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South AfricaWe generated genome sequences from 218 cases of Ebola virus disease (EVD) in Sierra Leone (SLE) during 2014–2015 to complement available datasets, particularly by including cases from a period of low sequence coverage during peak transmission of Ebola virus (EBOV) in the highly-affected Western Area division of SLE. The combined dataset was utilized to produce phylogenetic and phylodynamic inferences, to study sink–source dynamics and virus dispersal from highly-populated transmission hotspots. We identified four districts in SLE where EBOV was introduced and transmission occurred without onward exportation to other districts. We also identified six districts that substantially contributed to the dispersal of the virus and prolonged the EVD outbreak: five of these served as major hubs, with lots of movement in and out, and one acted primarily as a source, exporting the virus to other areas of the country. Positive correlations between case numbers, inter-district transition events, and district population sizes reaffirm that population size was a driver of EBOV transmission dynamics in SLE. The data presented here confirm the role of urban hubs in virus dispersal and of a delayed laboratory response in the expansion and perpetuation of the EVD outbreak in SLE.http://www.mdpi.com/1999-4915/11/1/71Ebola virusfilovirusFiloviridaephylodynamicsEbola virus diseaseSierra LeoneWest Africa |
| spellingShingle | Petrus Jansen van Vuren Jason T. Ladner Antoinette A. Grobbelaar Michael R. Wiley Sean Lovett Mushal Allam Arshad Ismail Chantel le Roux Jacqueline Weyer Naazneen Moolla Nadia Storm Joe Kgaladi Mariano Sanchez-Lockhart Ousman Conteh Gustavo Palacios Janusz T. Paweska Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone Viruses Ebola virus filovirus Filoviridae phylodynamics Ebola virus disease Sierra Leone West Africa |
| title | Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone |
| title_full | Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone |
| title_fullStr | Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone |
| title_full_unstemmed | Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone |
| title_short | Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone |
| title_sort | phylodynamic analysis of ebola virus disease transmission in sierra leone |
| topic | Ebola virus filovirus Filoviridae phylodynamics Ebola virus disease Sierra Leone West Africa |
| url | http://www.mdpi.com/1999-4915/11/1/71 |
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