In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks
To achieve maximum transmission chain tracking in the current Ebola outbreak, whole genome sequencing (WGS) has been proposed to provide optimal information. However, WGS remains a costly and time-intensive procedure that is poorly suited for the large numbers of samples being generated, especially...
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doaj-70ec56a399b34529941bfb26dae2cee12020-11-25T01:06:04ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-04-011010.3389/fmicb.2019.00857448515In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus OutbreaksTrudy M. Wassenaar0Visanu Wanchai1Gregory S. Buzard2David W. Ussery3Molecular Microbiology and Genomics Consultants, Zotzenheim, GermanyDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United StatesRetired, Middletown, MD, United StatesDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United StatesTo achieve maximum transmission chain tracking in the current Ebola outbreak, whole genome sequencing (WGS) has been proposed to provide optimal information. However, WGS remains a costly and time-intensive procedure that is poorly suited for the large numbers of samples being generated, especially under severe time and work-environment constraints as in the present DRC outbreak. To better prepare for future outbreaks, where an apparent single outbreak may actually represent overlapping outbreaks caused by independent variants, and where rapid identification of emerging new transmission chains will be essential, a more practical method would be to amplify and sequence genomic areas that reveal the highest information to differentiate EBOV variants. We have identified four highly informative polymorphism PCR sequencing targets, suitable for rapid tracing of transmission chains and identification of new sources of Ebola outbreaks, an approach which will be far more practical in the field than WGS.https://www.frontiersin.org/article/10.3389/fmicb.2019.00857/fullEbola virustransmission chainvirus evolutionmutation hotspotPCR sequencing |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Trudy M. Wassenaar Visanu Wanchai Gregory S. Buzard David W. Ussery |
spellingShingle |
Trudy M. Wassenaar Visanu Wanchai Gregory S. Buzard David W. Ussery In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks Frontiers in Microbiology Ebola virus transmission chain virus evolution mutation hotspot PCR sequencing |
author_facet |
Trudy M. Wassenaar Visanu Wanchai Gregory S. Buzard David W. Ussery |
author_sort |
Trudy M. Wassenaar |
title |
In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks |
title_short |
In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks |
title_full |
In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks |
title_fullStr |
In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks |
title_full_unstemmed |
In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks |
title_sort |
in silico selection of amplification targets for rapid polymorphism screening in ebola virus outbreaks |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2019-04-01 |
description |
To achieve maximum transmission chain tracking in the current Ebola outbreak, whole genome sequencing (WGS) has been proposed to provide optimal information. However, WGS remains a costly and time-intensive procedure that is poorly suited for the large numbers of samples being generated, especially under severe time and work-environment constraints as in the present DRC outbreak. To better prepare for future outbreaks, where an apparent single outbreak may actually represent overlapping outbreaks caused by independent variants, and where rapid identification of emerging new transmission chains will be essential, a more practical method would be to amplify and sequence genomic areas that reveal the highest information to differentiate EBOV variants. We have identified four highly informative polymorphism PCR sequencing targets, suitable for rapid tracing of transmission chains and identification of new sources of Ebola outbreaks, an approach which will be far more practical in the field than WGS. |
topic |
Ebola virus transmission chain virus evolution mutation hotspot PCR sequencing |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2019.00857/full |
work_keys_str_mv |
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