Cargando…

Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples

The frequency of epidemics caused by Dengue viruses 1–4, Zika virus and Chikungunya viruses have been on an upward trend in recent years driven primarily by uncontrolled urbanization, mobility of human populations and geographical spread of their shared vectors, Aedes aegypti and Aedes albopictus. I...

Descripción completa

Detalles Bibliográficos
Autores principales: Kamaraj, Uma Sangumathi, Tan, Jun Hao, Xin Mei, Ong, Pan, Louise, Chawla, Tanu, Uehara, Anna, Wang, Lin-Fa, Ooi, Eng Eong, Gubler, Duane J., Tissera, Hasitha, Ng, Lee Ching, Wilder-Smith, Annelies, de Sessions, Paola Florez, Barkham, Timothy, Anderson, Danielle E., Sessions, October Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6504110/
https://www.ncbi.nlm.nih.gov/pubmed/31022183
http://dx.doi.org/10.1371/journal.pntd.0007184
_version_ 1783416515879501824
author Kamaraj, Uma Sangumathi
Tan, Jun Hao
Xin Mei, Ong
Pan, Louise
Chawla, Tanu
Uehara, Anna
Wang, Lin-Fa
Ooi, Eng Eong
Gubler, Duane J.
Tissera, Hasitha
Ng, Lee Ching
Wilder-Smith, Annelies
de Sessions, Paola Florez
Barkham, Timothy
Anderson, Danielle E.
Sessions, October Michael
author_facet Kamaraj, Uma Sangumathi
Tan, Jun Hao
Xin Mei, Ong
Pan, Louise
Chawla, Tanu
Uehara, Anna
Wang, Lin-Fa
Ooi, Eng Eong
Gubler, Duane J.
Tissera, Hasitha
Ng, Lee Ching
Wilder-Smith, Annelies
de Sessions, Paola Florez
Barkham, Timothy
Anderson, Danielle E.
Sessions, October Michael
author_sort Kamaraj, Uma Sangumathi
collection PubMed
description The frequency of epidemics caused by Dengue viruses 1–4, Zika virus and Chikungunya viruses have been on an upward trend in recent years driven primarily by uncontrolled urbanization, mobility of human populations and geographical spread of their shared vectors, Aedes aegypti and Aedes albopictus. Infections by these viruses present with similar clinical manifestations making them challenging to diagnose; this is especially difficult in regions of the world hyperendemic for these viruses. In this study, we present a targeted-enrichment methodology to simultaneously sequence the complete viral genomes for each of these viruses directly from clinical samples. Additionally, we have also developed a customized computational tool (BaitMaker) to design these enrichment baits. This methodology is robust in its ability to capture diverse sequences and is amenable to large-scale epidemiological studies. We have applied this methodology to two large cohorts: a febrile study based in Colombo, Sri Lanka taken during the 2009–2015 dengue epidemic (n = 170) and another taken during the 2016 outbreak of Zika virus in Singapore (n = 162). Results from these studies indicate that we were able to cover an average of 97.04% ± 0.67% of the full viral genome from samples in these cohorts. We also show detection of one DENV3/ZIKV co-infected patient where we recovered full genomes for both viruses.
format Online
Article
Text
id pubmed-6504110
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-65041102019-05-09 Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples Kamaraj, Uma Sangumathi Tan, Jun Hao Xin Mei, Ong Pan, Louise Chawla, Tanu Uehara, Anna Wang, Lin-Fa Ooi, Eng Eong Gubler, Duane J. Tissera, Hasitha Ng, Lee Ching Wilder-Smith, Annelies de Sessions, Paola Florez Barkham, Timothy Anderson, Danielle E. Sessions, October Michael PLoS Negl Trop Dis Research Article The frequency of epidemics caused by Dengue viruses 1–4, Zika virus and Chikungunya viruses have been on an upward trend in recent years driven primarily by uncontrolled urbanization, mobility of human populations and geographical spread of their shared vectors, Aedes aegypti and Aedes albopictus. Infections by these viruses present with similar clinical manifestations making them challenging to diagnose; this is especially difficult in regions of the world hyperendemic for these viruses. In this study, we present a targeted-enrichment methodology to simultaneously sequence the complete viral genomes for each of these viruses directly from clinical samples. Additionally, we have also developed a customized computational tool (BaitMaker) to design these enrichment baits. This methodology is robust in its ability to capture diverse sequences and is amenable to large-scale epidemiological studies. We have applied this methodology to two large cohorts: a febrile study based in Colombo, Sri Lanka taken during the 2009–2015 dengue epidemic (n = 170) and another taken during the 2016 outbreak of Zika virus in Singapore (n = 162). Results from these studies indicate that we were able to cover an average of 97.04% ± 0.67% of the full viral genome from samples in these cohorts. We also show detection of one DENV3/ZIKV co-infected patient where we recovered full genomes for both viruses. Public Library of Science 2019-04-25 /pmc/articles/PMC6504110/ /pubmed/31022183 http://dx.doi.org/10.1371/journal.pntd.0007184 Text en © 2019 Kamaraj et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Kamaraj, Uma Sangumathi
Tan, Jun Hao
Xin Mei, Ong
Pan, Louise
Chawla, Tanu
Uehara, Anna
Wang, Lin-Fa
Ooi, Eng Eong
Gubler, Duane J.
Tissera, Hasitha
Ng, Lee Ching
Wilder-Smith, Annelies
de Sessions, Paola Florez
Barkham, Timothy
Anderson, Danielle E.
Sessions, October Michael
Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples
title Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples
title_full Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples
title_fullStr Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples
title_full_unstemmed Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples
title_short Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples
title_sort application of a targeted-enrichment methodology for full-genome sequencing of dengue 1-4, chikungunya and zika viruses directly from patient samples
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6504110/
https://www.ncbi.nlm.nih.gov/pubmed/31022183
http://dx.doi.org/10.1371/journal.pntd.0007184
work_keys_str_mv AT kamarajumasangumathi applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT tanjunhao applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT xinmeiong applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT panlouise applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT chawlatanu applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT ueharaanna applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT wanglinfa applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT ooiengeong applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT gublerduanej applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT tisserahasitha applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT ngleeching applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT wildersmithannelies applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT desessionspaolaflorez applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT barkhamtimothy applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT andersondaniellee applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples
AT sessionsoctobermichael applicationofatargetedenrichmentmethodologyforfullgenomesequencingofdengue14chikungunyaandzikavirusesdirectlyfrompatientsamples