Cargando…

Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea

Transmission trees can be established through detailed contact histories, statistical or phylogenetic inference, or a combination of methods. Each approach has its limitations, and the extent to which they succeed in revealing a ‘true’ transmission history remains unclear. In this study, we compared...

Descripción completa

Detalles Bibliográficos
Autores principales: Robert, Alexis, Tsui Lok Hei, Joseph, Watson, Conall H, Gsell, Pierre-Stéphane, Hall, Yper, Rambaut, Andrew, Longini, Ira M, Sakoba, Keïta, Kucharski, Adam J, Touré, Alhassane, Danmadji Nadlaou, Sévérine, Saidou Barry, Mamadou, Fofana, Thierno Oumar, Lansana Kaba, Ibrahima, Sylla, Lansana, Diaby, Mohamed Lamine, Soumah, Ousmane, Diallo, Abdourahime, Niare, Amadou, Diallo, Abdourahamane, Eggo, Rosalind M, Caroll, Miles W, Henao-Restrepo, Ana Maria, Edmunds, W John, Hué, Stéphane
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10013732/
https://www.ncbi.nlm.nih.gov/pubmed/36926449
http://dx.doi.org/10.1093/ve/vead007
_version_ 1784906837231927296
author Robert, Alexis
Tsui Lok Hei, Joseph
Watson, Conall H
Gsell, Pierre-Stéphane
Hall, Yper
Rambaut, Andrew
Longini, Ira M
Sakoba, Keïta
Kucharski, Adam J
Touré, Alhassane
Danmadji Nadlaou, Sévérine
Saidou Barry, Mamadou
Fofana, Thierno Oumar
Lansana Kaba, Ibrahima
Sylla, Lansana
Diaby, Mohamed Lamine
Soumah, Ousmane
Diallo, Abdourahime
Niare, Amadou
Diallo, Abdourahamane
Eggo, Rosalind M
Caroll, Miles W
Henao-Restrepo, Ana Maria
Edmunds, W John
Hué, Stéphane
author_facet Robert, Alexis
Tsui Lok Hei, Joseph
Watson, Conall H
Gsell, Pierre-Stéphane
Hall, Yper
Rambaut, Andrew
Longini, Ira M
Sakoba, Keïta
Kucharski, Adam J
Touré, Alhassane
Danmadji Nadlaou, Sévérine
Saidou Barry, Mamadou
Fofana, Thierno Oumar
Lansana Kaba, Ibrahima
Sylla, Lansana
Diaby, Mohamed Lamine
Soumah, Ousmane
Diallo, Abdourahime
Niare, Amadou
Diallo, Abdourahamane
Eggo, Rosalind M
Caroll, Miles W
Henao-Restrepo, Ana Maria
Edmunds, W John
Hué, Stéphane
author_sort Robert, Alexis
collection PubMed
description Transmission trees can be established through detailed contact histories, statistical or phylogenetic inference, or a combination of methods. Each approach has its limitations, and the extent to which they succeed in revealing a ‘true’ transmission history remains unclear. In this study, we compared the transmission trees obtained through contact tracing investigations and various inference methods to identify the contribution and value of each approach. We studied eighty-six sequenced cases reported in Guinea between March and November 2015. Contact tracing investigations classified these cases into eight independent transmission chains. We inferred the transmission history from the genetic sequences of the cases (phylogenetic approach), their onset date (epidemiological approach), and a combination of both (combined approach). The inferred transmission trees were then compared to those from the contact tracing investigations. Inference methods using individual data sources (i.e. the phylogenetic analysis and the epidemiological approach) were insufficiently informative to accurately reconstruct the transmission trees and the direction of transmission. The combined approach was able to identify a reduced pool of infectors for each case and highlight likely connections among chains classified as independent by the contact tracing investigations. Overall, the transmissions identified by the contact tracing investigations agreed with the evolutionary history of the viral genomes, even though some cases appeared to be misclassified. Therefore, collecting genetic sequences during outbreak is key to supplement the information contained in contact tracing investigations. Although none of the methods we used could identify one unique infector per case, the combined approach highlighted the added value of mixing epidemiological and genetic information to reconstruct who infected whom.
format Online
Article
Text
id pubmed-10013732
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-100137322023-03-15 Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea Robert, Alexis Tsui Lok Hei, Joseph Watson, Conall H Gsell, Pierre-Stéphane Hall, Yper Rambaut, Andrew Longini, Ira M Sakoba, Keïta Kucharski, Adam J Touré, Alhassane Danmadji Nadlaou, Sévérine Saidou Barry, Mamadou Fofana, Thierno Oumar Lansana Kaba, Ibrahima Sylla, Lansana Diaby, Mohamed Lamine Soumah, Ousmane Diallo, Abdourahime Niare, Amadou Diallo, Abdourahamane Eggo, Rosalind M Caroll, Miles W Henao-Restrepo, Ana Maria Edmunds, W John Hué, Stéphane Virus Evol Research Article Transmission trees can be established through detailed contact histories, statistical or phylogenetic inference, or a combination of methods. Each approach has its limitations, and the extent to which they succeed in revealing a ‘true’ transmission history remains unclear. In this study, we compared the transmission trees obtained through contact tracing investigations and various inference methods to identify the contribution and value of each approach. We studied eighty-six sequenced cases reported in Guinea between March and November 2015. Contact tracing investigations classified these cases into eight independent transmission chains. We inferred the transmission history from the genetic sequences of the cases (phylogenetic approach), their onset date (epidemiological approach), and a combination of both (combined approach). The inferred transmission trees were then compared to those from the contact tracing investigations. Inference methods using individual data sources (i.e. the phylogenetic analysis and the epidemiological approach) were insufficiently informative to accurately reconstruct the transmission trees and the direction of transmission. The combined approach was able to identify a reduced pool of infectors for each case and highlight likely connections among chains classified as independent by the contact tracing investigations. Overall, the transmissions identified by the contact tracing investigations agreed with the evolutionary history of the viral genomes, even though some cases appeared to be misclassified. Therefore, collecting genetic sequences during outbreak is key to supplement the information contained in contact tracing investigations. Although none of the methods we used could identify one unique infector per case, the combined approach highlighted the added value of mixing epidemiological and genetic information to reconstruct who infected whom. Oxford University Press 2023-03-07 /pmc/articles/PMC10013732/ /pubmed/36926449 http://dx.doi.org/10.1093/ve/vead007 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Robert, Alexis
Tsui Lok Hei, Joseph
Watson, Conall H
Gsell, Pierre-Stéphane
Hall, Yper
Rambaut, Andrew
Longini, Ira M
Sakoba, Keïta
Kucharski, Adam J
Touré, Alhassane
Danmadji Nadlaou, Sévérine
Saidou Barry, Mamadou
Fofana, Thierno Oumar
Lansana Kaba, Ibrahima
Sylla, Lansana
Diaby, Mohamed Lamine
Soumah, Ousmane
Diallo, Abdourahime
Niare, Amadou
Diallo, Abdourahamane
Eggo, Rosalind M
Caroll, Miles W
Henao-Restrepo, Ana Maria
Edmunds, W John
Hué, Stéphane
Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea
title Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea
title_full Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea
title_fullStr Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea
title_full_unstemmed Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea
title_short Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea
title_sort quantifying the value of viral genomics when inferring who infected whom in the 2014–16 ebola virus outbreak in guinea
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10013732/
https://www.ncbi.nlm.nih.gov/pubmed/36926449
http://dx.doi.org/10.1093/ve/vead007
work_keys_str_mv AT robertalexis quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT tsuilokheijoseph quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT watsonconallh quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT gsellpierrestephane quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT hallyper quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT rambautandrew quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT longiniiram quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT sakobakeita quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT kucharskiadamj quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT tourealhassane quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT danmadjinadlaouseverine quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT saidoubarrymamadou quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT fofanathiernooumar quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT lansanakabaibrahima quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT syllalansana quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT diabymohamedlamine quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT soumahousmane quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT dialloabdourahime quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT niareamadou quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT dialloabdourahamane quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT eggorosalindm quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT carollmilesw quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT henaorestrepoanamaria quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT edmundswjohn quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea
AT huestephane quantifyingthevalueofviralgenomicswheninferringwhoinfectedwhominthe201416ebolavirusoutbreakinguinea