Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization

Megan E. Carey; Zoe A. Dyson; Silvia Argimón; Louise Cerdeira; Corin Yeats; David Aanensen; Gerald Mboowa; Stephen Baker; Sofonias K. Tessema; Anthony M. Smith; Iruka N. Okeke; Kathryn E. Holt

doi:10.1093/ofid/ofad044

Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization

Megan E. Carey, Zoe A. Dyson, Silvia Argimón, Louise Cerdeira, Corin Yeats, David Aanensen, Gerald Mboowa, Stephen Baker, Sofonias K. Tessema, Anthony M. Smith, Iruka N. Okeke, Kathryn E. Holt

Vector Biology

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

Abstract

The global response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrated the value of timely and open sharing of genomic data with standardized metadata to facilitate monitoring of the emergence and spread of new variants. Here, we make the case for the value of Salmonella Typhi (S. Typhi) genomic data and demonstrate the utility of freely available platforms and services that support the generation, analysis, and visualization of S. Typhi genomic data on the African continent and more broadly by introducing the Africa Centres for Disease Control and Prevention's Pathogen Genomics Initiative, SEQAFRICA, Typhi Pathogenwatch, TyphiNET, and the Global Typhoid Genomics Consortium.

Original language	English
Pages (from-to)	S38-S46
Journal	Open Forum Infectious Diseases
Volume	10
DOIs	https://doi.org/10.1093/ofid/ofad044
Publication status	Published - 2 Jun 2023

Keywords

analytic tools
data visualisation
genomics
Salmonella Typhi
typhoid fever

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Ofad044Final published version, 899 KBLicence: CC BY

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Carey, M. E., Dyson, Z. A., Argimón, S., Cerdeira, L., Yeats, C., Aanensen, D., Mboowa, G., Baker, S., Tessema, S. K., Smith, A. M., Okeke, I. N., & Holt, K. E. (2023). Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization. Open Forum Infectious Diseases, 10, S38-S46. https://doi.org/10.1093/ofid/ofad044

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title = "Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization",

abstract = "The global response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrated the value of timely and open sharing of genomic data with standardized metadata to facilitate monitoring of the emergence and spread of new variants. Here, we make the case for the value of Salmonella Typhi (S. Typhi) genomic data and demonstrate the utility of freely available platforms and services that support the generation, analysis, and visualization of S. Typhi genomic data on the African continent and more broadly by introducing the Africa Centres for Disease Control and Prevention's Pathogen Genomics Initiative, SEQAFRICA, Typhi Pathogenwatch, TyphiNET, and the Global Typhoid Genomics Consortium.",

keywords = "analytic tools, data visualisation, genomics, Salmonella Typhi, typhoid fever",

author = "Carey, \{Megan E.\} and Dyson, \{Zoe A.\} and Silvia Argim{\'o}n and Louise Cerdeira and Corin Yeats and David Aanensen and Gerald Mboowa and Stephen Baker and Tessema, \{Sofonias K.\} and Smith, \{Anthony M.\} and Okeke, \{Iruka N.\} and Holt, \{Kathryn E.\}",

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month = jun,

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doi = "10.1093/ofid/ofad044",

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volume = "10",

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Carey, ME, Dyson, ZA, Argimón, S, Cerdeira, L, Yeats, C, Aanensen, D, Mboowa, G, Baker, S, Tessema, SK, Smith, AM, Okeke, IN & Holt, KE 2023, 'Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization', Open Forum Infectious Diseases, vol. 10, pp. S38-S46. https://doi.org/10.1093/ofid/ofad044

TY - JOUR

T1 - Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization

AU - Carey, Megan E.

AU - Dyson, Zoe A.

AU - Argimón, Silvia

AU - Cerdeira, Louise

AU - Yeats, Corin

AU - Aanensen, David

AU - Mboowa, Gerald

AU - Baker, Stephen

AU - Tessema, Sofonias K.

AU - Smith, Anthony M.

AU - Okeke, Iruka N.

AU - Holt, Kathryn E.

PY - 2023/6/2

Y1 - 2023/6/2

N2 - The global response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrated the value of timely and open sharing of genomic data with standardized metadata to facilitate monitoring of the emergence and spread of new variants. Here, we make the case for the value of Salmonella Typhi (S. Typhi) genomic data and demonstrate the utility of freely available platforms and services that support the generation, analysis, and visualization of S. Typhi genomic data on the African continent and more broadly by introducing the Africa Centres for Disease Control and Prevention's Pathogen Genomics Initiative, SEQAFRICA, Typhi Pathogenwatch, TyphiNET, and the Global Typhoid Genomics Consortium.

AB - The global response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrated the value of timely and open sharing of genomic data with standardized metadata to facilitate monitoring of the emergence and spread of new variants. Here, we make the case for the value of Salmonella Typhi (S. Typhi) genomic data and demonstrate the utility of freely available platforms and services that support the generation, analysis, and visualization of S. Typhi genomic data on the African continent and more broadly by introducing the Africa Centres for Disease Control and Prevention's Pathogen Genomics Initiative, SEQAFRICA, Typhi Pathogenwatch, TyphiNET, and the Global Typhoid Genomics Consortium.

KW - analytic tools

KW - data visualisation

KW - genomics

KW - Salmonella Typhi

KW - typhoid fever

U2 - 10.1093/ofid/ofad044

DO - 10.1093/ofid/ofad044

M3 - Article

SN - 2328-8957

VL - 10

SP - S38-S46

JO - Open Forum Infectious Diseases

JF - Open Forum Infectious Diseases

ER -

Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization

Abstract

Keywords

UN SDGs

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