GENOMIC SURVEILLANCE TO CONTROL PATHOGEN INFECTIONS IN AFRICA

Project Information

GenPath Africa

Grant agreement ID: 101103171

DOI

10.3030/101103171

EC signature date 28 August 2023

Start date 1 May 2023

End date 30 April 2027

Funded under

• Health

Total cost

€ 4 999 170,25

EU contribution

€ 4 999 170,25

Coordinated by

STELLENBOSCH UNIVERSITY
South Africa

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (25)

Isolation of viable <i>Mycobacterium bovis</i> from faeces of naturally infected free-ranging rural domestic cattle ( <i>Bos taurus</i> )

Author(s): Rachiel Gumbo, Tristen Lourens, Deborah M Cooke, Tanya J Kerr, Robin M Warren, Michele A Miller, Giovanni Ghielmetti, Wynand J Goosen
Published in: Journal of Applied Microbiology, Issue 136, 2025, ISSN 1365-2672
Publisher: Oxford University Press (OUP)
DOI: 10.1093/JAMBIO/LXAF281

A microbial safari: finding evidence of <i>Mycobacterium bovis</i> DNA in soil from the Kruger National Park, South Africa

Author(s): M. C. Matthews, M. E. M. Toorians, T. J. Davies, R. D. Stewart, W. J. Goosen, M. A. Miller
Published in: Microbiology Spectrum, Issue 14, 2025, ISSN 2165-0497
Publisher: American Society for Microbiology
DOI: 10.1128/SPECTRUM.01658-25

Detection of Mycobacterium bovis in nasal swabs from communal goats (Capra hircus) in rural KwaZulu-Natal, South Africa

Author(s): Deborah M. Cooke; Charlene Clarke; Tanya J. Kerr; Robin M. Warren; Carmel Witte, Michele A. Miller; Wynand J. Goosen
Published in: Frontiers in Microbiology, Issue 15:1349163, 2024, ISSN 1664-302X
Publisher: Frontiers Media S.A.
DOI: 10.3389/fmicb.2024.1349163

Genomic Surveillance of Climate-Amplified Cholera Outbreak, Malawi, 2022–2023

Author(s): Lucious Chabuka, Wonderful T. Choga, Carla N. Mavian, Monika Moir, Christian Morgenstern, Houriiyah Tegaly, Abhinav Sharma, Eduan Wilkinson, Yeshnee Naidoo, Rhys Inward, Samir Bhatt, G.R. WilliamWint, Kamran Khan, Isaac I. Bogoch, Moritz U.G. Kraemer, José Lourenço, Cheryl Baxter, Massimiliano Tagliamonte, Marco Salemi, Richard J. Lessells, Collins Mitambo, Ronald Chitatanga, Joseph Bitilinyu-Bango, Mabvuto Chiwaula, Yollamu Chavula, Mphatso Bukhu, Happy Manda, Moses Chitenje, Innocent Malolo, Alex Mwanyongo, Bernard Mvula, Mirrium Nyenje, Tulio de Oliveira, Mathew Kagoli
Published in: Emerging Infectious Diseases, Issue 31, 2025, ISSN 1080-6040
Publisher: Centers for Disease Control and Prevention (CDC)
DOI: 10.3201/EID3106.240930

Evaluation of DNA extraction methods from clinical Mycobacterium tuberculosis primary liquid culture for whole-genome sequencing

Author(s): Emilyn Costa Conceição, Mishka Haffejee, Felicia Wells, Brendon Mann, Tim Heupink, Astrid Paulse, Jennifer Williams, Anzaan Dippenaar, Yonas Ghebrekristos, Megan Burger, Vincent Rennie, Miguel de Diego Fuertes, Ilham Al-Talib, Nabila Ismail, Melanie Grobbelaar, Elizabeth Maria Streicher, Túlio de Oliveira, Gian Van der Spuy, Annelies Van Rie, Robin Warren
Published in: BMC Genomics, 2026, ISSN 1471-2164
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/S12864-026-12812-W

CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation

Author(s): Massimiliano S Tagliamonte, Abhinav Sharma, Alberto Riva, Monika Moir, Marco Salemi, Cheryl Baxter, Tulio de Oliveira, Carla N Mavian, Eduan Wilkinson
Published in: Bioinformatics, Issue 42, 2026, ISSN 1367-4811
Publisher: Oxford University Press (OUP)
DOI: 10.1093/BIOINFORMATICS/BTAF665

The third era of genomics is at risk of being dismantled across the global south

Author(s): Tulio de Oliveira
Published in: Science, Issue 386:6718, 2024, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.adt484

Mixed nontuberculous mycobacteria in an immunocompromised patient with probable progressive multifocal leukoencephalopathy

Author(s): Christoffel Opperman, Janet Scott, Janre Steyn, Sarishna Singh, Yonas Ghebrekristos, Roland Croxford, Robin Warren, Aliasgar Esmail, Giovanni Ghielmetti, Wynand Goosen
Published in: IJID Regions, Issue 14, 2025, ISSN 2772-7076
Publisher: Elsevier BV
DOI: 10.1016/J.IJREGI.2024.100502

Mycobacterium avium DNA extraction: Implications for NTM identification and amplicon sequencing

Author(s): Christoffel J. Opperman, Salim Ben Amor, Greshan Kisten, Brendon C. Mann, Janré Steyn, Sarishna Singh, Yonas Ghebrekristos, Robin Warren, Wynand Goosen
Published in: Southern African Journal of Infectious Diseases, Issue 40, 2025, ISSN 2312-0053
Publisher: AOSIS
DOI: 10.4102/SAJID.V40I1.717

Genomic Characterization of Circulating Dengue Virus, Ethiopia, 2022–2023

Author(s): Adugna Abera, Houriiyah Tegally, Geremew Tasew, Eduan Wilkinson, Abraham Ali, Feyisa Regasa, Molalegne Bitew, Mahlet Belachew, Lucious Chabuka, Gaspary Mwanyika, Derek Tshiabuila, Jennifer Giandhari, Sureshnee Pillay, Jenicca Poogavanan, Monika Moir, Moritz U.G. Kraemer, Kamran Khan, Carmen Huber, Getachew Tollera, Tobias F. Rinke de Wit, Cheryl Baxter, Richard Lessells, Dawit Wolday, Dereje Beyene, Tulio de Oliveira, null null
Published in: Emerging Infectious Diseases, Issue 31, 2025, ISSN 1080-6040
Publisher: Centers for Disease Control and Prevention (CDC)
DOI: 10.3201/EID3103.240996

Dengue virus importation risks in Africa: a modelling study

Author(s): Jenicca Poongavanan, José Lourenço, Joseph L-H Tsui, Vittoria Colizza, Yajna Ramphal, Cheryl Baxter, Moritz U G Kraemer, Marcel Dunaiski, Tulio de Oliveira, Houriiyah Tegally
Published in: The Lancet Planetary Health, Issue 8, 2024, ISSN 2542-5196
Publisher: Elsevier BV
DOI: 10.1016/S2542-5196(24)00272-9

Mycobacterium tuberculosis cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis

Author(s): Emilyn C. Conceição, Felicia Wells, Abhinav Sharma, Mishka Haffejee, Brendon Mann, Justice T. Ngom, Shatha Omar, Johannes Loubser​, Miguel de Diego Fuertes, Vincent Rennie, Anzaan Dippenaar, Tim
Published in: Microbial Genomics, Issue Volume 11, Issue 11, 2025, ISSN 2057-5858
Publisher: Microbiological Society
DOI: 10.1099/MGEN.0.001565

An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable for Genomic Surveillance Within Clinical Diagnostic Settings

Author(s): Derek Tshiabuila, Wonderful Choga, James E. San, Tongai Maponga, Gert Van Zyl, Jennifer Giandhari, Sureshnee Pillay, Wolfgang Preiser, Yeshnee Naidoo, Cheryl Baxter, Darren P. Martin, Tulio de Oliveira
Published in: International Journal of Molecular Sciences, Issue 25, 2024, ISSN 1422-0067
Publisher: MDPI AG
DOI: 10.3390/ijms252111702

Evidence of Mycobacterium bovis DNA in shared water sources at livestock–wildlife–human interfaces in KwaZulu-Natal, South Africa

Author(s): Megan C. Matthews, Deborah M. Cooke, Tanya J. Kerr, Andre G. Loxton, Robin M. Warren, Giovanni Ghielmetti, Elizabeth M. Streicher, Carmel S. Witte, Michele A. Miller, Wynand J. Goosen
Published in: Frontiers in Veterinary Science, Issue 12, 2025, ISSN 2297-1769
Publisher: Frontiers Media SA
DOI: 10.3389/FVETS.2025.1483162

A decade of dengue disease burden in Africa (2013–2023): a systematic review

Author(s): Gaspary O. Mwanyika, Monika Moir, Abdualmoniem O. Musa, Jenicca Poongavanan, Graeme Dor, Eduan Wilkinson, Cheryl Baxter, Tulio de Oliveira, Houriiyah Tegally
Published in: Travel Medicine and Infectious Disease, Issue 67, 2025, ISSN 1477-8939
Publisher: Elsevier BV
DOI: 10.1016/J.TMAID.2025.102897

Spatiotemporal patterns of Rift Valley fever virus in Africa: a retrospective genomic epidemiology and phylodynamic modelling study

Author(s): John Juma, Houriiyah Tegally, Samson L Konongoi, Kristina Roesel, Rosemary Sang, Tulio de Oliviera, M Kariuki Njenga, Alan Christoffels, Bernard Bett, Simon Dellicour, Samuel O Oyola
Published in: The Lancet Microbe, Issue 7, 2026, ISSN 2666-5247
Publisher: Elsevier BV
DOI: 10.1016/J.LANMIC.2025.101251

Insights into mycobacteriome composition in Mycobacterium bovis-infected African buffalo (Syncerus caffer) tissue samples

Author(s): Giovanni Ghielmetti; Tanya J. Kerr; Netanya Bernit; Sinegugu K. Mhlophe; Elizma Streicher; Andre G. Loxton; Robin M. Warren; Michele A. Miller; Wynand J. Goosen
Published in: Scientific Reports, Issue 14:17537, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-68189-x

Hyperendemicity of Rift Valley Fever in Southwestern Uganda Associated With the Rapidly Evolving Lineage C Viruses

Author(s): Barnabas Bakamutumaho, John Juma, Erin Clancey, Luke Nyakarahuka, Silvia Situma, Raymond Odinoh, Jeanette Dawa, Carolyne Nasimiyu, Evan A Eskew, Stephen Balinandi, Sophia Mulei, John Kayiwa, John D Klena, Trevor R Shoemaker, Shannon L M Whitmer, Joel M Montgomery, John Schieffelin, Julius Lutwama, Allan Muruta, Henry Kyobe Bosa, Scott L Nuismer, Samuel O Oyola, Robert F Breiman, M Kariuki Njenga
Published in: The Journal of Infectious Diseases, Issue 233, 2026, ISSN 0022-1899
Publisher: Oxford University Press (OUP)
DOI: 10.1093/INFDIS/JIAF417

Whole-genome sequencing reveals genetic diversity and transmission dynamics of Mycobacterium bovis in South African wildlife

Author(s): Abisola Okunola, Johannes Loubser, Giovanni Ghielmetti, Rachiel Gumbo, Elizabeth M. Streicher, Pamela Ncube, Anzaan Dippenaar, Wynand J. Goosen, Ana Marcia Sá Guimarães, Robin M. Warren, Andre G. Loxton, Michele A. Miller, Tanya J. Kerr
Published in: Microbial Genomics, Issue 12, 2026, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/MGEN.0.001646

Disseminated Mycobacterium avium: A multi-organ system investigation

Author(s): Christoffel Johannes Opperman, Sarishna Singh, Yons Ghebrekristos, Michael Linström, Lourens Jacobsz, Wynand Goosen
Published in: International Journal of Infectious Diseases, Issue 165, 2026, ISSN 1201-9712
Publisher: Elsevier BV
DOI: 10.1016/J.IJID.2026.108475

Genomic Epidemiology of Rift Valley Fever Virus Involved in the 2018 and 2022 Outbreaks in Livestock in Rwanda

Author(s): Isidore Nsengimana; John Juma; Kristina Roesel; Methode N. Gasana; Fabrice Ndayisenga; Claude M. Muvunyi; Emmanuel Hakizimana; Jean N. Hakizimana; Gillian Eastwood; Augustino A. Chengula; Bernard Bett; Christopher J. Kasanga; Samuel O. Oyola
Published in: Viruses, Issue 16(7):1148, 2024, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v16071148

Identification and molecular characterization of Mycobacterium bovis DNA in GeneXpert® MTB/RIF ultra-positive, culture-negative sputum from a rural community in South Africa

Author(s): Wynand J. Goosen; Sashen Moodley; Giovanni Ghielmetti; Yumna Moosa; Thando Zulu; Theresa Smit; Vukuzazi Team; Leanie Kleynhans; Tanya J. Kerr; Elizabeth M. Streicher; Willem A. Hanekom; Robin M. Warren; Emily B. Wong; Michele A. Miller
Published in: One Health, Issue 18:100702, 2024, ISSN 2352-7714
Publisher: Elsevier
DOI: 10.1016/j.onehlt.2024.100702

Culture-independent detection of Mycobacterium tuberculosis complex DNA using targeted next generation sequencing in African buffalo (Syncerus caffer) oronasal swabs in South Africa

Author(s): Sinegugu Kholeka Mhlophe, Charlene Clarke, Giovanni Ghielmetti, Megan Matthews, Tanya Jane Kerr, Michele Ann Miller, Wynand Johan Goosen
Published in: Frontiers in Veterinary Science, Issue 12, 2025, ISSN 2297-1769
Publisher: Frontiers Media SA
DOI: 10.3389/FVETS.2025.1523628

Conserved recombination patterns across hepatitis B genotypes: a retrospective study

Author(s): Derek Tshiabuila, James E. San, Eduan Wilkinson, Graeme Dor, Houriiyah Tegally, Tongai G. Maponga, Marion Delphin, Philippa C. Matthews, Darren P. Martin, Cheryl Baxter, Tulio de Oliveira
Published in: Virology Journal, Issue 22, 2025, ISSN 1743-422X
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/S12985-025-02829-0

Targeted deep sequencing of mycobacteria species from extrapulmonary sites not identified by routine line probe assays: a retrospective laboratory analysis of stored clinical cultures

Author(s): Christoffel Opperman, Janré Steyn, Megan Ceris Matthews, Sarishna Singh, Yonas Ghebrekristos, Tanya Jane Kerr, Michele Miller, Aliasgar Esmail, Helen Cox, Robin Warren, Giovanni Ghielmetti, Wynand Goosen
Published in: IJID Regions, 2024, ISSN 2772-7076
Publisher: Elsevier BV
DOI: 10.1016/j.ijregi.2024.100464