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2023;2023 6638714.

PHINDaccess Hackathons for COVID-19 and Host-Pathogen Interaction: Lessons Learned and Recommendations for Low- and Middle-Income Countries.

Kais Ghedira, Hamza Dallali, Monia Ardhaoui, Zied Bouslema, Yosr Hamdi, Salma Feki Ben-Salah, Hanen Chelbi, Chiraz Atri, Melek Chaouch, Naira Dekhil, Afef Rais, Saifeddine Azouz, Manel Gharbi, Fatma Guerfali, Chaima Hkimi, Selim Kamoun, Ayoub Ksouri, Imen Moumni, Houyem Ouragini, Raghda Bsibes, Zeineb Afifi, Khouloud Youssfi, Hichem Ben Hassine, Najet Hadhri, Helmi Mardassi, Houcemeddine Othman, Oussema Khamessi
Author Information
  1. Kais Ghedira: Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia. ORCID
  2. Hamza Dallali: Laboratory of Biomedical Genomics and Oncogenetics (LR20IPT05), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia. ORCID
  3. Monia Ardhaoui: Department of Human and Experimentally Anatomic Pathology, Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia. ORCID
  4. Zied Bouslema: Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia. ORCID
  5. Yosr Hamdi: Laboratory of Biomedical Genomics and Oncogenetics (LR20IPT05), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia. ORCID
  6. Salma Feki Ben-Salah: Laboratory of Virus, Vector and Hosts (LR20IPT02), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia. ORCID
  7. Hanen Chelbi: Laboratory of Medical Parasitology, Biotechnology and Biomolecules, LR16IPT06, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis Belvédère 1002, Tunisia. ORCID
  8. Chiraz Atri: Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR16IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis Belvédère 1002, Tunisia. ORCID
  9. Melek Chaouch: Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia. ORCID
  10. Naira Dekhil: Laboratory of Molecular Microbiology, Vaccinology, And Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia. ORCID
  11. Afef Rais: Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR16IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis Belvédère 1002, Tunisia. ORCID
  12. Saifeddine Azouz: Genomics Platform, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia. ORCID
  13. Manel Gharbi: Laboratory of Epidemiology and Veterinary Microbiology. Group of Bacteriology and Biotechnology Institut Pasteur of Tunisia, University of Tunis El Manar (UTM), Tunis 1002, Tunisia. ORCID
  14. Fatma Guerfali: Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR16IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis Belvédère 1002, Tunisia. ORCID
  15. Chaima Hkimi: Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia. ORCID
  16. Selim Kamoun: Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia. ORCID
  17. Ayoub Ksouri: Laboratory of Venom, Toxins and Therapeutic Molecules, Institut Pasteur Tunis, University Tunis El Manar, Tunis, Tunisia. ORCID
  18. Imen Moumni: Laboratory of Molecular and Cellular Hematology, LR16IPT07, Pasteur Institute of Tunis, University of Tunis El Manar, Tunisia. ORCID
  19. Houyem Ouragini: Laboratory of Molecular and Cellular Hematology, LR16IPT07, Pasteur Institute of Tunis, University of Tunis El Manar, Tunisia. ORCID
  20. Raghda Bsibes: Grant Office, Institut Pasteur de Tunis, Tunis, Tunisia. ORCID
  21. Zeineb Afifi: Grant Office, Institut Pasteur de Tunis, Tunis, Tunisia.
  22. Khouloud Youssfi: Specialized Unit "Communication, Science and Society", Institut Pasteur de Tunis, Tunis, Tunisia.
  23. Hichem Ben Hassine: Specialized Unit "Communication, Science and Society", Institut Pasteur de Tunis, Tunis, Tunisia. ORCID
  24. Najet Hadhri: Grant Office, Institut Pasteur de Tunis, Tunis, Tunisia.
  25. Helmi Mardassi: Laboratory of Molecular Microbiology, Vaccinology, And Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia. ORCID
  26. Houcemeddine Othman: Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. ORCID
  27. Oussema Khamessi: Laboratory of Venoms and Therapeutic Molecules LR11IPT08, Institut Pasteur de Tunis, University of Tunis El Manar, 13 Place Pasteur BP74Belvédère, Tunis Belvédère, Tunisia. ORCID
PMID: 37854792 DOI: 10.1155/2023/6638714

Abstract

Hackathons are collaborative events that bring together diverse groups to solve predefined challenges. The COVID-19 pandemic caused by SARS-CoV-2 has emphasized the need for portable and reproducible genomics analysis pipelines to study the genetic susceptibility of the human host and investigate human-SARS-CoV-2 protein interactions. To build and strengthen institutional capacities in OMICS data analysis applied to host-pathogen interaction (HPI), the PHINDaccess project organized two hackathons in 2020 and 2021. These hackathons are aimed at developing bioinformatics pipelines related to the SARS-CoV-2 viral genome, its phylodynamic transmission, and the identification of human genome host variants, with a focus on addressing global health challenges, particularly in low- and middle-income countries (LMIC). This paper outlines the preparation, proceedings, and lessons learned from these hackathons, including the challenges faced by participants and our recommendations based on our experience for organizing hackathons in LMIC and beyond.

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MeSH Term

Humans
COVID-19
SARS-CoV-2
Developing Countries
Pandemics
Host-Pathogen Interactions
Journal Article
Article has an altmetric score of 1

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