PHINDaccess Hackathons for COVID-19 and Host-Pathogen Interaction: Lessons Learned and Recommendations for Low- and Middle-Income Countries-Reference-Cited by-同舟云学术

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

Published:2023-10-10 Issue: Volume:2023 Page:1-12
ISSN:2314-6141
Container-title:BioMed Research International
language:en
Short-container-title:BioMed Research International

Author:

Ghedira Kais¹^ORCID,Dallali Hamza²^ORCID,Ardhaoui Monia³⁴^ORCID,Bouslema Zied⁵⁶^ORCID,Hamdi Yosr²^ORCID,Feki Ben-Salah Salma⁷^ORCID,Chelbi Hanen⁸^ORCID,Atri Chiraz⁹^ORCID,Chaouch Melek¹^ORCID,Dekhil Naira¹⁰^ORCID,Rais Afef⁹^ORCID,Azouz Saifeddine¹¹^ORCID,Gharbi Manel¹²^ORCID,Guerfali Fatma⁹^ORCID,Hkimi Chaima¹^ORCID,Kamoun Selim¹^ORCID,Ksouri Ayoub¹³^ORCID,Moumni Imen¹⁴^ORCID,Ouragini Houyem¹⁴^ORCID,Bsibes Raghda¹⁵^ORCID,Afifi Zeineb¹⁵,Youssfi Khouloud¹⁶,Ben Hassine Hichem¹⁶^ORCID,Hadhri Najet¹⁵,Mardassi Helmi¹⁰^ORCID,Othman Houcemeddine¹⁷¹⁸¹⁹^ORCID,Khamessi Oussema²⁰²¹^ORCID

Affiliation:

1. Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia

2. Laboratory of Biomedical Genomics and Oncogenetics (LR20IPT05), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia

3. 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

4. Laboratory of Molecular Epidemiology and Experimental Pathology, Tunisia

5. Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia

6. University of Tunis El Manar, Tunis, Tunisia

7. Laboratory of Virus, Vector and Hosts (LR20IPT02), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia

8. Laboratory of Medical Parasitology, Biotechnology and Biomolecules, LR16IPT06, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis Belvédère 1002, Tunisia

9. Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR16IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis Belvédère 1002, Tunisia

10. Laboratory of Molecular Microbiology, Vaccinology, And Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia

11. Genomics Platform, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia

12. Laboratory of Epidemiology and Veterinary Microbiology. Group of Bacteriology and Biotechnology Institut Pasteur of Tunisia, University of Tunis El Manar (UTM), Tunis 1002, Tunisia

13. Laboratory of Venom, Toxins and Therapeutic Molecules, Institut Pasteur Tunis, University Tunis El Manar, Tunis, Tunisia

14. Laboratory of Molecular and Cellular Hematology, LR16IPT07, Pasteur Institute of Tunis, University of Tunis El Manar, Tunisia

15. Grant Office, Institut Pasteur de Tunis, Tunis, Tunisia

16. Specialized Unit “Communication, Science and Society”, Institut Pasteur de Tunis, Tunis, Tunisia

17. Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa

18. Department of Genetics, Farhat Hached University Hospital, Sousse, Tunisia

19. Laboratory of Cytogenetics, Molecular Genetics, and Reproductive Biology (LR03SP02), Farhat Hached University Hospital, Sousse, Tunisia

20. Laboratory of Venoms and Therapeutic Molecules LR11IPT08, Institut Pasteur de Tunis, University of Tunis El Manar, 13 Place Pasteur BP74Belvédère, Tunis Belvédère, Tunisia

21. High Institute of Biotechnology of Sidi Thabet, University of Manouba, Ariana BP-66, Manouba 2010, Tunisia

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.

Funder

Tunisian Ministry of Higher Education and Research

Publisher

Hindawi Limited

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine

Link

http://downloads.hindawi.com/journals/bmri/2023/6638714.pdf

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