Building Pathogen Genomic Sequencing Capacity in Africa: Centre for Epidemic Response and Innovation Fellowship

Abstract

The World Health Organization African region has the greatest infectious disease burden in the world. However, many African countries have limited capacity to rapidly detect, report, and respond to public health events. The Centre for Epidemic Response and Innovation (CERI), KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) in South Africa, and global Climate Amplified Diseases and Epidemics (CLIMADE) consortium are investing in building the capacity of African scientists in pathogen genomics and bioinformatics. A two-week long (11-21 April 2023) intensive training in wet-laboratory genomic data production, bioinformatics, and phylogenetic analyses of viral and bacterial pathogens was held in Cape Town, South Africa. Training was provided to 36 fellows with diverse backgrounds from 16 countries, 14 of which were low- and middle-income African countries. In this report, we, the fellows, share our collective experiences and describe how the learnt skills have been integrated into the operations of our home institutions to advance genomic surveillance capabilities. We identified the in-person and hands-on learning format of the training, taught by genomics experts and field application specialists, as the most impactful elements of this training event. Adaptation and miniaturisation of protocols to detect other pathogens is a great enhancement over the traditional method of using a single protocol for a pathogen. We note the duration of the training as the largest limiting factor, particularly for the computationally intensive bioinformatics sessions. We recommend this programme continue to build pathogen genomics capacity in Africa.

Keywords: bioinformatics; capacity building; genomic surveillance; lessons; pathogens; training.

Figure 1

Map of Africa depicting the location and affiliation of the fellows who participated in the training (red circles). The location of CERI, where the training was hosted, is shown with a gold circle. Country colour displays the number of SARS-CoV-2 genomes publicly available on the Global Initiative on Sharing All Influenza Data (GISAID) as a proxy for pathogen genomic sequencing capacity (data accessed on 17 July 2023). Map produced with Quantum GIS [12].

Figure 2

Rating of fellows’ bioinformatics (red) and wet-laboratory (blue) skills. The number of respondents depicts the number of fellows possessing each skill prior to attending the training opportunity (PCR: polymerase chain reaction).

Figure 3

Novel aspects of the training are grouped into the categories of Content, Environment, and Delivery. The number of figure icons indicates how many fellows listed each aspect in their questionnaire responses.