Enhancing SARS-CoV-2 Response Capacity in Africa and Other CREID Centers through a Collaborative Training Program

To the Editor,

The COVID-19 pandemic has exposed critical vulnerabilities in global public health infrastructure, particularly in genomic surveillance capacity across low- and middle-income countries (LMICs). Although major investments have been made to improve access to sequencing platforms, reagents, and computational infrastructure, many LMICs still face limitations in the technical and analytical skills required to generate, interpret, and act on genomic data in real-time. As underscored by the World Health Organization, building a trained workforce capable of integrating genomics into public health decision-making remains a major challenge in pandemic preparedness efforts [1–3].

To address this gap, an international consortium of institutions organized a regional training program focused on strengthening SARS-CoV-2 genomic surveillance in Africa. The workshop was held in Dakar, Senegal, from 10 to 14 October 2022, and was hosted by the Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation (IRESSEF). The initiative was co-led by the Oswaldo Cruz Foundation (FIOCRUZ, Brazil), the Università Campus Bio-Medico di Roma (Italy), and the Centre for Epidemic Response and Innovation (CERI, South Africa). The program was delivered within the framework of the NIH/NIAID-funded Centers for Research in Emerging Infectious Diseases (CREID) network and was supported by the World Health Organization (WHO), Africa Centres for Disease Control and Prevention (Africa CDC), and the Pan American Health Organization (PAHO).

The training program adopted a hybrid format to maximize reach and inclusivity. A total of 35 participants from 15 countries across Africa, Asia, and the Americas joined the initial virtual phase, benefiting from lectures and interactive discussions. Following this, 28 trainees were selected for an intensive, in-person hands-on workshop in Dakar. The selection ensured geographic and institutional diversity, with participants representing national public health laboratories, research institutes, and academic centers actively engaged in pandemic response activities. Importantly, participants were selected with the expectation that they would transfer knowledge within their home institutions, thereby amplifying the impact of the training across multiple countries.

The hands-on curriculum was centered on the end-to-end process of SARS-CoV-2 genomic surveillance using Oxford Nanopore Technologies (ONT). Practical modules included sample processing, library preparation using tiled amplicons [8], sequencing, base calling, quality control, consensus genome generation, and data submission. Additionally, trainees were guided through reference-based alignment using ViralMSA [9], alignment visualization and editing with AliView [10], and phylogenetic reconstruction using IQ-TREE2 [11] and TreeTime [12]. These sessions equipped participants with the capacity to establish or strengthen sequencing workflows upon return to their national laboratories.

As part of the practical component, participants sequenced 22 SARS-CoV-2–positive nasopharyngeal swabs collected in Dakar, Senegal. All 22 samples yielded high-quality consensus genomes, which were analyzed in real time during the workshop. Phylogenetic and lineage assignment revealed the co-circulation of multiple Omicron sublineages, including BA.4, BA.5, and BQ.1—variants that were dominant globally during that period. Trainees learned to detect defining spike mutations, classify sequences using the Pango nomenclature system, and interpret lineage distributions in the context of local and global transmission dynamics. All sequences were uploaded to the GISAID platform [7], directly contributing to international surveillance and supporting contemporaneous outbreak investigations in Senegal. These findings were immediately shared with local public health authorities, providing timely information on the variants circulating in the country. Beyond the immediate public health relevance, the training also reinforced sequencing capacity in Senegal and enabled participants from other countries to transfer the same protocols to their home institutions, where they are now being applied not only to SARS-CoV-2 but also to other emerging pathogens.

This initiative demonstrated measurable outcomes on multiple levels. First, it significantly improved the technical capacity of participating laboratories to conduct SARS-CoV-2 genomic surveillance independently. Since the training, several participants have successfully applied these protocols in their national settings, directly generating genomes that informed local outbreak responses. Second, it fostered collaborative links among laboratories in Africa and between continents, strengthening a global network of trained professionals capable of responding to emerging infectious diseases with genomic tools. Participants have continued to collaborate through follow-up projects, knowledge-sharing forums, and joint submissions to international databases, ensuring sustainability beyond the event itself. Figure 1 illustrates the geographic distribution of participating countries and coordinating institutions, highlighting the transcontinental scope of the training and the central role played by regional hubs in genomic capacity-building.

In conclusion, this training model—combining virtual knowledge exchange with in-person sequencing and bioinformatics—demonstrated tangible and measurable outcomes. During the workshop, 22 high-quality SARS-CoV-2 genomes were generated, analyzed, and shared on GISAID, directly informing global and local monitoring of circulating Omicron sublineages in Senegal. Beyond these immediate outputs, the program effectively transferred technical skills to 28 participants from 15 countries, many of whom have since integrated these protocols into their national surveillance systems and contributed new genomic data to international platforms. The initiative also catalyzed capacity building that extended beyond SARS-CoV-2, with trainees now applying genomic methods to other emerging pathogens of regional concern. The initiative also strengthened regional and intercontinental collaborations, establishing a sustainable network of trained professionals embedded within global frameworks such as CREID, WHO, and Africa CDC. We therefore advocate for the continued expansion of such regional programs, as they provide a scalable and impactful model to close the genomic surveillance gap, ensuring more timely detection, monitoring, and control of emerging pathogens. I express my sincere gratitude to the organizers for the opportunity to contribute to this impactful initiative.

Supplementary Material

Data availability

Newly generated sequences have been deposited in GISAID under accession numbers EPI_ISL_1921452- EPI_ISL_19214540.