Two years of genomic surveillance capacity development in Guinea: an operational roadmap for local implementation in low-income countries and tracking of SARS-CoV-2 circulation dynamics

Introduction The COVID-19 pandemic significantly accelerated the development of genomic surveillance capabilities worldwide, though equitable access remains a challenge. On 12 March 2020, Guinea, a low-income country in West Africa, reported its first COVID-19 case; however, no local genomic infrastructure was available at the time. A year later, a long-term mentorship program was initiated to establish a SARS-CoV-2 nanopore sequencing unit at the Centre de Recherche en Virologie, Laboratoire des Fièvres Hémorragiques Virales de Guinée (CRV-LFHVG) in Conakry, Guinea. Here, we describe the establishment of this capacity and its role in uncovering SARS-CoV-2 circulation dynamics in the region. Methods We established a local hub for sequencing training where SARS-CoV-2-positive samples, collected as part of routine diagnostic activities from July 2020 to July 2022, were retrospectively and prospectively sequenced using MinION nanopore. Consensus genomes were generated for variant typing and GISAID-submission. Retrospective phylodynamic analysis was performed. Results By July 2022, the laboratory had generated 238 SARS-CoV-2 consensus sequences with a median genomic recovery of 98.1 % [range: 90.5-99.4], representing 0.64% of the 37,464 confirmed cases reported in the country as of 29 July 2022. These sequences encompassed four waves of infection, with the Delta (21A, 21I and 21J) and Omicron (21K and 21L) variants of concern (VOCs) accounting for 84% of all identified lineages. Notably, phylogeographic reconstructions unveiled introductions of Delta/B.1.617.2 and Delta/AY.37, as well as of Omicron/BA.1.1 and Omicron/BA.1.15.1, from the neighboring Western, Eastern and Middle African regions at dates close to their estimated emergence. Sequencing output was >0.5% of the total positive samples and resulted in the timely delivery of two preliminary variant identification reports to national health authorities, followed by six official reports. Conclusion This work underscores key findings during a global health crisis and offers operational guidance to support future genomic surveillance initiatives in low- and middle-income countries. Sustained financial investment, dedicated time, specialized expertise, efficient logistics, and local ownership are essential for long-term implementation of such capacities.