Two years of SARS-CoV-2 genomic surveillance capacity development in Guinea.

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 training program 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. We established a local hub for comprehensive sequencing training (wet-lab and bioinformatics), 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 the ONT MinION device. Consensus genomes were generated for variant typing and GISAID-submission. Retrospective phylodynamic analysis was performed. 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 (21 A, 21I and 21 J) and Omicron (21 K and 21 L) variants of concern (VOCs) accounting for 84% of all identified lineages. Phylogeographic reconstructions revealed 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, potentially from the neighboring Western, Eastern and Middle African regions. Retrospective and prospective sequencing output was > 0.5% of the total positive samples and the results were communicated to the health authorities during the pandemic as in two preliminary variant identification reports, followed by six official reports. 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.