Genomic diversity of SARS-CoV-2 carriage in a cohort of schoolchildren in Côte d’ivoire during COVID-19 pandemics: insights from pre-delta emergence

Background: After the first case of COVID-19 was reported in Côte d’Ivoire in March 2020, the virus spread significantly, with several epidemic waves. During a carriage study conducted from November 2020 to April 2021 to examine the oropharyngeal microbiome of school children, the presence of several other pathogens was investigated. This study characterised the diversity of SARS-CoV-2 detected in a cohort of school children in Côte d’Ivoire. Methods: Oropharyngeal swabs from participants in Korhogo (n = 37) and Abidjan (n = 39) were analysed. RNA was extracted from the samples, followed by RT-qPCR detection of Coronaviruses. Sequencing was done on an Oxford Nanopore platform and data analysed in GISAID. Results: Out of 445 samples collected, 15 (3.37%; 5 in Abidjan and 10 in Korhogo) tested positive for SARS-CoV-2 and were sequenced. Genomic coverage of over 70% was obtained for 12 genome sequences (80%). There was a significant difference in SARS-CoV-2 carriage over season per sampling visit (p < 0.05). The variants identified were of type Eta and Beta, including variant of concern (VOC) B.1.351 (6.7%), Variants of Interest (VOI) B.1.525 (60%) and other unclassified lineages B.1.1.318 (6.7%), A.19 (13,3%) and A.27 (13,3%). D614G mutation (n = 11, 73,33%) located on the S gene was the most common, followed by the T205I (n = 8, 53,33%) located on the N gene in this collection of genomes. Conclusions: This study highlights the diversity of SARS-CoV-2 that circulated in a cohort of children in Côte d’Ivoire and reports carriage of the A.19 lineage, a variant which circulated more frequently in West Africa during the study period. Clinical trial number: Not applicable.