Genomic Surveillance of SARS-CoV-2 in Ibadan, Oyo State, Nigeria

Oyo State, Nigeria, reported its first coronavirus disease 2019 (COVID-19) case on 21 March 2020 and subsequently recorded the fifth highest number of cases in Nigeria, most in the capital city Ibadan. We aimed to identify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that were circulating in Ibadan between August 2021 and August 2022 and to assess the utility of healthcare worker (HCW)-associated infections for endemic COVID-19 surveillance.

Following ethical approval, SARS-CoV-2 real-time quantitative polymerase chain reaction (RT-qPCR)-confirmed samples were reverse-transcribed and sequenced on an Illumina MiSeq using ARTIC SARS-CoV-2 RT-PCR and sequencing protocols. Genomes were assembled using the nf-core/viralrecon pipeline. Quality control, phylogenetic, analysis, and variant identification were performed using publicly available software implemented in a custom Nextflow pipeline. Biodata and relevant clinical information were obtained from electronic case investigation forms.

We analyzed 258 samples with minimum non-N coverage of 70% and identified 12 SARS-CoV-2 lineages and 7 clades, all but one aligning with global lineages. Lineages BA.1 (22%) and BA.1.1 (48%) were the most common. Delta lineage predominated from August to September 2021, and was replaced by Omicron lineage from December 2021. Samples from HCWs (n = 60; 23%) accounted for a third (4 of 12) of all major lineages observed.

We contributed 258 genomes from Oyo State to the GSAID repository and identified Delta and Omicron lineages circulating in Ibadan, in temporal alignment with global circulating lineages. As clinical testing declines HCWs are useful sentinels for genomic epidemiology capturing much of the diversity.