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

## TL;DR

This study tracks SARS-CoV-2 variants in Ibadan, Nigeria, from 2021 to 2022, showing Delta and Omicron dominance and the role of healthcare workers in surveillance.

## Contribution

The study provides genomic data from Nigeria and highlights healthcare workers as effective sentinels for variant tracking post-widespread testing.

## Key findings

- Delta variants were predominant in Ibadan from August to September 2021.
- Omicron variants replaced Delta from December 2021 onward.
- Healthcare workers contributed to the detection of major lineages despite reduced clinical testing.

## Abstract

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.

SARS-CoV-2 from COVID-19 patients in Ibadan were predominantly Delta variants (Aug-Sept 2021), and Omicron variants (Dec 2021-July 2022). The commonest lineages were recovered from health workers, who could be employed for variant tracking now that extensive testing has ceased.