Akande Elizabeth T, Fowotade Adeola A, Odih Erkison Ewomazino, Oaikhena Anderson O, Olisa Olasunkanmi, Sunmonu Gabriel Temitope, Adebiyi Boluwatife, Akinlabi Olabisi C, Popoola Oluwafemi A, Alonge Temitope O, Okeke Iruka N
Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria.
Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria.
Clin Infect Dis. 2025 Jul 22;80(Supplement_1):S29-S36. doi: 10.1093/cid/ciaf056.
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.
尼日利亚奥约州于2020年3月21日报告了首例2019冠状病毒病（COVID-19）病例，随后记录的病例数在尼日利亚排第五，其中大多数病例在首府伊巴丹。我们旨在确定2021年8月至2022年8月期间在伊巴丹传播的严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变体，并评估医护人员（HCW）相关感染在地方性COVID-19监测中的作用。
在获得伦理批准后，对经SARS-CoV-2实时定量聚合酶链反应（RT-qPCR）确认的样本进行逆转录，并使用ARTIC SARS-CoV-2 RT-PCR和测序方案在Illumina MiSeq上进行测序。使用nf-core/viralrecon流程组装基因组。使用在定制的Nextflow流程中实现的公开可用软件进行质量控制、系统发育分析和变体鉴定。从电子病例调查表中获取生物数据和相关临床信息。
我们分析了258个样本，最小非N覆盖率为70%，确定了12个SARS-CoV-2谱系和7个进化枝，除一个外均与全球谱系一致。BA.1（22%）和BA.1.1（48%）谱系最为常见。Delta谱系在2021年8月至9月占主导地位，2021年12月被Omicron谱系取代。医护人员的样本（n = 60；23%）占所有观察到的主要谱系的三分之一（12个中的4个）。
我们将来自奥约州的258个基因组提交到全球共享流感数据倡议组织（GSAID）数据库，并确定了在伊巴丹传播的Delta和Omicron谱系，与全球传播谱系在时间上一致。随着临床检测减少，医护人员是基因组流行病学的有用哨兵，能够捕捉到大部分的多样性。
