Whole genome sequencing and phylogenetic analysis of SARS-CoV-2 strains isolated during the COVID-19 pandemic in Nigeria

Adedolapo B Olorunfemi; Salma A R Suliman; Tung T Tran; Babatunde Ayorinde; Muinah A Fowora; Bamidele A Iwalokun; Olugbenga A Olowe; Oluyinka O Opaleye; Mohamed Osman; Babatunde L Salako; Richard Adegbola; Bolaji N Thomas; Srinivas Reddy Pallerla; Thirumalaisamy P Velavan; Olusola Ojurongbe

doi:10.1016/j.ijregi.2024.01.005

Whole genome sequencing and phylogenetic analysis of SARS-CoV-2 strains isolated during the COVID-19 pandemic in Nigeria

IJID Reg. 2024 Jan 17:10:174-178. doi: 10.1016/j.ijregi.2024.01.005. eCollection 2024 Mar.

Authors

Adedolapo B Olorunfemi^{1

2}, Salma A R Suliman³, Tung T Tran⁴, Babatunde Ayorinde^{5

6}, Muinah A Fowora^{5

6}, Bamidele A Iwalokun^{5

6}, Olugbenga A Olowe^{1

2}, Oluyinka O Opaleye^{1

2}, Mohamed Osman^{3

7}, Babatunde L Salako^{5

6}, Richard Adegbola^{5

6}, Bolaji N Thomas⁸, Srinivas Reddy Pallerla^{9

10}, Thirumalaisamy P Velavan^{4

10}, Olusola Ojurongbe^{1

2}

Affiliations

¹ Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria.
² Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria.
³ Institute of Endemic Diseases, University of Khartoum, Sudan.
⁴ Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam.
⁵ Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria.
⁶ Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria.
⁷ York Biomedical Research Institute, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
⁸ Department of Biomedical Sciences, College of Health Sciences and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA.
⁹ Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany.
¹⁰ Institute of Tropical Medicine, Universitätsklinikum Tübingen, Universität Tübingen, Germany.

Abstract

Objectives: The emergence and spread of SARS-CoV-2 have stimulated ongoing research into the virus transmission dynamics, circulating variants, and potential mutations. This study was conducted to understand the genomic dynamics of the epidemic in Nigeria.

Design: Whole genome sequencing was conducted on SARS-CoV-2 samples collected during the first and second outbreaks using the Oxford Nanopore MinION sequencing platform. Phylogenetic analysis was conducted, and genomes were grouped into different pangolin lineages.

Results: The study revealed four circulating SARS-CoV-2 variants. The Alpha (B.1.1.7) variant was the most prevalent (32.7%), followed by Beta (B.1 B.1.1, L.3, and B.1.1.318) (30.8%), Eta (B.1.525) (28.9%), and Delta (B.1.617, AY.1, AY.109, and AY.36) (7.7%). Phylogenetic analysis revealed three clusters with four Nextstrain clades (20I, 20B, 21D, and 21J). The Alpha lineages (B.1.1.7) clustered with references from Italy. The Beta lineages (Clade 20B) (B.11, B.11318, and L3) and sub-lineage B.11 were distinct. Sub-lineage B.11318 is clustered with references from the USA, whereas sub-lineage L3 is clustered with references from Russia, the Philippines, Australia, and Japan. The 21D and 21J, belonging to two Pango lineages, Eta (B.1525) and Delta (B.1.617 and AY.109), showed high genetic similarity.

Conclusion: The phylogenetic relatedness of the lineages suggests multiple virus introduction, which could be a source of more virulent, locally adapted variants.

Keywords: COVID-19; MinION; Nigeria; Pandemic; SARS-CoV-2; Whole genome sequencing.