Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria

Olawoye, Idowu B.; Oluniyi, Paul E.; Oguzie, Judith; Uwanibe, Jessica N.; Kayode, Adeyemi T.; Olumade, Testimony; Ajogbasile, Fehintola V.; Parker, Edyth; Eromon, Philomena; Abechi, Priscilla; Sobajo, Tope; Ugwu, Chinedu; George, Uwem; Ayoade, Femi; Akano, Kazeem; Oyejide, Nicholas E.; Nosamiefan, Iguosadolo; Fred-Akintunwa, Iyanuoluwa; Kemi, Adedotun-Sulaiman; Brimmo, Farida; Adegboyega, Babatunde B.; Philip, Courage; Adeleke, Richard Ayomide; Chukwu, Grace Chizaramu; Ahmed, Muhammad I.; Ope-ewe, Oludayo Oluwaseyi; Otitoola, Shobi; Ogunsanya, Olusola A.; Saibu, Mudasiru F.; Sijuwola, Ayotunde E.; Ezekiel, Grace Opemipo; John, Oluwagboadurami G.; Akin-John, Julie Oreoluwa; Akinlo, Oluwasemilogo Oluwasekunolami; Fayemi, Olanrewaju O.; Ipaye, Testimony Oluwatise; Nwodo, Deborah Chisom; Omoniyi, Abolade Esther; Omwanghe, Iyobosa B.; Terkuma, Christabel Anamuma; Okolie, Johnson; Ayo-Ale, Olubukola; Odia, Ikponmwosa; Ebo, Benevolence; Naregose, Grace O.; Patience, Akhilomen E.; Blessing, Osiemi; Micheal, Airende; Agbukor, Jacqueline; Aiyepada, John; Ebhodaghe, Paulson; Omiunu, Racheal; Rita, Esumeh; Rosemary, Giwa E.; Ehikhametalor, Solomon; Anieno, Ekanem; Edna, Yerumoh; Chris, Aire O.; Donatus, Adomeh; Ogbaini-Emovon, Ephraim; Tatfeng, Mirabeau Youtchou; Omunakwe, Hannah E; Bob-Manuel, Mienye; Ahmed, Rahaman A.; Onwuamah, Chika; Shaibu, Joseph Ojonugwa; Okuruawe, Azuka; Ataga, A. E.; Bock-Oruma, Andrew; Daramola, Funmi; Yusuf, Ibrahim F.; Fajola, Akinwumi; Ntia, Nsikak-Abasi; Ekpo, Julie J.; Moses, Anietie; Moore-Igwe, Beatrice W.; Fakayode, Oluwatosin; Akinola, Monilade; Kida, Ibrahim Musa; Oderinde, Bamidele Soji; Wudiri, Zara; Adeyemi, Oluwapelumi O.; Akanbi, Olusola Anuoluwapo; Ahumibe, Anthony; Akinpelu, Afolabi; Ayansola, Oyeronke; Babatunde, Olajumoke; Omoare, Adesuyi A.; Chukwu, Chimaobi; Nwando, G.; Omoruyi, Ewean Chukwuma; Olisa, Olasunkanmi; Akande, Olatunji K.; Nwafor, Ifeanyi Emmanuel; Ekeh, Matthew; Ndoma, Erim; Ewah, Richard; Duruihuoma, Rosemary O.; Abu, Augustine; Odeh, Elizabeth; Onyia, Venatius; Ojide, Chiedozie Kingsley; Okoro, Sylvanus; Igwe, Daniel; Ogah, Emeka Onwe; Khan, Kamran; Ajayi, Nnennaya A.; Ugwu, Collins Nwachi; Ukwaja, Kingsley Nnanna; Ugwu, Ngozi Immaculata; Abejegah, Chukwuyem; Adedosu, Nelson; Ayodeji, Oladele Oluwafemi; Liasu, Ahmed A.; Isamotu, Rafiu Olasunkanmi; Gadzama, Galadima; Petros, Brittany A.; Siddle, Katherine J.; Schaffner, Stephen F.; Akpede, George O.; Erameh, Cyril; Baba, Marycelin; Oladiji, Femi; Audu, Rosemary; Ndodo, Nnaemeka; Fowotade, Adeola; Sylvanus, Okogbenin; Okokhere, Peter O; Park, Danny; MacInnis, Bronwyn; Adetifa, Ifedayo; Ihekweazu, Chikwe; Salako, Babatunde Lawal; Blumberg, Lucille; Happi, Anise N.; Folarin, Onikepe A.; Andersen, Kristian G.; Sabeti, Pardis C.; Happi, Christian T.

doi:10.1038/s41467-023-36449-5

Cited by 13 publications

(7 citation statements)

References 54 publications

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“…Shortly after its detection, sub-variants BA4 and BA5 were identified in South Africa [ 12 ]. Elsewhere on the continent, A23.1 was detected in Uganda and Rwanda [ 13 ] and B.1.525 in Nigeria [ 14 ]. In addition, A.30 was originally detected in Angola but is thought to originate in Tanzania [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022

Sisay

Tshiabuila

Wyk

et al. 2023

Genes

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Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499,000 cases, and ~7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was outcompeted by the Delta variant. Notably, Ethiopia’s lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia’s role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.

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Section: Introductionmentioning

confidence: 99%

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022

Sisay

Tshiabuila

Wyk

et al. 2023

Genes

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“…Interestingly, September and October of 2020 also have a high prevalence of clade 20D (B.1.1.1), peaking at above 25% frequency despite never reaching more than 2% globally. Subsequently, in January of 2021, we see the emergence of the Alpha VOC in the region, followed by the introduction of the 21D clade (Eta VOI) that was highly prevalent in West Africa at this time [ 26 – 28 ]. The Delta variant emerged in May of 2021 and became dominant by July ( Fig 1D ).…”

Section: Resultsmentioning

confidence: 99%

Genomic characterization of SARS-CoV-2 in Guinea, West Africa

Sow,

Togo,

Simons

et al. 2024

PLoS ONE

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SARS-CoV-2 has claimed several million lives since its emergence in late 2019. The ongoing evolution of the virus has resulted in the periodic emergence of new viral variants with distinct fitness advantages, including enhanced transmission and immune escape. While several SARS-CoV-2 variants of concern trace their origins back to the African continent—including Beta, Eta, and Omicron–most countries in Africa remain under-sampled in global genomic surveillance efforts. In an effort to begin filling these knowledge gaps, we conducted retrospective viral genomic surveillance in Guinea from October 2020 to August 2021. We found that SARS-CoV-2 clades 20A, 20B, and 20C dominated throughout 2020 until the coincident emergence of the Alpha and Eta variants of concern in January 2021. The Alpha variant remained dominant throughout early 2021 until the arrival of the Delta variant in July. Surprisingly, despite the small sample size of our study, we also found the persistence of the early SARS-CoV-2 clade 19B as late as April 2021. Together, these data help fill in our understanding of the SARS-CoV-2 population dynamics in West Africa early in the COVID-19 pandemic.

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“…Nigeria experienced four major waves of COVID-19 to date. Wave one was from February 2020 to August 2020 and was dominated by the ancestral Wuhan strain (D614G), wave two from September 2020 to March 2021, was dominated by the eta and alpha variants, while the delta variant was the dominant wave three and lasted from April 2021 to November 2021 ( 13 ). Wave four, the omicron wave, began in December 2021 until today ( Figure 3A ).…”

Section: Resultsmentioning

confidence: 99%

Immunological insights into COVID-19 in Southern Nigeria

Ugwu,

Alao,

John

et al. 2024

Front. Immunol.

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IntroductionOne of the unexpected outcomes of the COVID-19 pandemic was the relatively low levels of morbidity and mortality in Africa compared to the rest of the world. Nigeria, Africa's most populous nation, accounted for less than 0.01% of the global COVID-19 fatalities. The factors responsible for Nigeria's relatively low loss of life due to COVID-19 are unknown. Also, the correlates of protective immunity to SARS-CoV-2 and the impact of pre-existing immunity on the outcome of the COVID-19 pandemic in Africa are yet to be elucidated. Here, we evaluated the natural and vaccine-induced immune responses from vaccinated, non-vaccinated and convalescent individuals in Southern Nigeria throughout the three waves of the COVID-19 pandemic in Nigeria. We also examined the pre-existing immune responses to SARS-CoV-2 from samples collected prior to the COVID-19 pandemic.MethodsWe used spike RBD and N- IgG antibody ELISA to measure binding antibody responses, SARS-CoV-2 pseudotype assay protocol expressing the spike protein of different variants (D614G, Delta, Beta, Omicron BA1) to measure neutralizing antibody responses and nucleoprotein (N) and spike (S1, S2) direct ex vivo interferon gamma (IFNγ) T cell ELISpot to measure T cell responses. ResultOur study demonstrated a similar magnitude of both binding (N-IgG (74% and 62%), S-RBD IgG (70% and 53%) and neutralizing (D614G (49% and 29%), Delta (56% and 47%), Beta (48% and 24%), Omicron BA1 (41% and 21%)) antibody responses from symptomatic and asymptomatic survivors in Nigeria. A similar magnitude was also seen among vaccinated participants. Interestingly, we revealed the presence of preexisting binding antibodies (N-IgG (60%) and S-RBD IgG (44%)) but no neutralizing antibodies from samples collected prior to the pandemic. DiscussionThese findings revealed that both vaccinated, non-vaccinated and convalescent individuals in Southern Nigeria make similar magnitude of both binding and cross-reactive neutralizing antibody responses. It supported the presence of preexisting binding antibody responses among some Nigerians prior to the COVID-19 pandemic. Lastly, hybrid immunity and heterologous vaccine boosting induced the strongest binding and broadly neutralizing antibody responses compared to vaccine or infection-acquired immunity alone.

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Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria

Cited by 13 publications

References 54 publications

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022

Genomic characterization of SARS-CoV-2 in Guinea, West Africa

Immunological insights into COVID-19 in Southern Nigeria

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