Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria
Idowu B. Olawoye, Paul E. Oluniyi, Judith U. Oguzie, Jessica N. Uwanibe, Adeyemi T. Kayode, Testimony Olumade, Fehintola V. Ajogbasile, Edyth Parker, Philomena Eromon, Priscilla Abechi, Tope Sobajo, Chinedu Ugwu, Uwem E. George, Femi Ayoade, Kazeem Akano, Nicholas Oyejide, Iguosadolo Nosamiefan, Iyanuoluwa Fred-Akintunwa, Adedotun-Sulaiman Kemi, Farida Oluwabukola Brimmo, Babatunde B. Adegboyega, Courage Philip, Richard Adeleke, Grace C. Chukwu, Muhammad I. Ahmed, Oludayo O. Ope-ewe, Shobi G. Otitoola, Olusola Ogunsanya, Mudasiru F. Saibu, Ayotunde E. Sijuwola, Grace O. Ezekiel, Oluwagboadurami G. John, Julie O. Akin-John, Oluwasemilogo O. Akinlo, Olanrewaju O. Fayemi, Testimony O. Ipaye, Deborah C. Nwodo, Abolade E. Omoniyi, Iyobosa B. Omwanghe, Christabel A. Terkuma, Johnson Okolie, Olubukola Ayo-Ale, Ikponmwosa Odia, Benevolence Ebo, Grace O. Naregose, Akhilomen E. Patience, Osiemi Blessing, Airende Micheal, Jacqueline Agbukor, John Aiyepada, Paulson Ebhodaghe, Omiunu Racheal, Rita Esumeh, Giwa E. Rosemary, Solomon Ehikhametalor, Anieno Ekanem, Yerumoh Edna, Aire O. Chris, Adomeh Donatus, Ephraim Ogbaini-Emovon, Mirabeau Youtchou Tatfeng, Hannah E. Omunakwe, Mienye Bob-Manuel, Rahaman A. Ahmed, Chika Onwuamah, Joseph Ojonugwa Shaibu, Azuka Patrick Okwuraiwe, A. E. Ataga, Andrew Bock-Oruma, Funmi Daramola, Ibrahim F. Yusuf, Akinwumi Fajola, Nsikak-Abasi Ntia, Julie J. Ekpo, Anietie Moses, Beatrice W. Moore-Igwe, Oluwatosin Fakayode, Monilade Akinola, Ibrahim Musa Kida, Bamidele Soji Oderinde, Zara Wudiri, Oluwapelumi O. Adeyemi, Olusola Anuoluwapo Akanbi, Anthony Ahumibe, Afolabi Akinpelu, Oyeronke Ayansola, Olajumoke Babatunde, Adesuyi Ayodeji Omoare, Chimaobi Chukwu, Nwando G. Mba, Ewean Chukwuma Omoruyi, Olasunkanmi Olisa, Olatunji K. Akande, Ifeanyi Emmanuel Nwafor, Matthew A. Ekeh, Erim Ndoma, Richard L. Ewah, Rosemary O. Duruihuoma, Augustine Abu, Elizabeth Odeh
Abstract
Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates.