Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria
Authors: Olawoye Idowu B. , Oluniyi Paul E. , Oguzie Judith U. , Uwanibe Jessica N. , Kayode Tolulope A. , Olumade Testimony J. , Ajogbasile Fehintola V. , Parker Edyth , Eromon Philomena E. , Abechi Priscilla , Sobajo Tope A. , Ugwu Chinedu A. , George Uwem E. , Ayoade Femi , Akano Kazeem , Oyejide Nicholas E. , Nosamiefan Iguosadolo , Fred-Akintunwa Iyanuoluwa , Adedotun-Sulaiman Kemi , Brimmo Farida B. , Adegboyega Babatunde B. , Philip Courage , Adeleke Richard A. , Chukwu Grace C. , Ahmed Muhammad I. , Ope-Ewe Oludayo O. , Otitoola Shobi G. , Ogunsanya Olusola A. , Saibu Mudasiru F. , Sijuwola Ayotunde E. , Ezekiel Grace O. , John Oluwagboadurami G. , Akin-John Julie O. , Akinlo Oluwasemilogo O. , Fayemi Olanrewaju O. , Ipaye Testimony O. , Nwodo Deborah C. , Omoniyi Abolade E. , Omwanghe Iyobosa B. , Terkuma Christabel A. , Okolie Johnson , Ayo-Ale Olubukola , Ikponmwosa Odia , Benevolence Ebo , Naregose Grace O. , Patience Akhilomen E. , Blessing Osiemi , Micheal Airende , Jacqueline Agbukor , Aiyepada John O. , Ebhodaghe Paulson , Racheal Omiunu , Rita Esumeh , Rosemary Giwa E. , Solomon Ehikhametalor , Anieno Ekanem , Edna Yerumoh , Chris Aire O. , Donatus Adomeh I. , Ogbaini-Emovon Ephraim , Tatfeng Mirabeau Y. , Omunakwe Hannah E. , Bob-Manuel Mienye , Ahmed Rahaman A. , Onwuamah Chika K. , Shaibu Joseph O. , Okwuraiwe Azuka , Ataga Anthony E. , Bock-Oruma Andrew , Daramola Funmi , Yusuf Ibrahim F. , Fajola Akinwumi , Ntia Nsikak-Abasi , Ekpo Julie J. , Moses Anietie E. , Moore-Igwe Beatrice W. , Fakayode Oluwatosin E. , Akinola Monilade , Kida Ibrahim M. , Oderinde Bamidele S. , Wudiri Zara W. , Adeyemi Oluwapelumi O. , Akanbi Olusola A. , Ahumibe Anthony , Akinpelu Afolabi , Ayansola Oyeronke , Babatunde Olajumoke , Omoare Adesuyi A. , Chukwu Chimaobi , Mba Nwando G. , Omoruyi Ewean C. , Olisa Olasunkanmi , Akande Olatunji K. , Nwafor Ifeanyi E. , Ekeh Matthew A. , Ndoma Erim , Ewah Richard L. , Duruihuoma Rosemary O. , Abu Augustine , Odeh Elizabeth , Onyia Venatius , Ojide Chiedozie K. , Okoro Sylvanus , Igwe Daniel , Ogah Emeka O. , Khan Kamran , Ajayi Nnennaya A. , Ugwu Collins N. , Ukwaja Kingsley N. , Ugwu Ngozi I. , Abejegah Chukwuyem , Adedosu Nelson , Ayodeji Olufemi , Liasu Ahmed A. , Isamotu Rafiu O. , Gadzama Galadima , Petros Brittany A. , Siddle Katherine J. , Schaffner Stephen F. , Akpede George , Erameh Cyril Oshomah , Baba Marycelin M. , Oladiji Femi , Audu Rosemary , Ndodo Nnaemeka , Fowotade Adeola , Okogbenin Sylvanus , Okokhere Peter O. , Park Danny J. , Mcannis Bronwyn L. , Adetifa Ifedayo M. , Ihekweazu Chikwe , Salako Babatunde L. , Tomori Oyewale , Happi Anise N. , Folarin Onikepe A. , Andersen Kristian G. , Sabeti Pardis C. , Happi Christian T. 
Published: February 2023

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.