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 Adeyemi T. , Olumade Testimony J. , Ajogbasile Fehintola V. , Parker Edyth , Eromon Philomena E. , Abechi Priscilla , Sobajo Tope , Ugwu Chinedu , Uwem George , Ayoade Femi , Akano Kazeem , Oyejide Nicholas , Fred-Akintunwa Iyanuoluwa , Adedotun-Sulaiman Kemi , Brimmo Farida , Adegboyega Benjamin , Philip Courage , Adeleke Ayomide , Chukwu Grace C. , Muhammad Ahmed I. , Ope-ewe Oludayo O. , Otitoola Shobi , 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 Okonofua , Patience Akhilomen , Blessing Osiemi , Micheal Airende , Jacqueline Agbukor , John Aiyepada , Ebhodaghe Paulson , Racheal Omiunu , Rita Esumeh , Rosemary Giwa , Solomon Ehikhametalor , Anieno Ekanem , Edna Yerumoh , Chris Aire , Donatus Adomeh , Ogbaini Ephraim , Tatfeng Mirabeau Y. , Omunakwe Hannah E. , Bob-Manuel Mienye , Ahmed Rahaman , Onwuamah Chika , Shaibu Joseph , Okwuraiwe Azuka , Atage Anthony E. , Bock-Oruma Andrew , Daramola Funmi , Fajola Akinwumi , Ntia Nsikak-Abasi , Ekpo Julie J. , Moses Anietie , Moore-Igwe Worbianueri B. , Yusuf Ibrahim F. , Fakayode Enoch O. , Akinola Monilade , Kida Ibrahim , Oderinde Bamidele S. , Wudiri Zara , Adeyemi Olufemi O. , Akanbi Olusola , Ahumibe Anthony , Akinpelu Afolabi , Ayansola Oyeronke , Babatunde Olajumoke , Omoare Adesuyi , Chukwu Chimaobi , Mba Nwando , Omoruyi Ewean C. , Adeniji Johnson A. , Adewunmi Moses O. , Olayinka Oluseyi , Olasunkanmi Olisa , Akande Olatunji , Nwafor Ifeanyi , Ekeh Matthew , Ndoma Erim , Ewah Richard , Duruihuoma Rosemary , Abu Augustine , Odeh Elizabeth , Onyia Venatious , Ojide Kingsley C. , Okoro Sylvanus , Igwe Daniel , Khan Kamran , Ajayi Anthony N. , Ugwu Ebhodaghe Ngozi , Ugwu Collins N. , Ukwuaja Kingsley , Ogah Emeka O. , Abejegah Chukwuyem , Adedosu Nelson , Ayodeji Olufemi , Isamotu Rafiu O. , Gadzama Galadima , Petros Brittany , Siddle Katherine J. , Schaffner Stephen , Akpede George , Erameh Cyril Oshomah , Baba Marycelin , Oladiji Femi , Audu Rosemary , Ndodo Nnaemeka , Fowotade Adeola , Okogbenin Sylvanus , Okokhere Peter , Park Danny , Mcannis Bronwyn , Adetifa Ifedayo , Ihekweazu Chikwe , Salako Babatunde L. , Tomori Oyewale , Happi Anise N. , Folarin Onikepe A. , Andersen Kristian G. , Sabeti Pardis C. , Happi Christian T. 
Published: September 2022

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 B.1.1.318 and B.1.525 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 emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Our results show how regional connectivity in downsampled regions like Africa can often influence virus transmissions between neighbouring countries. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission in the region, generating actionable information for public health decision makers in the region.