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

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.

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