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

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.

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, 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 and Christian T. Happi ()
Additional contact information
Idowu B. Olawoye: Redeemer’s University
Paul E. Oluniyi: Redeemer’s University
Judith U. Oguzie: Redeemer’s University
Jessica N. Uwanibe: Redeemer’s University
Tolulope A. Kayode: Redeemer’s University
Testimony J. Olumade: Redeemer’s University
Fehintola V. Ajogbasile: Redeemer’s University
Edyth Parker: The Scripps Research Institute
Philomena E. Eromon: Redeemer’s University
Priscilla Abechi: Redeemer’s University
Tope A. Sobajo: Redeemer’s University
Chinedu A. Ugwu: Redeemer’s University
Uwem E. George: Redeemer’s University
Femi Ayoade: Redeemer’s University
Kazeem Akano: Redeemer’s University
Nicholas E. Oyejide: Redeemer’s University
Iguosadolo Nosamiefan: Redeemer’s University
Iyanuoluwa Fred-Akintunwa: Redeemer’s University
Kemi Adedotun-Sulaiman: Redeemer’s University
Farida B. Brimmo: Redeemer’s University
Babatunde B. Adegboyega: Redeemer’s University
Courage Philip: Redeemer’s University
Richard A. Adeleke: Redeemer’s University
Grace C. Chukwu: Redeemer’s University
Muhammad I. Ahmed: Redeemer’s University
Oludayo O. Ope-Ewe: Redeemer’s University
Shobi G. Otitoola: Redeemer’s University
Olusola A. Ogunsanya: Redeemer’s University
Mudasiru F. Saibu: Redeemer’s University
Ayotunde E. Sijuwola: Redeemer’s University
Grace O. Ezekiel: Redeemer’s University
Oluwagboadurami G. John: Redeemer’s University
Julie O. Akin-John: Redeemer’s University
Oluwasemilogo O. Akinlo: Redeemer’s University
Olanrewaju O. Fayemi: Redeemer’s University
Testimony O. Ipaye: Redeemer’s University
Deborah C. Nwodo: Redeemer’s University
Abolade E. Omoniyi: Redeemer’s University
Iyobosa B. Omwanghe: Redeemer’s University
Christabel A. Terkuma: Redeemer’s University
Johnson Okolie: Redeemer’s University
Olubukola Ayo-Ale: Redeemer’s University
Odia Ikponmwosa: Irrua Specialist Teaching Hospital
Ebo Benevolence: Irrua Specialist Teaching Hospital
Grace O. Naregose: Irrua Specialist Teaching Hospital
Akhilomen E. Patience: Irrua Specialist Teaching Hospital
Osiemi Blessing: Irrua Specialist Teaching Hospital
Airende Micheal: Irrua Specialist Teaching Hospital
Agbukor Jacqueline: Irrua Specialist Teaching Hospital
John O. Aiyepada: Irrua Specialist Teaching Hospital
Paulson Ebhodaghe: Irrua Specialist Teaching Hospital
Omiunu Racheal: Irrua Specialist Teaching Hospital
Esumeh Rita: Irrua Specialist Teaching Hospital
Giwa E. Rosemary: Irrua Specialist Teaching Hospital
Ehikhametalor Solomon: Irrua Specialist Teaching Hospital
Ekanem Anieno: Irrua Specialist Teaching Hospital
Yerumoh Edna: Irrua Specialist Teaching Hospital
Aire O. Chris: Irrua Specialist Teaching Hospital
Adomeh I. Donatus: Irrua Specialist Teaching Hospital
Ephraim Ogbaini-Emovon: Irrua Specialist Teaching Hospital
Mirabeau Y. Tatfeng: Niger Delta University
Hannah E. Omunakwe: Rivers State University Teaching Hospital
Mienye Bob-Manuel: Rivers State University Teaching Hospital
Rahaman A. Ahmed: The Nigerian Institute of Medical Research
Chika K. Onwuamah: The Nigerian Institute of Medical Research
Joseph O. Shaibu: The Nigerian Institute of Medical Research
Azuka Okwuraiwe: The Nigerian Institute of Medical Research
Anthony E. Ataga: University of Port Harcourt
Andrew Bock-Oruma: Family Physician, SPDC
Funmi Daramola: Clinical Health, SPDC
Ibrahim F. Yusuf: Clinical Health, SPDC
Akinwumi Fajola: Regional Community Health, SPDC
Nsikak-Abasi Ntia: Occupational Health, SPDC
Julie J. Ekpo: University of Uyo
Anietie E. Moses: University of Uyo
Beatrice W. Moore-Igwe: Rivers State University
Oluwatosin E. Fakayode: Ministry of Health
Monilade Akinola: University of Maiduguri Teaching Hospital
Ibrahim M. Kida: University of Maiduguri Teaching Hospital
Bamidele S. Oderinde: University of Maiduguri Teaching Hospital
Zara W. Wudiri: University of Maiduguri Teaching Hospital
Oluwapelumi O. Adeyemi: University of Ilorin
Olusola A. Akanbi: Nigeria Centre for Disease Control
Anthony Ahumibe: Nigeria Centre for Disease Control
Afolabi Akinpelu: Nigeria Centre for Disease Control
Oyeronke Ayansola: Nigeria Centre for Disease Control
Olajumoke Babatunde: Nigeria Centre for Disease Control
Adesuyi A. Omoare: Nigeria Centre for Disease Control
Chimaobi Chukwu: Nigeria Centre for Disease Control
Nwando G. Mba: Nigeria Centre for Disease Control
Ewean C. Omoruyi: University of Ibadan
Olasunkanmi Olisa: University of Ibadan
Olatunji K. Akande: University of Ibadan
Ifeanyi E. Nwafor: Alex Ekwueme Federal University Teaching Hospital
Matthew A. Ekeh: Alex Ekwueme Federal University Teaching Hospital
Erim Ndoma: Alex Ekwueme Federal University Teaching Hospital
Richard L. Ewah: Alex Ekwueme Federal University Teaching Hospital
Rosemary O. Duruihuoma: Alex Ekwueme Federal University Teaching Hospital
Augustine Abu: Alex Ekwueme Federal University Teaching Hospital
Elizabeth Odeh: Alex Ekwueme Federal University Teaching Hospital
Venatius Onyia: Alex Ekwueme Federal University Teaching Hospital
Chiedozie K. Ojide: Alex Ekwueme Federal University Teaching Hospital
Sylvanus Okoro: Alex Ekwueme Federal University Teaching Hospital
Daniel Igwe: Alex Ekwueme Federal University Teaching Hospital
Emeka O. Ogah: Alex Ekwueme Federal University Teaching Hospital
Kamran Khan: University of Toronto
Nnennaya A. Ajayi: Alex Ekwueme Federal University Teaching Hospital
Collins N. Ugwu: Alex Ekwueme Federal University Teaching Hospital
Kingsley N. Ukwaja: Alex Ekwueme Federal University Teaching Hospital
Ngozi I. Ugwu: Alex Ekwueme Federal University Teaching Hospital
Chukwuyem Abejegah: Federal Medical Center
Nelson Adedosu: Federal Medical Center
Olufemi Ayodeji: Federal Medical Center
Ahmed A. Liasu: Federal Medical Center
Rafiu O. Isamotu: Ministry of Health
Galadima Gadzama: University of Maiduguri Teaching Hospital
Brittany A. Petros: Broad Institute of Harvard and MIT
Katherine J. Siddle: Broad Institute of Harvard and MIT
Stephen F. Schaffner: Broad Institute of Harvard and MIT
George Akpede: Irrua Specialist Teaching Hospital
Cyril Oshomah Erameh: Irrua Specialist Teaching Hospital
Marycelin M. Baba: University of Maiduguri Teaching Hospital
Femi Oladiji: University of Ilorin
Rosemary Audu: The Nigerian Institute of Medical Research
Nnaemeka Ndodo: Nigeria Centre for Disease Control
Adeola Fowotade: Alex Ekwueme Federal University Teaching Hospital
Sylvanus Okogbenin: Irrua Specialist Teaching Hospital
Peter O. Okokhere: Irrua Specialist Teaching Hospital
Danny J. Park: Broad Institute of Harvard and MIT
Bronwyn L. Mcannis: Broad Institute of Harvard and MIT
Ifedayo M. Adetifa: Nigeria Centre for Disease Control
Chikwe Ihekweazu: Nigeria Centre for Disease Control
Babatunde L. Salako: The Nigerian Institute of Medical Research
Oyewale Tomori: Redeemer’s University
Anise N. Happi: Redeemer’s University
Onikepe A. Folarin: Redeemer’s University
Kristian G. Andersen: The Scripps Research Institute
Pardis C. Sabeti: Broad Institute of Harvard and MIT
Christian T. Happi: Redeemer’s University

Nature Communications, 2023, vol. 14, issue 1, 1-10

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-36449-5

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