Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria.
Olawoye IB., Oluniyi PE., Oguzie JU., Uwanibe JN., Kayode TA., Olumade TJ., Ajogbasile FV., Parker E., Eromon PE., Abechi P., Sobajo TA., Ugwu CA., George UE., Ayoade F., Akano K., Oyejide NE., Nosamiefan I., Fred-Akintunwa I., Adedotun-Sulaiman K., Brimmo FB., Adegboyega BB., Philip C., Adeleke RA., Chukwu GC., Ahmed MI., Ope-Ewe OO., Otitoola SG., Ogunsanya OA., Saibu MF., Sijuwola AE., Ezekiel GO., John OG., Akin-John JO., Akinlo OO., Fayemi OO., Ipaye TO., Nwodo DC., Omoniyi AE., Omwanghe IB., Terkuma CA., Okolie J., Ayo-Ale O., Ikponmwosa O., Benevolence E., Naregose GO., Patience AE., Blessing O., Micheal A., Jacqueline A., Aiyepada JO., Ebhodaghe P., Racheal O., Rita E., Rosemary GE., Solomon E., Anieno E., Edna Y., Chris AO., Donatus AI., Ogbaini-Emovon E., Tatfeng MY., Omunakwe HE., Bob-Manuel M., Ahmed RA., Onwuamah CK., Shaibu JO., Okwuraiwe A., Ataga AE., Bock-Oruma A., Daramola F., Yusuf IF., Fajola A., Ntia N-A., Ekpo JJ., Moses AE., Moore-Igwe BW., Fakayode OE., Akinola M., Kida IM., Oderinde BS., Wudiri ZW., Adeyemi OO., Akanbi OA., Ahumibe A., Akinpelu A., Ayansola O., Babatunde O., Omoare AA., Chukwu C., Mba NG., Omoruyi EC., Olisa O., Akande OK., Nwafor IE., Ekeh MA., Ndoma E., Ewah RL., Duruihuoma RO., Abu A., Odeh E., Onyia V., Ojide CK., Okoro S., Igwe D., Ogah EO., Khan K., Ajayi NA., Ugwu CN., Ukwaja KN., Ugwu NI., Abejegah C., Adedosu N., Ayodeji O., Liasu AA., Isamotu RO., Gadzama G., Petros BA., Siddle KJ., Schaffner SF., Akpede G., Erameh CO., Baba MM., Oladiji F., Audu R., Ndodo N., Fowotade A., Okogbenin S., Okokhere PO., Park DJ., Mcannis BL., Adetifa IM., Ihekweazu C., Salako BL., Tomori O., Happi AN., Folarin OA., Andersen KG., Sabeti PC., Happi CT.
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.