Author:
Parker Edyth,Omah Ifeanyi F.,Varilly Patrick,Magee Andrew,Ayinla Akeemat Opeyemi,Sijuwola Ayotunde E.,Ahmed Muhammad I.,Ope-ewe Oludayo O.,Ogunsanya Olusola Akinola,Olono Alhaji,Eromon Philomena,Tomkins-Tinch Christopher H,Otieno James Richard,Akanbi Olusola,Egwuenu Abiodun,Ehiakhamen Odianosen,Chukwu Chimaobi,Suleiman Kabiru,Akinpelu Afolabi,Ahmad Adama,Imam Khadijah Isa,Ojedele Richard,Oripenaye Victor,Ikeata Kenneth,Adelakun Sophiyah,Olajumoke Babatunde,Djuicy Delia Doreen,Messanga Essengue Loique Landry,Moumbeket Yifomnjou Moïse Henri,Zeller Mark,Gangavarapu Karthik,O’Toole Áine,Park Daniel J,Mboowa Gerald,Tessema Sofonias Kifle,Tebeje Yenew Kebede,Folarin Onikepe,Happi Anise,Lemey Philippe,Suchard Marc A,Andersen Kristian G.,Sabeti Pardis,Rambaut Andrew,Njoum Richard,Ihekweazu Chikwe,Jide Idriss,Adetifa Ifedayo,Happi Christian T
Abstract
Five years before the 2022–2023 global mpox outbreak Nigeria reported its first cases in nearly 40 years, with the ongoing epidemic since driven by sustained human-to-human transmission. However, limited genomic data has left questions about the timing and origin of the mpox virus’ (MPXV) emergence. Here we generated 112 MPXV genomes from Nigeria from 2021-2023. We identify the closest zoonotic outgroup to the human epidemic in southern Nigeria, and estimate that the lineage transmitting from human-to-human emerged around July 2014, circulating cryptically until detected in September 2017. The epidemic originated in Southern Nigeria, particularly Rivers State, which also acted as a persistent and dominant source of viral dissemination to other states. We show that APOBEC3 activity increased MPXV’s evolutionary rate twenty-fold during human-to-human transmission. We also show how Delphy, a tool for near-real-time Bayesian phylogenetics, can aid rapid outbreak analytics. Our study sheds light on MPXV’s establishment in West Africa before the 2022–2023 global outbreak and highlights the need for improved pathogen surveillance and response.
Publisher
Cold Spring Harbor Laboratory