Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans
Parker, E.; Omah, I.; Varilly, P.; Magee, A.; Ayinla, A. O.; Sijuwola, A. E.; Ahmed, M. I.; Ope-Ewe, O. O.; Ogunsanya, O. A.; Olono, A.; Eromon, P.; Tomkins-Tinch, C. H.; Otieno, J. R.; Akanbi, O.; Egwuenu, A.; Ehiakhamen, O.; Chukwu, C.; Suleiman, K.; Akinpelu, A.; Ahmad, A.; Imam, K. I.; Ojedele, R.; Oripenaye, V.; Ikeata, K.; Adelakun, S.; Olajumoke, B.; Essengue, L. L. M.; Djuicy, D. D.; Yifomnjou, M. H. M.; Zeller, M.; Gangavarapu, K.; O'Toole, A.; Park, D.; Mbowa, G.; Kiffle Tessema, S.; Tebeje, Y. K.; Folarin, O.; Happi, A.; Lemey, P.; Suchard, M. A.; Andersen, K. G.; Sabeti, P.; Rambau
10.1101/2024.06.18.24309104 medRxivShow 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 MPXVs 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 MPXVs establishment in West Africa before the 2022-2023 global outbreak and highlights the need for improved pathogen surveillance and response.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria 97%
- Predicting the evolution of Lassa Virus endemic area and population at risk over the next decades 96%
- Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential 95%
Similar papers in this journal
- High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study 95%
- Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa 95%
- Identification of a molnupiravir-associated mutational signature in SARS-CoV-2 sequencing databases 94%
Similar papers in this journal
- Persistence of SARS-CoV-2 immunity, Omicron’s footprints, and projections of epidemic resurgences in South African population cohorts 95%
- Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria 94%
- Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data 93%
Similar papers in this journal
- Unrecognized introductions of SARS-CoV-2 into the state of Georgia shaped the early epidemic 95%
- Emerging phylogenetic structure of the SARS-CoV-2 pandemic 95%
- Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.