Evidence map›Paper›PMID 38947052›Full record

ArticlemedRxiv : the preprint server for health sciences2024

Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans.

Edyth Parker, Ifeanyi F Omah, Patrick Varilly, Andrew Magee, Akeemat Opeyemi Ayinla, Ayotunde E Sijuwola, Muhammad I Ahmed, Oludayo O Ope-Ewe, Olusola Akinola Ogunsanya, Alhaji Olono and 38 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

48 authors.

Edyth ParkerAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
Ifeanyi F OmahInstitute of Ecology and Evolution, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FL, UK.
Patrick VarillyThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Andrew MageeDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Akeemat Opeyemi AyinlaAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
Ayotunde E SijuwolaAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
Muhammad I AhmedAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
Oludayo O Ope-EweAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
Olusola Akinola OgunsanyaAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
Alhaji OlonoAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
Philomena EromonAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
Christopher H Tomkins-TinchThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
James Richard OtienoTheiagen Genomics, Highlands Ranch, CO, USA.
Olusola AkanbiNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Abiodun EgwuenuNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Odianosen EhiakhamenNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Chimaobi ChukwuNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Kabiru SuleimanNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Afolabi AkinpeluNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Adama AhmadNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Khadijah Isa ImamNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Richard OjedeleNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Victor OripenayeNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Kenneth IkeataNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Sophiyah AdelakunNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Babatunde OlajumokeNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Delia Doreen DjuicyVirology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274.
Loique Landry Messanga EssengueVirology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274.
Moïse Henri Moumbeket YifomnjouVirology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274.
Mark ZellerDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
Karthik GangavarapuDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
Áine O'TooleInstitute of Ecology and Evolution, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FL, UK.
Daniel J ParkThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Gerald MboowaAfrica Centres for Disease Control and Prevention, P.O. Box 3243, Addis Ababa, Ethiopia.
Sofonias Kifle TessemaAfrica Centres for Disease Control and Prevention, P.O. Box 3243, Addis Ababa, Ethiopia.
Yenew Kebede TebejeAfrica Centres for Disease Control and Prevention, P.O. Box 3243, Addis Ababa, Ethiopia.
Onikepe FolarinAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
Anise HappiAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
Philippe LemeyDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
Marc A SuchardDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Kristian G AndersenDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
Pardis SabetiThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Andrew RambautInstitute of Ecology and Evolution, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FL, UK.
Richard NjoumVirology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274.
Chikwe IhekweazuNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Idriss JideNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Ifedayo AdetifaNigeria Centre for Disease Control and Prevention, Abuja, Nigeria.
Christian T HappiAfrican Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI SABETI, PARDIS CHRISTINE · 2014 to 2024
$66.5M
Technology CoreU19AI135995 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Kristian Graugaard Andersen · 2018 to 2026
$32.0M
West African Emerging Infectious Disease Research Center (WA-EIDRC)U01AI151812 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI ANDERSEN, KRISTIAN GRAUGAARD, GARRY, ROBERT F · 2020 to 2024
$13.2M
Utilize Microbial Metagenomics for Viral Pathogen CharacterizationU54HG007480 · NHGRI · REDEEMER'S UNIVERSITY · PI HAPPI, CHRISTIAN T. · 2017 to 2022
$5.5M
Fast and flexible Bayesian phylogenetics via modern machine learningR01AI162611 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI MATSEN, FREDERICK ALBERT · 2021 to 2025
$3.8M
Statistical Innovation to Integrate Sequences and Phenotypes for Scalable Phylodynamic InferenceR01AI153044 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Marc A. Suchard · 2021 to 2026
$2.4M
Host and Microbial Genetic Determinants of Febrile Illness in West AfricaU01HG007480 · NHGRI · REDEEMER'S UNIVERSITY · PI HAPPI, CHRISTIAN T. · 2013 to 2016
$1.6M
NHGRI NIH HHS U01 HG007480NHGRI NIH HHS U54 HG007480NIAID NIH HHS R01 AI153044NIAID NIH HHS R01 AI162611NIAID NIH HHS U01 AI151812NIAID NIH HHS U19 AI110818NIAID NIH HHS U19 AI135995Wellcome Trust
6 · The paper itself

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.

Identifiers

PMID38947052
PMCPMC11213064

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.