Geographic Structuring and Divergence Time Frame of Monkeypox Virus in the Endemic Region.
Orthopoxvirus
molecular dating
monkeypox virus
population structure
Journal
The Journal of infectious diseases
ISSN: 1537-6613
Titre abrégé: J Infect Dis
Pays: United States
ID NLM: 0413675
Informations de publication
Date de publication:
28 03 2023
28 03 2023
Historique:
received:
09
03
2022
accepted:
12
07
2022
medline:
29
3
2023
pubmed:
15
7
2022
entrez:
14
7
2022
Statut:
ppublish
Résumé
Monkeypox is an emerging zoonosis endemic to Central and West Africa. Monkeypox virus (MPXV) is genetically structured in 2 major clades (clades 1 and 2/3), but its evolution is poorly explored. We retrieved MPXV genomes from public repositories and we analyzed geographic patterns using STRUCTURE. Molecular dating was performed using a using a Bayesian approach. We show that the population transmitted in West Africa (clades 2/3) experienced limited drift. Conversely, clade 1 (transmitted in the Congo Basin) possibly underwent a bottleneck or founder effect. Depending on the model used, we estimated that the 2 clades separated ∼560-860 (highest posterior density: 450-960) years ago, a period characterized by expansions and contractions of rainforest areas, possibly creating the ecological conditions for the MPXV reservoir(s) to migrate. In the Congo Basin, MPXV diversity is characterized by 4 subpopulations that show no geographic structuring. Conversely, clades 2/3 are spatially structured with 2 populations located West and East of the Dahomey Gap. The distinct histories of the 2 clades may derive from differences in MPXV ecology in West and Central Africa.
Sections du résumé
BACKGROUND
Monkeypox is an emerging zoonosis endemic to Central and West Africa. Monkeypox virus (MPXV) is genetically structured in 2 major clades (clades 1 and 2/3), but its evolution is poorly explored.
METHODS
We retrieved MPXV genomes from public repositories and we analyzed geographic patterns using STRUCTURE. Molecular dating was performed using a using a Bayesian approach.
RESULTS
We show that the population transmitted in West Africa (clades 2/3) experienced limited drift. Conversely, clade 1 (transmitted in the Congo Basin) possibly underwent a bottleneck or founder effect. Depending on the model used, we estimated that the 2 clades separated ∼560-860 (highest posterior density: 450-960) years ago, a period characterized by expansions and contractions of rainforest areas, possibly creating the ecological conditions for the MPXV reservoir(s) to migrate. In the Congo Basin, MPXV diversity is characterized by 4 subpopulations that show no geographic structuring. Conversely, clades 2/3 are spatially structured with 2 populations located West and East of the Dahomey Gap.
CONCLUSIONS
The distinct histories of the 2 clades may derive from differences in MPXV ecology in West and Central Africa.
Identifiants
pubmed: 35831941
pii: 6643513
doi: 10.1093/infdis/jiac298
pmc: PMC10044091
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
742-751Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of the Infectious Diseases Society of America.
Déclaration de conflit d'intérêts
Potential conflicts of interest. All authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest.
Références
Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16262-7
pubmed: 20805472
Philos Trans R Soc Lond B Biol Sci. 2020 Nov 23;375(1812):20190572
pubmed: 33012235
Nat Microbiol. 2020 Jul;5(7):955-965
pubmed: 32341480
Emerg Infect Dis. 2013 Feb;19(2):237-45
pubmed: 23347770
Bioinformatics. 2000 Sep;16(9):847-8
pubmed: 11108709
Ann Intern Med. 2022 Aug;175(8):1175-1176
pubmed: 35605243
Curr Biol. 2016 Dec 19;26(24):3407-3412
pubmed: 27939314
Nat Med. 2022 Aug;28(8):1569-1572
pubmed: 35750157
Sci Rep. 2021 Jun 22;11(1):13085
pubmed: 34158533
Genetics. 2000 Jun;155(2):945-59
pubmed: 10835412
Curr Biol. 2021 Nov 8;31(21):4689-4696.e5
pubmed: 34478645
Science. 2020 Jul 24;369(6502):
pubmed: 32703849
J Virol. 2011 Sep;85(18):9527-42
pubmed: 21752919
Lancet Infect Dis. 2019 Aug;19(8):872-879
pubmed: 31285143
Theor Popul Biol. 1975 Apr;7(2):256-76
pubmed: 1145509
Viruses. 2017 Oct 03;9(10):
pubmed: 28972544
Viruses. 2015 Apr 22;7(4):2168-84
pubmed: 25912718
Proc Natl Acad Sci U S A. 1979 Oct;76(10):5269-73
pubmed: 291943
R Soc Open Sci. 2018 Jan 31;5(1):171089
pubmed: 29410823
Methods Ecol Evol. 2016 Jan;7(1):80-89
pubmed: 27110344
Virus Evol. 2018 Jun 08;4(1):vey016
pubmed: 29942656
Mol Ecol. 2005 Jul;14(8):2611-20
pubmed: 15969739
Emerg Infect Dis. 2014 Feb;20(2):232-9
pubmed: 24457084
PLoS Negl Trop Dis. 2019 Oct 16;13(10):e0007791
pubmed: 31618206
Emerg Infect Dis. 2014 Jun;20(6):1009-11
pubmed: 24857667
PLoS Negl Trop Dis. 2022 Feb 11;16(2):e0010141
pubmed: 35148313
Emerg Infect Dis. 2006 Dec;12(12):1827-33
pubmed: 17326932
Vaccine. 2020 Jul 14;38(33):5077-5081
pubmed: 32417140
Virology. 2005 Sep 15;340(1):46-63
pubmed: 16023693
Mol Biol Evol. 2018 Jan 1;35(1):247-251
pubmed: 29029186
Lancet Infect Dis. 2022 Jul;22(7):941-942
pubmed: 35690074
Front Public Health. 2018 Sep 04;6:241
pubmed: 30234087
Nat Rev Microbiol. 2019 May;17(5):321-328
pubmed: 30518814
J Gen Virol. 2005 Oct;86(Pt 10):2661-2672
pubmed: 16186219
J Virol. 2016 Jul 27;90(16):7184-95
pubmed: 27252529
J Infect Dis. 2022 Apr 19;225(8):1367-1376
pubmed: 32880628
Trends Ecol Evol. 2019 May;34(5):474-486
pubmed: 30904189
Genetics. 1989 Nov;123(3):585-95
pubmed: 2513255
Lancet Infect Dis. 2018 Mar;18(3):246
pubmed: 29361427
Mol Ecol Resour. 2017 Sep;17(5):981-990
pubmed: 28028941
Microbiol Resour Announc. 2020 Mar 5;9(10):
pubmed: 32139560
Mol Biol Evol. 2014 Jul;31(7):1929-36
pubmed: 24739305
Viruses. 2020 Dec 30;13(1):
pubmed: 33396609
Genetics. 2003 Aug;164(4):1567-87
pubmed: 12930761