{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T21:05:19Z","timestamp":1784840719549,"version":"3.55.0"},"reference-count":16,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T00:00:00Z","timestamp":1772236800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Mpox is a zoonosis caused by the monkeypox virus. Here, we report Mali\u2019s index Mpox case, which was clinically identified at the Mali\u2013Guinea border by the national telemedicine center and confirmed by PCR. The library prepared with NextGenPCR\u2122 MPXV Sequencing Library Prep and sequenced on Minion MK1C revealed a genome length of 197,122 bp with an average depth of 1284.4\u00d7. The strain belonged to Clade IIb G1 lineage and exhibited 85 mutations relative to NC_063383.1. To decipher genomic epidemiology, genomes \u2265 195 kb were retrieved from NCBI and aligned with MAFFT. Time-resolved phylogenetic reconstruction and ancestral trait inference were performed with TreeTime v0.11.4. A median joining network was built with Popart v1.7. Phylogeographic analysis revealed clustering with Clade IIb (G.1 lineage) linked to the May 2025 outbreak in Sierra Leone.<\/jats:p>","DOI":"10.3390\/v18030294","type":"journal-article","created":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T14:55:01Z","timestamp":1772463301000},"page":"294","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genomic Characterization of the Index Case of Human Monkeypox Virus Infection in Mali, 2025"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7138-6164","authenticated-orcid":false,"given":"Noumou Yakhouba","family":"Keita","sequence":"first","affiliation":[{"name":"Institut National de Sant\u00e9 Pulique, Hippodrome Route de Koulikoro Rue 235 Porte 52, Bamako BP 1771, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahamadou","family":"Abdou","sequence":"additional","affiliation":[{"name":"Institut National de Sant\u00e9 Pulique, Hippodrome Route de Koulikoro Rue 235 Porte 52, Bamako BP 1771, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed","family":"Ag Bara\u00efka","sequence":"additional","affiliation":[{"name":"Institut National de Sant\u00e9 Pulique, Hippodrome Route de Koulikoro Rue 235 Porte 52, Bamako BP 1771, Mali"},{"name":"Faculty of Pharmacy, Universit\u00e9 des Sciences des Techniques et des Technologies de Bamako, Point G Campus, Bamako BP 1805, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8008-3517","authenticated-orcid":false,"given":"Klema Marcel","family":"Kone","sequence":"additional","affiliation":[{"name":"Institut National de Sant\u00e9 Pulique, Hippodrome Route de Koulikoro Rue 235 Porte 52, Bamako BP 1771, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8868-9483","authenticated-orcid":false,"given":"Ousmane","family":"Kamena","sequence":"additional","affiliation":[{"name":"Institut National de Sant\u00e9 Pulique, Hippodrome Route de Koulikoro Rue 235 Porte 52, Bamako BP 1771, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elysabette","family":"Coulibaly","sequence":"additional","affiliation":[{"name":"Institut National de Sant\u00e9 Pulique, Hippodrome Route de Koulikoro Rue 235 Porte 52, Bamako BP 1771, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariam Sama","family":"Sangare","sequence":"additional","affiliation":[{"name":"Institut National de Sant\u00e9 Pulique, Hippodrome Route de Koulikoro Rue 235 Porte 52, Bamako BP 1771, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Korika","family":"Diakite","sequence":"additional","affiliation":[{"name":"Institut National de Sant\u00e9 Pulique, Hippodrome Route de Koulikoro Rue 235 Porte 52, Bamako BP 1771, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dorcas Waruguru","family":"Wanjohi","sequence":"additional","affiliation":[{"name":"Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa P.O. Box 3243, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boubacar","family":"Doumbia","sequence":"additional","affiliation":[{"name":"Institut National de Sant\u00e9 Pulique, Hippodrome Route de Koulikoro Rue 235 Porte 52, Bamako BP 1771, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7298-4921","authenticated-orcid":false,"given":"Harris","family":"Onywera","sequence":"additional","affiliation":[{"name":"Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa P.O. Box 3243, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5461-5623","authenticated-orcid":false,"given":"Moussa Moise","family":"Diagne","sequence":"additional","affiliation":[{"name":"Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3130-4763","authenticated-orcid":false,"given":"Ibrehima","family":"Guindo","sequence":"additional","affiliation":[{"name":"Institut National de Sant\u00e9 Pulique, Hippodrome Route de Koulikoro Rue 235 Porte 52, Bamako BP 1771, Mali"},{"name":"Faculty of Pharmacy, Universit\u00e9 des Sciences des Techniques et des Technologies de Bamako, Point G Campus, Bamako BP 1805, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1016\/j.cmi.2023.08.008","article-title":"Emergence of Mpox in the Post-Smallpox Era\u2014A Narrative Review on Mpox Epidemiology","volume":"29","author":"Hoff","year":"2023","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Bunge, E.M., Hoet, B., Chen, L., Lienert, F., Weidenthaler, H., Baer, L.R., and Steffen, R. (2022). The Changing Epidemiology of Human Monkeypox\u2014A Potential Threat? A Systematic Review. PLoS Neglected Trop. Dis., 16.","DOI":"10.1371\/journal.pntd.0010141"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1038\/s41467-024-46949-7","article-title":"Monkeypox Virus Genomic Accordion Strategies","volume":"15","author":"Varona","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2791","DOI":"10.1038\/s41591-024-03130-3","article-title":"Sustained Human Outbreak of a New MPXV Clade I Lineage in Eastern Democratic Republic of the Congo","volume":"30","author":"Vakaniaki","year":"2024","journal-title":"Nat. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/s43856-025-01203-z","article-title":"First Imported Cases of MPXV Clade Ib from Goma, Democratic Republic of the Congo","volume":"5","author":"Merritt","year":"2025","journal-title":"Commun. Med."},{"key":"ref_6","unstructured":"AfricaCDC (2025, December 01). Africa CDC Declares Mpox A Public Health Emergency of Continental Security, Mobilizing Resources Across the Continent. Available online: https:\/\/africacdc.org\/news-item\/africa-cdc-declares-mpox-a-public-health-emergency-of-continental-security-mobilizing-resources-across-the-continent\/."},{"key":"ref_7","unstructured":"World Health Organization (2025, December 03). WHO Director-General Declares Mpox Outbreak a Public Health Emergency of International Concern. Available online: https:\/\/www.who.int\/news\/item\/14-08-2024-who-director-general-declares-mpox-outbreak-a-public-health-emergency-of-international-concern."},{"key":"ref_8","unstructured":"World Health Organization (2025, December 03). Global Mpox Trends. Available online: https:\/\/worldhealthorg.shinyapps.io\/mpx_global\/."},{"key":"ref_9","unstructured":"Matthijs, W., Jonges, M. (2025, November 01). Monkeypox Virus Whole Genome Sequencing Using Combination of NextGenPCR and Oxford Nanopore V.1. Available online: https:\/\/www.protocols.io\/view\/monkeypox-virus-whole-genome-sequencing-using-comb-n2bvj6155lk5\/v1."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise Alignment for Nucleotide Sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve Years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2906","DOI":"10.21105\/joss.02906","article-title":"Augur: A Bioinformatics Toolkit for Phylogenetic Analyses of Human Pathogens","volume":"6","author":"Huddleston","year":"2021","journal-title":"J. Open Source Softw."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Campbell, A.K.O., Sandi, J.D., Omah, I.F., Faye, M., Parker, E., Brock-Fisher, T., Gigante, C.M., Folorunso, V., Kamara, M.S., and Williams, A.J. (2025). Genomic Epidemiology Uncovers the Origin of the Mpox Epidemic in Sierra Leone. medRxiv.","DOI":"10.1101\/2025.10.15.25337823"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"Popart: Full-Feature Software for Haplotype Network Construction","volume":"6","author":"Leigh","year":"2015","journal-title":"Methods Ecol. Evol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"232","DOI":"10.3201\/eid2002.130118","article-title":"Genomic Variability of Monkeypox Virus among Humans, Democratic Republic of the Congo","volume":"20","author":"Kugelman","year":"2014","journal-title":"Emerg. Infect. Dis. J."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Yadav, R., Chaudhary, A.A., Srivastava, U., Gupta, S., Rustagi, S., Rudayni, H.A., Kashyap, V.K., and Kumar, S. (2025). Mpox 2022 to 2025 Update: A Comprehensive Review on Its Complications, Transmission, Diagnosis, and Treatment. Viruses, 17.","DOI":"10.3390\/v17060753"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/3\/294\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T14:58:02Z","timestamp":1772463482000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/3\/294"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,28]]},"references-count":16,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,3]]}},"alternative-id":["v18030294"],"URL":"https:\/\/doi.org\/10.3390\/v18030294","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,28]]}}}