{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T18:58:54Z","timestamp":1774292334076,"version":"3.50.1"},"reference-count":79,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2023,6,21]],"date-time":"2023-06-21T00:00:00Z","timestamp":1687305600000},"content-version":"vor","delay-in-days":20,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Medical Virology"],"published-print":{"date-parts":[[2023,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    A large outbreak of Monkeypox virus (MPXV) infections has arisen in May 2022 in nonendemic countries. Here, we performed DNA metagenomics using next\u2010generation sequencing with Illumina or Nanopore technologies for clinical samples from MPXV\u2010infected patients diagnosed between June and July 2022. Classification of the MPXV genomes and determination of their mutational patterns were performed using Nextclade. Twenty\u2010five samples from 25 patients were studied. A MPXV genome was obtained for 18 patients, essentially from skin lesions and rectal swabbing. All 18 genomes were classified in clade IIb, lineage B.1, and we identified four B.1 sublineages (B.1.1, B.1.10, B.1.12, B.1.14). We detected a high number of mutations (range, 64\u221273) relatively to a 2018 Nigerian genome (genome GenBank Accession no. NC_063383.1), which were harbored by a large part of a set of 3184 MPXV genomes of lineage B.1 recovered from GenBank and Nextstrain; and we detected 35 mutations relatively to genome ON563414.3 (a B.1 lineage reference genome). Nonsynonymous mutations occurred in genes encoding central proteins, among which transcription factors and core and envelope proteins, and included two mutations that would truncate a RNA polymerase subunit and a phospholipase\n                    <jats:sc>d<\/jats:sc>\n                    \u2010like protein, suggesting an alternative start codon and gene inactivation, respectively. A large majority (94%) of nucleotide substitutions were G\u2009&gt;\u2009A or C\u2009&gt;\u2009U, suggesting the action of human APOBEC3 enzymes. Finally, &gt;1000 reads were identified as from\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    and\n                    <jats:italic>Streptococcus pyogenes<\/jats:italic>\n                    for 3 and 6 samples, respectively. These findings warrant a close genomic monitoring of MPXV to get a better picture of the\u00a0genetic micro\u2010evolution and mutational patterns of this virus, and a close clinical monitoring of skin bacterial superinfection in monkeypox patients.\n                  <\/jats:p>","DOI":"10.1002\/jmv.28799","type":"journal-article","created":{"date-parts":[[2023,6,21]],"date-time":"2023-06-21T15:09:34Z","timestamp":1687360174000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Sequencing of monkeypox virus from infected patients reveals viral genomes with APOBEC3\u2010like editing, gene inactivation, and bacterial agents of skin superinfection"],"prefix":"10.1002","volume":"95","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6285-0308","authenticated-orcid":false,"given":"Philippe","family":"Colson","sequence":"first","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI) Aix\u2010Marseille Univ. Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gwilherm","family":"Penant","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeremy","family":"Delerce","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C\u00e9line","family":"Boschi","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI) Aix\u2010Marseille Univ. Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathalie","family":"Wurtz","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marielle","family":"Bedotto","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"St\u00e9phanie","family":"Branger","sequence":"additional","affiliation":[{"name":"Service de M\u00e9decine Interne Infectiologie A\u00efgue Polyvalente, Centre hospitalier d'Avignon Avignon France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippe","family":"Brouqui","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI) Aix\u2010Marseille Univ. Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippe","family":"Parola","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI) Aix\u2010Marseille Univ. Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Vecteurs \u2010 Infections Tropicales et M\u00e9diterran\u00e9ennes (VITROME) Aix\u2010Marseille Univ. Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean\u2010Christophe","family":"Lagier","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI) Aix\u2010Marseille Univ. Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadim","family":"Cassir","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI) Aix\u2010Marseille Univ. Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Herv\u00e9","family":"Tissot\u2010Dupont","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI) Aix\u2010Marseille Univ. Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthieu","family":"Million","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI) Aix\u2010Marseille Univ. Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah","family":"Aherfi","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI) Aix\u2010Marseille Univ. Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8006-7704","authenticated-orcid":false,"given":"Bernard","family":"La Scola","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Institut de Recherche pour le D\u00e9veloppement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI) Aix\u2010Marseille Univ. Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2023,6,21]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01495-21","article-title":"Ancient gene capture and recent gene loss shape the evolution of Or\u2010thopoxvirus\u2010Host interaction genes","volume":"12","author":"Senkevitch TG","year":"2021","journal-title":"mBio"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-022-00776-z"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiaa559"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-92315-8"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-01907-y"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tmaid.2022.102402"},{"key":"e_1_2_10_8_1","doi-asserted-by":"crossref","unstructured":"WangL ShangJ WengS et al. Genomic annotation and molecular evolution of monkeypox virus outbreak in 2022.J Med Virol. Published online July 29 2022.doi:10.1002\/jmv.28036","DOI":"10.1002\/jmv.28036"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(22)00153-7"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2022.27.36.2200620"},{"key":"e_1_2_10_11_1","doi-asserted-by":"crossref","unstructured":"BragazziNL KongJD WuJ. Is monkeypox a new emerging sexually transmitted disease? A rapid review of the literature.J Med Virol.2023;95:e28145.doi:10.1002\/jmv.28145","DOI":"10.1002\/jmv.28145"},{"key":"e_1_2_10_12_1","unstructured":"IsidroJ BorgesV PintoM et al. First draft genome sequence of Monkeypox virus associated with the suspected multi\u2010country outbreak May 2022 (confirmed case in Portugal). Virological.org. 2022.https:\/\/virological.org\/t\/first-draft-genome-sequence-of-monkeypox-virus-associated-with-the-suspected-multi-country-outbreak-may-2022-confirmed-case-in-portugal\/799"},{"key":"e_1_2_10_13_1","unstructured":"CrovilleG MathildaW Jean\u2010LucG Jean\u2010MichelM ChristopheP JacquesI. First French draft genome sequence of Monkeypox virus may 2022. Virological.org. 2022.https:\/\/virological.org\/t\/first-french-draft-genome-sequence-of-monkeypox-virus-may-2022\/819"},{"key":"e_1_2_10_14_1","article-title":"Genetic variability, including gene duplication and deletion, in early sequences from the 2022 European monkeypox outbreak","author":"Jones TC","year":"2022","journal-title":"bioRxiv"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.28366"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msq088"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid2812.221440"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1373\/clinchem.2006.068635"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0016142"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.786233"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.21105\/joss.03773"},{"key":"e_1_2_10_23_1","article-title":"Haplotype\u2010based variant detection from short\u2010read sequencing","author":"Garrison E","year":"2012","journal-title":"arXiv"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12493-y"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1002\/gch2.1018"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu300"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msy096"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty407"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1135"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-3-r46"},{"key":"e_1_2_10_32_1","doi-asserted-by":"publisher","DOI":"10.3390\/v14112393"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz1164"},{"key":"e_1_2_10_34_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.77.13.7590-7600.2003"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00987-06"},{"key":"e_1_2_10_36_1","doi-asserted-by":"publisher","DOI":"10.3390\/v9090253"},{"key":"e_1_2_10_37_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1921098117"},{"key":"e_1_2_10_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.antiviral.2011.11.010"},{"key":"e_1_2_10_39_1","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.030460-0"},{"key":"e_1_2_10_40_1","doi-asserted-by":"publisher","DOI":"10.1111\/jam.15806"},{"key":"e_1_2_10_41_1","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.28493"},{"key":"e_1_2_10_42_1","article-title":"APOBEC3F is the main source of editing identified during the 2022 outbreak of human monkeypox virus","author":"Susp\u00e8ne R","year":"2023","journal-title":"bioRxiv"},{"key":"e_1_2_10_43_1","unstructured":"O'TooleA RambautA. Initial observations about putative APOBEC3 deaminase editing driving short\u2010term evolution of MPXV since 2017. Virological. org.\u00a02022.https:\/\/virological.org\/t\/initial-observations-about-putative-apobec3-deaminase-editing-driving-short-term-evolution-of-mpxv-since-2017\/830"},{"key":"e_1_2_10_44_1","doi-asserted-by":"publisher","DOI":"10.1038\/nm1273"},{"key":"e_1_2_10_45_1","first-page":"132","article-title":"Functional diversity of ankyrin repeats in microbial proteins","volume":"18","author":"Al\u2010Khodor S","year":"2010","journal-title":"TIM"},{"key":"e_1_2_10_46_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13062-015-0043-z"},{"key":"e_1_2_10_47_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.75.23.11720-11734.2001"},{"key":"e_1_2_10_48_1","doi-asserted-by":"publisher","DOI":"10.3390\/v2102356"},{"key":"e_1_2_10_49_1","doi-asserted-by":"publisher","DOI":"10.1128\/msphere.00062-23"},{"key":"e_1_2_10_50_1","article-title":"Genomic deletions and rearrangements in monkeypox virus from the 2022 outbreak, USA","author":"Gigante CM","year":"2022","journal-title":"bioRxiv"},{"issue":"12","key":"e_1_2_10_51_1","first-page":"824","article-title":"Recombination shapes the 2022 monkeypox (mpox) outbreak","volume":"3","author":"Yeh TY","year":"2022","journal-title":"Med (New York, N.Y.)"},{"key":"e_1_2_10_52_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2136653100"},{"key":"e_1_2_10_53_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.add4153"},{"key":"e_1_2_10_54_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02154-17"},{"key":"e_1_2_10_55_1","doi-asserted-by":"publisher","DOI":"10.1021\/cr200296t"},{"key":"e_1_2_10_56_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0912737107"},{"key":"e_1_2_10_57_1","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.28536"},{"key":"e_1_2_10_58_1","doi-asserted-by":"publisher","DOI":"10.3390\/v2091933"},{"key":"e_1_2_10_59_1","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01526-22"},{"key":"e_1_2_10_60_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2220415120"},{"key":"e_1_2_10_61_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid2002.130118"},{"key":"e_1_2_10_62_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2012.00091"},{"key":"e_1_2_10_63_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(02)00665-7"},{"key":"e_1_2_10_64_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0002628"},{"key":"e_1_2_10_65_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1006594107"},{"key":"e_1_2_10_66_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002950"},{"key":"e_1_2_10_67_1","doi-asserted-by":"publisher","DOI":"10.1159\/000320964"},{"key":"e_1_2_10_68_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-022-01181-x"},{"key":"e_1_2_10_69_1","doi-asserted-by":"publisher","DOI":"10.1038\/nri1489"},{"key":"e_1_2_10_70_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00584-08"},{"key":"e_1_2_10_71_1","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.28322"},{"key":"e_1_2_10_72_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1153201"},{"key":"e_1_2_10_73_1","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2017.22.8.30468"},{"key":"e_1_2_10_74_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tmaid.2022.102417"},{"key":"e_1_2_10_75_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa143"},{"key":"e_1_2_10_76_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(22)00411-X"},{"key":"e_1_2_10_77_1","doi-asserted-by":"crossref","DOI":"10.1136\/bmj-2022-072410","article-title":"Clinical features and novel presentations of human monkeypox in a central London centre during the 2022 outbreak: descriptive case series","volume":"378","author":"Patel A","year":"2022","journal-title":"BMJ"},{"key":"e_1_2_10_78_1","unstructured":"World Health Organization (WHO). Clinical management and infection prevention and control for monkeypox: Interim rapid response guidance 10 June 2022.\u00a0Accessed\u00a0September 12 2022.\u00a0https:\/\/www.who.int\/publications\/i\/item\/WHO-MPX-Clinical-and-IPC-2022.1"},{"key":"e_1_2_10_79_1","unstructured":"Centers for Disease Control and Prevention (CDC). Monkeypox\u2014treatment information for healthcare professionals. 2022. 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