{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T04:54:28Z","timestamp":1778561668552,"version":"3.51.4"},"reference-count":30,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2022,12,22]],"date-time":"2022-12-22T00:00:00Z","timestamp":1671667200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Department of Clinical Investigation at Brooke Army Medical Center"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Monkeypox has been a neglected, zoonotic tropical disease for over 50 years. Since the 2022 global outbreak, hundreds of human clinical samples have been subjected to next-generation sequencing (NGS) worldwide with raw data deposited in public repositories. However, sequence analysis for in-depth investigation of viral evolution remains hindered by the lack of a curated, whole genome Monkeypox virus (MPXV) database (DB) and efficient bioinformatics pipelines. To address this, we developed a customized MPXV DB for integration with \u201cready-to-use\u201d workflows in the CLC Microbial Genomics Module for whole genomic and metagenomic analysis. After database construction (218 MPXV genomes), whole genome alignment, pairwise comparison, and evolutionary analysis of all genomes were analyzed to autogenerate tabular outputs and visual displays (collective runtime: 16 min). The clinical utility of the MPXV DB was demonstrated by using a Chimpanzee fecal, hybrid-capture NGS dataset (publicly available) for metagenomic, phylogenomic, and viral\/host integration analysis. The clinically relevant MPXV DB embedded in CLC workflows proved to be a rapid method of sequence analysis useful for phylogenomic exploration and a wide range of applications in translational science.<\/jats:p>","DOI":"10.3390\/v15010040","type":"journal-article","created":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T03:02:15Z","timestamp":1671764535000},"page":"40","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["A Customized Monkeypox Virus Genomic Database (MPXV DB v1.0) for Rapid Sequence Analysis and Phylogenomic Discoveries in CLC Microbial Genomics"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0876-9338","authenticated-orcid":false,"given":"Jane","family":"Shen-Gunther","sequence":"first","affiliation":[{"name":"Department of Clinical Investigation, Gynecologic Oncology & Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX 78234, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong","family":"Cai","sequence":"additional","affiliation":[{"name":"Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA"},{"name":"South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9959-4149","authenticated-orcid":false,"given":"Yufeng","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA"},{"name":"South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1111\/j.1699-0463.1959.tb00328.x","article-title":"A pox-like disease in cynomolgus monkeys","volume":"46","author":"Magnus","year":"1959","journal-title":"Acta Pathol. Microbiol. Scand."},{"key":"ref_2","first-page":"277","article-title":"Smallpox and monkeypox in non-human primates","volume":"39","author":"Arita","year":"1968","journal-title":"Bull. World Health Organ."},{"key":"ref_3","first-page":"593","article-title":"A human infection caused by monkeypox virus in Basankusu Territory, Democratic Republic of the Congo","volume":"46","author":"Ladnyj","year":"1972","journal-title":"Bull World Health Organ"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"772","DOI":"10.3390\/idr14050079","article-title":"Monkeypox: From A Neglected Tropical Disease to a Public Health Threat","volume":"14","author":"Antunes","year":"2022","journal-title":"Infect. Dis. Rep."},{"key":"ref_5","unstructured":"(2022, November 10). World Health Organization (WHO). Available online: https:\/\/www.who.int\/director-general\/speeches\/detail\/who-director-general-s-statement-on-the-press-conference-following-IHR-emergency-committee-regarding-the-multi--country-outbreak-of-monkeypox--23-july-2022."},{"key":"ref_6","unstructured":"(2022, November 10). Center for Disease Control and Prevention. 2022 Monkeypox Outbreak Global Map, Available online: https:\/\/www.cdc.gov\/poxvirus\/monkeypox\/response\/2022\/world-map.html."},{"key":"ref_7","unstructured":"Howley, P.M., and Knipe, P.M. (2022). Poxviridae: The Viruses and Their Replication. Fields Virology. DNA Viruses, Wolters Kluwer. [7th ed.]."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/S0014-5793(01)03144-1","article-title":"Human monkeypox and smallpox viruses: Genomic comparison","volume":"509","author":"Shchelkunov","year":"2001","journal-title":"FEBS Lett."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1006\/viro.2002.1446","article-title":"Analysis of the monkeypox virus genome","volume":"297","author":"Shchelkunov","year":"2002","journal-title":"Virology"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.virol.2005.05.030","article-title":"Virulence differences between monkeypox virus isolates from West Africa and the Congo basin","volume":"340","author":"Chen","year":"2005","journal-title":"Virology"},{"key":"ref_11","unstructured":"National Center for Biotechnology Information (2022, November 10). Virus, Available online: https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/#\/."},{"key":"ref_12","unstructured":"National Center for Biotechnology Information (2022, November 10). Sequence Read Archive, Available online: https:\/\/www.ncbi.nlm.nih.gov\/sra."},{"key":"ref_13","unstructured":"International Committee on Taxonomy of Viruses (ICTV) (2022, November 10). Taxonomy. Available online: https:\/\/ictv.global\/taxonomy."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e0005321","DOI":"10.1128\/MMBR.00053-21","article-title":"The Baltimore Classification of Viruses 50 Years Later: How Does It Stand in the Light of Virus Evolution?","volume":"85","author":"Koonin","year":"2021","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Happi, C., Adetifa, I., Mbala, P., Njouom, R., Nakoune, E., Happi, A., Ndodo, N., Ayansola, O., Mboowa, G., and Bedford, T. (2022). Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. PLoS Biol., 20.","DOI":"10.1371\/journal.pbio.3001769"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"13085","DOI":"10.1038\/s41598-021-92315-8","article-title":"Genomic history of human monkey pox infections in the Central African Republic between 2001 and 2018","volume":"11","author":"Berthet","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2168","DOI":"10.3390\/v7042168","article-title":"A phylogeographic investigation of African monkeypox","volume":"7","author":"Nakazawa","year":"2015","journal-title":"Viruses"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"307","DOI":"10.4314\/ajcem.v19i4.9","article-title":"Re-emergence of monkeypox in Nigeria: A cause for concern and public enlightenment","volume":"19","author":"Fowotade","year":"2018","journal-title":"Afr. J. Clin. Exp. Microbiol."},{"key":"ref_19","unstructured":"(2022, November 10). Qiagen Digital Insights. Available online: https:\/\/digitalinsights.qiagen.com\/technical-support\/system-requirements\/."},{"key":"ref_20","unstructured":"(2022, November 10). Qiagen Digital Insights. Available online: https:\/\/digitalinsights.qiagen.com\/products-overview\/plugins\/."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1038\/s41564-020-0706-0","article-title":"Monkeypox virus emergence in wild chimpanzees reveals distinct clinical outcomes and viral diversity","volume":"5","author":"Patrono","year":"2020","journal-title":"Nat. Microbiol."},{"key":"ref_22","unstructured":"National Center for Biotechnology Information (2022, November 10). Assembly, Available online: https:\/\/www.ncbi.nlm.nih.gov\/assembly\/GCF_002880755.1."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.1038\/s41591-022-01907-y","article-title":"Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus","volume":"28","author":"Isidro","year":"2022","journal-title":"Nat. Med."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Shen-Gunther, J., Cai, H., and Wang, Y. (2022). HPV Integration Site Mapping: A Rapid Method of Viral Integration Site (VIS) Analysis and Visualization Using Automated Workflows in CLC Microbial Genomics. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23158132"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2241","DOI":"10.1056\/NEJMicm2033620","article-title":"Orbital Cowpox","volume":"384","author":"Kiernan","year":"2021","journal-title":"New Engl. J. Med."},{"key":"ref_26","unstructured":"National Public Radio (2022, November 10). COVID Sewage Surveillance Labs Join the Hunt for Monkeypox. Available online: https:\/\/www.npr.org\/sections\/health-shots\/2022\/08\/08\/1115455190\/covid-sewage-surveillance-labs-join-the-hunt-for-monkeypox."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"D311","DOI":"10.1093\/nar\/gki110","article-title":"Poxvirus Bioinformatics Resource Center: A comprehensive Poxviridae informational and analytical resource","volume":"33","author":"Lefkowitz","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1385\/1-59259-789-0:347","article-title":"Poxvirus bioinformatics","volume":"269","author":"Upton","year":"2004","journal-title":"Vaccinia Virus Poxvirology"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1007\/978-1-4939-9593-6_2","article-title":"Bioinformatics for Analysis of Poxvirus Genomes","volume":"Volume 2023","author":"Mercer","year":"2019","journal-title":"Vaccinia Virus. Methods in Molecular Biology"},{"key":"ref_30","unstructured":"Qiagen (2022, November 10). QIAseq xHYB Viral and Bacterial Panels. Available online: https:\/\/www.qiagen.com\/us\/products\/next-generation-sequencing\/metagenomics\/targeted-metagenomics\/qiaseq-xhyb-viral-and-bacterial-panels\/?catno=333397."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/1\/40\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:48:07Z","timestamp":1760147287000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/1\/40"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,22]]},"references-count":30,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,1]]}},"alternative-id":["v15010040"],"URL":"https:\/\/doi.org\/10.3390\/v15010040","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,22]]}}}