Shen-Gunther, JaneCai, HongWang, Yufeng2023-01-202023-01-202022-12-22Viruses 15 (1): 40 (2023)https://hdl.handle.net/20.500.12588/1590Monkeypox 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 "ready-to-use" 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.Attribution 4.0 United Stateshttps://creativecommons.org/licenses/by/4.0/bioinformaticsdisease outbreaksmonkeypoxmonkeypox virusnext generation sequencingphylogenypoxvirustaxonomic classificationvirus databaseArticle2023-01-20