{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:19:12Z","timestamp":1785406752588,"version":"3.56.0"},"reference-count":45,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T00:00:00Z","timestamp":1780099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012759","name":"Ohio Department of Health","doi-asserted-by":"crossref","award":["#53183"],"award-info":[{"award-number":["#53183"]}],"id":[{"id":"10.13039\/100012759","id-type":"DOI","asserted-by":"crossref"}]},{"award":["#53183"],"award-info":[{"award-number":["#53183"]}],"id":[{"id":"https:\/\/ror.org\/0436zyg08","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Clinical surveillance of infectious diseases caused by viruses, such as SARS-CoV-2, is important for effective intervention and preventing potential epidemics or pandemics. The development of cost-effective whole genome sequencing technologies has facilitated worldwide efforts to sequence viral genomes. The array of sequence data generated across the globe offers diverse opportunities to study SARS-CoV-2 evolutionary dynamics and serves as a foundation for different research questions in the future. Even though bioinformatics tools are rapidly developed for accessing and analyzing large-scale data from public repositories, surveillance labs lack streamlined pipelines to handle high sample volumes and efficiently identify mutations for variant reporting with minimal computational expertise. Methods: We have developed a SARS-CoV-2 mutational analysis pipeline using Workflow Description Language (WDL), which is open-source and combines various steps in an analysis workflow with human-readable syntax. Thus, users with minimal informatics background can easily adapt the workflow while creating a local data repository within their institution. The pipeline processes input FASTA files and quality control files from Ion Torrent S5, performs clade and variant assignments, integrates patient metadata, and stores the results into a REDCap database. Results: In this framework, REDCap acts as the core data backbone for run-level tracking and result storage. To further enhance the utility of our REDCap-based data capture system, we have developed an intuitive interactive dashboard. This interface seamlessly connects with the REDCap data sources, providing real-time monitoring, interactive visualization, and the ability to create a consolidated variant report. Conclusions: Our overall approach streamlines processes in managing complex genomic data and offers easy adaptation to empower other molecular labs.<\/jats:p>","DOI":"10.3390\/genes17060632","type":"journal-article","created":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T06:17:31Z","timestamp":1780467451000},"page":"632","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["From Bench to Insight: Rapid Pathogen Genomic Surveillance Workflow for SARS-CoV-2 and Emerging Pathogens"],"prefix":"10.3390","volume":"17","author":[{"given":"Chelsea","family":"Zimmer","sequence":"first","affiliation":[{"name":"Office of Research, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Selena","family":"McVay","sequence":"additional","affiliation":[{"name":"Office of Research, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keely","family":"Starke","sequence":"additional","affiliation":[{"name":"Office of Research, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimily","family":"Hughley","sequence":"additional","affiliation":[{"name":"Office of Research, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5416-8621","authenticated-orcid":false,"given":"Sara N.","family":"Koenig","sequence":"additional","affiliation":[{"name":"Office of Research, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Venkat Sundar","family":"Gadepalli","sequence":"additional","affiliation":[{"name":"Office of Research, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1098\/rstb.2001.0888","article-title":"Risk factors for human disease emergence","volume":"356","author":"Taylor","year":"2001","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Jiang, X., Fan, Z., Li, S., and Yin, H. (2023). A Review on Zoonotic Pathogens Associated with Non-Human Primates: Understanding the Potential Threats to Humans. Microorganisms, 11.","DOI":"10.3390\/microorganisms11020246"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2671","DOI":"10.1016\/j.biocel.2008.05.019","article-title":"Human H5N1 influenza: Current insight into pathogenesis","volume":"40","author":"Thanh","year":"2008","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1126\/science.abp8715","article-title":"The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic","volume":"377","author":"Worobey","year":"2022","journal-title":"Science"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.ijsu.2020.04.018","article-title":"The socio-economic implications of the coronavirus pandemic (COVID-19): A review","volume":"78","author":"Nicola","year":"2020","journal-title":"Int. J. Surg."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e00940-20","DOI":"10.1128\/JVI.00940-20","article-title":"Broad and Differential Animal Angiotensin-Converting Enzyme 2 Receptor Usage by SARS-CoV-2","volume":"94","author":"Zhao","year":"2020","journal-title":"J. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Cocherie, T., Zafilaza, K., Leducq, V., Marot, S., Calvez, V., Marcelin, A.-G., and Todesco, E. (2022). Epidemiology and Characteristics of SARS-CoV-2 Variants of Concern: The Impacts of the Spike Mutations. Microorganisms, 11.","DOI":"10.3390\/microorganisms11010030"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1016\/j.cell.2020.06.043","article-title":"Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus","volume":"182","author":"Korber","year":"2020","journal-title":"Cell"},{"key":"ref_10","first-page":"2002106","article-title":"Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020","volume":"26","author":"Leung","year":"2020","journal-title":"Eurosurveillance"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1016\/j.chom.2021.06.006","article-title":"SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity","volume":"29","author":"Motozono","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3426","DOI":"10.1016\/j.cell.2021.04.025","article-title":"Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant","volume":"184","author":"Deng","year":"2021","journal-title":"Cell"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1038\/s41591-021-01285-x","article-title":"SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma","volume":"27","author":"Wibmer","year":"2021","journal-title":"Nat. Med."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1038\/s41586-021-04266-9","article-title":"Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation","volume":"602","author":"Saito","year":"2021","journal-title":"Nature"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"20503121231208273","DOI":"10.1177\/20503121231208273","article-title":"Social stigma during COVID-19: A systematic review","volume":"11","author":"SeyedAlinaghi","year":"2023","journal-title":"SAGE Open Med."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Des Jarlais, D.C., Lieff, S., Grivel, M., Meltzer, G., Choi, J., Weng, C.A., Feelemyer, J.P., Chang, V.W., and Yang, L. (2023). COVID-19 stigmatization after the development of effective vaccines: Vaccination behavior, attitudes, and news sources. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0283467"},{"key":"ref_17","unstructured":"Group, W.V. (2023). Tracking SARS-CoV-2 Variants, WHO."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/s41564-021-00932-w","article-title":"SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse","volume":"6","author":"Konings","year":"2021","journal-title":"Nat. Microbiol."},{"key":"ref_19","unstructured":"@CDCgov (2023). SARS-CoV-2 Variant Classifications and Definitions, National Center for Immunization and Respiratory Diseases (U.S.) Division of Viral Diseases."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/S0140-6736(20)30251-8","article-title":"Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding","volume":"395","author":"Lu","year":"2020","journal-title":"Lancet"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1093\/bib\/bbaa297","article-title":"Next generation sequencing of SARS-CoV-2 genomes: Challenges, applications and opportunities","volume":"22","author":"Chiara","year":"2021","journal-title":"Brief. Bioinform."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1007\/s10096-023-04590-0","article-title":"A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2","volume":"42","author":"Carbo","year":"2023","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis. Off. Publ. Eur. Soc. Clin. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e0064921","DOI":"10.1128\/JCM.00649-21","article-title":"Whole-Genome Sequencing of SARS-CoV-2: Assessment of the Ion Torrent AmpliSeq Panel and Comparison with the Illumina MiSeq ARTIC Protocol","volume":"59","author":"Plitnick","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.46234\/ccdcw2021.255","article-title":"GISAID\u2019s Role in Pandemic Response","volume":"3","author":"Khare","year":"2021","journal-title":"China CDC Wkly."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: Clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2023","journal-title":"J. Open Source Softw."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1038\/s41564-020-0770-5","article-title":"A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology","volume":"5","author":"Rambaut","year":"2020","journal-title":"Nat. Microbiol."},{"key":"ref_27","first-page":"veab064","article-title":"Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool","volume":"7","author":"Scher","year":"2023","journal-title":"Virus Evol."},{"key":"ref_28","unstructured":"(2024, December 20). WHO Coronavirus (COVID-19) Dashboard. Available online: https:\/\/data.who.int\/dashboards\/covid19\/summary."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Dezordi, F.Z., da Silva Neto, A.M., de Lima Campos, T., Jeronimo, P.M.C., Aksenen, C.F., Almeida, S.P., Wallau, G.L., and On Behalf of The Fiocruz Covid-Genomic Surveillance Network (2022). ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection. Viruses, 14.","DOI":"10.3390\/v14020217"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"105521","DOI":"10.1016\/j.meegid.2023.105521","article-title":"CoVEx: SARS-CoV-2 Mutation Explorer for genomic surveillance","volume":"116","year":"2023","journal-title":"Infect. Genet. Evol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1093\/bib\/bbaa232","article-title":"Computational strategies to combat COVID-19: Useful tools to accelerate SARS-CoV-2 and coronavirus research","volume":"22","author":"Hufsky","year":"2021","journal-title":"Brief. Bioinform."},{"key":"ref_32","first-page":"1381","article-title":"Full-Stack Genomics Pipelining with GATK4 + WDL + Cromwell","volume":"6","author":"Voss","year":"2017","journal-title":"F1000Research"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/j.jbi.2008.08.010","article-title":"Research electronic data capture (REDCap)\u2013a metadata-driven methodology and workflow process for providing translational research informatics support","volume":"42","author":"Harris","year":"2009","journal-title":"J. Biomed. Inf."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"103208","DOI":"10.1016\/j.jbi.2019.103208","article-title":"The REDCap consortium: Building an international community of software platform partners","volume":"95","author":"Harris","year":"2019","journal-title":"J. Biomed. Inf."},{"key":"ref_35","unstructured":"Chang, W., Cheng, J., Allaire, J.J., Sievert, C., Schloerke, B., Xie, Y., Allen, J., McPherson, J., Dipert, A., and Borges, B. (2026, May 26). Shiny: Web Application Framework for R. Available online: https:\/\/cran.r-project.org\/web\/packages\/shiny\/index.html."},{"key":"ref_36","unstructured":"Lin, G. (2026, May 26). Reactable: Interactive Data Tables for R. Available online: https:\/\/glin.github.io\/reactable\/."},{"key":"ref_37","unstructured":"Sievert, C., Parmer, C., Hocking, T., Chamberlain, S., Ram, K., Corvellec, M., Despouy, P., Br\u00fcggemann, S., and Plotly Technologies Inc. (2026, May 26). Plotly: Create Interactive Web Graphics via Plotly.js. Available online: https:\/\/plotly.r-universe.dev\/plotly."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw."},{"key":"ref_39","unstructured":"Wickham, H. (2026, May 26). Tidyverse: Easily Install and Load the Tidyverse. Available online: https:\/\/tidyverse.tidyverse.org\/."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Sievert, C. (2020). Interactive Web-Based Data Visualization with R, Plotly, and Shiny, Chapman and Hall\/CRC.","DOI":"10.1201\/9780429447273"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"103871","DOI":"10.1016\/j.jbi.2021.103871","article-title":"REDCap on FHIR: Clinical Data Interoperability Services","volume":"121","author":"Cheng","year":"2021","journal-title":"J. Biomed. Inf."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"21680","DOI":"10.1038\/s41598-021-99288-8","article-title":"Design considerations for workflow management systems use in production genomics research and the clinic","volume":"11","author":"Ahmed","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Lambisia, A.W., Mohammed, K.S., Makori, T.O., Ndwiga, L., Mburu, M.W., Morobe, J.M., Moraa, E.O., Musyoki, J., Murunga, N., and Mwangi, J.N. (2022). Optimization of the SARS-CoV-2 ARTIC Network V4 Primers and Whole Genome Sequencing Protocol. Front. Med., 9.","DOI":"10.3389\/fmed.2022.836728"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Sitharam, N., Tegally, H., Silva, D.d.C., Baxter, C., de Oliveira, T., and Xavier, J.S. (2024). SARS-CoV-2 Genomic Epidemiology Dashboards: A Review of Functionality and Technological Frameworks for the Public Health Response. Genes, 15.","DOI":"10.3390\/genes15070876"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"e0147924","DOI":"10.1128\/aac.01479-24","article-title":"Pathogen genomics in healthcare: Overcoming barriers to proactive surveillance","volume":"69","author":"Sundermann","year":"2024","journal-title":"Antimicrob. Agents Chemother."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/6\/632\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T04:47:17Z","timestamp":1780548437000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/6\/632"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,30]]},"references-count":45,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["genes17060632"],"URL":"https:\/\/doi.org\/10.3390\/genes17060632","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,30]]}}}