ArticleMethods in molecular biology (Clifton, N.J.)2025
BV-BRC Zoonosis or Reverse Zoonosis Example.
Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This bioinformatics workflow utilizes the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) to investigate a potential zoonotic or reverse zoonotic transmission event on a North Carolina swine farm in 2022 (Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, Dempsey DM, Dickerman A, Dietrich EM, Kenyon RW, Kuscuoglu M, Lefkowitz EJ, Lu J, Machi D, Macken C, Mao C, Niewiadomska A, Nguyen M, Olsen GJ, Overbeek JC, Parrello B, Parrello V, Porter JS, Pusch GD, Shukla M, Singh I, Stewart L, Tan G, Thomas C, VanOeffelen M, Vonstein V, Wallace ZS, Warren AS, Wattam AR, Xia F, Yoo H, Zhang Y, Zmasek CM, Scheuermann RH, Stevens RL, Nucleic Acids Res 51(D1):D678-D689, 2023). The BV-BRC contains a genomic sequence database featuring NIH/NIAID and an integrated platform for comprehensive bioinformatic analysis in the bacterial and virology space. The workflow involves dataset assembly, annotation, multiple sequence alignment, meta-CATS sequence comparison, phylogenetic analysis, subspecies classification, and PCR primer design. The tools in BV-BRC, including MAFFT, RAxML, and meta-CATS, facilitate a detailed comparative genomics analysis of HA protein sequences from birds and humans, as an example of the integrative functionality of the BV-BRC. The results contribute valuable insights into the potential transmission dynamics, supporting high-quality scientific analysis, and provide a robust methodology for researchers exploring similar scenarios. In the following subheadings, we describe use cases with examples of how the BV-BRC can be utilized for large-scale analysis.
Indexed as
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.