Publications

BV-BRC Zoonosis or Reverse Zoonosis Example

Capria A, Singh I, Zmasek C, Lefkowitz EJ, Scheuermann R

PMID: 40455156

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.