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Volume 31, Supplement—April 2025
SUPPLEMENT ISSUE
Supplement

Respiratory Virus Detection and Sequencing from SARS-CoV-2–Negative Rapid Antigen Tests

Emmanuela Jules1, Charlie Decker1, Brianna Jeanne Bixler1, Alaa Ahmed, Zijing (Carol) Zhou, Itika Arora, Henok Tafesse, Hannah Dakanay, Andrei Bombin, Ethan Wang, Jessica Ingersoll, Kathy Bifulco, Jennifer K. Frediani, Richard Parsons, Julie Sullivan, Morgan Greenleaf, Jesse J. Waggoner, Greg S. Martin, Wilbur A. Lam, and Anne PiantadosiComments to Author 
Author affiliation: Emory University School of Medicine, Atlanta, Georgia, USA (E. Jules, C. Decker, B.J. Bixler, A. Ahmed, Z.(C.) Zhou, I. Arora, H. Tafesse, H. Dakanay, A. Bombin, E. Wang, J. Ingersoll, J. Sullivan, J.J. Waggoner, W.A. Lam, A. Piantadosi); Emory Integrated Genomics Core, Winship Cancer Institute of Emory University, Atlanta (A. Ahmed); Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta (K. Bifulco, J.K. Frediani, R. Parsons); The Atlanta Center for Microsystems Engineered Point-of-Care Technologies, Atlanta (J.K. Frediani, R. Parsons, J. Sullivan, M. Greenleaf); Georgia Clinical and Translational Science Alliance, Atlanta (M. Greenleaf); Emory University Division of Pulmonary, Allergy, Critical Care Medicine and Sleep Medicine, Atlanta (G.S. Martin); Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta (W.A. Lam); Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, Atlanta (W.A. Lam)

Main Article

Figure 3

Plot of the viral taxa (rows) that were detected in each sample (columns) in study of respiratory virus detection and sequencing from SARS-CoV-2–negative rapid antigen tests. A) Results from samples used in this study; B) results from negative controls. Dark blue boxes indicate viruses that were detected by both KrakenUniq (https://github.com/fbreitwieser/krakenuniq) and blastn (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) and were confirmed by reference mapping (covering >3 distinct regions or 10% of the reference virus genome). Light blue boxes indicate viruses that were detected by both KrakenUniq and blastn but not confirmed by reference mapping. This figure only includes results for which >1 read mapped to a reference genome sequence. Further detail including sample identifiers is shown in Appendix 1 Figures 3,4.

Figure 3. Plot of the viral taxa (rows) that were detected in each sample (columns) in study of respiratory virus detection and sequencing from SARS-CoV-2–negative rapid antigen tests. A) Results from samples used in this study; B) results from negative controls. Dark blue boxes indicate viruses that were detected by both KrakenUniq (https://github.com/fbreitwieser/krakenuniq) and blastn (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) and were confirmed by reference mapping (covering >3 distinct regions or 10% of the reference virus genome). Light blue boxes indicate viruses that were detected by both KrakenUniq and blastn but not confirmed by reference mapping. This figure only includes results for which >1 read mapped to a reference genome sequence. Further detail including sample identifiers is shown in Appendix 1 Figures 3,4.

Main Article

1These first authors contributed equally to this article.

Page created: March 31, 2025
Page updated: April 23, 2025
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