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Establishing Methods to Monitor Influenza (A)H5N1 Virus in Dairy Cattle Milk, Massachusetts, USA
Elyse Stachler
, Andreas Gnirke, Kyle McMahon, Michael Gomez, Liam Stenson, Charelisse Guevara-Reyes, Hannah Knoll, Toni Hill, Sellers Hill, Katelyn S. Messer, Jon Arizti-Sanz, Fatinah Albeez, Elizabeth Curtis, Pedram Samani, Natalia Wewior, David H. O’Connor, William Vuyk, Sophia E. Khoury, Matthew K. Schnizlein, Nicole C. Rockey, Zachariah Broemmel, Michael Mina, Lawrence C. Madoff, Shirlee Wohl, Lorraine O’Connor, Catherine M. Brown, Al Ozonoff, Daniel J. Park, Bronwyn L. MacInnis
1, and Pardis C. Sabeti
1
Author affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA (E. Stachler, A. Gnirke, K. McMahon, M. Gomez, L. Stenson, C. Guevara-Reyes, H. Knoll, T. Hill, S. Hill, K.S. Messer, J. Arizti-Sanz, F. Albeez, E. Curtis, P. Samani, N. Wewior, A. Ozonoff, D.J. Park, B.L. MacInnis, P.C. Sabeti); University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico, USA (C. Guevara-Reyes); Harvard University, Cambridge (P. Samani, B.L. MacInnis, P.C. Sabeti); University College London, London, UK (P. Samani); University of Wisconsin-Madison, Madison, Wisconsin, USA (D.H. O’Connor, W. Vuyk); The University of Texas at Austin, Austin, Texas, USA (S.E. Khoury); Michigan State University, East Lansing, Michigan, USA (M.K. Schnizlein); Duke University, Durham, North Carolina, USA (N.C. Rockey, Z. Broemmel); Immune Observatory, Boston, Massachusetts, USA (M. Mina); University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA (L.C. Madoff); Massachusetts Department of Public Health, Boston (L.C. Madoff, S. Wohl, C.M. Brown); Brigham and Women’s Hospital, Boston (S. Wohl); Massachusetts Department of Agricultural Resources, Boston (L. O’Connor); Boston Children’s Hospital, Boston (A. Ozonoff); Harvard Medical School, Boston (A. Ozonoff); Howard Hughes Medical Institute, Chevy Chase, Maryland, USA (P.C. Sabeti)
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Figure 5
Figure 5. Virus genome assemblies from retail milk samples in study of methods to monitor influenza A(H5N1) virus in dairy cattle milk, Massachusetts, USA. A) Completeness of H5N1 genome assemblies generated by RNA-Seq, virus-enriched (hsRNA-Seq), and targeted H5N1 Amp-Seq as a function of H5N1 copies per milliliter of RNA. B) The most complete H5N1 assembly produced for each sample sorted by length and the underlying sequencing approach. Asterisks (*) above bars indicate ultrapasteurized samples. Amp-Seq, amplicon sequencing; hsRNA-Seq, hybrid-selected metagenomics; RNA-Seq, unbiased metagenomics.
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