A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples von Naccache, Samia N, Federman, Scot, Veeraraghavan, Narayanan, Zaharia, Matei, Lee, Deanna, Samayoa, Erik, Bouquet, Jerome, Greninger, Alexander L, Luk, Ka-Cheung, Enge, Barryett, Wadford, Debra A, Messenger, Sharon L, Genrich, Gillian L, Pellegrino, Kristen, Grard, Gilda, Leroy, Eric, Schneider, Bradley S, Fair, Joseph N, Martínez, Miguel A, Isa, Pavel, Crump, John A, DeRisi, Joseph L, Sittler, Taylor, Hackett, Jr, John, Miller, Steve, Chiu, Charles Y

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Case Definitions, Diagnostic Algorithms, and Priorities in Encephalitis: Consensus Statement of the International Encephalitis Consortium von Venkatesan, A., Tunkel, A. R., Bloch, K. C., Lauring, A. S., Sejvar, J., Bitnun, A., Stahl, J-P., Mailles, A., Drebot, M., Rupprecht, C. E., Yoder, J., Cope, J. R., Wilson, M. R., Whitley, R. J., Sullivan, J., Granerod, J., Jones, C., Eastwood, K., Ward, K. N., Durrheim, D. N., Solbrig, M. V., Guo-Dong, L., Glaser, C. A.

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A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012–14): a retrospective cohort study von Greninger, Alexander L, MD, Naccache, Samia N, PhD, Messacar, Kevin, MD, Clayton, Anna, BSc, Yu, Guixia, BSc, Somasekar, Sneha, BSc, Federman, Scot, BA, Stryke, Doug, BSc, Anderson, Christopher, BSc, Yagi, Shigeo, PhD, Messenger, Sharon, PhD, Wadford, Debra, PhD, Xia, Dongxiang, MD, Watt, James P, MD, Van Haren, Keith, MD, Dominguez, Samuel R, MD, Glaser, Carol, MD, Aldrovandi, Grace, Prof, Chiu, Charles Y, Dr

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A forty-year review of Rocky Mountain spotted fever cases in California shows clinical and epidemiologic changes von Kjemtrup, Anne M, Padgett, Kerry, Paddock, Christopher D, Messenger, Sharon, Hacker, Jill K, Feiszli, Tina, Melgar, Michael, Metzger, Marco E, Hu, Renjie, Kramer, Vicki L

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Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016 von Chiu, Charles Y, Coffey, Lark L, Murkey, Jamie, Symmes, Kelly, Sample, Hannah A, Wilson, Michael R, Naccache, Samia N, Arevalo, Shaun, Somasekar, Sneha, Federman, Scot, Stryke, Doug, Vespa, Paul, Schiller, Gary, Messenger, Sharon, Humphries, Romney, Miller, Steve, Klausner, Jeffrey D

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Evaluation of co-circulating pathogens and microbiome from COVID-19 infections von Thissen, James B, Morrison, Michael D, Mulakken, Nisha, Nelson, William C, Daum, Chris, Messenger, Sharon, Wadford, Debra A, Jaing, Crystal

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Travel-Associated Zika Cases and Threat of Local Transmission during Global Outbreak, California, USA von Porse, Charsey Cole, Messenger, Sharon, Vugia, Duc J, Jilek, Wendy, Salas, Maria, Watt, James, Kramer, Vicki

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Evaluation of co-circulating pathogens and microbiome from COVID-19 infections von Thissen, James B., Morrison, Michael D., Mulakken, Nisha, Nelson, William C., Daum, Chris, Messenger, Sharon, Wadford, Debra A., Jaing, Crystal, Onwuamah, ed., Chika Kingsley

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New Exposure Location for Hantavirus Pulmonary Syndrome Case, California, USA, 2018 von Kjemtrup, Anne M, Messenger, Sharon, Meza, Amy M, Feiszli, Tina, Yoshimizu, Melissa Hardstone, Padgett, Kerry, Singh, Sunita

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Emerging Epidemiology of Bat-Associated Cryptic Cases of Rabies in Humans in the United States von Messenger, Sharon L., Smith, Jean S., Rupprecht, Charles E.

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West Nile virus in California, 2003-2018: A persistent threat von Snyder, Robert E, Feiszli, Tina, Foss, Leslie, Messenger, Sharon, Fang, Ying, Barker, Christopher M, Reisen, William K, Vugia, Duc J, Padgett, Kerry A, Kramer, Vicki L

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Epidemiologic and environmental characterization of the Re-emergence of St. Louis Encephalitis Virus in California, 2015-2020 von Danforth, Mary E, Snyder, Robert E, Feiszli, Tina, Bullick, Teal, Messenger, Sharon, Hanson, Carl, Padgett, Kerry, Coffey, Lark L, Barker, Christopher M, Reisen, William K, Kramer, Vicki L

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Long-Term Rodent Surveillance after Outbreak of Hantavirus Infection, Yosemite National Park, California, USA, 2012 von Danforth, Mary E, Messenger, Sharon, Buttke, Danielle, Weinburke, Matthew, Carroll, George, Hacker, Gregory, Niemela, Michael, Andrews, Elizabeth S, Jackson, Bryan T, Kramer, Vicki, Novak, Mark

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The Eco-epidemiology of Pacific Coast Tick Fever in California von Padgett, Kerry A, Bonilla, Denise, Eremeeva, Marina E, Glaser, Carol, Lane, Robert S, Porse, Charsey Cole, Castro, Martin B, Messenger, Sharon, Espinosa, Alex, Hacker, Jill, Kjemtrup, Anne, Ryan, Bonnie, Scott, Jamesina J, Hu, Renjie, Yoshimizu, Melissa Hardstone, Dasch, Gregory A, Kramer, Vicki

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Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples von Kimbrel, Jeffrey, Moon, Joseph, Avila-Herrera, Aram, Martí, Jose Manuel, Thissen, James, Mulakken, Nisha, Sandholtz, Sarah H, Ferrell, Tyshawn, Daum, Chris, Hall, Sara, Segelke, Brent, Arrildt, Kathryn T, Messenger, Sharon, Wadford, Debra A, Jaing, Crystal, Allen, Jonathan E, Borucki, Monica K

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Novel Focus of Sin Nombre Virus in Peromyscus eremicus Mice, Death Valley National Park, California, USA von Burns, Joseph E, Metzger, Marco E, Messenger, Sharon, Fritz, Curtis L, Vilcins, Inger-Marie E, Enge, Barryett, Bronson, Lawrence R, Kramer, Vicki L, Hu, Renjie

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Hantavirus infections among overnight visitors to Yosemite National Park, California, USA, 2012 von Núñez, Jonathan J, Fritz, Curtis L, Knust, Barbara, Buttke, Danielle, Enge, Barryett, Novak, Mark G, Kramer, Vicki, Osadebe, Lynda, Messenger, Sharon, Albariño, César G, Ströher, Ute, Niemela, Michael, Amman, Brian R, Wong, David, Manning, Craig R, Nichol, Stuart T, Rollin, Pierre E, Xia, Dongxiang, Watt, James P, Vugia, Duc J

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Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission von Borucki, Monica K, Chen-Harris, Haiyin, Lao, Victoria, Vanier, Gilda, Wadford, Debra A, Messenger, Sharon, Allen, Jonathan E

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Bat-associated rabies virus in Skunks von Leslie, Mira J, Messenger, Sharon, Rohde, Rodney E, Smith, Jean, Cheshier, Ronald, Hanlon, Cathleen, Rupprecht, Charles E

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RICKETTSIA SPP. 364D CAUSING A CLUSTER OF ESCHAR-ASSOCIATED ILLNESS, CALIFORNIA von JOHNSTON, Samantha H, GLASER, Carol A, HSIEH, Charlotte, MESSENGER, Sharon L, PADGETT, Kerry, WADFORD, Debra A, ESPINOSA, Alex, ESPINOSA, Natasha, EREMEEVA, Marina E, TAIT, Karen, HOBSON, Barbara, SHTIVELMAN, Sarit

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