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1. Introduction and Spread of Dengue Virus 3, Florida, USA, May 2022-April 2023

Author

Jones, Forrest K., Morrison, Andrea M., Santiago, Gilberto A., Rysava, Kristyna, Zimler, Rebecca A., Heberlein, Lea A., Kopp, Edgar, Team, Florida Department of Health Bureau of Public Health Laboratory, Saunders, Katharine E., Baudin, Samantha, Rico, Edhelene, Mejia-Echeverri, Alvaro, Taylor-Salmon, Emma, Hill, Verity, Breban, Mallery I., Vogels, Chantal B.F., Grubaugh, Nathan D., Paul, Lauren M., Michael, Scott F., Johansson, Michael A., Adams, Laura E., Munoz-Jordan, Jorge, Paz-Bailey, Gabriela, and Stanek, Danielle R.

Subjects
United States. Centers for Disease Control and Prevention, Genomics -- Health aspects, Infection -- Health aspects, Travelers -- Health aspects, Dengue viruses -- Health aspects, Health
Abstract

Dengue virus (DENV) is not endemic in the continental United States (1); most cases occur among travelers to DENV-endemic areas (2). In Florida, USA, DENV infections are primarily reported among [...]

Published
2024
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2. Instructional Models for Course-Based Research Experience (CRE) Teaching

Author

Hanauer, David I, Graham, Mark J, Arnold, Rachel J, Ayuk, Mary A, Balish, Mitchell F, Beyer, Andrea R, Butela, Kristen A, Byrum, Christine A, Chia, Catherine P, Chung, Hui-Min, Clase, Kari L, Conant, Stephanie, Coomans, Roy J, D’Elia, Tom, Diaz, Jason, Diaz, Arturo, Doty, Jean A, Edgington, Nicholas P, Edwards, Dustin C, Eivazova, Elvira, Emmons, Christine B, Fast, Kayla M, Fisher, Emily J, Fleischacker, Christine L, Frederick, Gregory D, Freise, Amanda C, Gainey, Maria D, Gissendanner, Chris R, Golebiewska, Urszula P, Guild, Nancy A, Hendrickson, Heather L, Herren, Christopher D, Hopson-Fernandes, Margaret S, Hughes, Lee E, Jacobs-Sera, Deborah, Johnson, Allison A, Kirkpatrick, Bridgette L, Klyczek, Karen K, Koga, Ann P, Kotturi, Hari, LeBlanc-Straceski, Janine, Lee-Soety, Julia Y, Leonard, Justin E, Mastropaolo, Matthew D, Merkhofer, Evan C, Michael, Scott F, Mitchell, Jon C, Mohan, Swarna, Monti, Denise L, Noutsos, Christos, Nsa, Imade Y, Peters, Nick T, Plymale, Ruth, Pollenz, Richard S, Porter, Megan L, Rinehart, Claire A, Rosas-Acosta, German, Ross, Joseph F, Rubin, Michael R, Scherer, Anne E, Schroeder, Stephanie C, Shaffer, Christopher D, Sprenkle, Amy B, Sunnen, C Nicole, Swerdlow, Sarah J, Tobiason, Deborah, Tolsma, Sara S, Tsourkas, Philippos K, Ward, Robert E, Ware, Vassie C, Warner, Marcie H, Washington, Jacqueline M, Westover, Kristi M, White, Simon J, Whitefleet-Smith, JoAnn L, Williams, Daniel C, Wolyniak, Michael J, Zeilstra-Ryalls, Jill H, Asai, David J, Hatfull, Graham F, and Sivanathan, Viknesh

Subjects
Curriculum and Pedagogy, Education Systems, Education, Quality Education, Engineering, Faculty, Humans, Mathematics, Models, Educational, Students, Teaching, Curriculum and pedagogy
Abstract

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.

Published
2022

3. Instructional Models for Course-Based Research Experience (CRE) Teaching

Author

Hanauer, David I., Graham, Mark J., Arnold, Rachel J., Ayuk, Mary A., Balish, Mitchell F., Beyer, Andrea R., Butela, Kristen A., Byrum, Christine A., Chia, Catherine P., Chung, Hui-Min, Clase, Kari L., Conant, Stephanie, Coomans, Roy J., D'Elia, Tom, Diaz, Jason, Diaz, Arturo, Doty, Jean A., Edgington, Nicholas P., Edwards, Dustin C., Eivazova, Elvira, Emmons, Christine B., Fast, Kayla M., Fisher, Emily J., Fleischacker, Christine L., Frederick, Gregory D., Freise, Amanda C., Gainey, Maria D., Gissendanner, Chris R., Golebiewska, Urszula P., Guild, Nancy A., Hendrickson, Heather L., Herren, Christopher D., Hopson-Fernandes, Margaret S., Hughes, Lee E., Jacobs-Sera, Deborah, Johnson, Allison A., Kirkpatrick, Bridgette L., Klyczek, Karen K., Koga, Ann P., Kotturi, Hari, LeBlanc-Straceski, Janine, Lee-Soety, Julia Y., Leonard, Justin E., Mastropaolo, Matthew D., Merkhofer, Evan C., Michael, Scott F., Mitchell, Jon C., Mohan, Swarna, Monti, Denise L., Noutsos, Christos, Nsa, Imade Y., Peters, Nick T., Plymale, Ruth, Pollenz, Richard S., Porter, Megan L., Rinehart, Claire A., Rosas-Acosta, German, Ross, Joseph F., Rubin, Michael R., Scherer, Anne E., Schroeder, Stephanie C., Shaffer, Christopher D., Sprenkle, Amy B., Sunnen, C. Nicole, Swerdlow, Sarah J., Tobiason, Deborah, Tolsma, Sara S., Tsourkas, Philippos K., Ward, Robert E., Ware, Vassie C., Warner, Marcie H., Washington, Jacqueline M., Westover, Kristi M., White, Simon J., Whitefleet-Smith, JoAnn L., Williams, Daniel C., Wolyniak, Michael J., Zeilstra-Ryalls, Jill H., Asai, David J., Hatfull, Graham F., and Sivanathan, Viknesh

Abstract

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: (1) being a scientist and generating data; (2) teaching procedural knowledge; and (3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.

Published
2022
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4. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus

Author

Vogels, Chantal B. F., primary, Hill, Verity, additional, Breban, Mallery I., additional, Chaguza, Chrispin, additional, Paul, Lauren M., additional, Sodeinde, Afeez, additional, Taylor-Salmon, Emma, additional, Ott, Isabel M., additional, Petrone, Mary E., additional, Dijk, Dennis, additional, Jonges, Marcel, additional, Welkers, Matthijs R. A., additional, Locksmith, Timothy, additional, Dong, Yibo, additional, Tarigopula, Namratha, additional, Tekin, Omer, additional, Schmedes, Sarah, additional, Bunch, Sylvia, additional, Cano, Natalia, additional, Jaber, Rayah, additional, Panzera, Charles, additional, Stryker, Ian, additional, Vergara, Julieta, additional, Zimler, Rebecca, additional, Kopp, Edgar, additional, Heberlein, Lea, additional, Herzog, Kaylee S., additional, Fauver, Joseph R., additional, Morrison, Andrea M., additional, Michael, Scott F., additional, and Grubaugh, Nathan D., additional

Published
2024
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5. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean

Author

Taylor-Salmon, Emma, primary, Hill, Verity, additional, Paul, Lauren M., additional, Koch, Robert T., additional, Breban, Mallery I., additional, Chaguza, Chrispin, additional, Sodeinde, Afeez, additional, Warren, Joshua L., additional, Bunch, Sylvia, additional, Cano, Natalia, additional, Cone, Marshall, additional, Eysoldt, Sarah, additional, Garcia, Alezaundra, additional, Gilles, Nicadia, additional, Hagy, Andrew, additional, Heberlein, Lea, additional, Jaber, Rayah, additional, Kassens, Elizabeth, additional, Colarusso, Pamela, additional, Davis, Amanda, additional, Baudin, Samantha, additional, Rico, Edhelene, additional, Mejía-Echeverri, Álvaro, additional, Scott, Blake, additional, Stanek, Danielle, additional, Zimler, Rebecca, additional, Muñoz-Jordán, Jorge L., additional, Santiago, Gilberto A., additional, Adams, Laura E., additional, Paz-Bailey, Gabriela, additional, Spillane, Melanie, additional, Katebi, Volha, additional, Paulino-Ramírez, Robert, additional, Mueses, Sayira, additional, Peguero, Armando, additional, Sánchez, Nelissa, additional, Norman, Francesca F., additional, Galán, Juan-Carlos, additional, Huits, Ralph, additional, Hamer, Davidson H., additional, Vogels, Chantal B. F., additional, Morrison, Andrea, additional, Michael, Scott F., additional, and Grubaugh, Nathan D., additional

Published
2024
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7. Models of classroom assessment for course-based research experiences

Author

Hanauer, David I., primary, Zhang, Tong, additional, Graham, Mark J., additional, Adams, Sandra D., additional, Ahumada-Santos, Yesmi Patricia, additional, Alvey, Richard M., additional, Antunes, Mauricio S., additional, Ayuk, Mary A., additional, Elena Báez-Flores, María, additional, Bancroft, Christa T., additional, Bates, Tonya C., additional, Bechman, Meghan J., additional, Behr, Elizabeth, additional, Beyer, Andrea R., additional, Bortz, Rebecca L., additional, Bowder, Dane M., additional, Briggs, Laura A., additional, Brown-Kennerly, Victoria, additional, Buckholt, Michael A., additional, Bullock, Sharon K., additional, Butela, Kristen A., additional, Byrum, Christine A., additional, Caruso, Steven M., additional, Chia, Catherine P., additional, Chong, Rebecca A., additional, Chung, Hui-Min, additional, Clase, Kari L., additional, Coleman, Sean T., additional, Parks Collins, D., additional, Conant, Stephanie B., additional, Condon, Brett M., additional, Connerly, Pamela L., additional, Connors, Bernadette J., additional, Cook-Easterwood, Jennifer E., additional, Crump, Katie E., additional, D’Elia, Tom, additional, Dennis, Megan K., additional, DeVeaux, Linda C., additional, Diacovich, Lautaro, additional, Duffy, Iain, additional, Edgington, Nicholas P., additional, Edwards, Dustin C., additional, Egwuatu, Tenny O. G., additional, Eivazova, Elvira R., additional, Fallest-Strobl, Patricia C., additional, Fillman, Christy L., additional, Findley, Ann M., additional, Fisher, Emily, additional, Fisher, Matthew R., additional, Fogarty, Marie P., additional, Freise, Amanda C., additional, Frost, Victoria J., additional, Gainey, Maria D., additional, Garcia Costas, Amaya M., additional, Garza, Atenea A., additional, Gavin, Hannah E., additional, Ghittoni, Raffaella, additional, Gibb, Bryan, additional, Golebiewska, Urszula P., additional, Grinath, Anna S., additional, Gurney, Susan M. R., additional, Hare, Rebekah F., additional, Heninger, Steven G., additional, Hinz, John M., additional, Hughes, Lee E., additional, Jayachandran, Pradeepa, additional, Johnson, Kristen C., additional, Johnson, Allison A., additional, Kanther, Michelle, additional, Kenna, Margaret, additional, Kirkpatrick, Bridgette L., additional, Klyczek, Karen K., additional, Kohl, Kathryn P., additional, Kuchka, Michael, additional, LaPeruta, Amber J., additional, Lee-Soety, Julia Y., additional, Lewis, Lynn O., additional, Lindberg, Heather M., additional, Madden, Jaclyn A., additional, Markov, Sergei A., additional, Mastropaolo, Matthew D., additional, Mathur, Vinayak, additional, McClory, Sean P., additional, Merkhofer, Evan C., additional, Merkle, Julie A., additional, Michael, Scott F., additional, Mitchell, Jon C., additional, Molloy, Sally D., additional, Monti, Denise L., additional, Mussi, María Alejandra, additional, Nance, Holly, additional, Nieto-Fernandez, Fernando E., additional, Nissen, Jillian C., additional, Nsa, Imade Y., additional, O’Donnell, Mary G., additional, Page, Shallee T., additional, Panagakis, Andrea, additional, Parra-Unda, Jesús Ricardo, additional, Pelletier, Tara A., additional, Perez Morales, Tiara G., additional, Peters, Nick T., additional, Phuntumart, Vipaporn, additional, Pollenz, Richard S., additional, Preuss, Mary L., additional, Puthoff, David P., additional, Raifu, Muideen K., additional, Reyna, Nathan S., additional, Rinehart, Claire A., additional, Rocheleau, Jessica M., additional, Rossier, Ombeline, additional, Rudner, Adam D., additional, Rueschhoff, Elizabeth E., additional, Ryan, Amy, additional, Saha, Sanghamitra, additional, Shaffer, Christopher D., additional, Smith, Mary Ann V., additional, Sprenkle, Amy B., additional, Strong, Christy L., additional, Sunnen, C. Nicole, additional, Tarbox, Brian P., additional, Temple, Louise, additional, Thoemke, Kara R., additional, Thomas, Michael A., additional, Tobiason, Deborah M., additional, Tolsma, Sara S., additional, Garcia, Julie Torruellas, additional, Valentine, Megan S., additional, Vazquez, Edwin, additional, Ward, Robert E., additional, Ward, Catherine M., additional, Ware, Vassie C., additional, Warner, Marcie H., additional, Washington, Jacqueline M., additional, Westholm, Daniel E., additional, Wheaton, Keith A., additional, Wilkes, Beth M., additional, Williams, Elizabeth C., additional, Biederman, William H., additional, Cresawn, Steven G., additional, Heller, Danielle M., additional, Jacobs-Sera, Deborah, additional, Hatfull, Graham F., additional, Asai, David J., additional, and Sivanathan, Viknesh, additional

Published
2023
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8. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean

Author

Taylor-Salmon, Emma, primary, Hill, Verity, additional, Paul, Lauren M., additional, Koch, Robert T., additional, Breban, Mallery I., additional, Chaguza, Chrispin, additional, Sodeinde, Afeez, additional, Warren, Joshua L., additional, Bunch, Sylvia, additional, Cano, Natalia, additional, Cone, Marshall, additional, Eysoldt, Sarah, additional, Garcia, Alezaundra, additional, Gilles, Nicadia, additional, Hagy, Andrew, additional, Heberlein, Lea, additional, Jaber, Rayah, additional, Kassens, Elizabeth, additional, Colarusso, Pamela, additional, Davis, Amanda, additional, Baudin, Samantha, additional, Rico, Edhelene, additional, Mejia-Echeverri, Alvaro, additional, Scott, Blake, additional, Stanek, Danielle, additional, Zimler, Rebecca, additional, Munoz-Jordan, Jorge L., additional, Santiago, Gilberto A., additional, Adams, Laura E., additional, Paz-Bailey, Gabriela, additional, Spillane, Melanie, additional, Katebi, Volha, additional, Paulino-Ramirez, Robert, additional, Mueses, Sayira, additional, Peguero, Armando, additional, Sanchez, Nelissa, additional, Norman, Francesca F., additional, Galan, Juan-Carlos Galan, additional, Huits, Ralph Huits, additional, Hamer, Davidison H., additional, Vogels, Chantal B.F., additional, Morrison, Andrea Morrison, additional, Michael, Scott F., additional, and Grubaugh, Nathan D., additional

Published
2023
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9. DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus

Author

Vogels, Chantal B.F., primary, Hill, Verity, additional, Breban, Mallery I., additional, Chaguza, Chrispin, additional, Paul, Lauren M., additional, Sodeinde, Afeez, additional, Taylor-Salmon, Emma, additional, Ott, Isabel M., additional, Petrone, Mary E., additional, Dijk, Dennis, additional, Jonges, Marcel, additional, Welkers, Matthijs R.A., additional, Locksmith, Timothy, additional, Dong, Yibo, additional, Tarigopula, Namratha, additional, Tekin, Omer, additional, Schmedes, Sarah, additional, Bunch, Sylvia, additional, Cano, Natalia, additional, Jaber, Rayah, additional, Panzera, Charles, additional, Stryker, Ian, additional, Vergara, Julieta, additional, Zimler, Rebecca, additional, Kopp, Edgar, additional, Heberlein, Lea, additional, Morrison, Andrea M., additional, Michael, Scott F., additional, and Grubaugh, Nathan D., additional

Published
2023
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10. Field-deployable viral diagnostics using CRISPR-Cas13

Author

Myhrvold, Cameron, Freije, Catherine A., Gootenberg, Jonathan S., Abudayyeh, Omar O., Metsky, Hayden C., Durbin, Ann F., Kellner, Max J., Tan, Amanda L., Paul, Lauren M., Parham, Leda A., Garcia, Kimberly F., Barnes, Kayla G., Chak, Bridget, Mondini, Adriano, Nogueira, Mauricio L., Isern, Sharon, Michael, Scott F., Lorenzana, Ivette, Yozwiak, Nathan L., MacInnis, Bronwyn L., Bosch, Irene, Gehrke, Lee, Zhang, Feng, and Sabeti, Pardis C.

Published
2018

11. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Author

Grubaugh, Nathan D., Gangavarapu, Karthik, Quick, Joshua, Matteson, Nathaniel L., De Jesus, Jaqueline Goes, Main, Bradley J., Tan, Amanda L., Paul, Lauren M., Brackney, Doug E., Grewal, Saran, Gurfield, Nikos, Van Rompay, Koen K. A., Isern, Sharon, Michael, Scott F., Coffey, Lark L., Loman, Nicholas J., and Andersen, Kristian G.

Published
2019
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13. Design Principles of Lipid-like Ionic Liquids for Gene Delivery

Author

Siegel, David J., primary, Anderson, Grace I., additional, Paul, Lauren M., additional, Seibert, Philipp J., additional, Hillesheim, Patrick C., additional, Sheng, Yinghong, additional, Zeller, Matthias, additional, Taubert, Andreas, additional, Werner, Peter, additional, Balischewski, Christian, additional, Michael, Scott F., additional, and Mirjafari, Arsalan, additional

Published
2021
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14. Zika virus evolution and spread in the Americas

Author

Metsky, Hayden C., Matranga, Christian B., Wohl, Shirlee, Schaffner, Stephen F., Freije, Catherine A., Winnicki, Sarah M., West, Kendra, Qu, James, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Tomkins-Tinch, Christopher H., Ye, Simon H., Park, Daniel J., Luo, Cynthia Y., Barnes, Kayla G., Shah, Rickey R., Chak, Bridget, Barbosa-Lima, Giselle, Delatorre, Edson, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Barcellona, Carolyn M., Porcelli, Mario C., Vasquez, Chalmers, Cannons, Andrew C., Cone, Marshall R., Hogan, Kelly N., Kopp, Edgar W., Anzinger, Joshua J., Garcia, Kimberly F., Parham, Leda A., Ramrez, Rosa M. Glvez, Montoya, Maria C. Miranda, Rojas, Diana P., Brown, Catherine M., Hennigan, Scott, Sabina, Brandon, Scotland, Sarah, Gangavarapu, Karthik, Grubaugh, Nathan D., Oliveira, Glenn, Robles-Sikisaka, Refugio, Rambaut, Andrew, Gehrke, Lee, Smole, Sandra, Halloran, M. Elizabeth, Villar, Luis, Mattar, Salim, Lorenzana, Ivette, Cerbino-Neto, Jose, Valim, Clarissa, Degrave, Wim, Bozza, Patricia T., Gnirke, Andreas, Andersen, Kristian G., Isern, Sharon, Michael, Scott F., Bozza, Fernando A., Souza, Thiago M. L., Bosch, Irene, Yozwiak, Nathan L., MacInnis, Bronwyn L., and Sabeti, Pardis C.

Subjects
America -- Health aspects, Zika virus -- Natural history, Zika virus infection -- Distribution, Company distribution practices, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Hayden C. Metsky [1, 2]; Christian B. Matranga [1]; Shirlee Wohl [1, 3]; Stephen F. Schaffner [1, 3, 4]; Catherine A. Freije [1, 3]; Sarah M. Winnicki [1]; Kendra [...]

Published
2017
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15. Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Author

Grubaugh, Nathan D., Ladner, Jason T., Kraemer, Moritz U. G., Dudas, Gytis, Tan, Amanda L., Gangavarapu, Karthik, Wiley, Michael R., White, Stephen, Thz, Julien, Magnani, Diogo M., Prieto, Karla, Reyes, Daniel, Bingham, Andrea M., Paul, Lauren M., Robles-Sikisaka, Refugio, Oliveira, Glenn, Pronty, Darryl, Barcellona, Carolyn M., Metsky, Hayden C., Baniecki, Mary Lynn, Barnes, Kayla G., Chak, Bridget, Freije, Catherine A., Gladden-Young, Adrianne, Gnirke, Andreas, Luo, Cynthia, MacInnis, Bronwyn, Matranga, Christian B., Park, Daniel J., Qu, James, Schaffner, Stephen F., Tomkins-Tinch, Christopher, West, Kendra L., Winnicki, Sarah M., Wohl, Shirlee, Yozwiak, Nathan L., Quick, Joshua, Fauver, Joseph R., Khan, Kamran, Brent, Shannon E., Reiner, Robert C., Jr, Lichtenberger, Paola N., Ricciardi, Michael J., Bailey, Varian K., Watkins, David I., Cone, Marshall R., Kopp, Edgar W., IV, Hogan, Kelly N., Cannons, Andrew C., Jean, Reynald, Monaghan, Andrew J., Garry, Robert F., Loman, Nicholas J., Faria, Nuno R., Porcelli, Mario C., Vasquez, Chalmers, Nagle, Elyse R., Cummings, Derek A. T., Stanek, Danielle, Rambaut, Andrew, Sanchez-Lockhart, Mariano, Sabeti, Pardis C., Gillis, Leah D., Michael, Scott F., Bedford, Trevor, Pybus, Oliver G., Isern, Sharon, Palacios, Gustavo, and Andersen, Kristian G.

Subjects
Zika virus -- Health aspects -- Genetic aspects, Gene expression -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Nathan D. Grubaugh [1]; Jason T. Ladner [2]; Moritz U. G. Kraemer [3, 4, 5]; Gytis Dudas [6]; Amanda L. Tan [7]; Karthik Gangavarapu [1]; Michael R. Wiley [2, [...]

Published
2017
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16. Field-deployable viral diagnostics using CRISPR-Cas13

Author

McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Biological Engineering, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Myhrvold, Cameron, Freije, Catherine A., Gootenberg, Jonathan S, Abudayyeh, Omar O., Metsky, Hayden C., Durbin, Ann F, Kellner, Max J., Tan, Amanda L., Paul, Lauren M., Parham, Leda A., Garcia, Kimberly F., Barnes, Kayla G., Chak, Bridget, Mondini, Adriano, Nogueira, Mauricio L., Isern, Sharon, Michael, Scott F., Lorenzana, Ivette, Yozwiak, Nathan L., MacInnis, Bronwyn L., Bosch, Irene, Gehrke, Lee, Zhang, Feng, Sabeti, Pardis C., McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Biological Engineering, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Myhrvold, Cameron, Freije, Catherine A., Gootenberg, Jonathan S, Abudayyeh, Omar O., Metsky, Hayden C., Durbin, Ann F, Kellner, Max J., Tan, Amanda L., Paul, Lauren M., Parham, Leda A., Garcia, Kimberly F., Barnes, Kayla G., Chak, Bridget, Mondini, Adriano, Nogueira, Mauricio L., Isern, Sharon, Michael, Scott F., Lorenzana, Ivette, Yozwiak, Nathan L., MacInnis, Bronwyn L., Bosch, Irene, Gehrke, Lee, Zhang, Feng, and Sabeti, Pardis C.

Abstract

Mitigating global infectious disease requires diagnostic tools that are sensitive, specific, and rapidly field deployable. In this study, we demonstrate that the Cas13-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform can detect Zika virus (ZIKV) and dengue virus (DENV) in patient samples at concentrations as low as 1 copy per microliter. We developed HUDSON (heating unextracted diagnostic samples to obliterate nucleases), a protocol that pairs with SHERLOCK for viral detection directly from bodily fluids, enabling instrument-free DENV detection directly from patient samples in <2 hours. We further demonstrate that SHERLOCK can distinguish the four DENV serotypes, as well as region-specific strains of ZIKV from the 2015–2016 pandemic. Finally, we report the rapid (<1 week) design and testing of instrument-free assays to detect clinically relevant viral single-nucleotide polymorphisms., NIH (Grants AI-100190, 1R01-HG009761, 1R01-MH110049, and 1DP1-HL141201)

Published
2020

17. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

Author

Metsky, Hayden C, Siddle, Katherine J, Gladden-Young, Adrianne, Qu, James, Yang, David K, Brehio, Patrick, Goldfarb, Andrew, Piantadosi, Anne, Wohl, Shirlee, Carter, Amber, Lin, Aaron E, Barnes, Kayla G, Tully, Damien C, Corleis, Bjӧrn, Hennigan, Scott, Barbosa-Lima, Giselle, Vieira, Yasmine R, Paul, Lauren M, Tan, Amanda L, Garcia, Kimberly F, Parham, Leda A, Odia, Ikponmwosa, Eromon, Philomena, Folarin, Onikepe A, Goba, Augustine, Viral Hemorrhagic Fever Consortium, Simon-Lorière, Etienne, Hensley, Lisa, Balmaseda, Angel, Harris, Eva, Kwon, Douglas S, Allen, Todd M, Runstadler, Jonathan A, Smole, Sandra, Bozza, Fernando A, Souza, Thiago ML, Isern, Sharon, Michael, Scott F, Lorenzana, Ivette, Gehrke, Lee, Bosch, Irene, Ebel, Gregory, Grant, Donald S, Happi, Christian T, Park, Daniel J, Gnirke, Andreas, Sabeti, Pardis C, and Matranga, Christian B

Abstract

Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.

Published
2019

18. Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic

Author

Grubaugh, Nathan D., primary, Saraf, Sharada, additional, Gangavarapu, Karthik, additional, Watts, Alexander, additional, Tan, Amanda L., additional, Oidtman, Rachel J., additional, Ladner, Jason T., additional, Oliveira, Glenn, additional, Matteson, Nathaniel L., additional, Kraemer, Moritz U.G., additional, Vogels, Chantal B.F., additional, Hentoff, Aaron, additional, Bhatia, Deepit, additional, Stanek, Danielle, additional, Scott, Blake, additional, Landis, Vanessa, additional, Stryker, Ian, additional, Cone, Marshall R., additional, Kopp, Edgar W., additional, Cannons, Andrew C., additional, Heberlein-Larson, Lea, additional, White, Stephen, additional, Gillis, Leah D., additional, Ricciardi, Michael J., additional, Kwal, Jaclyn, additional, Lichtenberger, Paola K., additional, Magnani, Diogo M., additional, Watkins, David I., additional, Palacios, Gustavo, additional, Hamer, Davidson H., additional, Gardner, Lauren M., additional, Perkins, T. Alex, additional, Baele, Guy, additional, Khan, Kamran, additional, Morrison, Andrea, additional, Isern, Sharon, additional, Michael, Scott F., additional, and Andersen, Kristian G., additional

Published
2019
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19. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Author

Grubaugh, Nathan D, primary, Gangavarapu, Karthik, additional, Quick, Joshua, additional, Matteson, Nathaniel L., additional, De Jesus, Jaqueline Goes, additional, Main, Bradley J, additional, Tan, Amanda L, additional, Paul, Lauren M, additional, Brackney, Doug E, additional, Grewal, Saran, additional, Gurfield, Nikos, additional, Van Rompay, Koen KA, additional, Isern, Sharon, additional, Michael, Scott F, additional, Coffey, Lark L, additional, Loman, Nicholas J, additional, and Andersen, Kristian G, additional

Published
2018
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20. Zika virus evolution and spread in the Americas

Author

Institute for Medical Engineering and Science, Broad Institute of MIT and Harvard, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Metsky, Hayden C., Schaffner, Stephen F, Quigley, James Edwin, Ye, Simon Huang, Park, Daniel, Barnes, Kayla, Gehrke, Lee, Valim, Clarissa, Gnirke, Andreas, Andersen, Kristian, Bosch, Irene, Matranga, Christian B., Wohl, Shirlee, Freije, Catherine A., Winnicki, Sarah M., West, Kendra, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Tomkins-Tinch, Christopher H., Luo, Cynthia Y., Shah, Rickey R., Chak, Bridget, Barbosa-Lima, Giselle, Delatorre, Edson, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Barcellona, Carolyn M., Porcelli, Mario C., Vasquez, Chalmers, Cannons, Andrew C., Cone, Marshall R., Hogan, Kelly N., Kopp, Edgar W., Anzinger, Joshua J., Garcia, Kimberly F., Parham, Leda A., Ramírez, Rosa M. Gélvez, Montoya, Maria C. Miranda, Rojas, Diana P., Brown, Catherine M., Hennigan, Scott, Sabina, Brandon, Scotland, Sarah, Gangavarapu, Karthik, Grubaugh, Nathan D., Oliveira, Glenn, Robles-Sikisaka, Refugio, Rambaut, Andrew, Smole, Sandra, Halloran, M. Elizabeth, Villar, Luis, Mattar, Salim, Lorenzana, Ivette, Cerbino-Neto, Jose, Degrave, Wim, Bozza, Patricia T., Isern, Sharon, Michael, Scott F., Bozza, Fernando A., Souza, Thiago M. L., Yozwiak, Nathan L., MacInnis, Bronwyn L., Sabeti, Pardis C., Institute for Medical Engineering and Science, Broad Institute of MIT and Harvard, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Metsky, Hayden C., Schaffner, Stephen F, Quigley, James Edwin, Ye, Simon Huang, Park, Daniel, Barnes, Kayla, Gehrke, Lee, Valim, Clarissa, Gnirke, Andreas, Andersen, Kristian, Bosch, Irene, Matranga, Christian B., Wohl, Shirlee, Freije, Catherine A., Winnicki, Sarah M., West, Kendra, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Tomkins-Tinch, Christopher H., Luo, Cynthia Y., Shah, Rickey R., Chak, Bridget, Barbosa-Lima, Giselle, Delatorre, Edson, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Barcellona, Carolyn M., Porcelli, Mario C., Vasquez, Chalmers, Cannons, Andrew C., Cone, Marshall R., Hogan, Kelly N., Kopp, Edgar W., Anzinger, Joshua J., Garcia, Kimberly F., Parham, Leda A., Ramírez, Rosa M. Gélvez, Montoya, Maria C. Miranda, Rojas, Diana P., Brown, Catherine M., Hennigan, Scott, Sabina, Brandon, Scotland, Sarah, Gangavarapu, Karthik, Grubaugh, Nathan D., Oliveira, Glenn, Robles-Sikisaka, Refugio, Rambaut, Andrew, Smole, Sandra, Halloran, M. Elizabeth, Villar, Luis, Mattar, Salim, Lorenzana, Ivette, Cerbino-Neto, Jose, Degrave, Wim, Bozza, Patricia T., Isern, Sharon, Michael, Scott F., Bozza, Fernando A., Souza, Thiago M. L., Yozwiak, Nathan L., MacInnis, Bronwyn L., and Sabeti, Pardis C.

Abstract

Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests., National Institutes of Health (U.S.) (Grant NIAID U19AI110818)

Published
2017

22. Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

Author

Grubaugh, Nathan D, primary, Ladner, Jason T, additional, Kraemer, Moritz UG, additional, Dudas, Gytis, additional, Tan, Amanda L, additional, Gangavarapu, Karthik, additional, Wiley, Michael R, additional, White, Stephen, additional, Thézé, Julien, additional, Magnani, Diogo M, additional, Prieto, Karla, additional, Reyes, Daniel, additional, Bingham, Andrea, additional, Paul, Lauren M, additional, Robles-Sikisaka, Refugio, additional, Oliveira, Glenn, additional, Pronty, Darryl, additional, Metsky, Hayden C, additional, Baniecki, Mary Lynn, additional, Barnes, Kayla G, additional, Chak, Bridget, additional, Freije, Catherine A, additional, Gladden-Young, Adrianne, additional, Gnirke, Andreas, additional, Luo, Cynthia, additional, MacInnis, Bronwyn, additional, Matranga, Christian B, additional, Park, Daniel J, additional, Qu, James, additional, Schaffner, Stephen F, additional, Tomkins-Tinch, Christopher, additional, West, Kendra L, additional, Winnicki, Sarah M, additional, Wohl, Shirlee, additional, Yozwiak, Nathan L, additional, Quick, Joshua, additional, Fauver, Joseph R, additional, Khan, Kamran, additional, Brent, Shannon E, additional, Reiner, Robert C, additional, Lichtenberger, Paola N, additional, Ricciardi, Michael, additional, Bailey, Varian K, additional, Watkins, David I, additional, Cone, Marshall R, additional, Kopp, Edgar W, additional, Hogan, Kelly N, additional, Cannons, Andrew C, additional, Jean, Reynald, additional, Garry, Robert F, additional, Loman, Nicholas J, additional, Faria, Nuno R, additional, Porcelli, Mario C, additional, Vasquez, Chalmers, additional, Nagle, Elyse R, additional, Cummings, Derek AT, additional, Stanek, Danielle, additional, Rambaut, Andrew, additional, Sanchez-Lockhart, Mariano, additional, Sabeti, Pardis C, additional, Gillis, Leah D, additional, Michael, Scott F, additional, Bedford, Trevor, additional, Pybus, Oliver G, additional, Isern, Sharon, additional, Palacios, Gustavo, additional, and Andersen, Kristian G, additional

Published
2017
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23. Prophage-mediated defence against viral attack and viral counter-defence

Author

Dedrick, Rebekah M., primary, Jacobs-Sera, Deborah, additional, Bustamante, Carlos A. Guerrero, additional, Garlena, Rebecca A., additional, Mavrich, Travis N., additional, Pope, Welkin H., additional, Reyes, Juan C. Cervantes, additional, Russell, Daniel A., additional, Adair, Tamarah, additional, Alvey, Richard, additional, Bonilla, J. Alfred, additional, Bricker, Jerald S., additional, Brown, Bryony R., additional, Byrnes, Deanna, additional, Cresawn, Steven G., additional, Davis, William B., additional, Dickson, Leon A., additional, Edgington, Nicholas P., additional, Findley, Ann M., additional, Golebiewska, Urszula, additional, Grose, Julianne H., additional, Hayes, Cory F., additional, Hughes, Lee E., additional, Hutchison, Keith W., additional, Isern, Sharon, additional, Johnson, Allison A., additional, Kenna, Margaret A., additional, Klyczek, Karen K., additional, Mageeney, Catherine M., additional, Michael, Scott F., additional, Molloy, Sally D., additional, Montgomery, Matthew T., additional, Neitzel, James, additional, Page, Shallee T., additional, Pizzorno, Marie C., additional, Poxleitner, Marianne K., additional, Rinehart, Claire A., additional, Robinson, Courtney J., additional, Rubin, Michael R., additional, Teyim, Joseph N., additional, Vazquez, Edwin, additional, Ware, Vassie C., additional, Washington, Jacqueline, additional, and Hatfull, Graham F., additional

Published
2017
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25. Dengue virus antibodies enhance Zika virus infection

Author

Paul, Lauren M, primary, Carlin, Eric R, additional, Jenkins, Meagan M, additional, Tan, Amanda L, additional, Barcellona, Carolyn M, additional, Nicholson, Cindo O, additional, Michael, Scott F, additional, and Isern, Sharon, additional

Published
2016
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26. Dengue Virus Antibodies Enhance Zika Virus Infection

Author

Paul, Lauren M., primary, Carlin, Eric R., additional, Jenkins, Meagan M., additional, Tan, Amanda L., additional, Barcellona, Carolyn M., additional, Nicholson, Cindo O., additional, Trautmann, Lydie, additional, Michael, Scott F., additional, and Isern, Sharon, additional

Published
2016
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27. Correction: Biomimetic design of protic lipidic ionic liquids with enhanced fluidity

Author

O'Brien, Richard A., primary, Zayas, Manuel Sanchez, additional, Nestor, Stephen T., additional, Gaitor, Jamie C., additional, Paul, Lauren M., additional, Edhegard, Forrest A., additional, Minkowicz, Samuel, additional, Sykora, Richard E., additional, Sheng, Yinghong, additional, Michael, Scott F., additional, Isern, Sharon, additional, and Mirjafari, Arsalan, additional

Published
2016
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28. Biomimetic design of protic lipidic ionic liquids with enhanced fluidity

Author

O'Brien, Richard A., primary, Zayas, Manuel Sanchez, additional, Nestor, Stephen T., additional, Gaitor, Jamie C., additional, Paul, Lauran M., additional, Edhegard, Forrest A., additional, Minkowicz, Samuel, additional, Sykora, Richard E., additional, Sheng, Yinghong, additional, Michael, Scott F., additional, Isern, Sharon, additional, and Mirjafari, Arsalan, additional

Published
2016
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29. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean.

Author

Taylor-Salmon E, Hill V, Paul LM, Koch RT, Breban MI, Chaguza C, Sodeinde A, Warren JL, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán JL, Santiago GA, Adams LE, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman FF, Galán JC, Huits R, Hamer DH, Vogels CBF, Morrison A, Michael SF, and Grubaugh ND

Abstract

Dengue is the most prevalent mosquito-borne viral disease in humans, and cases are continuing to rise globally. In particular, islands in the Caribbean have experienced more frequent outbreaks, and all four dengue virus (DENV) serotypes have been reported in the region, leading to hyperendemicity and increased rates of severe disease. However, there is significant variability regarding virus surveillance and reporting between islands, making it difficult to obtain an accurate understanding of the epidemiological patterns in the Caribbean. To investigate this, we used travel surveillance and genomic epidemiology to reconstruct outbreak dynamics, DENV serotype turnover, and patterns of spread within the region from 2009-2022. We uncovered two recent DENV-3 introductions from Asia, one of which resulted in a large outbreak in Cuba, which was previously under-reported. We also show that while outbreaks can be synchronized between islands, they are often caused by different serotypes. Our study highlights the importance of surveillance of infected travelers to provide a snapshot of local introductions and transmission in areas with limited local surveillance and suggests that the recent DENV-3 introductions may pose a major public health threat in the region.

Published
2023
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30. DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus.

Author

Vogels CBF, Hill V, Breban MI, Chaguza C, Paul LM, Sodeinde A, Taylor-Salmon E, Ott IM, Petrone ME, Dijk D, Jonges M, Welkers MRA, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Morrison AM, Michael SF, and Grubaugh ND

Abstract

Background: The increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing of all four dengue virus serotypes., Results: We developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (>95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 10 1 -10 2 RNA copies/μL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments., Conclusions: DengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance., Competing Interests: Competing interests The authors declare that they have no competing interests.

Published
2023
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31. Instructional Models for Course-Based Research Experience (CRE) Teaching.

Author

Hanauer DI, Graham MJ, Arnold RJ, Ayuk MA, Balish MF, Beyer AR, Butela KA, Byrum CA, Chia CP, Chung HM, Clase KL, Conant S, Coomans RJ, D'Elia T, Diaz J, Diaz A, Doty JA, Edgington NP, Edwards DC, Eivazova E, Emmons CB, Fast KM, Fisher EJ, Fleischacker CL, Frederick GD, Freise AC, Gainey MD, Gissendanner CR, Golebiewska UP, Guild NA, Hendrickson HL, Herren CD, Hopson-Fernandes MS, Hughes LE, Jacobs-Sera D, Johnson AA, Kirkpatrick BL, Klyczek KK, Koga AP, Kotturi H, LeBlanc-Straceski J, Lee-Soety JY, Leonard JE, Mastropaolo MD, Merkhofer EC, Michael SF, Mitchell JC, Mohan S, Monti DL, Noutsos C, Nsa IY, Peters NT, Plymale R, Pollenz RS, Porter ML, Rinehart CA, Rosas-Acosta G, Ross JF, Rubin MR, Scherer AE, Schroeder SC, Shaffer CD, Sprenkle AB, Sunnen CN, Swerdlow SJ, Tobiason D, Tolsma SS, Tsourkas PK, Ward RE, Ware VC, Warner MH, Washington JM, Westover KM, White SJ, Whitefleet-Smith JL, Williams DC, Wolyniak MJ, Zeilstra-Ryalls JH, Asai DJ, Hatfull GF, and Sivanathan V

Subjects
Engineering, Faculty, Humans, Mathematics, Teaching, Models, Educational, Students
Abstract

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.

Published
2022
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32. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.

Author

Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A, Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, and Matranga CB

Subjects
Animals, Culicidae virology, Disease Outbreaks, Gene Library, Genetic Variation, Genomics, High-Throughput Nucleotide Sequencing, Humans, Lassa Fever virology, Nigeria epidemiology, Oligonucleotide Probes, Oligonucleotides genetics, Sequence Analysis, DNA, Virus Diseases, Computational Biology methods, Genome, Viral, Metagenome, Metagenomics
Abstract

Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.

Published
2019
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33. Genome Sequences of 19 Rhodococcus erythropolis Cluster CA Phages.

Author

Bonilla JA, Isern S, Findley AM, Klyczek KK, Michael SF, Saha MS, Buchser WJ, Forsyth MH, Paudel S, Gissendanner CR, Wiedemeier AMD, Alonzo FL, Garlena RA, Russell DA, Pope WH, Cresawn SG, Jacobs-Sera D, and Hatfull GF

Abstract

We report the complete genome sequences of 19 cluster CA bacteriophages isolated from environmental samples using Rhodococcus erythropolis as a host. All of the phages are Siphoviridae , have similar genome lengths (46,314 to 46,985 bp) and G+C contents (58.5 to 58.8%), and share nucleotide sequence similarity., (Copyright © 2017 Bonilla et al.)

Published
2017
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