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

Author

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

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

Author

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

Published
2024
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6. 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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7. 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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8. 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

9. 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

10. Genome sequencing reveals Zika virus diversity and spread in the Americas

Author

Metsky, Hayden C, Matranga, Christian B, Wohl, Shirlee, Schaffner, Stephen F., Freije, Catherine A, Winnicki, Sarah, West, Kendra, Qu, J, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Christopher, Tomkins-Tinch, Ye, S.H, Park, Daniel J, Luo, Cynthia, Barnes, Kayla G, Shah, R.R., Chak, Bridget, Barbosa-Lima, G., Delatorre, E., Vieira, Y.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 IV, Edgar W, Anzinger, J.J., Garcia, K.F., Parhap, L.A., Gelvez Ramirez, R.M., Montoya, Miranda, Rojas, D.P., Brown, C.M., Hennigan, S., Sabina, B., Scotland, S., Gangavarapu, K., Grubaugh, N.D., Oliveira, G., Robles-Sikisaka, R., Rambaut, Andrew, Gehrke, L., Smole, S., Halloran, M.E., Villar Centeno, L.A., Mattar, S., Lorenzana, I., Cerbino-Neto, J., Valim, C., Degrave, W., Bozza, P.T., Souza, T.M.L., Bosch, I., Yozwiak, N.L., MacInnis, B.L., and Sabeti, P.C.

Abstract

Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part due to a lack of genomic data. We applied 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 analyzed 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 US. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of viral surveillance. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those potentially relevant to the effectiveness of diagnostic tests.

Published
2017

11. 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

12. 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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13. 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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