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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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4. 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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6. 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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7. 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

9. 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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10. 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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11. 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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12. 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

13. 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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14. 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

15. 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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17. 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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18. 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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19. 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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20. 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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21. 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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22. 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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