8 results on '"Barnes, Kayla G."'
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2. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems
- Author
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Barnes, Kayla G., Levy, Joshua I., Gauld, Jillian, Rigby, Jonathan, Kanjerwa, Oscar, Uzzell, Christopher B., Chilupsya, Chisomo, Anscombe, Catherine, Tomkins-Tinch, Christopher, Mbeti, Omar, Cairns, Edward, Thole, Herbert, McSweeney, Shannon, Chibwana, Marah G., Ashton, Philip M., Jere, Khuzwayo C., Meschke, John Scott, Diggle, Peter, Cornick, Jennifer, Chilima, Benjamin, Jambo, Kondwani, Andersen, Kristian G., Kawalazira, Gift, Paterson, Steve, Nyirenda, Tonney S., Feasey, Nicholas, Barnes, Kayla G., Levy, Joshua I., Gauld, Jillian, Rigby, Jonathan, Kanjerwa, Oscar, Uzzell, Christopher B., Chilupsya, Chisomo, Anscombe, Catherine, Tomkins-Tinch, Christopher, Mbeti, Omar, Cairns, Edward, Thole, Herbert, McSweeney, Shannon, Chibwana, Marah G., Ashton, Philip M., Jere, Khuzwayo C., Meschke, John Scott, Diggle, Peter, Cornick, Jennifer, Chilima, Benjamin, Jambo, Kondwani, Andersen, Kristian G., Kawalazira, Gift, Paterson, Steve, Nyirenda, Tonney S., and Feasey, Nicholas
- Abstract
The COVID-19 pandemic has profoundly impacted health systems globally and robust surveillance has been critical for pandemic control, however not all countries can currently sustain community pathogen surveillance programs. Wastewater surveillance has proven valuable in high-income settings, but less is known about the utility of water surveillance of pathogens in low-income countries. Here we show how wastewater surveillance of SAR-CoV-2 can be used to identify temporal changes and help determine circulating variants quickly. In Malawi, a country with limited community-based COVID-19 testing capacity, we explore the utility of rivers and wastewater for SARS-CoV-2 surveillance. From May 2020–May 2022, we collect water from up to 112 river or defunct wastewater treatment plant sites, detecting SARS-CoV-2 in 8.3% of samples. Peak SARS-CoV-2 detection in water samples predate peaks in clinical cases. Sequencing of water samples identified the Beta, Delta, and Omicron variants, with Delta and Omicron detected well in advance of detection in patients. Our work highlights how wastewater can be used to detect emerging waves, identify variants of concern, and provide an early warning system in settings with no formal sewage systems.
- Published
- 2023
3. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics
- Author
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Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Kotliar, Dylan, Lin, Aaron E, Logue, James, Hughes, Travis K, Khoury, Nadine M, Raju, Siddharth S, Wadsworth, Marc H, Chen, Han, Kurtz, Jonathan R, Dighero-Kemp, Bonnie, Bjornson, Zach B, Mukherjee, Nilanjan, Sellers, Brian A, Tran, Nancy, Bauer, Matthew R, Adams, Gordon C, Adams, Ricky, Rinn, John L, Melé, Marta, Schaffner, Stephen F, Nolan, Garry P, Barnes, Kayla G, Hensley, Lisa E, McIlwain, David R, Shalek, Alex K, Sabeti, Pardis C, Bennett, Richard S, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Kotliar, Dylan, Lin, Aaron E, Logue, James, Hughes, Travis K, Khoury, Nadine M, Raju, Siddharth S, Wadsworth, Marc H, Chen, Han, Kurtz, Jonathan R, Dighero-Kemp, Bonnie, Bjornson, Zach B, Mukherjee, Nilanjan, Sellers, Brian A, Tran, Nancy, Bauer, Matthew R, Adams, Gordon C, Adams, Ricky, Rinn, John L, Melé, Marta, Schaffner, Stephen F, Nolan, Garry P, Barnes, Kayla G, Hensley, Lisa E, McIlwain, David R, Shalek, Alex K, Sabeti, Pardis C, and Bennett, Richard S
- Abstract
© 2020 The Author(s) Single-cell profiling of circulating immune cells during Ebola virus (EBOV) infection in non-human primates resolves molecular correlates of viral tropism, characterizes replication dynamics within infected cells, and distinguishes expression changes that are mediated by viral infection from those due to cytokine signaling.
- Published
- 2022
4. Field-deployable viral diagnostics using CRISPR-Cas13
- Author
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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
5. Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum
- Author
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Whitaker College of Health Sciences and Technology, Broad Institute of MIT and Harvard, Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Park, Daniel J., Schaffner, Stephen F., Neafsey, Daniel E., Cortese, Joseph F., Daniels, Rachel F., Johnson, Charles A., Shlyakhter, Ilya, Grossman, Sharon Rachel, Karlsson, Elinor K., Birren, Bruce W., Wiegand, Roger C., Wirth, Dyann F., Volkman, Sarah K., Sabeti, Pardis C., Tyne, Daria Van, Angelino, Elaine, Barnes, Kayla G., Rosen, David M., Lukens, Amanda K., Milner, Danny A., Becker, Justin S., Yamins, Daniel, Ndiaye, Daouda, Sarr, Ousmane, Mboup, Soulyemane, Happi, Christian, Furlotte, Nicholas A., Eskin, Eleazar, Kang, Hyun Min, Hartl, Daniel L., Whitaker College of Health Sciences and Technology, Broad Institute of MIT and Harvard, Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Park, Daniel J., Schaffner, Stephen F., Neafsey, Daniel E., Cortese, Joseph F., Daniels, Rachel F., Johnson, Charles A., Shlyakhter, Ilya, Grossman, Sharon Rachel, Karlsson, Elinor K., Birren, Bruce W., Wiegand, Roger C., Wirth, Dyann F., Volkman, Sarah K., Sabeti, Pardis C., Tyne, Daria Van, Angelino, Elaine, Barnes, Kayla G., Rosen, David M., Lukens, Amanda K., Milner, Danny A., Becker, Justin S., Yamins, Daniel, Ndiaye, Daouda, Sarr, Ousmane, Mboup, Soulyemane, Happi, Christian, Furlotte, Nicholas A., Eskin, Eleazar, Kang, Hyun Min, and Hartl, Daniel L.
- Abstract
The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (~1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome., Bill & Melinda Gates Foundation, Ellison Medical Foundation, Exxon Mobil Foundation, Fogarty International Center, National Institute of Allergy and Infectious Diseases (U.S.), Burroughs Wellcome Fund, David & Lucile Packard Foundation, National Science Foundation (U.S.). Graduate Research Fellowship Program
- Published
- 2012
6. Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum
- Author
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Whitaker College of Health Sciences and Technology, Broad Institute of MIT and Harvard, Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Park, Daniel J., Schaffner, Stephen F., Neafsey, Daniel E., Cortese, Joseph F., Daniels, Rachel F., Johnson, Charles A., Shlyakhter, Ilya, Grossman, Sharon Rachel, Karlsson, Elinor K., Birren, Bruce W., Wiegand, Roger C., Wirth, Dyann F., Volkman, Sarah K., Sabeti, Pardis C., Tyne, Daria Van, Angelino, Elaine, Barnes, Kayla G., Rosen, David M., Lukens, Amanda K., Milner, Danny A., Becker, Justin S., Yamins, Daniel, Ndiaye, Daouda, Sarr, Ousmane, Mboup, Soulyemane, Happi, Christian, Furlotte, Nicholas A., Eskin, Eleazar, Kang, Hyun Min, Hartl, Daniel L., Park, Daniel, Schaffner, Stephen F, Karlsson, Elinor, Lander, Eric Steven, Sabeti, Pardis, Whitaker College of Health Sciences and Technology, Broad Institute of MIT and Harvard, Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Park, Daniel J., Schaffner, Stephen F., Neafsey, Daniel E., Cortese, Joseph F., Daniels, Rachel F., Johnson, Charles A., Shlyakhter, Ilya, Grossman, Sharon Rachel, Karlsson, Elinor K., Birren, Bruce W., Wiegand, Roger C., Wirth, Dyann F., Volkman, Sarah K., Sabeti, Pardis C., Tyne, Daria Van, Angelino, Elaine, Barnes, Kayla G., Rosen, David M., Lukens, Amanda K., Milner, Danny A., Becker, Justin S., Yamins, Daniel, Ndiaye, Daouda, Sarr, Ousmane, Mboup, Soulyemane, Happi, Christian, Furlotte, Nicholas A., Eskin, Eleazar, Kang, Hyun Min, Hartl, Daniel L., Park, Daniel, Schaffner, Stephen F, Karlsson, Elinor, Lander, Eric Steven, and Sabeti, Pardis
- Abstract
The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (~1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome., Bill & Melinda Gates Foundation, Ellison Medical Foundation, Exxon Mobil Foundation, Fogarty International Center, National Institute of Allergy and Infectious Diseases (U.S.), Burroughs Wellcome Fund, David & Lucile Packard Foundation, National Science Foundation (U.S.). Graduate Research Fellowship Program
- Published
- 2012
7. Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum.
- Author
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Van Tyne, Daria, Van Tyne, Daria, Park, Daniel J, Schaffner, Stephen F, Neafsey, Daniel E, Angelino, Elaine, Cortese, Joseph F, Barnes, Kayla G, Rosen, David M, Lukens, Amanda K, Daniels, Rachel F, Milner, Danny A, Johnson, Charles A, Shlyakhter, Ilya, Grossman, Sharon R, Becker, Justin S, Yamins, Daniel, Karlsson, Elinor K, Ndiaye, Daouda, Sarr, Ousmane, Mboup, Souleymane, Happi, Christian, Furlotte, Nicholas A, Eskin, Eleazar, Kang, Hyun Min, Hartl, Daniel L, Birren, Bruce W, Wiegand, Roger C, Lander, Eric S, Wirth, Dyann F, Volkman, Sarah K, Sabeti, Pardis C, Van Tyne, Daria, Van Tyne, Daria, Park, Daniel J, Schaffner, Stephen F, Neafsey, Daniel E, Angelino, Elaine, Cortese, Joseph F, Barnes, Kayla G, Rosen, David M, Lukens, Amanda K, Daniels, Rachel F, Milner, Danny A, Johnson, Charles A, Shlyakhter, Ilya, Grossman, Sharon R, Becker, Justin S, Yamins, Daniel, Karlsson, Elinor K, Ndiaye, Daouda, Sarr, Ousmane, Mboup, Souleymane, Happi, Christian, Furlotte, Nicholas A, Eskin, Eleazar, Kang, Hyun Min, Hartl, Daniel L, Birren, Bruce W, Wiegand, Roger C, Lander, Eric S, Wirth, Dyann F, Volkman, Sarah K, and Sabeti, Pardis C
- Abstract
The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (∼ 1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome.
- Published
- 2011
8. Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum.
- Author
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Van Tyne, Daria, Moran, Nancy A1, Van Tyne, Daria, Park, Daniel J, Schaffner, Stephen F, Neafsey, Daniel E, Angelino, Elaine, Cortese, Joseph F, Barnes, Kayla G, Rosen, David M, Lukens, Amanda K, Daniels, Rachel F, Milner, Danny A, Johnson, Charles A, Shlyakhter, Ilya, Grossman, Sharon R, Becker, Justin S, Yamins, Daniel, Karlsson, Elinor K, Ndiaye, Daouda, Sarr, Ousmane, Mboup, Souleymane, Happi, Christian, Furlotte, Nicholas A, Eskin, Eleazar, Kang, Hyun Min, Hartl, Daniel L, Birren, Bruce W, Wiegand, Roger C, Lander, Eric S, Wirth, Dyann F, Volkman, Sarah K, Sabeti, Pardis C, Van Tyne, Daria, Moran, Nancy A1, Van Tyne, Daria, Park, Daniel J, Schaffner, Stephen F, Neafsey, Daniel E, Angelino, Elaine, Cortese, Joseph F, Barnes, Kayla G, Rosen, David M, Lukens, Amanda K, Daniels, Rachel F, Milner, Danny A, Johnson, Charles A, Shlyakhter, Ilya, Grossman, Sharon R, Becker, Justin S, Yamins, Daniel, Karlsson, Elinor K, Ndiaye, Daouda, Sarr, Ousmane, Mboup, Souleymane, Happi, Christian, Furlotte, Nicholas A, Eskin, Eleazar, Kang, Hyun Min, Hartl, Daniel L, Birren, Bruce W, Wiegand, Roger C, Lander, Eric S, Wirth, Dyann F, Volkman, Sarah K, and Sabeti, Pardis C
- Abstract
The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (∼ 1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome.
- Published
- 2011
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