6 results on '"Sharon Reed"'
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2. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission
- Author
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Smruthi Karthikeyan, Joshua I. Levy, Peter De Hoff, Greg Humphrey, Amanda Birmingham, Kristen Jepsen, Sawyer Farmer, Helena M. Tubb, Tommy Valles, Caitlin E. Tribelhorn, Rebecca Tsai, Stefan Aigner, Shashank Sathe, Niema Moshiri, Benjamin Henson, Adam M. Mark, Abbas Hakim, Nathan A. Baer, Tom Barber, Pedro Belda-Ferre, Marisol Chacón, Willi Cheung, Evelyn S. Cresini, Emily R. Eisner, Alma L. Lastrella, Elijah S. Lawrence, Clarisse A. Marotz, Toan T. Ngo, Tyler Ostrander, Ashley Plascencia, Rodolfo A. Salido, Phoebe Seaver, Elizabeth W. Smoot, Daniel McDonald, Robert M. Neuhard, Angela L. Scioscia, Alysson M. Satterlund, Elizabeth H. Simmons, Dismas B. Abelman, David Brenner, Judith C. Bruner, Anne Buckley, Michael Ellison, Jeffrey Gattas, Steven L. Gonias, Matt Hale, Faith Hawkins, Lydia Ikeda, Hemlata Jhaveri, Ted Johnson, Vince Kellen, Brendan Kremer, Gary Matthews, Ronald W. McLawhon, Pierre Ouillet, Daniel Park, Allorah Pradenas, Sharon Reed, Lindsay Riggs, Alison Sanders, Bradley Sollenberger, Angela Song, Benjamin White, Terri Winbush, Christine M. Aceves, Catelyn Anderson, Karthik Gangavarapu, Emory Hufbauer, Ezra Kurzban, Justin Lee, Nathaniel L. Matteson, Edyth Parker, Sarah A. Perkins, Karthik S. Ramesh, Refugio Robles-Sikisaka, Madison A. Schwab, Emily Spencer, Shirlee Wohl, Laura Nicholson, Ian H. McHardy, David P. Dimmock, Charlotte A. Hobbs, Omid Bakhtar, Aaron Harding, Art Mendoza, Alexandre Bolze, David Becker, Elizabeth T. Cirulli, Magnus Isaksson, Kelly M. Schiabor Barrett, Nicole L. Washington, John D. Malone, Ashleigh Murphy Schafer, Nikos Gurfield, Sarah Stous, Rebecca Fielding-Miller, Richard S. Garfein, Tommi Gaines, Cheryl Anderson, Natasha K. Martin, Robert Schooley, Brett Austin, Duncan R. MacCannell, Stephen F. Kingsmore, William Lee, Seema Shah, Eric McDonald, Alexander T. Yu, Mark Zeller, Kathleen M. Fisch, Christopher Longhurst, Patty Maysent, David Pride, Pradeep K. Khosla, Louise C. Laurent, Gene W. Yeo, Kristian G. Andersen, and Rob Knight
- Subjects
Wastewater-Based Epidemiological Monitoring ,Multidisciplinary ,SARS-CoV-2 ,Sequence Analysis, RNA ,COVID-19 ,Humans ,RNA, Viral ,Wastewater - Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
- Published
- 2022
3. Development of primers specific for detection of Litylenchus crenatae, the causal agent of beech leaf disease, in plant tissue
- Author
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David Burke, Adam Hoke, Sharon Reed, Danielle Martin, Sarah Kyker, Mary Pitts, and Samantha Battinger
- Subjects
Plant Science ,Agronomy and Crop Science - Abstract
Beech leaf disease (BLD), an emerging threat to American beech (Fagus grandifolia) in the northern U.S. and Canada, was recently confirmed to be caused by the nematode, Litylenchus crenatae subsp. mccannii (hereafter L. crenatae). Consequently, there is a need for a rapid, sensitive, and accurate method for detecting L. crenatae for both diagnostic as well as control purposes. This research developed a new set of DNA primers that specifically amplify L. crenatae and allow for accurate detection of the nematode in plant tissue. These primers have also been used in quantitative PCR (qPCR) to determine relative differences in gene copy number between samples. This primer set provides an improved, effective tool for monitoring and detection of L. crenatae in temperate tree leaf tissue which is necessary to understand the spread of this emerging forest pest and to develop management strategies.
- Published
- 2023
4. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission
- Author
-
Smruthi Karthikeyan, Joshua I Levy, Peter De Hoff, Greg Humphrey, Amanda Birmingham, Kristen Jepsen, Sawyer Farmer, Helena M. Tubb, Tommy Valles, Caitlin E Tribelhorn, Rebecca Tsai, Stefan Aigner, Shashank Sathe, Niema Moshiri, Benjamin Henson, Adam M. Mark, Abbas Hakim, Nathan A Baer, Tom Barber, Pedro Belda-Ferre, Marisol Chacón, Willi Cheung, Evelyn S Cresini, Emily R Eisner, Alma L Lastrella, Elijah S Lawrence, Clarisse A Marotz, Toan T Ngo, Tyler Ostrander, Ashley Plascencia, Rodolfo A Salido, Phoebe Seaver, Elizabeth W Smoot, Daniel McDonald, Robert M Neuhard, Angela L Scioscia, Alysson M. Satterlund, Elizabeth H Simmons, Dismas B. Abelman, David Brenner, Judith C. Bruner, Anne Buckley, Michael Ellison, Jeffrey Gattas, Steven L. Gonias, Matt Hale, Faith Hawkins, Lydia Ikeda, Hemlata Jhaveri, Ted Johnson, Vince Kellen, Brendan Kremer, Gary Matthews, Ronald W. McLawhon, Pierre Ouillet, Daniel Park, Allorah Pradenas, Sharon Reed, Lindsay Riggs, Alison Sanders, Bradley Sollenberger, Angela Song, Benjamin White, Terri Winbush, Christine M Aceves, Catelyn Anderson, Karthik Gangavarapu, Emory Hufbauer, Ezra Kurzban, Justin Lee, Nathaniel L Matteson, Edyth Parker, Sarah A Perkins, Karthik S Ramesh, Refugio Robles-Sikisaka, Madison A Schwab, Emily Spencer, Shirlee Wohl, Laura Nicholson, Ian H Mchardy, David P Dimmock, Charlotte A Hobbs, Omid Bakhtar, Aaron Harding, Art Mendoza, Alexandre Bolze, David Becker, Elizabeth T Cirulli, Magnus Isaksson, Kelly M Schiabor Barrett, Nicole L Washington, John D Malone, Ashleigh Murphy Schafer, Nikos Gurfield, Sarah Stous, Rebecca Fielding-Miller, Richard S. Garfein, Tommi Gaines, Cheryl Anderson, Natasha K. Martin, Robert Schooley, Brett Austin, Duncan R. MacCannell, Stephen F Kingsmore, William Lee, Seema Shah, Eric McDonald, Alexander T. Yu, Mark Zeller, Kathleen M Fisch, Christopher Longhurst, Patty Maysent, David Pride, Pradeep K. Khosla, Louise C. Laurent, Gene W Yeo, Kristian G Andersen, and Rob Knight
- Abstract
SummaryAs SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
- Published
- 2021
5. Molecular Evaluation of Resistance to Rifampicin and Isoniazid of Tuberculosis Patients by test 'Genotype® MTBDR Plus' in Senegal
- Author
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Papa Amadou Lamine Gueye, Babacar Faye, Sharon Reed, Alioune Dieye, Cheikh Tidiane Ndour, Issa Jessika, Fatoumata Ba, Michael P. Grillo, Marie Sarr, and Mame Cheikh Seck
- Subjects
0301 basic medicine ,03 medical and health sciences ,Tuberculosis ,business.industry ,030106 microbiology ,Genotype ,Isoniazid ,medicine ,business ,medicine.disease ,Virology ,Rifampicin ,medicine.drug - Published
- 2018
6. Nutrient and suspended solid concentrations, loads, and yields in rivers across the Lake Winnipeg Basin: A twenty year trend assessment
- Author
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Adam G. Yates, Robert B. Brua, Arthur Friesen, Sharon Reedyk, and Glenn Benoy
- Subjects
WRTDS ,Total phosphorus ,Total nitrogen ,Total suspended solids ,Discharge ,Concentration-discharge ,Physical geography ,GB3-5030 ,Geology ,QE1-996.5 - Abstract
Study region: The Lake Winnipeg Basin in the northern Great Plains of North America Study focus: Assessment of trends in total nitrogen (TN), total phosphorus (TP) and total suspended solids (TSS) for 18 river stations in the Lake Winnipeg Basin for the period of 1996–2016 using a Weighted Regressions on Time, Discharge and Season (WRTDS) modeling approach. New hydrological insights for the region: We observed rapidly increasing concentrations, loads, and yields of TN, TP and TSS at most of the evaluated river monitoring stations in the eastern half of the basin. In contrast, nutrient and suspended solid loads tended to exhibit decreasing or stationary trends at most of the more western stations. Trends in nutrients and suspended solids typically corresponded to discharge, particularly in the Red-Assiniboine subdrainage where rapidly increasing nutrient loads were almost exclusively associated with runoff patterns. Our findings will serve as a baseline against which future trend assessments can be compared. Moreover, our findings suggest that land management practices aimed at reducing nutrient loads to Lake Winnipeg should be prioritized towards the rivers of the eastern subdrainages of the Lake Winnipeg basin.
- Published
- 2022
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