HomeStockWeather reportNetworkAwardees
Back to network

Development and Proof-of-Concept Implementation of the South Florida Miami RADx-rad SARS-CoV-2 Wastewater-Based Surveillance Infrastructure

University of Miami Coral Gables

Helena Solo-Gabriele

Wastewater
Website

Related publications

Framework for a Community Health Observing System for the Gulf of Mexico Region: Preparing for Future Disasters.

Written by Paul Sandifer, Landon Knapp, Maureen Lichtveld, Ruth Manley, David Abramson, Rex Caffey, David Cochran, Tracy Collier, Kristie Ebi, Lawrence Engel, John Farrington, Melissa Finucane, Christine Hale, David Halpern, Emily Harville, Leslie Hart, Yulin Hswen, Barbara Kirkpatrick, Bruce McEwen, Glenn Morris, Raymond Orbach, Lawrence Palinkas, Melissa Partyka, Dwayne Porter, Aric A Prather, Teresa Rowles, Geoffrey Scott, Teresa Seeman, Helena Solo-Gabriele, Erik Svendsen, Terry Tincher, Juli Trtanj, Ann Hayward Walker, Rachel Yehuda, Fuyuen Yip, David Yoskowitz, Burton Singer
October 15, 2020

The Gulf of Mexico (GoM) region is prone to disasters, including recurrent oil spills, hurricanes, floods, industrial accidents, harmful algal blooms, and the current COVID-19 pandemic. The GoM and other…

Fecal indicator bacteria levels at a marine beach before, during, and after the COVID-19 shutdown period and associations with decomposing seaweed and human presence.

Written by Afeefa A Abdool-Ghany, Peter J Sahwell, James Klaus, Maribeth L Gidley, Christopher D Sinigalliano, Helena M Solo-Gabriele
August 27, 2022

Studies are limited that evaluate seaweed as a source of bacteria to beach waters. The objective of the current study was to evaluate whether seaweed, along with humans and other…

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications.

Written by Keith J M Moore, Jeremy Cahill, Guy Aidelberg, Rachel Aronoff, Ali Bektaş, Daniela Bezdan, Daniel J Butler, Sridar V Chittur, Martin Codyre, Fernan Federici, Nathan A Tanner, Scott W Tighe, Randy True, Sarah B Ware, Anne L Wyllie, Evan E Afshin, Andres Bendesky, Connie B Chang, Richard Dela Rosa, Eran Elhaik, David Erickson, Andrew S Goldsborough, George Grills, Kathrin Hadasch, Andrew Hayden, Seong-Young Her, Julie A Karl, Chang Hee Kim, Alison J Kriegel, Thomas Kunstman, Zeph Landau, Kevin Land, Bradley W Langhorst, Ariel B Lindner, Benjamin E Mayer, Lee A McLaughlin, Matthew T McLaughlin, Jenny Molloy, Christopher Mozsary, Jerry L Nadler, Melinee D'Silva, David Ng, David H O'Connor, Jerry E Ongerth, Olayinka Osuolale, Ana Pinharanda, Dennis Plenker, Ravi Ranjan, Michael Rosbash, Assaf Rotem, Jacob Segarra, Stephan Schürer, Scott Sherrill-Mix, Helena Solo-Gabriele, Shaina To, Merly C Vogt, Albert D Yu, Christopher E Mason

As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is…

Relationships between SARS-CoV-2 in Wastewater and COVID-19 Clinical Cases and Hospitalizations, with and without Normalization against Indicators of Human Waste.

Written by Qingyu Zhan, Kristina M Babler, Mark E Sharkey, Ayaaz Amirali, Cynthia C Beaver, Melinda M Boone, Samuel Comerford, Daniel Cooper, Elena M Cortizas, Benjamin B Currall, Jonathan Foox, George S Grills, Erin Kobetz, Naresh Kumar, Jennifer Laine, Walter E Lamar, Alejandro M A Mantero, Christopher E Mason, Brian D Reding, Maria Robertson, Matthew A Roca, Krista Ryon, Stephan C Schürer, Bhavarth S Shukla, Natasha Schaefer Solle, Mario Stevenson, John J Tallon, Collette Thomas, Tori Thomas, Dušica Vidović, Sion L Williams, Xue Yin, Helena M Solo-Gabriele
November 11, 2022

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in wastewater has been used to track community infections of coronavirus disease-2019 (COVID-19), providing critical information for public health interventions. Since levels in wastewater…

Degradation rates influence the ability of composite samples to represent 24-hourly means of SARS-CoV-2 and other microbiological target measures in wastewater.

Written by Kristina M Babler, Mark E Sharkey, Samantha Abelson, Ayaaz Amirali, Aymara Benitez, Gabriella A Cosculluela, George S Grills, Naresh Kumar, Jennifer Laine, Walter Lamar, Erik D Lamm, Jiangnan Lyu, Christopher E Mason, Philip M McCabe, Joshi Raghavender, Brian D Reding, Matthew A Roca, Stephan C Schürer, Mario Stevenson, Angela Szeto, John J Tallon, Dusica Vidović, Yalda Zarnegarnia, Helena M Solo-Gabriele
April 1, 2023

The utility of using severe-acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA for assessing the prevalence of COVID-19 within communities begins with the design of the sample collection program. The objective of…

COVID-19 Prediction using Genomic Footprint of SARS-CoV-2 in Air, Surface Swab and Wastewater

Written by Helena Solo-Gabriele, Shelja Kumar, Abelson Samantha, Jonathon Penso, Kristina M. Babler, Contreras Axel Julio, Mark Sharkey, Alejandro Mantero, Christopher Mason, Sion Llewleyn Williams, Erin Kobetz, Stephan Schuerer, Dusica Vidovic, George S. Grills, Walter Lamar, John Tallon, Natasha Solle, Richard John Kenney, Bhavarth Shukla, Dushyantha Jayaweera, Mehdi Mirsaeidi, Naresh Kumar
March 17, 2022

ImportanceGenomic footprints of pathogens shed by infected individuals can be traced in environmental samples. Analysis of these samples can be employed for noninvasive surveillance of infectious diseases.

ObjectiveTo evaluate the…

Predicting COVID-19 cases using SARS-CoV-2 RNA in air, surface swab and wastewater samples.

Written by Helena M Solo-Gabriele, Shelja Kumar, Samantha Abelson, Johnathon Penso, Julio Contreras, Kristina M Babler, Mark E Sharkey, Alejandro M A Mantero, Walter E Lamar, John J Tallon, Erin Kobetz, Natasha Schaefer Solle, Bhavarth S Shukla, Richard J Kenney, Christopher E Mason, Stephan C Schürer, Dusica Vidovic, Sion L Williams, George S Grills, Dushyantha T Jayaweera, Mehdi Mirsaeidi, Naresh Kumar
October 4, 2022

Genomic footprints of pathogens shed by infected individuals can be traced in environmental samples, which can serve as a noninvasive method of infectious disease surveillance. The research evaluates the efficacy…

Lessons learned from SARS-CoV-2 measurements in wastewater.

Written by Mark E Sharkey, Naresh Kumar, Alejandro M A Mantero, Kristina M Babler, Melinda M Boone, Yoslayma Cardentey, Elena M Cortizas, George S Grills, James Herrin, Jenny M Kemper, Richard Kenney, Erin Kobetz, Jennifer Laine, Walter E Lamar, Christopher C Mader, Christopher E Mason, Anda Z Quintero, Brian D Reding, Matthew A Roca, Krista Ryon, Natasha Schaefer Solle, Stephan C Schürer, Bhavarth Shukla, Mario Stevenson, Thomas Stone, John J Tallon, Sreeharsha S Venkatapuram, Dusica Vidovic, Sion L Williams, Benjamin Young, Helena M Solo-Gabriele
December 1, 2021

Standardized protocols for wastewater-based surveillance (WBS) for the RNA of SARS-CoV-2, the virus responsible for the current COVID-19 pandemic, are being developed and refined worldwide for early detection of disease…

A Rapid, Isothermal, and Point-of-Care System for COVID-19 Diagnostics.

Written by Christopher Mozsary, Duncan McCloskey, Kristina M Babler, Juan Boza, Daniel Butler, Benjamin Currall, Sion Williams, Anne Wiley, Evan E Afshin, George S Grills, Mark E Sharkey, Prem Premsrirut, Helena Solo-Gabriele, Yoslayma Cardentey, David Erickson, Christopher E Mason

The COVID-19 pandemic has had a profound, detrimental effect on economies and societies worldwide. Where the pandemic has been controlled, extremely high rates of diagnostic testing for the SARS-CoV-2 virus…

COVID-19 Case and Mortality Surveillance using Daily SARS-CoV-2 in Wastewater Samples adjusting for Meteorological Conditions and Sample pH

Written by Abelson Samantha, Bader Alsuliman, Jonathon Penso, Kristina Babler, Mark Sharkey, Christopher Mason, George S. Grills, Helena Solo-Gabriele, Naresh Kumar
July 12, 2023

BackgroundWastewater monitoring is increasingly used for community surveillance of infectious diseases, especially after the COVID-19 pandemic as the genomic footprints of pathogens shed by infected individuals can be traced in…

Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights.

Written by Dorottya Nagy-Szakal, Mara Couto-Rodriguez, Heather L Wells, Joseph E Barrows, Marilyne Debieu, Kristin Butcher, Siyuan Chen, Agnes Berki, Courteny Hager, Robert J Boorstein, Mariah K Taylor, Colleen B Jonsson, Christopher E Mason, Niamh B O'Hara
October 31, 2021

The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic…

SARS-CoV-2 genome diversity at the binding sites of oligonucleotides used for COVID-19 diagnosis

Written by Renan Valieris, Michal Kowaslki, Alina Frolova, Witold Wydmanski, Johnathan Foox, Giovana Torrezan, Ewelina Pospiech, Wojciech Branicki, Kasthuri Venkateswaran, Bharath Prithiviraj, Ramasamy Dhamodharan, Klas Udekwu, Diana Nunes, Dirce Carraro, Christopher Mason, Pawel Labaj, Israel Silva, Emmanuel Dias-Neto
December 11, 2020

ImportanceSARS-CoV-2 genomic variants impacts the overall sensitivity of COVID-19 diagnosis, leading to false-negative diagnosis and the continued spread of the virus.

ObjectiveTo evaluate how nucleotide variability in target primer binding…

Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.

Written by Chantal B F Vogels, Mallery I Breban, Isabel M Ott, Tara Alpert, Mary E Petrone, Anne E Watkins, Chaney C Kalinich, Rebecca Earnest, Jessica E Rothman, Jaqueline Goes de Jesus, Ingra Morales Claro, Giulia Magalhães Ferreira, Myuki A E Crispim, Lavanya Singh, Houriiyah Tegally, Ugochukwu J Anyaneji, Emma B Hodcroft, Christopher E Mason, Gaurav Khullar, Jessica Metti, Joel T Dudley, Matthew J MacKay, Megan Nash, Jianhui Wang, Chen Liu, Pei Hui, Steven Murphy, Caleb Neal, Eva Laszlo, Marie L Landry, Anthony Muyombwe, Randy Downing, Jafar Razeq, Tulio de Oliveira, Nuno R Faria, Ester C Sabino, Richard A Neher, Joseph R Fauver, Nathan D Grubaugh
May 7, 2021

With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted…

Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States.

Written by Tara Alpert, Anderson F Brito, Erica Lasek-Nesselquist, Jessica Rothman, Andrew L Valesano, Matthew J MacKay, Mary E Petrone, Mallery I Breban, Anne E Watkins, Chantal B F Vogels, Chaney C Kalinich, Simon Dellicour, Alexis Russell, John P Kelly, Matthew Shudt, Jonathan Plitnick, Erasmus Schneider, William J Fitzsimmons, Gaurav Khullar, Jessica Metti, Joel T Dudley, Megan Nash, Nike Beaubier, Jianhui Wang, Chen Liu, Pei Hui, Anthony Muyombwe, Randy Downing, Jafar Razeq, Stephen M Bart, Ardath Grills, Stephanie M Morrison, Steven Murphy, Caleb Neal, Eva Laszlo, Hanna Rennert, Melissa Cushing, Lars Westblade, Priya Velu, Arryn Craney, Lin Cong, David R Peaper, Marie L Landry, Peter W Cook, Joseph R Fauver, Christopher E Mason, Adam S Lauring, Kirsten St George, Duncan R MacCannell, Nathan D Grubaugh
May 13, 2021

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2,500 COVID-19 cases…

Viral Dynamics of SARS-CoV-2 Variants in Vaccinated and Unvaccinated Persons.

Written by Stephen M Kissler, Joseph R Fauver, Christina Mack, Caroline G Tai, Mallery I Breban, Anne E Watkins, Radhika M Samant, Deverick J Anderson, Jessica Metti, Gaurav Khullar, Rachel Baits, Matthew MacKay, Daisy Salgado, Tim Baker, Joel T Dudley, Christopher E Mason, David D Ho, Nathan D Grubaugh, Yonatan H Grad
December 23, 2021

Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection

Written by Justin Frere, Sonja M Best, Henry Cope, Viktorija Zaksas, Amanda Saravia-Butler, Cem Meydan, Jonathan Foox, Christopher Mozsary, Yared H Kidane, Waldemar Priebe, Mark Emmett, Robert Meller, Urminder Singh, Yaron Bram, Benjamin R. tenOever, Mark T. Heise, Nathaniel J. Moorman, Emily A. Madden, Sharon A. Taft-Benz, Elizabeth J. Anderson, Wes A. Sanders, Rebekah J. Dickmander, Victoria K. Baxter, Stephen Baylin, Eve Wurtele, Pedro Moraes-vieira, Christopher Mason, Jonathan C Schisler, Robert E. Schwartz, Afshin Beheshti
February 22, 2022

Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription…

The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing.

Written by Matthew J MacKay, Anna C Hooker, Ebrahim Afshinnekoo, Marc Salit, Jason Kelly, Jonathan V Feldstein, Nick Haft, Doug Schenkel, Subhalaxmi Nambi, Yizhi Cai, Feng Zhang, George Church, Junbiao Dai, Cliff L Wang, Shawn Levy, Jeff Huber, Hanlee P Ji, Alison Kriegel, Anne L Wyllie, Christopher E Mason

SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.

Written by Nicolae Sapoval, Medhat Mahmoud, Michael D Jochum, Yunxi Liu, R A Leo Elworth, Qi Wang, Dreycey Albin, Huw A Ogilvie, Michael D Lee, Sonia Villapol, Kyle M Hernandez, Irina Maljkovic Berry, Jonathan Foox, Afshin Beheshti, Krista Ternus, Kjersti M Aagaard, David Posada, Christopher E Mason, Fritz J Sedlazeck, Todd J Treangen
February 18, 2021

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively…

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

Written by Nicolae Sapoval, Medhat Mahmoud, Michael D. Jochum, Yunxi Liu, R.A. Leo Elworth, Qi Wang, Dreycey Albin, Huw Ogilvie, Michael D. Lee, Sonia Villapol, Kyle Hernandez, Irina Maljkovic Berry, Jon Foox, Afshin Beheshti, Krista Ternus, Kjersti M. Aagaard, David Posada, Christopher Mason, Fritz J Sedlazeck, Todd J Treangen
July 2, 2020

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively…

End-to-End Protocol for the Detection of SARS-CoV-2 from Built Environments.

Written by Ceth W Parker, Nitin Singh, Scott Tighe, Adriana Blachowicz, Jason M Wood, Arman Seuylemezian, Parag Vaishampayan, Camilla Urbaniak, Ryan Hendrickson, Pheobe Laaguiby, Kevin Clark, Brian G Clement, Niamh B O'Hara, Mara Couto-Rodriguez, Daniela Bezdan, Christopher E Mason, Kasthuri Venkateswaran
October 6, 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019, is a respiratory virus primarily transmitted person to person through inhalation of droplets or aerosols, laden…

COVID-19 drug practices risk antimicrobial resistance evolution.

Written by Ebrahim Afshinnekoo, Chandrima Bhattacharya, Ana Burguete-García, Eduardo Castro-Nallar, Youping Deng, Christelle Desnues, Emmanuel Dias-Neto, Eran Elhaik, Gregorio Iraola, Soojin Jang, Paweł P Łabaj, Christopher E Mason, Niranjan Nagarajan, Michael Poulsen, Bharath Prithiviraj, Rania Siam, Tieliu Shi, Haruo Suzuki, Johannes Werner, Maria Mercedes Zambrano, Malay Bhattacharyya
February 24, 2021

Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Written by Daniel J Butler, Christopher Mozsary, Cem Meydan, David C Danko, Jonathan Foox, Joel Rosiene, Alon Shaiber, Ebrahim Afshinnekoo, Matthew MacKay, Fritz J Sedlazeck, Nikolay A Ivanov, Maria A Sierra, Diana Pohle, Michael Zietz, Undina Gisladottir, Vijendra Ramlall, Craig D Westover, Krista Ryon, Benjamin Young, Chandrima Bhattacharya, Phyllis Ruggiero, Bradley W Langhorst, Nathan A Tanner, Justyna Gawrys, Dmitry Meleshko, Dong Xu, Peter A D Steel, Amos J Shemesh, Jenny Xiang, Jean Thierry-Mieg, Danielle Thierry-Mieg, Robert E Schwartz, Angelika Iftner, Daniela Bezdan, John Sipley, Lin Cong, Arryn Craney, Priya Velu, Ari Melnick, Iman Hajirasouliha, Stacy M Horner, Thomas Iftner, Mirella Salvatore, Massimo Loda, Lars F Westblade, Shawn Levy, Melissa Cushing, Shixiu Wu, Nicholas P Tatonetti, Marcin Imielinski, Hanna Rennert, Christopher Mason
April 20, 2020

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted…

Effectiveness of SARS-CoV-2 Decontamination and Containment in a COVID-19 ICU.

Written by Zarina Brune, Cyrus E Kuschner, Joseph Mootz, Karina W Davidson, Robert C F Pena, Mustafa H Ghanem, Austin Fischer, Michael Gitman, Lewis Teperman, Christopher Mason, Lance B Becker
March 3, 2021

Background: Health care systems in the United States are continuously expanding and contracting spaces to treat patients with coronavirus disease 2019 (COVID-19) in intensive care units (ICUs). As a result,…

Precision health diagnostic and surveillance network uses S gene target failure (SGTF) combined with sequencing technologies to track emerging SARS-CoV-2 variants.

Written by Rafael Guerrero-Preston, Vanessa Rivera-Amill, Karem Caraballo, Sebastian Rodríguez-Torres, Ana Purcell-Wiltz, Andrea A García, Raphael S Torres, Fernando T Zamuner, Claudio Zanettini, Matthew J MacKay, Rachel Baits, Daisy Salgado, Gaurav Khullar, Jessica Metti, Timothy Baker, Joel Dudley, Keilyn Vale, Gabriela Pérez, Lorena De Jesús, Yaima Miranda, Denise Ortiz, Amanda García-Negrón, Liliana Viera, Alberto Ortiz, Jorge A Canabal, Josefina Romaguera, Ivonne Jiménez-Velázquez, Luigi Marchionni, José F Rodríguez-Orengo, Adriana Baez, Christopher E Mason, David Sidransky

INTRODUCTION: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic revealed a worldwide lack of effective molecular surveillance networks at local, state, and national levels, which are essential to identify,…

The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response.

Written by Francisco J Enguita, Ana Lúcia Leitão, J Tyson McDonald, Viktorija Zaksas, Saswati Das, Diego Galeano, Deanne Taylor, Eve Syrkin Wurtele, Amanda Saravia-Butler, Stephen B Baylin, Robert Meller, D Marshall Porterfield, Douglas C Wallace, Jonathan C Schisler, Christopher E Mason, Afshin Beheshti
May 9, 2022

Rationale: Viral infections are complex processes based on an intricate network of molecular interactions. The infectious agent hijacks components of the cellular machinery for its profit, circumventing the natural defense…

Role of miR-2392 in driving SARS-CoV-2 infection.

Written by J Tyson McDonald, Francisco J Enguita, Deanne Taylor, Robert J Griffin, Waldemar Priebe, Mark R Emmett, Mohammad M Sajadi, Anthony D Harris, Jean Clement, Joseph M Dybas, Nukhet Aykin-Burns, Joseph W Guarnieri, Larry N Singh, Peter Grabham, Stephen B Baylin, Aliza Yousey, Andrea N Pearson, Peter M Corry, Amanda Saravia-Butler, Thomas R Aunins, Sadhana Sharma, Prashant Nagpal, Cem Meydan, Jonathan Foox, Christopher Mozsary, Bianca Cerqueira, Viktorija Zaksas, Urminder Singh, Eve Syrkin Wurtele, Sylvain V Costes, Gustavo Gastão Davanzo, Diego Galeano, Alberto Paccanaro, Suzanne L Meinig, Robert S Hagan, Natalie M Bowman, Matthew C Wolfgang, Selin Altinok, Nicolae Sapoval, Todd J Treangen, Pedro M Moraes-Vieira, Charles Vanderburg, Douglas C Wallace, Jonathan C Schisler, Christopher E Mason, Anushree Chatterjee, Robert Meller, Afshin Beheshti
October 19, 2021

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provide an exciting avenue toward antiviral therapeutics. From patient transcriptomic…

The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection

Written by J. Tyson McDonald, Francisco Javier Enguita, Robert J Griffin, Waldemar Priebe, Mark R Emmett, Mohammad Sajadi, Anthony D Harris, Jean Clement, Nukhet Aykin-Burns, Peter Grabham, Stephen Baylin, Aliza Yousey, Andrea N Pearson, Peter M Corry, Amanda Saravia-Butler, Thomas R Aunins, Sadhana Sharma, Prashant Nagpal, Cem Meydan, Jonathan Foox, Christopher Mozsary, Bianca Cerqueira, Viktorija Zaksas, Urminder Singh, Eve Syrkin Wurtele, Sylvain V Costes, Gustavo Gastao Davanzo, Diego Galeano, Alberto Paccanaro, Suzanne L Meinig, Robert S Hagan, Natalie M Bowman, - UNC COVID-19 Pathobiology Consortium, Matthew C Wolfgang, Selin Altinok, Nicolae Sapoval, Todd J Treangen, Pedro M. Moraes-Vieira, Charles Vanderburg, Jonathan C Schisler, Christopher Mason, Anushree Chatterjee, Robert Meller, Afshin Beheshti
April 23, 2021

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic…

The spatial landscape of lung pathology during COVID-19 progression.

Written by André F Rendeiro, Hiranmayi Ravichandran, Yaron Bram, Vasuretha Chandar, Junbum Kim, Cem Meydan, Jiwoon Park, Jonathan Foox, Tyler Hether, Sarah Warren, Youngmi Kim, Jason Reeves, Steven Salvatore, Christopher E Mason, Eric C Swanson, Alain C Borczuk, Olivier Elemento, Robert E Schwartz
March 29, 2021

Recent studies have provided insights into the pathology of and immune response to COVID-191-8. However, a thorough investigation of the interplay between infected cells and the immune system at sites…

Host transcriptional responses in nasal swabs identify potential SARS-CoV-2 infection in PCR negative patients.

Written by Amanda M Saravia-Butler, Jonathan C Schisler, Deanne Taylor, Afshin Beheshti, Dan Butler, Cem Meydan, Jonathon Foox, Kyle Hernandez, Chris Mozsary, Christopher E Mason, Robert Meller
November 18, 2022

We analyzed RNA sequencing data from nasal swabs used for SARS-CoV-2 testing. 13% of 317 PCR-negative samples contained over 100 reads aligned to multiple regions of the SARS-CoV-2 genome. Differential…

Betacoronavirus-specific alternate splicing.

Written by Guy Karlebach, Bruce Aronow, Stephen B Baylin, Daniel Butler, Jonathan Foox, Shawn Levy, Cem Meydan, Christopher Mozsary, Amanda M Saravia-Butler, Deanne M Taylor, Eve Wurtele, Christopher E Mason, Afshin Beheshti, Peter N Robinson
January 22, 2022

Viruses can subvert a number of cellular processes including splicing in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to…

A history of the MetaSUB consortium: Tracking urban microbes around the globe.

Written by Krista A Ryon, Braden T Tierney, Alina Frolova, Andre Kahles, Christelle Desnues, Christos Ouzounis, Cynthis Gibas, Daniela Bezdan, Youping Deng, Ding He, Emmanuel Dias-Neto, Eran Elhaik, Evan Afshin, George Grills, Gregorio Iraola, Haruo Suzuki, Johannes Werner, Klas Udekwu, Lynn Schriml, Malay Bhattacharyya, Manuela Oliveira, Maria Mercedes Zambrano, Nur Hazlin Hazrin-Chong, Olayinka Osuolale, Paweł P Łabaj, Prisca Tiasse, Sampath Rapuri, Silvia Borras, Sofya Pozdniakova, Tieliu Shi, Ugur Sezerman, Xavier Rodo, Zehra Hazal Sezer, Christopher E Mason
November 18, 2022

The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the…

System-wide transcriptome damage and tissue identity loss in COVID-19 patients.

Written by Jiwoon Park, Jonathan Foox, Tyler Hether, David C Danko, Sarah Warren, Youngmi Kim, Jason Reeves, Daniel J Butler, Christopher Mozsary, Joel Rosiene, Alon Shaiber, Evan E Afshin, Matthew MacKay, André F Rendeiro, Yaron Bram, Vasuretha Chandar, Heather Geiger, Arryn Craney, Priya Velu, Ari M Melnick, Iman Hajirasouliha, Afshin Beheshti, Deanne Taylor, Amanda Saravia-Butler, Urminder Singh, Eve Syrkin Wurtele, Jonathan Schisler, Samantha Fennessey, André Corvelo, Michael C Zody, Soren Germer, Steven Salvatore, Shawn Levy, Shixiu Wu, Nicholas P Tatonetti, Sagi Shapira, Mirella Salvatore, Lars F Westblade, Melissa Cushing, Hanna Rennert, Alison J Kriegel, Olivier Elemento, Marcin Imielinski, Charles M Rice, Alain C Borczuk, Cem Meydan, Robert E Schwartz, Christopher E Mason
February 15, 2022

The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory…

Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection.

Written by Vijendra Ramlall, Phyllis M Thangaraj, Cem Meydan, Jonathan Foox, Daniel Butler, Jacob Kim, Ben May, Jessica K De Freitas, Benjamin S Glicksberg, Christopher E Mason, Nicholas P Tatonetti, Sagi D Shapira
August 3, 2020

Understanding the pathophysiology of SARS-CoV-2 infection is critical for therapeutic and public health strategies. Viral-host interactions can guide discovery of disease regulators, and protein structure function analysis points to several…

Betacoronavirus-specific alternate splicing

Written by Guy Karlebach, Stephen J Baylin, Daniel Butler, Jonathan Foox, Shawn Levy, Cem Meydan, Christopher Mozsary, Amanda M Saravia-Butler, Eve Wurtele, Christopher Mason, Afshin Beheshti, Peter N. Robinson
July 2, 2021

Viruses can subvert a number of cellular processes in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global…

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.

Written by Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang, Sami Smalling, Liz-Audrey Kounatse Djomnang, Joan Sesing Lenz, Randy Longman, Amy Steadman, Luis G Gómez-Escobar, Edward J Schenck, Mirella Salvatore, Michael J Satlin, Manikkam Suthanthiran, John R Lee, Christopher E Mason, Darshana Dadhania, Iwijn De Vlaminck
July 21, 2022

Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we…

Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study.

Written by James A Hay, Stephen M Kissler, Joseph R Fauver, Christina Mack, Caroline G Tai, Radhika M Samant, Sarah Connolly, Deverick J Anderson, Gaurav Khullar, Matthew MacKay, Miral Patel, Shannan Kelly, April Manhertz, Isaac Eiter, Daisy Salgado, Tim Baker, Ben Howard, Joel T Dudley, Christopher E Mason, Manoj Nair, Yaoxing Huang, John DiFiori, David D Ho, Nathan D Grubaugh, Yonatan H Grad
November 16, 2022

BACKGROUND: The combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear. METHODS: We characterized 1,280 infections from the National Basketball Association occupational health cohort…

Transcriptional response modules characterize IL-1β and IL-6 activity in COVID-19.

Written by Lucy C K Bell, Cem Meydan, Jacob Kim, Jonathan Foox, Daniel Butler, Christopher E Mason, Sagi D Shapira, Mahdad Noursadeghi, Gabriele Pollara
January 22, 2021

Dysregulated IL-1β and IL-6 responses have been implicated in the pathogenesis of severe Coronavirus Disease 2019 (COVID-19). Innovative approaches for evaluating the biological activity of these cytokines in vivo are…

Ozone Disinfection for Elimination of Bacteria and Degradation of SARS-CoV2 RNA for Medical Environments.

Written by Craig Westover, Savlatjon Rahmatulloev, David Danko, Evan E Afshin, Niamh B O'Hara, Rachid Ounit, Daniela Bezdan, Christopher E Mason
December 28, 2022

Pathogenic bacteria and viruses in medical environments can lead to treatment complications and hospital-acquired infections. Current disinfection protocols do not address hard-to-access areas or may be beyond line-of-sight treatment, such…

Identification of Immune complement function as a determinant of adverse SARS-CoV-2 infection outcome

Written by Vijendra Ramlall, Phyllis Thangaraj, Cem Meydan, Jonathan Foox, Daniel Butler, Ben May, Jessica de Freitas, Benjamin S Glicksberg, Christopher Mason, Nicholas P Tatonetti, Sagi D Shapira
May 13, 2020

SO_SCPLOWUMMARYC_SCPLOWUnderstanding the pathophysiology of SARS-CoV-2 infection is critical for therapeutics and public health intervention strategies. Viral-host interactions can guide discovery of regulators of disease outcomes, and protein structure function analysis…

Connecting omics signatures and revealing biological mechanisms with iLINCS.

Written by Marcin Pilarczyk, Mehdi Fazel-Najafabadi, Michal Kouril, Behrouz Shamsaei, Juozas Vasiliauskas, Wen Niu, Naim Mahi, Lixia Zhang, Nicholas A Clark, Yan Ren, Shana White, Rashid Karim, Huan Xu, Jacek Biesiada, Mark F Bennett, Sarah E Davidson, John F Reichard, Kurt Roberts, Vasileios Stathias, Amar Koleti, Dusica Vidovic, Daniel J B Clarke, Stephan C Schürer, Avi Ma'ayan, Jarek Meller, Mario Medvedovic
August 9, 2022

There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses and visualization that do not require programming skills. Here we present…

Umbilical cord mesenchymal stem cells for COVID-19 acute respiratory distress syndrome: A double-blind, phase 1/2a, randomized controlled trial.

Written by Giacomo Lanzoni, Elina Linetsky, Diego Correa, Shari Messinger Cayetano, Roger A Alvarez, Dimitrios Kouroupis, Ana Alvarez Gil, Raffaella Poggioli, Phillip Ruiz, Antonio C Marttos, Khemraj Hirani, Crystal A Bell, Halina Kusack, Lisa Rafkin, David Baidal, Andrew Pastewski, Kunal Gawri, Clarissa Leñero, Alejandro M A Mantero, Sarah W Metalonis, Xiaojing Wang, Luis Roque, Burlett Masters, Norma S Kenyon, Enrique Ginzburg, Xiumin Xu, Jianming Tan, Arnold I Caplan, Marilyn K Glassberg, Rodolfo Alejandro, Camillo Ricordi
January 5, 2021

Acute respiratory distress syndrome (ARDS) in COVID-19 is associated with high mortality. Mesenchymal stem cells are known to exert immunomodulatory and anti-inflammatory effects and could yield beneficial effects in COVID-19…

Contextualizing covid-19 spread: a county level analysis, urban versus rural, and implications for preparing for the next wave

Written by J. Sunil Rao, Hang Zhang, Alejandro Mantero
April 29, 2020

Paraphrasing [Morano and Holt, 2017], contextual determinants of health including social, environmental, healthcare and others, are a so-called deck of cards one is dealt. The ability to modify health outcomes…

Development of a Standardized Data Collection Tool for Evaluation and Management of Coronavirus Disease 2019.

Written by Stephen R Morris, Yoichiro Natori, Douglas Salguero, Alejandro Mantero, Ruixuan Ma, Daniela F de Lima Corvino, Anmary Fernandez, Alex Lazo, Christine A Vu, Lauren Bjork, David Serota, Jennifer Quevedo, Ana Vega, Meshell Maxam, Kailynn DeRonde, Pablo Barreiro, Patricia Raccamarich, Maria Romero Alvarez, Dimitra Skiada, Shuba Balan, Maya Ramanathan, Gregory Holt, Jose Gonzales-Zamora, Gio J Baracco, Susanne Doblecki-Lewis, Lilian M Abbo, Paola N Lichtenberger, Maria L Alcaide
July 29, 2020

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 ) is responsible for coronavirus disease 2019 (COVID-19), a disease that had not been previously described and for which clinicians need to…

A Longitudinal Analysis of SARS-CoV-2 Antibody Responses Among People With HIV.

Written by Maria L Alcaide, Nicholas F Nogueira, Ana S Salazar, Emily K Montgomerie, Violeta J Rodriguez, Patricia D Raccamarich, Irma T Barreto, Angela McGaugh, Mark E Sharkey, Alejandro M Mantero, Allan E Rodriguez, Laura Beauchamps, Deborah L Jones
March 7, 2022

Background: The concentration and duration of antibodies (Ab) to SARS-CoV-2 infection predicts the severity of the disease and the clinical outcomes. Older people and those with HIV have impaired immune…

Infection with SARS-CoV-2 is associated with menstrual irregularities among women of reproductive age.

Written by Emily M Cherenack, Ana S Salazar, Nicholas F Nogueira, Patricia Raccamarich, Violeta J Rodriguez, Alejandro M Mantero, Allison Marsh, Sophia Gerard, Marissa Maddalon, Deborah L Jones, Nichole R Klatt, Maria L Alcaide
October 26, 2022

BACKGROUND: Biological and psychological mechanisms may be responsible for menstrual irregularities occurring among women during the COVID-19 pandemic. STUDY DESIGN: From January 2019 to September 2021, women (18- to 45-years-old…

A history of the MetaSUB consortium: Tracking urban microbes around the globe.

Written by Krista A Ryon, Braden T Tierney, Alina Frolova, Andre Kahles, Christelle Desnues, Christos Ouzounis, Cynthis Gibas, Daniela Bezdan, Youping Deng, Ding He, Emmanuel Dias-Neto, Eran Elhaik, Evan Afshin, George Grills, Gregorio Iraola, Haruo Suzuki, Johannes Werner, Klas Udekwu, Lynn Schriml, Malay Bhattacharyya, Manuela Oliveira, Maria Mercedes Zambrano, Nur Hazlin Hazrin-Chong, Olayinka Osuolale, Paweł P Łabaj, Prisca Tiasse, Sampath Rapuri, Silvia Borras, Sofya Pozdniakova, Tieliu Shi, Ugur Sezerman, Xavier Rodo, Zehra Hazal Sezer, Christopher E Mason
November 18, 2022

The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the…

Transcriptional response modules characterise IL-1 and IL-6 activity in COVID-19

Written by Lucy C K Bell, Cem Meydan, Jacob Kim, Jonathan Foox, Daniel Butler, Christopher E Mason, Sagi D Shapira, Mahdad Noursadeghi, Gabriele Pollara
July 23, 2020

Dysregulated IL-1{beta} and IL-6 responses have been implicated in the pathogenesis of severe Coronavirus Disease 2019 (COVID-19). Innovative approaches for evaluating the biological activity of these cytokines in vivo are…

Molecular determinants of disease severity in urinary tract infection.

Written by Ines Ambite, Daniel Butler, Murphy Lam Yim Wan, Therese Rosenblad, Thi Hien Tran, Sing Ming Chao, Catharina Svanborg
June 15, 2021

The most common and lethal bacterial pathogens have co-evolved with the host. Pathogens are the aggressors, and the host immune system is responsible for the defence. However, immune responses can…

Head and neck oncological ablation and reconstruction in the COVID-19 era - our experience to date.

Written by Daniel Butler, Cameron Davies-Husband, Jagtar Dhanda, Ian Francis, Aakshay Gulati, Karan Kapoor, Laurence Newman, Paul Norris, Zaid Sadiq, Christian Surwald, Navdeep Upile, Tim Vorster, Brian Bisase
June 17, 2020

The COVID-19 pandemic has caused unprecedented disruption to the routine operations of healthcare services across the world. As the potential duration of the pandemic remains uncertain, the need to develop…

Do undergraduate general practice placements propagate the 'inverse care law'?

Written by Daniel Butler, Diarmuid O'Donovan, Alice McClung, Nigel Hart
June 29, 2022

INTRODUCTION: Fifty years since Dr Tudor-Hart's publication of the 'Inverse Care Law', all-cause mortality rates and COVID-19 mortality rates are higher in more deprived areas. Part of the solution is…

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.

Written by Daniel Butler, Christopher Mozsary, Cem Meydan, Jonathan Foox, Joel Rosiene, Alon Shaiber, David Danko, Ebrahim Afshinnekoo, Matthew MacKay, Fritz J Sedlazeck, Nikolay A Ivanov, Maria Sierra, Diana Pohle, Michael Zietz, Undina Gisladottir, Vijendra Ramlall, Evan T Sholle, Edward J Schenck, Craig D Westover, Ciaran Hassan, Krista Ryon, Benjamin Young, Chandrima Bhattacharya, Dianna L Ng, Andrea C Granados, Yale A Santos, Venice Servellita, Scot Federman, Phyllis Ruggiero, Arkarachai Fungtammasan, Chen-Shan Chin, Nathaniel M Pearson, Bradley W Langhorst, Nathan A Tanner, Youngmi Kim, Jason W Reeves, Tyler D Hether, Sarah E Warren, Michael Bailey, Justyna Gawrys, Dmitry Meleshko, Dong Xu, Mara Couto-Rodriguez, Dorottya Nagy-Szakal, Joseph Barrows, Heather Wells, Niamh B O'Hara, Jeffrey A Rosenfeld, Ying Chen, Peter A D Steel, Amos J Shemesh, Jenny Xiang, Jean Thierry-Mieg, Danielle Thierry-Mieg, Angelika Iftner, Daniela Bezdan, Elizabeth Sanchez, Thomas R Campion, John Sipley, Lin Cong, Arryn Craney, Priya Velu, Ari M Melnick, Sagi Shapira, Iman Hajirasouliha, Alain Borczuk, Thomas Iftner, Mirella Salvatore, Massimo Loda, Lars F Westblade, Melissa Cushing, Shixiu Wu, Shawn Levy, Charles Chiu, Robert E Schwartz, Nicholas Tatonetti, Hanna Rennert, Marcin Imielinski, Christopher E Mason
March 12, 2021

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused…

Molnupiravir plus usual care versus usual care alone as early treatment for adults with COVID-19 at increased risk of adverse outcomes (PANORAMIC): an open-label, platform-adaptive randomised controlled trial.

Written by Christopher C Butler, F D Richard Hobbs, Oghenekome A Gbinigie, Najib M Rahman, Gail Hayward, Duncan B Richards, Jienchi Dorward, David M Lowe, Joseph F Standing, Judith Breuer, Saye Khoo, Stavros Petrou, Kerenza Hood, Jonathan S Nguyen-Van-Tam, Mahendra G Patel, Benjamin R Saville, Joe Marion, Emma Ogburn, Julie Allen, Heather Rutter, Nick Francis, Nicholas P B Thomas, Philip Evans, Melissa Dobson, Tracie-Ann Madden, Jane Holmes, Victoria Harris, May Ee Png, Mark Lown, Oliver van Hecke, Michelle A Detry, Christina T Saunders, Mark Fitzgerald, Nicholas S Berry, Lazaro Mwandigha, Ushma Galal, Sam Mort, Bhautesh D Jani, Nigel D Hart, Haroon Ahmed, Daniel Butler, Micheal McKenna, Jem Chalk, Layla Lavallee, Elizabeth Hadley, Lucy Cureton, Magdalena Benysek, Monique Andersson, Maria Coates, Sarah Barrett, Clare Bateman, Jennifer C Davies, Ivy Raymundo-Wood, Andrew Ustianowski, Andrew Carson-Stevens, Ly-Mee Yu, Paul Little
December 22, 2022

BACKGROUND: The safety, effectiveness, and cost-effectiveness of molnupiravir, an oral antiviral medication for SARS-CoV-2, has not been established in vaccinated patients in the community at increased risk of morbidity and…

Betacoronavirus-specific alternate splicing.

Written by Guy Karlebach, Bruce Aronow, Stephen B Baylin, Daniel Butler, Jonathan Foox, Shawn Levy, Cem Meydan, Christopher Mozsary, Amanda M Saravia-Butler, Deanne M Taylor, Eve Wurtele, Christopher E Mason, Afshin Beheshti, Peter N Robinson
January 22, 2022

Viruses can subvert a number of cellular processes including splicing in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to…

System-wide transcriptome damage and tissue identity loss in COVID-19 patients.

Written by Jiwoon Park, Jonathan Foox, Tyler Hether, David C Danko, Sarah Warren, Youngmi Kim, Jason Reeves, Daniel J Butler, Christopher Mozsary, Joel Rosiene, Alon Shaiber, Evan E Afshin, Matthew MacKay, André F Rendeiro, Yaron Bram, Vasuretha Chandar, Heather Geiger, Arryn Craney, Priya Velu, Ari M Melnick, Iman Hajirasouliha, Afshin Beheshti, Deanne Taylor, Amanda Saravia-Butler, Urminder Singh, Eve Syrkin Wurtele, Jonathan Schisler, Samantha Fennessey, André Corvelo, Michael C Zody, Soren Germer, Steven Salvatore, Shawn Levy, Shixiu Wu, Nicholas P Tatonetti, Sagi Shapira, Mirella Salvatore, Lars F Westblade, Melissa Cushing, Hanna Rennert, Alison J Kriegel, Olivier Elemento, Marcin Imielinski, Charles M Rice, Alain C Borczuk, Cem Meydan, Robert E Schwartz, Christopher E Mason
February 15, 2022

The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory…

Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection.

Written by Vijendra Ramlall, Phyllis M Thangaraj, Cem Meydan, Jonathan Foox, Daniel Butler, Jacob Kim, Ben May, Jessica K De Freitas, Benjamin S Glicksberg, Christopher E Mason, Nicholas P Tatonetti, Sagi D Shapira
August 3, 2020

Understanding the pathophysiology of SARS-CoV-2 infection is critical for therapeutic and public health strategies. Viral-host interactions can guide discovery of disease regulators, and protein structure function analysis points to several…

Betacoronavirus-specific alternate splicing

Written by Guy Karlebach, Stephen J Baylin, Daniel Butler, Jonathan Foox, Shawn Levy, Cem Meydan, Christopher Mozsary, Amanda M Saravia-Butler, Eve Wurtele, Christopher Mason, Afshin Beheshti, Peter N. Robinson
July 2, 2021

Viruses can subvert a number of cellular processes in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global…

Transcriptional response modules characterize IL-1β and IL-6 activity in COVID-19.

Written by Lucy C K Bell, Cem Meydan, Jacob Kim, Jonathan Foox, Daniel Butler, Christopher E Mason, Sagi D Shapira, Mahdad Noursadeghi, Gabriele Pollara
January 22, 2021

Dysregulated IL-1β and IL-6 responses have been implicated in the pathogenesis of severe Coronavirus Disease 2019 (COVID-19). Innovative approaches for evaluating the biological activity of these cytokines in vivo are…

Identification of Immune complement function as a determinant of adverse SARS-CoV-2 infection outcome

Written by Vijendra Ramlall, Phyllis Thangaraj, Cem Meydan, Jonathan Foox, Daniel Butler, Ben May, Jessica de Freitas, Benjamin S Glicksberg, Christopher Mason, Nicholas P Tatonetti, Sagi D Shapira
May 13, 2020

SO_SCPLOWUMMARYC_SCPLOWUnderstanding the pathophysiology of SARS-CoV-2 infection is critical for therapeutics and public health intervention strategies. Viral-host interactions can guide discovery of regulators of disease outcomes, and protein structure function analysis…