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Discovery and Clinical Validation of Host Biomarkers of Disease Severity and Multi-System Inflammatory Syndrome in Children (MIS-C) with COVID-19

University of California, San Francisco

Charles Yen Chiu

PreVAIL kIds
Website

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Timely intervention and control of a novel coronavirus (COVID-19) outbreak at a large skilled nursing facility-San Francisco, California, 2020.

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Comprehensive understanding of the serological response to SARS-CoV-2 infection is important for both pathophysiologic insight and diagnostic development. Here, we generate a pan-human coronavirus programmable phage display assay to perform…

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August 24, 2020

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Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. Genome sequencing of SARS-CoV-2 strains allows for the…

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Interpretation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serosurveillance studies is limited by poorly defined performance of antibody assays over time in individuals with different clinical presentations. We measured…

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As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because…

An intranasal ASO therapeutic targeting SARS-CoV-2

Written by Chi Zhu, Justin Y. Lee, Jia Z. Woo, Lei Xu, Xammy Nguyenla, Livia H. Yamashiro, Fei Ji, Scott B. Biering, Erik Van Dis, Federico Gonzalez, Douglas Fox, Arjun Rustagi, Benjamin A. Pinsky, Catherine A. Blish, Charles Chiu, Eva Harris, Ruslan I. Sadreyev, Sarah Stanley, Sakari Kauppinen, Silvi Rouskin, Anders M. Näär
May 18, 2021

The COVID-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and that may partially evade vaccine and antibody immunity1. Rapid deployment…

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Written by Mary A Rodgers, Ana Olivo, Barbara J Harris, Chris Lark, Xinxin Luo, Michael G Berg, Todd V Meyer, Aurash Mohaimani, Gregory S Orf, Yitz Goldstein, Amy S Fox, Julie Hirschhorn, William B Glen, Frederick Nolte, Alan Landay, Cheryl Jennings, James Moy, Venice Servellita, Charles Chiu, Rahul Batra, Luke B Snell, Gaia Nebbia, Sam Douthwaite, Amilcar Tanuri, Lavanya Singh, Tulio de Oliveira, Ambroise Ahouidi, Souleymane Mboup, Gavin A Cloherty
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BACKGROUND: Viral diversity presents an ongoing challenge for diagnostic tests, which need to accurately detect all circulating variants. The Abbott Global Surveillance program monitors severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)…

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An outbreak of betacoronavirus severe acute respiratory syndrome (SARS)-CoV-2 began in Wuhan, China in December 2019. COVID-19, the disease associated with SARS-CoV-2 infection, rapidly spread to produce a global pandemic.…

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The impact of vaccination on SARS-CoV-2 infectiousness is not well understood. We compared longitudinal viral shedding dynamics in unvaccinated and fully vaccinated adults. SARS-CoV-2-infected adults were enrolled within 5 days…

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Written by Catherine DeVoe, Shraddha Pandey, Dayana Shariff, Shagun Arora, Timothy J Henrich, Deborah S Yokoe, Charles R Langelier, Venice Servellita, Charles Chiu, Steve Miller, Jennifer M Babik, Peter Chin-Hong, Monica Fung
April 15, 2022

The effect of vaccination on severity of subsequent COVID-19 in patients with hematologic malignancies (HM) is unknown. In this single-center retrospective cohort study, we found no difference in severity of…

Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants.

Written by Venice Servellita, Abdullah M Syed, Mary Kate Morris, Noah Brazer, Prachi Saldhi, Miguel Garcia-Knight, Bharath Sreekumar, Mir M Khalid, Alison Ciling, Pei-Yi Chen, G Renuka Kumar, Amelia S Gliwa, Jenny Nguyen, Alicia Sotomayor-Gonzalez, Yueyuan Zhang, Edwin Frias, John Prostko, John Hackett, Raul Andino, Debra A Wadford, Carl Hanson, Jennifer Doudna, Melanie Ott, Charles Y Chiu
April 28, 2022

Virus-like particle (VLP) and live virus assays were used to investigate neutralizing immunity against Delta and Omicron SARS-CoV-2 variants in 259 samples from 128 vaccinated individuals. Following Delta breakthrough infection,…

Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination.

Written by Rahul K Suryawanshi, Irene P Chen, Tongcui Ma, Abdullah M Syed, Noah Brazer, Prachi Saldhi, Camille R Simoneau, Alison Ciling, Mir M Khalid, Bharath Sreekumar, Pei-Yi Chen, G Renuka Kumar, Mauricio Montano, Ronne Gascon, Chia-Lin Tsou, Miguel A Garcia-Knight, Alicia Sotomayor-Gonzalez, Venice Servellita, Amelia Gliwa, Jenny Nguyen, Ines Silva, Bilal Milbes, Noah Kojima, Victoria Hess, Maria Shacreaw, Lauren Lopez, Matthew Brobeck, Fred Turner, Frank W Soveg, Ashley F George, Xiaohui Fang, Mazharul Maishan, Michael Matthay, Mary Kate Morris, Debra Wadford, Carl Hanson, Warner C Greene, Raul Andino, Lee Spraggon, Nadia R Roan, Charles Y Chiu, Jennifer A Doudna, Melanie Ott
May 18, 2022

SARS-CoV-2 Delta and Omicron are globally relevant variants of concern (VOCs). While individuals infected with Delta are at risk to develop severe lung disease, infection with Omicron often causes milder…

Individualized Constellation of Killer Cell Immunoglobulin-Like Receptors and Cognate HLA Class I Ligands that Controls Natural Killer Cell Antiviral Immunity Predisposes COVID-19.

Written by Stalinraja Maruthamuthu, Karan Rajalingam, Navchetan Kaur, Maelig G Morvan, Jair Soto, Nancy Lee, Denice Kong, Zicheng Hu, Kevin Reyes, Dianna Ng, Atul J Butte, Charles Chiu, Raja Rajalingam
February 22, 2022

Background: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection causes coronavirus disease-2019 (COVID-19) in some individuals, while the majority remain asymptomatic. Natural killer (NK) cells play an essential role in…

The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters.

Written by Timothy Carroll, Douglas Fox, Neeltje van Doremalen, Erin Ball, Mary Kate Morris, Alicia Sotomayor-Gonzalez, Venice Servellita, Arjun Rustagi, Claude Kwe Yinda, Linda Fritts, Julia Rebecca Port, Zhong-Min Ma, Myndi G Holbrook, Jonathan Schulz, Catherine A Blish, Carl Hanson, Charles Y Chiu, Vincent Munster, Sarah Stanley, Christopher J Miller
February 10, 2022

As novel SARS-CoV-2 variants continue to emerge, it is critical that their potential to cause severe disease and evade vaccine-induced immunity is rapidly assessed in humans and studied in animal…

Magnitude and determinants of SARS-CoV-2 household transmission: a longitudinal cohort study.

Written by J Daniel Kelly, Scott Lu, Khamal Anglin, Miguel Garcia-Knight, Jesus Pineda-Ramirez, Sarah A Goldberg, Michel Tassetto, Amethyst Zhang, Kevin Donohue, Michelle C Davidson, Mariela Romero, Ruth Diaz Sanchez, Manuella Djomaleu, Sujata Mathur, Jessica Y Chen, Carrie A Forman, Venice Servellita, Rubi D Montejano, Joshua R Shak, George W Rutherford, Steven G Deeks, Glen R Abedi, Melissa A Rolfes, Sharon Saydah, Melissa Briggs-Hagen, Michael J Peluso, Charles Chiu, Claire M Midgley, Raul Andino, Jeffrey N Martin
July 5, 2022

BACKGROUND: Households have emerged as important venues for SARS-CoV-2 transmission. Little is known, however, regarding the magnitude and determinants of household transmission in increasingly vaccinated populations. METHODS: From September 2020…

An intranasal ASO therapeutic targeting SARS-CoV-2.

Written by Chi Zhu, Justin Y Lee, Jia Z Woo, Lei Xu, Xammy Nguyenla, Livia H Yamashiro, Fei Ji, Scott B Biering, Erik Van Dis, Federico Gonzalez, Douglas Fox, Eddie Wehri, Arjun Rustagi, Benjamin A Pinsky, Julia Schaletzky, Catherine A Blish, Charles Chiu, Eva Harris, Ruslan I Sadreyev, Sarah Stanley, Sakari Kauppinen, Silvi Rouskin, Anders M Näär
August 3, 2022

The COVID-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and that may partially evade vaccine and antibody immunity. Rapid deployment…

Infectious viral shedding of SARS-CoV-2 Delta following vaccination: A longitudinal cohort study.

Written by Miguel Garcia-Knight, Khamal Anglin, Michel Tassetto, Scott Lu, Amethyst Zhang, Sarah A Goldberg, Adam Catching, Michelle C Davidson, Joshua R Shak, Mariela Romero, Jesus Pineda-Ramirez, Ruth Diaz-Sanchez, Paulina Rugart, Kevin Donohue, Jonathan Massachi, Hannah M Sans, Manuella Djomaleu, Sujata Mathur, Venice Servellita, David McIlwain, Brice Gaudiliere, Jessica Chen, Enrique O Martinez, Jacqueline M Tavs, Grace Bronstone, Jacob Weiss, John T Watson, Melissa Briggs-Hagen, Glen R Abedi, George W Rutherford, Steven G Deeks, Charles Chiu, Sharon Saydah, Michael J Peluso, Claire M Midgley, Jeffrey N Martin, Raul Andino, J Daniel Kelly
September 12, 2022

The impact of vaccination on SARS-CoV-2 infectiousness is not well understood. We compared longitudinal viral shedding dynamics in unvaccinated and fully vaccinated adults. SARS-CoV-2-infected adults were enrolled within 5 days…

COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme.

Written by Clare L Fasching, Venice Servellita, Bridget McKay, Vaishnavi Nagesh, James P Broughton, Alicia Sotomayor-Gonzalez, Baolin Wang, Noah Brazer, Kevin Reyes, Jessica Streithorst, Rachel N Deraney, Emma Stanfield, Carley G Hendriks, Becky Fung, Steve Miller, Jesus Ching, Janice S Chen, Charles Y Chiu
June 29, 2022

Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants can potentially guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here, we…

A lateral flow-based at-home test for detection of SARS-CoV-2

Written by Peng Xu, Venice Servellita, Krzysztof Langer, Dan Weisgerber, Gordon Murtaugh, Adam R Abate, Charles Chiu
March 11, 2021

We have developed a highly sensitive and specific LAMP(loop-mediated amplification)-based assay for thedetection of SARS-CoV-2 that can potentially be used for at-home and point-of-care (POC) testing. The assayincludes only three…

Neutralizing immunity induced against the Omicron BA.1 and BA.2 variants in vaccine breakthrough infections.

Written by Noah Brazer, Mary Kate Morris, Venice Servellita, Khamal Anglin, Prachi Saldhi, Miguel Garcia-Knight, Sutana Bethancourt, Alicia Sotomayor-Gonzalez, Baolin Wang, Abiodun Foresythe, Jenny Nguyen, Amelia S Gliwa, Jesus Pineda-Ramirez, Ruth Diaz Sanchez, Yueyuan Zhang, Melanie Ott, Debra A Wadford, Raul Andino, J Daniel Kelly, Carl Hanson, Charles Chiu
September 22, 2022

BACKGROUND: As of early 2022, the Omicron variants are the predominant circulating lineages globally. Understanding neutralizing antibody responses against Omicron BA.1 and BA.2 following vaccine breakthrough infections will provide insights…

Cell-free DNA tissues of origin by methylation profiling reveals significant cell, tissue, and organ-specific injury related to COVID-19 severity.

Written by Alexandre Pellan Cheng, Matthew Pellan Cheng, Wei Gu, Joan Sesing Lenz, Elaine Hsu, Erwin Schurr, Guillaume Bourque, Mathieu Bourgey, Jerome Ritz, Francisco M Marty, Charles Y Chiu, Donald C Vinh, Iwijn De Vlaminck
April 9, 2021

BACKGROUND: Coronavirus disease 2019 (COVID-19) primarily affects the lungs, but evidence of systemic disease with multi-organ involvement is emerging. Here, we developed a blood test to broadly quantify cell-, tissue-,…

Unlocking capacities of genomics for the COVID-19 response and future pandemics.

Written by Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Pelin Icer Baykal, Zoia Comarova, Angela Lu, Yuri Porozov, Tetyana I Vasylyeva, Joel O Wertheim, Braden T Tierney, Charles Y Chiu, Ren Sun, Aiping Wu, Malak S Abedalthagafi, Victoria M Pak, Shivashankar H Nagaraj, Adam L Smith, Pavel Skums, Bogdan Pasaniuc, Andrey Komissarov, Christopher E Mason, Eric Bortz, Philippe Lemey, Fyodor Kondrashov, Niko Beerenwinkel, Tommy Tsan-Yuk Lam, Nicholas C Wu, Alex Zelikovsky, Rob Knight, Keith A Crandall, Serghei Mangul

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…

SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling.

Written by Scott B Biering, Francielle Tramontini Gomes de Sousa, Laurentia V Tjang, Felix Pahmeier, Chi Zhu, Richard Ruan, Sophie F Blanc, Trishna S Patel, Caroline M Worthington, Dustin R Glasner, Bryan Castillo-Rojas, Venice Servellita, Nicholas T N Lo, Marcus P Wong, Colin M Warnes, Daniel R Sandoval, Thomas Mandel Clausen, Yale A Santos, Douglas M Fox, Victoria Ortega, Anders M Näär, Ralph S Baric, Sarah A Stanley, Hector C Aguilar, Jeffrey D Esko, Charles Y Chiu, John E Pak, P Robert Beatty, Eva Harris
December 9, 2022

Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction within the lung as well as in distal organs. While it is appreciated that an exaggerated inflammatory response is associated…

A lateral flow-based at-home test for detection of SARS-CoV-2

Written by Peng Xu, Venice Servellita, Krzysztof Langer, Dan Weisgerber, Gordon Murtaugh, Adam R Abate, Charles Chiu
December 14, 2022

This protocol was a finalist in the XPRIZE Global Rapid Covid Testing competitionWe have developed a highly sensitive and specific LAMP(loop-mediated amplification)-based assay for thedetection of SARS-CoV-2 that can potentially…

A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood.

Written by Dianna L Ng, Andrea C Granados, Yale A Santos, Venice Servellita, Gregory M Goldgof, Cem Meydan, Alicia Sotomayor-Gonzalez, Andrew G Levine, Joanna Balcerek, Lucy M Han, Naomi Akagi, Kent Truong, Neil M Neumann, David N Nguyen, Sagar P Bapat, Jing Cheng, Claudia Sanchez-San Martin, Scot Federman, Jonathan Foox, Allan Gopez, Tony Li, Ray Chan, Cynthia S Chu, Chiara A Wabl, Amelia S Gliwa, Kevin Reyes, Chao-Yang Pan, Hugo Guevara, Debra Wadford, Steve Miller, Christopher E Mason, Charles Y Chiu
February 3, 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA sequencing to analyze 286 nasopharyngeal (NP)…

Association of culturable-virus detection and household transmission of SARS-CoV-2 - California and Tennessee, 2020-2022.

Written by Jessica E Deyoe, J Daniel Kelly, Carlos G Grijalva, Gaston Bonenfant, Scott Lu, Khamal Anglin, Miguel Garcia-Knight, Jesus Pineda-Ramirez, Melissa Briggs Hagen, Sharon Saydah, Glen R Abedi, Sarah A Goldberg, Michel Tassetto, Amethyst Zhang, Kevin C Donohue, Michelle C Davidson, Ruth Diaz Sanchez, Manuella Djomaleu, Sujata Mathur, Joshua R Shak, Steven G Deeks, Michael J Peluso, Charles Y Chiu, Yuwei Zhu, Natasha B Halasa, James D Chappell, Alexandra Mellis, Carrie Reed, Raul Andino, Jeffrey N Martin, Bin Zhou, H Keipp Talbot, Claire M Midgley, Melissa A Rolfes
January 27, 2023

From two SARS-CoV-2 household transmission studies (enrolling April 2020 - January 2022) with rapid enrollment and specimen collection for 14 days, 61% (43/70) of primary cases had culturable-virus detected ≥6…