1
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Mwakibete L, Greening SS, Kalantar K, Ahyong V, Anis E, Miller EA, Needle DB, Oglesbee M, Thomas WK, Sevigny JL, Gordon LM, Nemeth NM, Ogbunugafor CB, Ayala AJ, Faith SA, Neff N, Detweiler AM, Baillargeon T, Tanguay S, Simpson SD, Murphy LA, Ellis JC, Tato CM, Gagne RB. Metagenomics for Pathogen Detection During a Mass Mortality Event in Songbirds. J Wildl Dis 2024; 60:362-374. [PMID: 38345467 DOI: 10.7589/jwd-d-23-00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/02/2024] [Indexed: 04/06/2024]
Abstract
Mass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria forming the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes, including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events.
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Affiliation(s)
| | - Sabrina S Greening
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Eman Anis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
- Department of Pathobiology, PADLS New Bolton Center, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Erica A Miller
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - David B Needle
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Michael Oglesbee
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Joseph L Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lawrence M Gordon
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Nicole M Nemeth
- Southeastern Cooperative Wildlife Disease Study and Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, USA
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Georgia 30602, USA
| | - C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Andrea J Ayala
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Seth A Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | | | - Tessa Baillargeon
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Stacy Tanguay
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Stephen D Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lisa A Murphy
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
- Department of Pathobiology, PADLS New Bolton Center, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Julie C Ellis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Cristina M Tato
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Roderick B Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
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2
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Lebel P, Elledge S, Wiener DM, Jeyakumar I, Phelps M, Jacobsen A, Huynh E, Charlton C, Puccinelli R, Mondal P, Saha S, Tato CM, Gómez-Sjöberg R. A handheld luminometer with sub-attomole limit of detection for distributed applications in global health. PLOS Glob Public Health 2024; 4:e0002766. [PMID: 38381748 PMCID: PMC10881016 DOI: 10.1371/journal.pgph.0002766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/08/2023] [Indexed: 02/23/2024]
Abstract
Luminescence is ubiquitous in biology research and medicine. Conceptually simple, the detection of luminescence nonetheless faces technical challenges because relevant signals can exhibit exceptionally low radiant power densities. Although low light detection is well-established in centralized laboratory settings, the cost, size, and environmental requirements of high-performance benchtop luminometers are not compatible with geographically-distributed global health studies or resource-constrained settings. Here we present the design and application of a ~$700 US handheld, battery-powered luminometer with performance on par with high-end benchtop instruments. By pairing robust and inexpensive Silicon Photomultiplier (SiPM) sensors with a low-profile shutter system, our design compensates for sensor non-idealities and thermal drift, achieving a limit of detection of 1.6E-19 moles of firefly luciferase. Using these devices, we performed two pilot cross-sectional serology studies to assess sars-cov-2 antibody levels: a cohort in the United States, as well as a field study in Bangladesh. Results from both studies were consistent with previous work and demonstrate the device's suitability for distributed applications in global health.
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Affiliation(s)
- Paul Lebel
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, United States of America
| | - Susanna Elledge
- University of California, San Francisco, California, United States of America
| | - Diane M. Wiener
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, United States of America
| | - Ilakkiyan Jeyakumar
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, United States of America
| | - Maíra Phelps
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, United States of America
| | - Axel Jacobsen
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, United States of America
| | - Emily Huynh
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, United States of America
| | - Chris Charlton
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, United States of America
| | - Robert Puccinelli
- University of California, Berkeley, California, United States of America
| | | | - Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Cristina M. Tato
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, United States of America
| | - Rafael Gómez-Sjöberg
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, United States of America
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3
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Chu VT, Nafees S, Waltari E, McNeil N, Caughell C, Sanchez-Guerrero E, Wang L, Stanley K, Cunningham G, Wong J, Phelps M, Tato CM, Miller S, DeRisi JL, Yokoe DS, Ramirez-Avila L, Langelier CR. Whole-genome sequencing rule-out of suspected hospital-onset Rhizopus outbreaks. Infect Control Hosp Epidemiol 2023; 44:2059-2061. [PMID: 37308466 PMCID: PMC10755156 DOI: 10.1017/ice.2023.85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 06/14/2023]
Abstract
Two independent temporal-spatial clusters of hospital-onset Rhizopus infections were evaluated using whole-genome sequencing (WGS). Phylogenetic analysis confirmed that isolates within each cluster were unrelated despite epidemiological suspicion of outbreaks. The ITS1 region alone was insufficient for accurate analysis. WGS has utility for rapid rule-out of suspected nosocomial Rhizopus outbreaks.
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Affiliation(s)
- Victoria T. Chu
- Division of Infectious Diseases and Global Health, Department of Pediatrics, University of California–San Francisco, San Francisco, California
| | - Saba Nafees
- Chan Zuckerberg Biohub, San Francisco, California
| | - Eric Waltari
- Chan Zuckerberg Biohub, San Francisco, California
| | - Nicole McNeil
- Department of Hospital Epidemiology and Infection Prevention, University of California–San Francisco, San Francisco, California
| | - Carolyn Caughell
- Department of Hospital Epidemiology and Infection Prevention, University of California–San Francisco, San Francisco, California
| | - Estella Sanchez-Guerrero
- Division of Infectious Diseases, Department of Medicine, University of California–San Francisco, San Francisco, California
| | - Lusha Wang
- Department of Hospital Epidemiology and Infection Prevention, University of California–San Francisco, San Francisco, California
| | - Kim Stanley
- Department of Hospital Epidemiology and Infection Prevention, University of California–San Francisco, San Francisco, California
| | - Gail Cunningham
- Department of Laboratory Medicine, University of California–San Francisco, San Francisco, California
| | - Joan Wong
- Chan Zuckerberg Biohub, San Francisco, California
| | - Maíra Phelps
- Chan Zuckerberg Biohub, San Francisco, California
| | | | | | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, California
- Department of Biochemistry and Biophysics, University of California–San Francisco, San Francisco, California
| | - Deborah S. Yokoe
- Department of Hospital Epidemiology and Infection Prevention, University of California–San Francisco, San Francisco, California
- Division of Infectious Diseases, Department of Medicine, University of California–San Francisco, San Francisco, California
| | - Lynn Ramirez-Avila
- Division of Infectious Diseases and Global Health, Department of Pediatrics, University of California–San Francisco, San Francisco, California
- Department of Hospital Epidemiology and Infection Prevention, University of California–San Francisco, San Francisco, California
| | - Charles R. Langelier
- Chan Zuckerberg Biohub, San Francisco, California
- Department of Hospital Epidemiology and Infection Prevention, University of California–San Francisco, San Francisco, California
- Division of Infectious Diseases, Department of Medicine, University of California–San Francisco, San Francisco, California
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4
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Horigan S, Kistler A, Ranaivoson HC, Andrianianina A, Andry S, Kettenburg G, Raharinosy V, Randriambolamanantsoa TH, Tato CM, Lacoste V, Heraud JM, Dussart P, Brook CE. Detection, characterization, and phylogenetic analysis of a near-whole genome sequence of a novel astrovirus in an endemic Malagasy fruit bat, Rousettus madagascariensis. bioRxiv 2023:2023.10.27.564436. [PMID: 37961349 PMCID: PMC10635015 DOI: 10.1101/2023.10.27.564436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Bats (order: Chiroptera ) are known to host a diverse range of viruses, some of which present a public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae ) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis . We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis , which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus . Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.
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5
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Mwakibete L, Takahashi S, Ahyong V, Black A, Rek J, Ssewanyana I, Kamya M, Dorsey G, Jagannathan P, Rodríguez-Barraquer I, Tato CM, Greenhouse B. Metagenomic next-generation sequencing to characterize potential etiologies of non-malarial fever in a cohort living in a high malaria burden area of Uganda. PLOS Glob Public Health 2023; 3:e0001675. [PMID: 37134083 PMCID: PMC10156012 DOI: 10.1371/journal.pgph.0001675] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/12/2023] [Indexed: 05/04/2023]
Abstract
Causes of non-malarial fevers in sub-Saharan Africa remain understudied. We hypothesized that metagenomic next-generation sequencing (mNGS), which allows for broad genomic-level detection of infectious agents in a biological sample, can systematically identify potential causes of non-malarial fevers. The 212 participants in this study were of all ages and were enrolled in a longitudinal malaria cohort in eastern Uganda. Between December 2020 and August 2021, respiratory swabs and plasma samples were collected at 313 study visits where participants presented with fever and were negative for malaria by microscopy. Samples were analyzed using CZ ID, a web-based platform for microbial detection in mNGS data. Overall, viral pathogens were detected at 123 of 313 visits (39%). SARS-CoV-2 was detected at 11 visits, from which full viral genomes were recovered from nine. Other prevalent viruses included Influenza A (14 visits), RSV (12 visits), and three of the four strains of seasonal coronaviruses (6 visits). Notably, 11 influenza cases occurred between May and July 2021, coinciding with when the Delta variant of SARS-CoV-2 was circulating in this population. The primary limitation of this study is that we were unable to estimate the contribution of bacterial microbes to non-malarial fevers, due to the difficulty of distinguishing bacterial microbes that were pathogenic from those that were commensal or contaminants. These results revealed the co-circulation of multiple viral pathogens likely associated with fever in the cohort during this time period. This study illustrates the utility of mNGS in elucidating the multiple potential causes of non-malarial febrile illness. A better understanding of the pathogen landscape in different settings and age groups could aid in informing diagnostics, case management, and public health surveillance systems.
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Affiliation(s)
- Lusajo Mwakibete
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Saki Takahashi
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Allison Black
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - John Rek
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Moses Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University, Kampala, Uganda
| | - Grant Dorsey
- Department of Medicine, Division of HIV, ID, and Global Medicine, University of California San Francisco, San Francisco, CA, United States of America
| | - Prasanna Jagannathan
- Department of Medicine, Stanford University, Palo Alto, CA, United States of America
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA, United States of America
| | - Isabel Rodríguez-Barraquer
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
| | - Cristina M. Tato
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Bryan Greenhouse
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
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6
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Byrum JR, Waltari E, Janson O, Guo SM, Folkesson J, Chhun BB, Vinden J, Ivanov IE, Forst ML, Li H, Larson AG, Blackmon L, Liu Z, Wu W, Ahyong V, Tato CM, McCutcheon KM, Hoh R, Kelly JD, Martin JN, Peluso MJ, Henrich TJ, Deeks SG, Prakash M, Greenhouse B, Mehta SB, Pak JE. MultiSero: An Open-Source Multiplex-ELISA Platform for Measuring Antibody Responses to Infection. Pathogens 2023; 12:671. [PMID: 37242341 PMCID: PMC10221076 DOI: 10.3390/pathogens12050671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
A multiplexed enzyme-linked immunosorbent assay (ELISA) that simultaneously measures antibody binding to multiple antigens can extend the impact of serosurveillance studies, particularly if the assay approaches the simplicity, robustness, and accuracy of a conventional single-antigen ELISA. Here, we report on the development of multiSero, an open-source multiplex ELISA platform for measuring antibody responses to viral infection. Our assay consists of three parts: (1) an ELISA against an array of proteins in a 96-well format; (2) automated imaging of each well of the ELISA array using an open-source plate reader; and (3) automated measurement of optical densities for each protein within the array using an open-source analysis pipeline. We validated the platform by comparing antibody binding to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antigens in 217 human sera samples, showing high sensitivity (0.978), specificity (0.977), positive predictive value (0.978), and negative predictive value (0.977) for classifying seropositivity, a high correlation of multiSero determined antibody titers with commercially available SARS-CoV-2 antibody tests, and antigen-specific changes in antibody titer dynamics upon vaccination. The open-source format and accessibility of our multiSero platform can contribute to the adoption of multiplexed ELISA arrays for serosurveillance studies, for SARS-CoV-2 and other pathogens of significance.
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Affiliation(s)
- Janie R. Byrum
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Eric Waltari
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Owen Janson
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, CA 94143, USA
- EPPIcenter Program, University of California, San Francisco, CA 94143, USA
| | - Syuan-Ming Guo
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Jenny Folkesson
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Bryant B. Chhun
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Joanna Vinden
- Infectious Diseases and Immunity Graduate Program, University of California, Berkeley, CA 94720-3370, USA
| | - Ivan E. Ivanov
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Marcus L. Forst
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Hongquan Li
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Adam G. Larson
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lena Blackmon
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Ziwen Liu
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Vida Ahyong
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Cristina M. Tato
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | | | - Rebecca Hoh
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, CA 94143, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| | - Michael J. Peluso
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, CA 94143, USA
| | - Timothy J. Henrich
- Division of Experimental Medicine, University of California, San Francisco, CA 94110, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, CA 94143, USA
| | - Manu Prakash
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Bryan Greenhouse
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, CA 94143, USA
- EPPIcenter Program, University of California, San Francisco, CA 94143, USA
| | - Shalin B. Mehta
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - John E. Pak
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
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7
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Perier C, Nasinghe E, Charles I, Ssetaba LJ, Ahyong V, Bangs D, Beatty PR, Czudnochowski N, Diallo A, Dugan E, Fabius JM, Fong Baker H, Gardner J, Isaacs S, Joanah B, Kalantar K, Kateete D, Knight M, Krasilnikov M, Krogan NJ, Langelier C, Lee E, Li LM, Licht D, Lien K, Lyons Z, Mboowa G, Mwebaza I, Mwesigwa S, Nalwadda G, Nichols R, Penaranda ME, Petnic S, Phelps M, Popper SJ, Rape M, Reingold A, Robbins R, Rosenberg OS, Savage DF, Schildhauer S, Settles ML, Sserwadda I, Stanley S, Tato CM, Tsitsiklis A, Van Dis E, Vanaerschot M, Vinden J, Cox JS, Joloba ML, Schaletzky J. Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries. Glob Health Action 2022; 15:2062175. [PMID: 35730550 PMCID: PMC9225690 DOI: 10.1080/16549716.2022.2062175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Science education and research have the potential to drive profound change in low- and middle-income countries (LMICs) through encouraging innovation, attracting industry, and creating job opportunities. However, in LMICs, research capacity is often limited, and acquisition of funding and access to state-of-the-art technologies is challenging. The Alliance for Global Health and Science (the Alliance) was founded as a partnership between the University of California, Berkeley (USA) and Makerere University (Uganda), with the goal of strengthening Makerere University’s capacity for bioscience research. The flagship program of the Alliance partnership is the MU/UCB Biosciences Training Program, an in-country, hands-on workshop model that trains a large number of students from Makerere University in infectious disease and molecular biology research. This approach nucleates training of larger and more diverse groups of students, development of mentoring and bi-directional research partnerships, and support of the local economy. Here, we describe the project, its conception, implementation, challenges, and outcomes of bioscience research workshops. We aim to provide a blueprint for workshop implementation, and create a valuable resource for bioscience research capacity strengthening in LMICs.
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Affiliation(s)
- Celine Perier
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
| | | | - Isabelle Charles
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Derek Bangs
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - P Robert Beatty
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Amy Diallo
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
| | - Hildy Fong Baker
- School of Public Health, Center for Global Public Health (CGPH), University of California, Berkeley, CA, USA
| | - Jackson Gardner
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Birungi Joanah
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | | | - David Kateete
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Matt Knight
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Maria Krasilnikov
- Department of Molecular Biology and Microbiology, Tufts Graduate School of Biomedical Sciences, Boston, MA, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA.,Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | | | - Eric Lee
- Graduate Group in Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, CA, USA
| | - Lucy M Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Daniel Licht
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Katie Lien
- Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Zilose Lyons
- California China Climate Institute, University of California, Berkeley, CA, USA
| | - Gerald Mboowa
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Ivan Mwebaza
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | | | | | - Robert Nichols
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Sarah Petnic
- Quality and Clinical Excellence Department, Providence Queen of the Valley Medical Center, Napa, CA, USA
| | | | - Stephen J Popper
- Sustainable Sciences Institute, San Francisco, CA, USA.,School of Public Health, Department of Infectious Disease and Vaccinology, University of California, Berkeley, CA, USA
| | - Michael Rape
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Arthur Reingold
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | | | - Oren S Rosenberg
- Department of Medicine, University of California, San Francisco, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | | | - Ivan Sserwadda
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Sarah Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | | | | | - Erik Van Dis
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Joanna Vinden
- Division of Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, CA, USA
| | - Jeffery S Cox
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Moses L Joloba
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Julia Schaletzky
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
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8
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Mercer T, Almond N, Crone MA, Chain PSG, Deshpande A, Eveleigh D, Freemont P, Fuchs S, Garlick R, Huggett J, Kammel M, Li PE, Milavec M, Marlowe EM, O'Sullivan DM, Page M, Pestano GA, Suliman S, Simen B, Sninsky JJ, Sopchak L, Tato CM, Vallone PM, Vandesompele J, White TJ, Zeichhardt H, Salit M. The Coronavirus Standards Working Group's roadmap for improved population testing. Nat Biotechnol 2022; 40:1563-1568. [PMID: 36323792 PMCID: PMC9628457 DOI: 10.1038/s41587-022-01538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tim Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland, Australia
| | - Neil Almond
- Medicines and Healthcare Products Regulatory Agency, Potters Bar, UK
| | - Michael A Crone
- London Biofoundry, Imperial College Translation and Innovation Hub, London, UK
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
- UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, UK
| | - Patrick S G Chain
- Biosecurity and Public Health, Bioscience Division, Los Alamos National Laboratory, Los Almos, NM, USA
| | - Alina Deshpande
- Biosecurity and Public Health, Bioscience Division, Los Alamos National Laboratory, Los Almos, NM, USA
| | | | - Paul Freemont
- London Biofoundry, Imperial College Translation and Innovation Hub, London, UK
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
- UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, UK
| | - Sebastien Fuchs
- Western University of Health Sciences, College of Osteopathic Medicine of the Pacific, Pomona, CA, USA
| | | | - Jim Huggett
- National Measurement Laboratory, LGC, Teddington, UK
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Martin Kammel
- INSTAND e.V. Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
- GBD Gesellschaft fuer Biotechnologische Diagnostik mbH, Berlin, Germany
| | - Po-E Li
- Biosecurity and Public Health, Bioscience Division, Los Alamos National Laboratory, Los Almos, NM, USA
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Denise M O'Sullivan
- National Measurement Laboratory, LGC, Teddington, UK
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Mark Page
- Medicines and Healthcare Products Regulatory Agency, Potters Bar, UK
| | | | - Sara Suliman
- Brigham and Women's Hospital, Division of Rheumatology, Inflammation and Immunity, Harvard Medical School, Boston, MA, USA
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Peter M Vallone
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Thomas J White
- Human Rights Center, School of Law, University of California, Berkeley, CA, USA
| | - Heinz Zeichhardt
- INSTAND e.V. Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
- GBD Gesellschaft fuer Biotechnologische Diagnostik mbH, Berlin, Germany
- IQVD GmbH, Institut fuer Qualitaetssicherung in der Virusdiagnostik, Berlin, Germany
| | - Marc Salit
- Departments of Pathology and Bioengineering, Stanford University, Stanford, CA, USA.
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
- MITRE Corporation, McLean, VA, USA.
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9
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Elledge SK, Eigl I, Phelps M, McClinton K, Zhou XX, Leung KK, Tato CM, Wells JA. Using Split Luminescent Biosensors for SARS-CoV-2 Antibody Detection in Serum, Plasma, and Blood Samples. Curr Protoc 2022; 2:e521. [PMID: 36200787 PMCID: PMC9793882 DOI: 10.1002/cpz1.521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Antibody detection assays are essential for evaluating immunity of individuals against a given virus, and this has been particularly relevant during the COVID-19 pandemic. Current serology assays either require a laboratory setting and take >1 hr (i.e., enzyme-linked immunosorbent assay [ELISA]) or are rapid but only qualitative in nature and cannot accurately track antibody levels over time (i.e., lateral flow assay [LFA]). Therefore, there is a need for development of a rapid and simple but also quantitative assay that can evaluate antibody levels in patients accurately over time. We have developed an assay that uses a split nanoluciferase fused to the spike or nucleocapsid proteins of the SARS-CoV-2 virus to enable luminescent-based detection of spike- or nucleocapsid-binding antibodies in serum, plasma, and whole blood samples. The resulting approach is simple, rapid, and quantitative and is highly amenable to low-/medium-throughput scale using plate-based assays, high-throughput scale using robotics, and point-of-care applications. In this article, we describe how to perform the assay in a laboratory setting using a plate reader or liquid-handling robotics and in a point-of-care setting using a handheld, battery-powered luminometer. Together, these assays allow antibody detection to be easily performed in multiple settings by simplifying and reducing assay time in a laboratory or clinical environment and by allowing for antibody detection in point-of-care, nonlaboratory settings. © 2022 Wiley Periodicals LLC. Basic Protocol: SARS-CoV-2 antibody detection using the split-luciferase assay on a medium-throughput scale with a laboratory luminometer Alternate Protocol 1: High-throughput-based protocol for SARS-CoV-2 antibody detection using a robotic platform Alternate Protocol 2: Point-of-care-based protocol for SARS-CoV-2 antibody detection using a handheld luminometer Support Protocol: Determining positive/negative cutoffs for test samples and standardizing the assay between days.
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Affiliation(s)
- Susanna K. Elledge
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia
| | - Ian Eigl
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia
| | | | | | - Xin X. Zhou
- Cancer BiologyDana Farber Cancer InstituteBostonMassachusetts
| | - Kevin K. Leung
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia
| | | | - James A. Wells
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia,Chan Zuckerberg BiohubSan FranciscoCalifornia,Department of Cellular and Molecular PharmacologyUniversity of CaliforniaSan FranciscoCalifornia
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10
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Yek C, Pacheco AR, Vanaerschot M, Bohl JA, Fahsbender E, Aranda-Díaz A, Lay S, Chea S, Oum MH, Lon C, Tato CM, Manning JE. Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead. Front Epidemiol 2022; 2:926695. [PMID: 36247976 PMCID: PMC9558322 DOI: 10.3389/fepid.2022.926695] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 06/16/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) is the process of sequencing all genetic material in a biological sample. The technique is growing in popularity with myriad applications including outbreak investigation, biosurveillance, and pathogen detection in clinical samples. However, mNGS programs are costly to build and maintain, and additional obstacles faced by low- and middle-income countries (LMICs) may further widen global inequities in mNGS capacity. Over the past two decades, several important infectious disease outbreaks have highlighted the importance of establishing widespread sequencing capacity to support rapid disease detection and containment at the source. Using lessons learned from the COVID-19 pandemic, LMICs can leverage current momentum to design and build sustainable mNGS programs, which would form part of a global surveillance network crucial to the elimination of infectious diseases.
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Affiliation(s)
- Christina Yek
- Department of Critical Care Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Andrea R. Pacheco
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Jennifer A. Bohl
- Vaccine Immunology Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | | | - Andrés Aranda-Díaz
- Chan Zuckerberg Initiative, Redwood City, CA, United States
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Sreyngim Lay
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sophana Chea
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Meng Heng Oum
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Chanthap Lon
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Jessica E. Manning
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
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11
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Yek C, Lay S, Bohl JA, Man S, Chea S, Lon C, Ahyong V, Tato CM, DeRisi JL, Sovannaroth S, Manning JE. Case Report: Cambodian National Malaria Surveillance Program Detection of Plasmodium knowlesi. Am J Trop Med Hyg 2022; 107:151-153. [PMID: 35895370 PMCID: PMC9294667 DOI: 10.4269/ajtmh.22-0039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/05/2022] [Indexed: 11/07/2022] Open
Abstract
Despite recent success in reducing the regional incidence of Plasmodium falciparum malaria, cases of zoonotic malaria are on the rise in Southeast Asia. The Cambodian National Malaria Surveillance Program has previously relied on rapid diagnostic tests and blood smear microscopy with confirmatory polymerase chain reaction (PCR) testing in a subset of cases to further distinguish P. falciparum, P. malariae, P. ovale, and P. vivax species. Here, metagenomic next-generation sequencing identified P. knowlesi mono-infection in six Cambodian patients initially diagnosed with P. malariae by blood smear microscopy in February–May 2020. These findings of recent human infections with P. knowlesi in Cambodia led to the incorporation of P. knowlesi–specific PCR diagnostics to national malaria surveillance efforts.
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Affiliation(s)
- Christina Yek
- Department of Critical Care Medicine, National Institutes of Health Clinical Center, Bethesda, Maryland
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Sreyngim Lay
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
| | - Jennifer A. Bohl
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Somnang Man
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
- National Center of Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Sophana Chea
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
| | - Chanthap Lon
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California
| | | | | | - Siv Sovannaroth
- National Center of Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Jessica E. Manning
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
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12
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Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, DeRisi JL, Gentles A, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, Dussart P, Heraud JM, Brook CE. Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade. Front Public Health 2022; 10:786060. [PMID: 35223729 PMCID: PMC8873168 DOI: 10.3389/fpubh.2022.786060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent ancestral sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.
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Affiliation(s)
- Gwenddolen Kettenburg
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Hafaliana Christian Ranaivoson
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Angelo Andrianiaina
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Santino Andry
- Department of Entomology, University of Antananarivo, Antananarivo, Madagascar
| | | | - Anecia Gentles
- Odum School of Ecology, University of Georgia, Athens, GA, United States
| | | | | | | | | | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cara E. Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
- *Correspondence: Cara E. Brook
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13
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Schubert RD, Hawes IA, Ramachandran PS, Ramesh A, Crawford ED, Pak JE, Wu W, Cheung CK, O'Donovan BD, Tato CM, Lyden A, Tan M, Sit R, Sowa GM, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL, Gelfand AA, Johnson-Kerner BL, Nash K, Krishnamoorthy KS, Chitnis T, Ding JZ, McMillan HJ, Chiu CY, Briggs B, Glaser CA, Yen C, Chu V, Wadford DA, Dominguez SR, Ng TFF, Marine RL, Lopez AS, Nix WA, Soldatos A, Gorman MP, Benson L, Messacar K, Konopka-Anstadt JL, Oberste MS, DeRisi JL, Wilson MR. Author Correction: Pan-viral serology implicates enteroviruses in acute flaccid myelitis. Nat Med 2021; 27:1849. [PMID: 34548659 DOI: 10.1038/s41591-021-01429-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ryan D Schubert
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Isobel A Hawes
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Prashanth S Ramachandran
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Akshaya Ramesh
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Emily D Crawford
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Brian D O'Donovan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Rene Sit
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gavin M Sowa
- School of Medicine, University of California, San Francisc, San Francisco, CA, USA
| | - Hannah A Sample
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Debarko Banerji
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Lillian M Khan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Riley Bove
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen L Hauser
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Amy A Gelfand
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Bethany L Johnson-Kerner
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Kendall Nash
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Tanuja Chitnis
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Joy Z Ding
- Division of Neurology, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Hugh J McMillan
- Division of Neurology, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Charles Y Chiu
- Department of Laboratory Medicine and Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin Briggs
- Department of Pediatrics, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Carol A Glaser
- Department of Pediatric Infectious Diseases, Kaiser Permanente Oakland Medical Center, Oakland, CA, USA
| | - Cynthia Yen
- Division of Communicable Disease Control, California Department of Public Health, Richmond, CA, USA
| | - Victoria Chu
- Division of Communicable Disease Control, California Department of Public Health, Richmond, CA, USA
| | - Debra A Wadford
- Division of Communicable Disease Control, California Department of Public Health, Richmond, CA, USA
| | - Samuel R Dominguez
- Children's Hospital Colorado and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Terry Fei Fan Ng
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rachel L Marine
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Adriana S Lopez
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - W Allan Nix
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ariane Soldatos
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mark P Gorman
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Leslie Benson
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Kevin Messacar
- Children's Hospital Colorado and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA. .,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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14
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Elledge SK, Zhou XX, Byrnes JR, Martinko AJ, Lui I, Pance K, Lim SA, Glasgow JE, Glasgow AA, Turcios K, Iyer NS, Torres L, Peluso MJ, Henrich TJ, Wang TT, Tato CM, Leung KK, Greenhouse B, Wells JA. Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection. Nat Biotechnol 2021. [PMID: 33767397 DOI: 10.1038/s41587-41021-00878-41588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Current serology tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies mainly take the form of enzyme-linked immunosorbent assays, chemiluminescent microparticle immunoassays or lateral flow assays, which are either laborious, expensive or lacking sufficient sensitivity and scalability. Here we present the development and validation of a rapid, low-cost, solution-based assay to detect antibodies in serum, plasma, whole blood and to a lesser extent saliva, using rationally designed split luciferase antibody biosensors. This new assay, which generates quantitative results in 30 min, substantially reduces the complexity and improves the scalability of coronavirus disease 2019 (COVID-19) antibody tests. This assay is well-suited for point-of-care, broad population testing, and applications in low-resource settings, for monitoring host humoral responses to vaccination or viral infection.
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Affiliation(s)
- Susanna K Elledge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - James R Byrnes
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | | | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Katarina Pance
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Shion A Lim
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Jeff E Glasgow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Anum A Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Keirstinne Turcios
- Division of Experimental Medicine, University of California, San Francisco, San Francisco CA, USA
| | - Nikita S Iyer
- Division of Experimental Medicine, University of California, San Francisco, San Francisco CA, USA
| | - Leonel Torres
- Division of Experimental Medicine, University of California, San Francisco, San Francisco CA, USA
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, San Francisco CA, USA
| | - Taia T Wang
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Departments of Medicine and of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Bryan Greenhouse
- Division of Experimental Medicine, University of California, San Francisco, San Francisco CA, USA
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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15
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Diagne MM, Ndione MHD, Gaye A, Barry MA, Diallo D, Diallo A, Mwakibete LL, Diop M, Ndiaye EH, Ahyong V, Diouf B, Mhamadi M, Diagne CT, Danfakha F, Diop B, Faye O, Loucoubar C, Fall G, Tato CM, Sall AA, Weaver SC, Diallo M, Faye O. Yellow Fever Outbreak in Eastern Senegal, 2020-2021. Viruses 2021; 13:v13081475. [PMID: 34452343 PMCID: PMC8402698 DOI: 10.3390/v13081475] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 01/07/2023] Open
Abstract
Yellow fever virus remains a major threat in low resource countries in South America and Africa despite the existence of an effective vaccine. In Senegal and particularly in the eastern part of the country, periodic sylvatic circulation has been demonstrated with varying degrees of impact on populations in perpetual renewal. We report an outbreak that occurred from October 2020 to February 2021 in eastern Senegal, notified and managed through the synergistic effort yellow fever national surveillance implemented by the Senegalese Ministry of Health in collaboration with the World Health Organization, the countrywide 4S network set up by the Ministry of Health, the Institut Pasteur de Dakar, and the surveillance of arboviruses and hemorrhagic fever viruses in human and vector populations implemented since mid 2020 in eastern Senegal. Virological analyses highlighted the implication of sylvatic mosquito species in virus transmission. Genomic analysis showed a close relationship between the circulating strain in eastern Senegal, 2020, and another one from the West African lineage previously detected and sequenced two years ago from an unvaccinated Dutch traveler who visited the Gambia and Senegal before developing signs after returning to Europe. Moreover, genome analysis identified a 6-nucleotide deletion in the variable domain of the 3′UTR with potential impact on the biology of the viral strain that merits further investigations. Integrated surveillance of yellow fever virus but also of other arboviruses of public health interest is crucial in an ecosystem such as eastern Senegal.
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Affiliation(s)
- Moussa Moïse Diagne
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
- Correspondence: ; Tel.: +221-77-405-9928
| | - Marie Henriette Dior Ndione
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Alioune Gaye
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - Diawo Diallo
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - Lusajo L. Mwakibete
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; (L.L.M.); (V.A.); (C.M.T.)
| | - Mamadou Diop
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - El Hadji Ndiaye
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; (L.L.M.); (V.A.); (C.M.T.)
| | - Babacar Diouf
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Moufid Mhamadi
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Cheikh Tidiane Diagne
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Fodé Danfakha
- Kedougou Medical Region, Ministry of Health, Kedougou 26005, Senegal;
| | - Boly Diop
- Prevention Department, Ministry of Health, Dakar 220, Senegal;
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - Gamou Fall
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Cristina M. Tato
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; (L.L.M.); (V.A.); (C.M.T.)
| | - Amadou Alpha Sall
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Mawlouth Diallo
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
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16
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Randremanana RV, Andriamandimby S, Rakotondramanga JM, Razanajatovo NH, Mangahasimbola RT, Randriambolamanantsoa TH, Ranaivoson HC, Rabemananjara HA, Razanajatovo I, Razafindratsimandresy R, Rabarison JH, Brook CE, Rakotomanana F, Rabetombosoa RM, Razafimanjato H, Ahyong V, Raharinosy V, Raharimanga V, Raharinantoanina SJ, Randrianarisoa MM, Bernardson B, Randrianasolo L, Randriamampionona LBN, Tato CM, DeRisi JL, Dussart P, Vololoniaina MC, Randriatsarafara FM, Randriamanantany ZA, Heraud J. The COVID-19 epidemic in Madagascar: clinical description and laboratory results of the first wave, march-september 2020. Influenza Other Respir Viruses 2021; 15:457-468. [PMID: 33586912 PMCID: PMC8013501 DOI: 10.1111/irv.12845] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Following the first detection of SARS-CoV-2 in passengers arriving from Europe on 19 March 2020, Madagascar took several mitigation measures to limit the spread of the virus in the country. METHODS Nasopharyngeal and/or oropharyngeal swabs were collected from travellers to Madagascar, suspected SARS-CoV-2 cases and contact of confirmed cases. Swabs were tested at the national reference laboratory using real-time RT-PCR. Data collected from patients were entered in an electronic database for subsequent statistical analysis. All distribution of laboratory-confirmed cases were mapped, and six genomes of viruses were fully sequenced. RESULTS Overall, 26,415 individuals were tested for SARS-CoV-2 between 18 March and 18 September 2020, of whom 21.0% (5,553/26,145) returned positive. Among laboratory-confirmed SARS-CoV-2-positive patients, the median age was 39 years (IQR: 28-52), and 56.6% (3,311/5,553) were asymptomatic at the time of sampling. The probability of testing positive increased with age with the highest adjusted odds ratio of 2.2 [95% CI: 1.9-2.5] for individuals aged 49 years and more. Viral strains sequenced belong to clades 19A, 20A and 20B indicative of several independent introduction of viruses. CONCLUSIONS Our study describes the first wave of the COVID-19 in Madagascar. Despite early strategies in place Madagascar could not avoid the introduction and spread of the virus. More studies are needed to estimate the true burden of disease and make public health recommendations for a better preparation to another wave.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Fanjasoa Rakotomanana
- Epidemiology and Clinical Research UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
| | | | | | | | | | - Vaomalala Raharimanga
- Epidemiology and Clinical Research UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
| | | | | | - Barivola Bernardson
- Epidemiology and Clinical Research UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
| | - Laurence Randrianasolo
- Epidemiology and Clinical Research UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
| | | | | | | | - Philippe Dussart
- Virology UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
| | | | | | | | - Jean‐Michel Heraud
- Virology UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
- Present address:
Virology DepartmentInstitut Pasteur de DakarDakarSenegal
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17
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Byrum JR, Waltari E, Janson O, Guo SM, Folkesson J, Chhun BB, Vinden J, Ivanov IE, Forst ML, Li H, Larson AG, Wu W, Tato CM, McCutcheon KM, Peluso MJ, Henrich TJ, Deeks SG, Prakash M, Greenhouse B, Pak JE, Mehta SB. multiSero: open multiplex-ELISA platform for analyzing antibody responses to SARS-CoV-2 infection. medRxiv 2021. [PMID: 34013298 PMCID: PMC8132273 DOI: 10.1101/2021.05.07.21249238] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Serology has provided valuable diagnostic and epidemiological data on antibody responses to SARS-CoV-2 in diverse patient cohorts. Deployment of high content, multiplex serology platforms across the world, including in low and medium income countries, can accelerate longitudinal epidemiological surveys. Here we report multiSero, an open platform to enable multiplex serology with up to 48 antigens in a 96-well format. The platform consists of three components: ELISA-array of printed proteins, a commercial or home-built plate reader, and modular python software for automated analysis (pysero). We validate the platform by comparing antibody titers against the SARS-CoV-2 Spike, receptor binding domain (RBD), and nucleocapsid (N) in 114 sera from COVID-19 positive individuals and 87 pre-pandemic COVID-19 negative sera. We report data with both a commercial plate reader and an inexpensive, open plate reader (nautilus). Receiver operating characteristic (ROC) analysis of classification with single antigens shows that Spike and RBD classify positive and negative sera with the highest sensitivity at a given specificity. The platform distinguished positive sera from negative sera when the reactivity of the sera was equivalent to the binding of 1 ng mL−1 RBD-specific monoclonal antibody. We developed normalization and classification methods to pool antibody responses from multiple antigens and multiple experiments. Our results demonstrate a performant and accessible pipeline for multiplexed ELISA ready for multiple applications, including serosurveillance, identification of viral proteins that elicit antibody responses, differential diagnosis of circulating pathogens, and immune responses to vaccines.
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18
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Chakraborty S, Mallajosyula V, Tato CM, Tan GS, Wang TT. SARS-CoV-2 vaccines in advanced clinical trials: Where do we stand? Adv Drug Deliv Rev 2021; 172:314-338. [PMID: 33482248 PMCID: PMC7816567 DOI: 10.1016/j.addr.2021.01.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 02/07/2023]
Abstract
The ongoing SARS-CoV-2 pandemic has led to the focused application of resources and scientific expertise toward the goal of developing investigational vaccines to prevent COVID-19. The highly collaborative global efforts by private industry, governments and non-governmental organizations have resulted in a number of SARS-CoV-2 vaccine candidates moving to Phase III trials in a period of only months since the start of the pandemic. In this review, we provide an overview of the preclinical and clinical data on SARS-CoV-2 vaccines that are currently in Phase III clinical trials and in few cases authorized for emergency use. We further discuss relevant vaccine platforms and provide a discussion of SARS-CoV-2 antigens that may be targeted to increase the breadth and durability of vaccine responses.
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Affiliation(s)
- Saborni Chakraborty
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | - Cristina M Tato
- Infectious Disease Initiative, Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gene S Tan
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; Department of Infectious Diseases, University of California San Diego, La Jolla, CA 92037, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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19
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Crawford E, Kamm J, Miller S, Li LM, Caldera S, Lyden A, Yokoe D, Nichols A, Tran NK, Barnard SE, Conner PM, Nambiar A, Zinter MS, Moayeri M, Serpa PH, Prince BC, Quan J, Sit R, Tan M, Phelps M, Derisi JL, Tato CM, Langelier C. Investigating Transfusion-related Sepsis Using Culture-Independent Metagenomic Sequencing. Clin Infect Dis 2021; 71:1179-1185. [PMID: 31563940 PMCID: PMC7442849 DOI: 10.1093/cid/ciz960] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/25/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Transfusion-related sepsis remains an important hospital infection control challenge. Investigation of septic transfusion events is often restricted by the limitations of bacterial culture in terms of time requirements and low yield in the setting of prior antibiotic administration. METHODS In 3 gram-negative septic transfusion cases, we performed metagenomic next-generation sequencing (mNGS) of direct clinical blood specimens in addition to standard culture-based approaches utilized for infection control investigations. Pathogen detection leveraged IDSeq, a new open-access microbial bioinformatics portal. Phylogenetic analysis was performed to assess microbial genetic relatedness and understand transmission events. RESULTS mNGS of direct clinical blood specimens afforded precision detection of pathogens responsible for each case of transfusion-related sepsis and enabled discovery of a novel Acinetobacter species in a platelet product that had become contaminated despite photochemical pathogen reduction. In each case, longitudinal assessment of pathogen burden elucidated the temporal sequence of events associated with each transfusion-transmitted infection. We found that informative data could be obtained from culture-independent mNGS of residual platelet products and leftover blood specimens that were either unsuitable or unavailable for culture or that failed to grow due to prior antibiotic administration. We additionally developed methods to enhance accuracy for detecting transfusion-associated pathogens that share taxonomic similarity to contaminants commonly found in mNGS library preparations. CONCLUSIONS Culture-independent mNGS of blood products afforded rapid and precise assessment of pathogen identity, abundance, and genetic relatedness. Together, these challenging cases demonstrated the potential for metagenomics to advance existing methods for investigating transfusion-transmitted infections.
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Affiliation(s)
- Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Microbiology and Immunology, University of California-San Francisco, San Francisco, California, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Lucy M Li
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Saharai Caldera
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Deborah Yokoe
- Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA.,Department of Hospital Epidemiology and Infection Prevention, University of California-San Francisco, San Francisco, California, USA
| | - Amy Nichols
- Department of Hospital Epidemiology and Infection Prevention, University of California-San Francisco, San Francisco, California, USA
| | - Nam K Tran
- Department of Pathology and Laboratory Medicine, University of California-Davis, Davis, California, USA
| | - Sarah E Barnard
- Department of Pathology and Laboratory Medicine, University of California-Davis, Davis, California, USA
| | - Peter M Conner
- Department of Pathology and Laboratory Medicine, University of California-Davis, Davis, California, USA
| | - Ashok Nambiar
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Matt S Zinter
- Division of Pulmonary and Critical Care Medicine, Department of Pediatrics, University of California-San Francisco, San Francisco, California, USA
| | - Morvarid Moayeri
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Paula Hayakawa Serpa
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Brian C Prince
- Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Jenai Quan
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rene Sit
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Michelle Tan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Joseph L Derisi
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California, USA
| | | | - Charles Langelier
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
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20
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Vanaerschot M, Mann SA, Webber JT, Kamm J, Bell SM, Bell J, Hong SN, Nguyen MP, Chan LY, Bhatt KD, Tan M, Detweiler AM, Espinosa A, Wu W, Batson J, Dynerman D, Wadford DA, Puschnik AS, Neff N, Ahyong V, Miller S, Ayscue P, Tato CM, Paul S, Kistler AL, DeRisi JL, Crawford ED. Identification of a Polymorphism in the N Gene of SARS-CoV-2 That Adversely Impacts Detection by Reverse Transcription-PCR. J Clin Microbiol 2020; 59:JCM.02369-20. [PMID: 33067272 DOI: 10.1101/2020.08.25.265074] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
AbstractWe identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection.Article Summary LineA SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.
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Affiliation(s)
| | - Sabrina A Mann
- Chan Zuckerberg Biohub, San Francisco, California, USA
- University of California, San Francisco, California, USA
| | | | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Sidney M Bell
- Chan Zuckerberg Initiative, Redwood City, California, USA
| | - John Bell
- California Department of Public Health, Richmond, California, USA
| | - Si Noon Hong
- Department of Public Health, Madera, California, USA
| | | | - Lienna Y Chan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Karan D Bhatt
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Michelle Tan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Alex Espinosa
- California Department of Public Health, Richmond, California, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Debra A Wadford
- California Department of Public Health, Richmond, California, USA
| | | | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Steve Miller
- University of California, San Francisco, California, USA
| | | | | | - Simon Paul
- Department of Public Health, Madera, California, USA
| | - Amy L Kistler
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, California, USA
- University of California, San Francisco, California, USA
| | - Emily D Crawford
- Chan Zuckerberg Biohub, San Francisco, California, USA
- University of California, San Francisco, California, USA
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21
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Crawford ED, Acosta I, Ahyong V, Anderson EC, Arevalo S, Asarnow D, Axelrod S, Ayscue P, Azimi CS, Azumaya CM, Bachl S, Bachmutsky I, Bhaduri A, Brown JB, Batson J, Behnert A, Boileau RM, Bollam SR, Bonny AR, Booth D, Borja MJB, Brown D, Buie B, Burnett CE, Byrnes LE, Cabral KA, Cabrera JP, Caldera S, Canales G, Castañeda GR, Chan AP, Chang CR, Charles-Orszag A, Cheung C, Chio U, Chow ED, Citron YR, Cohen A, Cohn LB, Chiu C, Cole MA, Conrad DN, Constantino A, Cote A, Crayton-Hall T, Darmanis S, Detweiler AM, Dial RL, Dong S, Duarte EM, Dynerman D, Egger R, Fanton A, Frumm SM, Fu BXH, Garcia VE, Garcia J, Gladkova C, Goldman M, Gomez-Sjoberg R, Gordon MG, Grove JCR, Gupta S, Haddjeri-Hopkins A, Hadley P, Haliburton J, Hao SL, Hartoularos G, Herrera N, Hilberg M, Ho KYE, Hoppe N, Hosseinzadeh S, Howard CJ, Hussmann JA, Hwang E, Ingebrigtsen D, Jackson JR, Jowhar ZM, Kain D, Kim JYS, Kistler A, Kreutzfeld O, Kulsuptrakul J, Kung AF, Langelier C, Laurie MT, Lee L, Leng K, Leon KE, Leonetti MD, Levan SR, Li S, Li AW, Liu J, Lubin HS, Lyden A, Mann J, Mann S, Margulis G, Marquez DM, Marsh BP, Martyn C, McCarthy EE, McGeever A, Merriman AF, Meyer LK, Miller S, Moore MK, Mowery CT, Mukhtar T, Mwakibete LL, Narez N, Neff NF, Osso LA, Oviedo D, Peng S, Phelps M, Phong K, Picard P, Pieper LM, Pincha N, Pisco AO, Pogson A, Pourmal S, Puccinelli RR, Puschnik AS, Rackaityte E, Raghavan P, Raghavan M, Reese J, Replogle JM, Retallack H, Reyes H, Rose D, Rosenberg MF, Sanchez-Guerrero E, Sattler SM, Savy L, See SK, Sellers KK, Serpa PH, Sheehy M, Sheu J, Silas S, Streithorst JA, Strickland J, Stryke D, Sunshine S, Suslow P, Sutanto R, Tamura S, Tan M, Tan J, Tang A, Tato CM, Taylor JC, Tenvooren I, Thompson EM, Thornborrow EC, Tse E, Tung T, Turner ML, Turner VS, Turnham RE, Turocy MJ, Vaidyanathan TV, Vainchtein ID, Vanaerschot M, Vazquez SE, Wandler AM, Wapniarski A, Webber JT, Weinberg ZY, Westbrook A, Wong AW, Wong E, Worthington G, Xie F, Xu A, Yamamoto T, Yang Y, Yarza F, Zaltsman Y, Zheng T, DeRisi JL. Rapid deployment of SARS-CoV-2 testing: The CLIAHUB. PLoS Pathog 2020; 16:e1008966. [PMID: 33112933 PMCID: PMC7592773 DOI: 10.1371/journal.ppat.1008966] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Emily D. Crawford
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Microbiology and Immunology, San Francisco, California, United States of America
| | - Irene Acosta
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Erika C. Anderson
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shaun Arevalo
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Daniel Asarnow
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shannon Axelrod
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Patrick Ayscue
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Camillia S. Azimi
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Caleigh M. Azumaya
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Stefanie Bachl
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Iris Bachmutsky
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Aparna Bhaduri
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jeremy Bancroft Brown
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Astrid Behnert
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Ryan M. Boileau
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Saumya R. Bollam
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alain R. Bonny
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - David Booth
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | | | - David Brown
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Bryan Buie
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Cassandra E. Burnett
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Lauren E. Byrnes
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Katelyn A. Cabral
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- University of California San Francisco, Institute for Neurodegenerative Diseases, San Francisco, California, United States of America
| | - Joana P. Cabrera
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Saharai Caldera
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
| | - Gabriela Canales
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Agnes Protacio Chan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Christopher R. Chang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Arthur Charles-Orszag
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Carly Cheung
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Unseng Chio
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Eric D. Chow
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Y. Rose Citron
- University of California, Berkeley, California, United States of America
| | - Allison Cohen
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Lillian B. Cohn
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Experimental Medicine, San Francisco, California, United States of America
| | - Charles Chiu
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Mitchel A. Cole
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Daniel N. Conrad
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Angela Constantino
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Andrew Cote
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Spyros Darmanis
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Rebekah L. Dial
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Shen Dong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Elias M. Duarte
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - David Dynerman
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Rebecca Egger
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Alison Fanton
- University of California, Berkeley, California, United States of America
| | - Stacey M. Frumm
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Becky Xu Hua Fu
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Valentina E. Garcia
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Julie Garcia
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Christina Gladkova
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Miriam Goldman
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - M. Grace Gordon
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - James C. R. Grove
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shweta Gupta
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alexis Haddjeri-Hopkins
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Pierce Hadley
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- University of California San Francisco, Institute for Neurodegenerative Diseases, San Francisco, California, United States of America
| | - John Haliburton
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Samantha L. Hao
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - George Hartoularos
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Nadia Herrera
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Melissa Hilberg
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Kit Ying E. Ho
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Nicholas Hoppe
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Conor J. Howard
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jeffrey A. Hussmann
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Elizabeth Hwang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Danielle Ingebrigtsen
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Julia R. Jackson
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Ziad M. Jowhar
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Danielle Kain
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - James Y. S. Kim
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Oriana Kreutzfeld
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Gladstone Institute, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Aileen W. Li
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- eSix Development, Oakland, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jennifer Mann
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sabrina Mann
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Gorica Margulis
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Diana M. Marquez
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Bryan P. Marsh
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Calla Martyn
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Elizabeth E. McCarthy
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Aaron McGeever
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Lauren K. Meyer
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Steve Miller
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Megan K. Moore
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Cody T. Mowery
- Gladstone Institute, San Francisco, California, United States of America
| | - Tanzila Mukhtar
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Noelle Narez
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Norma F. Neff
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Lindsay A. Osso
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Diter Oviedo
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Suping Peng
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Kiet Phong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Lindsey M. Pieper
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Angela Pogson
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Sergei Pourmal
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | | | | | - Elze Rackaityte
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Preethi Raghavan
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Madhura Raghavan
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - James Reese
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joseph M. Replogle
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Hanna Retallack
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Helen Reyes
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Donald Rose
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Marci F. Rosenberg
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Sydney M. Sattler
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Laura Savy
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Stephanie K. See
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Kristin K. Sellers
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Paula Hayakawa Serpa
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
| | - Maureen Sheehy
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jonathan Sheu
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sukrit Silas
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jessica A. Streithorst
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jack Strickland
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Doug Stryke
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Sara Sunshine
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Peter Suslow
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Renaldo Sutanto
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Serena Tamura
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jiongyi Tan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alice Tang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Cristina M. Tato
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jack C. Taylor
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Erin M. Thompson
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Edward C. Thornborrow
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Eric Tse
- Joint Bioengineering Graduate Program, University of California, Berkeley, California, United States of America
| | - Tony Tung
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Marc L. Turner
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Rigney E. Turnham
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Mary J. Turocy
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Trisha V. Vaidyanathan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Ilia D. Vainchtein
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Manu Vanaerschot
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sara E. Vazquez
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Anica M. Wandler
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Anne Wapniarski
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - James T. Webber
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Zara Y. Weinberg
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Allison W. Wong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Emily Wong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Fang Xie
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Albert Xu
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Terrina Yamamoto
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Ying Yang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Fauna Yarza
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Yefim Zaltsman
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Tina Zheng
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
- * E-mail:
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22
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Kalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, Han J, Holmes OB, Juan YF, King R, Kislyuk A, Lin MF, Mariano M, Morse T, Reynoso LV, Cruz DR, Sheu J, Tang J, Wang J, Zhang MA, Zhong E, Ahyong V, Lay S, Chea S, Bohl JA, Manning JE, Tato CM, DeRisi JL. IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. Gigascience 2020; 9:giaa111. [PMID: 33057676 PMCID: PMC7566497 DOI: 10.1093/gigascience/giaa111] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/28/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource-limited environments. FINDINGS We present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline, which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics that are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2. CONCLUSION The IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.
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Affiliation(s)
- Katrina L Kalantar
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Tiago Carvalho
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | | | - Boris Dimitrov
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Greg Dingle
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Rebecca Egger
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Julie Han
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Olivia B Holmes
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Yun-Fang Juan
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Ryan King
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Andrey Kislyuk
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Michael F Lin
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Maria Mariano
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Todd Morse
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Lucia V Reynoso
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - David Rissato Cruz
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Jonathan Sheu
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Jennifer Tang
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - James Wang
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Mark A Zhang
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Emily Zhong
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Vida Ahyong
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Sreyngim Lay
- Malaria and Vector Research Laboratory, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sophana Chea
- Malaria and Vector Research Laboratory, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Jennifer A Bohl
- Malaria and Vector Research Laboratory, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Jessica E Manning
- Malaria and Vector Research Laboratory, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Cristina M Tato
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
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23
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Elledge SK, Zhou XX, Byrnes JR, Martinko AJ, Lui I, Pance K, Lim SA, Glasgow JE, Glasgow AA, Turcios K, Iyer N, Torres L, Peluso MJ, Henrich TJ, Wang TT, Tato CM, Leung KK, Greenhouse B, Wells JA. Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection. medRxiv 2020:2020.08.17.20176925. [PMID: 32839788 PMCID: PMC7444307 DOI: 10.1101/2020.08.17.20176925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Current serology tests for SARS-CoV-2 antibodies mainly take the form of enzyme-linked immunosorbent assays or lateral flow assays, with the former being laborious and the latter being expensive and often lacking sufficient sensitivity and scalability. Here we present the development and validation of a rapid, low-cost solution-based assay to detect antibodies in serum, plasma, whole blood, and saliva, using rationally designed split luciferase antibody biosensors (spLUC). This new assay, which generates quantitative results in as short as 5 minutes, substantially reduces the complexity and improves the scalability of COVID-19 antibody tests for point-of-care and broad population testing.
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Affiliation(s)
- Susanna K. Elledge
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Xin X. Zhou
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - James R. Byrnes
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | | | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Katarina Pance
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Shion A. Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Jeff E. Glasgow
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Anum A. Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Keirstinne Turcios
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
| | - Nikita Iyer
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
| | - Leonel Torres
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
| | - Michael J. Peluso
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
| | - Timothy J. Henrich
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
| | - Taia T. Wang
- Chan Zuckerberg Biohub, San Francisco, California, 94158, USA
- Departments of Medicine and of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | | | - Kevin K. Leung
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
- Chan Zuckerberg Biohub, San Francisco, California, 94158, USA
| | - James A. Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
- Chan Zuckerberg Biohub, San Francisco, California, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, 94158, USA
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24
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Saha S, Malaker R, Sajib MSI, Hasanuzzaman M, Rahman H, Ahmed ZB, Islam MS, Islam M, Hooda Y, Ahyong V, Vanaerschot M, Batson J, Hao S, Kamm J, Kistler A, Tato CM, DeRisi JL, Saha SK. Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh. Microbiol Resour Announc 2020; 9:e00568-20. [PMID: 32527780 PMCID: PMC7291105 DOI: 10.1128/mra.00568-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 05/24/2020] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) isolate obtained from a nasopharyngeal swab from a patient with COVID-19 in Bangladesh is reported.
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Affiliation(s)
- Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Roly Malaker
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | | | | | | | | | | | - Yogesh Hooda
- Child Health Research Foundation, Dhaka, Bangladesh
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Samantha Hao
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
- Department of Microbiology, Dhaka Shishu Hospital, Bangladesh Institute of Child Health, Dhaka, Bangladesh
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25
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Manning JE, Bohl JA, Lay S, Chea S, Sovann L, Sengdoeurn Y, Heng S, Vuthy C, Kalantar K, Ahyong V, Tan M, Sheu J, Tato CM, DeRisi JL, Baril L, Duong V, Dussart P, Karlsson EA. Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia. bioRxiv 2020:2020.03.02.968818. [PMID: 32511296 PMCID: PMC7217139 DOI: 10.1101/2020.03.02.968818] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Rapid production and publication of pathogen genome sequences during emerging disease outbreaks provide crucial public health information. In resource-limited settings, especially near an outbreak epicenter, conventional deep sequencing or bioinformatics are often challenging. Here we successfully used metagenomic next generation sequencing on an iSeq100 Illumina platform paired with an open-source bioinformatics pipeline to quickly characterize Cambodia's first case of COVID-2019.
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Affiliation(s)
- Jessica E. Manning
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Jennifer A. Bohl
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sreyngim Lay
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sophana Chea
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Ly Sovann
- Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
| | - Yi Sengdoeurn
- Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
| | - Seng Heng
- Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
| | - Chan Vuthy
- Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Michelle Tan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jonathan Sheu
- Chan Zuckerberg Initiative, Redwood City, California, USA
| | | | | | | | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Erik A. Karlsson
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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26
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Woodworth MH, Dynerman D, Crawford ED, Doernberg SB, Ramirez-Avila L, Serpa PH, Nichols A, Li LM, Lyden A, Tato CM, Miller S, Derisi JL, Langelier C. Sentinel Case of Candida auris in the Western United States Following Prolonged Occult Colonization in a Returned Traveler from India. Microb Drug Resist 2019; 25:677-680. [PMID: 31163013 PMCID: PMC6555181 DOI: 10.1089/mdr.2018.0408] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Candida auris is an emerging multidrug-resistant yeast with high mortality. We report the sentinel C. auris case on the United States West Coast in a patient who relocated from India. We identified close phylogenetic relatedness to the South Asia clade and ERG11 Y132F and FKS1 S639Y mutations potentially explaining antifungal resistance.
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Affiliation(s)
- Michael H Woodworth
- 1 Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | | | | | - Sarah B Doernberg
- 3 Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Lynn Ramirez-Avila
- 4 Division of Pediatric Infectious Diseases and Global Health, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Paula Hayakawa Serpa
- 2 Chan Zuckerberg Biohub, San Francisco, California.,3 Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Amy Nichols
- 5 Hospital Epidemiology and Infection Control, University of California, San Francisco, San Francisco, California
| | - Lucy M Li
- 2 Chan Zuckerberg Biohub, San Francisco, California
| | - Amy Lyden
- 2 Chan Zuckerberg Biohub, San Francisco, California
| | | | - Steve Miller
- 6 Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California
| | - Joseph L Derisi
- 2 Chan Zuckerberg Biohub, San Francisco, California.,7 Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California
| | - Charles Langelier
- 2 Chan Zuckerberg Biohub, San Francisco, California.,3 Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California
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27
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Schubert RD, Hawes IA, Ramachandran PS, Ramesh A, Crawford ED, Pak JE, Wu W, Cheung CK, O'Donovan BD, Tato CM, Lyden A, Tan M, Sit R, Sowa GA, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL, Gelfand AA, Johnson-Kerner BL, Nash K, Krishnamoorthy KS, Chitnis T, Ding JZ, McMillan HJ, Chiu CY, Briggs B, Glaser CA, Yen C, Chu V, Wadford DA, Dominguez SR, Ng TFF, Marine RL, Lopez AS, Nix WA, Soldatos A, Gorman MP, Benson L, Messacar K, Konopka-Anstadt JL, Oberste MS, DeRisi JL, Wilson MR. Pan-viral serology implicates enteroviruses in acute flaccid myelitis. Nat Med 2019; 25:1748-1752. [PMID: 31636453 PMCID: PMC6858576 DOI: 10.1038/s41591-019-0613-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022]
Abstract
Since 2012, the United States has experienced a biennial spike in pediatric acute flaccid myelitis (AFM).1–6 Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF).2 We interrogated CSF from children with AFM (n=42) and pediatric other neurologic disease controls (n=58) for intrathecal anti-viral antibodies using a phage display library expressing 481,966 overlapping peptides derived from all known vertebrate and arboviruses (VirScan). We also performed metagenomic next-generation sequencing (mNGS) of AFM CSF RNA (n=20 cases), both unbiased and with targeted enrichment for EVs. Using VirScan, the only viral family significantly enriched by the CSF of AFM cases relative to controls was Picornaviridae, with the most enriched Picornaviridae peptides belonging to the genus Enterovirus (n=29/42 cases versus 4/58 controls). EV VP1 ELISA confirmed this finding (n=22/26 cases versus 7/50 controls). mNGS did not detect additional EV RNA. Despite rare detection of EV RNA, pan-viral serology identified frequently high levels of CSF EV-specific antibodies in AFM compared to controls, providing further evidence for a causal role of non-polio EVs in AFM.
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Affiliation(s)
- Ryan D Schubert
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Isobel A Hawes
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Prashanth S Ramachandran
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Akshaya Ramesh
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Emily D Crawford
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Brian D O'Donovan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Rene Sit
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gavin A Sowa
- School of Medicine, University of California, San Francisc, San Francisco, CA, USA
| | - Hannah A Sample
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Debarko Banerji
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Lillian M Khan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Riley Bove
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen L Hauser
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Amy A Gelfand
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Bethany L Johnson-Kerner
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Kendall Nash
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Tanuja Chitnis
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Joy Z Ding
- Division of Neurology, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Hugh J McMillan
- Division of Neurology, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Charles Y Chiu
- Department of Laboratory Medicine and Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin Briggs
- Department of Pediatrics, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Carol A Glaser
- Department of Pediatric Infectious Diseases, Kaiser Permanente Oakland Medical Center, Oakland, CA, USA
| | - Cynthia Yen
- Division of Communicable Disease Control, California Department of Public Health, Richmond, CA, USA
| | - Victoria Chu
- Division of Communicable Disease Control, California Department of Public Health, Richmond, CA, USA
| | - Debra A Wadford
- Division of Communicable Disease Control, California Department of Public Health, Richmond, CA, USA
| | - Samuel R Dominguez
- Children's Hospital Colorado and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Terry Fei Fan Ng
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rachel L Marine
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Adriana S Lopez
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - W Allan Nix
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ariane Soldatos
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mark P Gorman
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Leslie Benson
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Kevin Messacar
- Children's Hospital Colorado and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA. .,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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29
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Davis MM, Tato CM. Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? Seeing the Forest Rather than a Few Trees. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a028886. [PMID: 29038119 DOI: 10.1101/cshperspect.a028886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Preventing morbidity and mortality from infectious disease through the development and use of effective vaccines is one of medicine's greatest achievements and greatest frustrations. We are struggling with improving vaccine efficacy for some of the most globally widespread diseases, such as malaria and tuberculosis. In an effort to gain an edge, systems biology approaches have begun to be employed to more broadly investigate the pathways leading to protective vaccine responses. As such, we are now at a critical juncture, needing to evaluate how fruitful these approaches have been. Herein we discuss the level of success achieved as compared to the original promise of systems methodologies, and conclude that while we have indeed begun to make clear inroads into understanding the immune response to vaccines, we still have much to learn and gain from the more comprehensive approach of systems-level analysis.
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Affiliation(s)
- Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94304.,Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94304.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94304
| | - Cristina M Tato
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94304
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30
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Andres-Terre M, McGuire HM, Pouliot Y, Bongen E, Sweeney TE, Tato CM, Khatri P. Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses. Immunity 2016; 43:1199-211. [PMID: 26682989 PMCID: PMC4684904 DOI: 10.1016/j.immuni.2015.11.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/03/2015] [Accepted: 09/01/2015] [Indexed: 12/31/2022]
Abstract
Respiratory viral infections are a significant burden to healthcare worldwide. Many whole genome expression profiles have identified different respiratory viral infection signatures, but these have not translated to clinical practice. Here, we performed two integrated, multi-cohort analyses of publicly available transcriptional data of viral infections. First, we identified a common host signature across different respiratory viral infections that could distinguish (1) individuals with viral infections from healthy controls and from those with bacterial infections, and (2) symptomatic from asymptomatic subjects prior to symptom onset in challenge studies. Second, we identified an influenza-specific host response signature that (1) could distinguish influenza-infected samples from those with bacterial and other respiratory viral infections, (2) was a diagnostic and prognostic marker in influenza-pneumonia patients and influenza challenge studies, and (3) was predictive of response to influenza vaccine. Our results have applications in the diagnosis, prognosis, and identification of drug targets in viral infections. MVS is a common transcriptional host response to respiratory viral infection MVS could be used in clinics as a diagnostic and/or prognostic biomarker IMS distinguishes influenza from other viral and bacterial infections IMS correlates with infection symptomatology and vaccine response
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Affiliation(s)
- Marta Andres-Terre
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305, USA
| | - Helen M McGuire
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305, USA
| | - Yannick Pouliot
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305, USA
| | - Erika Bongen
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305, USA
| | - Timothy E Sweeney
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305, USA; Division of Biomedical Informatics, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Cristina M Tato
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305, USA; Division of Biomedical Informatics, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
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31
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Sweeney TE, Braviak L, Tato CM, Khatri P. Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis. Lancet Respir Med 2016; 4:213-24. [PMID: 26907218 DOI: 10.1016/s2213-2600(16)00048-5] [Citation(s) in RCA: 268] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND Active pulmonary tuberculosis is difficult to diagnose and treatment response is difficult to effectively monitor. A WHO consensus statement has called for new non-sputum diagnostics. The aim of this study was to use an integrated multicohort analysis of samples from publically available datasets to derive a diagnostic gene set in the peripheral blood of patients with active tuberculosis. METHODS We searched two public gene expression microarray repositories and retained datasets that examined clinical cohorts of active pulmonary tuberculosis infection in whole blood. We compared gene expression in patients with either latent tuberculosis or other diseases versus patients with active tuberculosis using our validated multicohort analysis framework. Three datasets were used as discovery datasets and meta-analytical methods were used to assess gene effects in these cohorts. We then validated the diagnostic capacity of the three gene set in the remaining 11 datasets. FINDINGS A total of 14 datasets containing 2572 samples from 10 countries from both adult and paediatric patients were included in the analysis. Of these, three datasets (N=1023) were used to discover a set of three genes (GBP5, DUSP3, and KLF2) that are highly diagnostic for active tuberculosis. We validated the diagnostic power of the three gene set to separate active tuberculosis from healthy controls (global area under the ROC curve (AUC) 0·90 [95% CI 0·85-0·95]), latent tuberculosis (0·88 [0·84-0·92]), and other diseases (0·84 [0·80-0·95]) in eight independent datasets composed of both children and adults from ten countries. Expression of the three-gene set was not confounded by HIV infection status, bacterial drug resistance, or BCG vaccination. Furthermore, in four additional cohorts, we showed that the tuberculosis score declined during treatment of patients with active tuberculosis. INTERPRETATION Overall, our integrated multicohort analysis yielded a three-gene set in whole blood that is robustly diagnostic for active tuberculosis, that was validated in multiple independent cohorts, and that has potential clinical application for diagnosis and monitoring treatment response. Prospective laboratory validation will be required before it can be used in a clinical setting. FUNDING National Institute of Allergy and Infectious Diseases, National Library of Medicine, the Stanford Child Health Research Institute, the Society for University Surgeons, and the Bill and Melinda Gates Foundation.
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Affiliation(s)
- Timothy E Sweeney
- Stanford Institute for Immunity, Transplantation and Infection, Stanford, CA, USA; Division of Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lindsay Braviak
- Stanford Institute for Immunity, Transplantation and Infection, Stanford, CA, USA
| | - Cristina M Tato
- Stanford Institute for Immunity, Transplantation and Infection, Stanford, CA, USA
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection, Stanford, CA, USA; Division of Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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32
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Lee JS, Tato CM, Joyce-Shaikh B, Gulen MF, Gulan F, Cayatte C, Chen Y, Blumenschein WM, Judo M, Ayanoglu G, McClanahan TK, Li X, Cua DJ. Interleukin-23-Independent IL-17 Production Regulates Intestinal Epithelial Permeability. Immunity 2015; 43:727-38. [PMID: 26431948 DOI: 10.1016/j.immuni.2015.09.003] [Citation(s) in RCA: 502] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 07/17/2015] [Accepted: 09/02/2015] [Indexed: 02/07/2023]
Abstract
Whether interleukin-17A (IL-17A) has pathogenic and/or protective roles in the gut mucosa is controversial and few studies have analyzed specific cell populations for protective functions within the inflamed colonic tissue. Here we have provided evidence for IL-17A-dependent regulation of the tight junction protein occludin during epithelial injury that limits excessive permeability and maintains barrier integrity. Analysis of epithelial cells showed that in the absence of signaling via the IL-17 receptor adaptor protein Act-1, the protective effect of IL-17A was abrogated and inflammation was enhanced. We have demonstrated that after acute intestinal injury, IL-23R(+) γδ T cells in the colonic lamina propria were the primary producers of early, gut-protective IL-17A, and this production of IL-17A was IL-23 independent, leaving protective IL-17 intact in the absence of IL-23. These results suggest that IL-17-producing γδ T cells are important for the maintenance and protection of epithelial barriers in the intestinal mucosa.
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Affiliation(s)
- Jacob S Lee
- Merck Research Laboratories, Palo Alto, CA 94304, USA
| | | | | | | | - Fatih Gulan
- Department of Immunology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | | | - Yi Chen
- Merck Research Laboratories, Palo Alto, CA 94304, USA
| | | | - Michael Judo
- Merck Research Laboratories, Palo Alto, CA 94304, USA
| | | | | | - Xiaoxia Li
- Department of Immunology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Daniel J Cua
- Merck Research Laboratories, Palo Alto, CA 94304, USA.
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Abstract
Using an elaborately evolved language of cytokines and chemokines as well as cell-cell interactions, the different components of the immune system communicate with each other and orchestrate a response (or wind one down). Immunological synapses are a key feature of the system in the ways in which they can facilitate and direct these responses. Studies analyzing the structure of an immune synapse as it forms between two cells have provided insight into how the stability and kinetics of this interaction ultimately affect the sensitivity, potency, and magnitude of a given response. Furthermore, we have gained an appreciation of how the immunological synapse provides directionality and contextual cues for downstream signaling and cellular decision-making. In this review, we discuss how using a variety of techniques, developed over the last decade, have allowed us to visualize and quantify key aspects of the dynamic synaptic interface and have furthered our understanding of their function. We describe some of the many characteristics of the immunological synapse that make it a vital part of intercellular communication and some of the questions that remain to be answered.
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Affiliation(s)
- Jianming Xie
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5323, USA
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Tato CM, Joyce-Shaikh B, Banerjee A, Chen Y, Sathe M, Ewald SE, Liu MR, Gorman D, McClanahan TK, Phillips JH, Heyworth PG, Cua DJ. The myeloid receptor PILRβ mediates the balance of inflammatory responses through regulation of IL-27 production. PLoS One 2012; 7:e31680. [PMID: 22479310 PMCID: PMC3313972 DOI: 10.1371/journal.pone.0031680] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 01/16/2012] [Indexed: 11/21/2022] Open
Abstract
Paired immunoglobulin-like receptors beta, PILRβ, and alpha, PILRα, are related to the Siglec family of receptors and are expressed primarily on cells of the myeloid lineage. PILRβ is a DAP12 binding partner expressed on both human and mouse myeloid cells. The potential ligand, CD99, is found on many cell types, such as epithelial cells where it plays a role in migration of immune cells to sites of inflammation. Pilrb deficient mice were challenged with the parasite Toxoplasma gondii in two different models of infection induced inflammation; one involving the establishment of chronic encephalitis and a second mimicking inflammatory bowel disease in order to understand the potential role of this receptor in persistent inflammatory responses. It was found that in the absence of activating signals from PILRβ, antigen-presenting cells (APCs) produced increased amounts of IL-27, p28 and promoted IL-10 production in effector T cells. The sustained production of IL-27 led ultimately to enhanced survival after challenge due to dampened immune pathology in the gut. Similar protection was also observed in the CNS during chronic T. gondii infection after i.p. challenge again providing evidence that PILRβ is important for regulating aberrant inflammatory responses.
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MESH Headings
- Animals
- Cells, Cultured
- Dendritic Cells/immunology
- Dendritic Cells/metabolism
- Encephalitis/genetics
- Encephalitis/immunology
- Encephalitis/metabolism
- Female
- Gene Expression
- Inflammation/genetics
- Inflammation/immunology
- Inflammation/metabolism
- Interferon-gamma/genetics
- Interferon-gamma/immunology
- Interferon-gamma/metabolism
- Interleukins/genetics
- Interleukins/immunology
- Interleukins/metabolism
- Macrophages/immunology
- Macrophages/metabolism
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred CBA
- Mice, Knockout
- Microglia/immunology
- Microglia/metabolism
- Receptors, Immunologic/deficiency
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Reverse Transcriptase Polymerase Chain Reaction
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Toxoplasma/immunology
- Toxoplasmosis, Animal/genetics
- Toxoplasmosis, Animal/immunology
- Toxoplasmosis, Animal/metabolism
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Affiliation(s)
- Cristina M. Tato
- Merck Research Laboratories, Palo Alto, California, United States of America
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California, United States of America
| | | | - Antara Banerjee
- Merck Research Laboratories, Palo Alto, California, United States of America
| | - Yi Chen
- Merck Research Laboratories, Palo Alto, California, United States of America
| | - Manjiri Sathe
- Merck Research Laboratories, Palo Alto, California, United States of America
| | - Sarah E. Ewald
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Man-Ru Liu
- Merck Research Laboratories, Palo Alto, California, United States of America
| | - Daniel Gorman
- Merck Research Laboratories, Palo Alto, California, United States of America
| | | | - Joseph H. Phillips
- Merck Research Laboratories, Palo Alto, California, United States of America
| | - Paul G. Heyworth
- Merck Research Laboratories, Palo Alto, California, United States of America
| | - Daniel J. Cua
- Merck Research Laboratories, Palo Alto, California, United States of America
- * E-mail:
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Ghoreschi K, Laurence A, Yang XP, Tato CM, McGeachy MJ, Konkel J, Ramos HL, Wei L, Davidson T, Bouladoux N, Grainger J, Chen Q, Kanno Y, Watford WT, Sun HW, Eberl G, Shevach E, Belkaid Y, Cua DJ, Chen W, O’Shea JJ. Generation of pathogenic T(H)17 cells in the absence of TGF-β signalling. Nature 2010; 467:967-71. [PMID: 20962846 PMCID: PMC3108066 DOI: 10.1038/nature09447] [Citation(s) in RCA: 1115] [Impact Index Per Article: 79.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 08/23/2010] [Indexed: 02/07/2023]
Abstract
CD4(+) T-helper cells that selectively produce interleukin (IL)-17 (T(H)17), are critical for host defence and autoimmunity. Although crucial for T(H)17 cells in vivo, IL-23 has been thought to be incapable of driving initial differentiation. Rather, IL-6 and transforming growth factor (TGF)-β1 have been proposed to be the factors responsible for initiating specification. Here we show that T(H)17 differentiation can occur in the absence of TGF-β signalling. Neither IL-6 nor IL-23 alone efficiently generated T(H)17 cells; however, these cytokines in combination with IL-1β effectively induced IL-17 production in naive precursors, independently of TGF-β. Epigenetic modification of the Il17a, Il17f and Rorc promoters proceeded without TGF-β1, allowing the generation of cells that co-expressed RORγt (encoded by Rorc) and T-bet. T-bet(+)RORγt(+) T(H)17 cells are generated in vivo during experimental allergic encephalomyelitis, and adoptively transferred T(H)17 cells generated with IL-23 without TGF-β1 were pathogenic in this disease model. These data indicate an alternative mode for T(H)17 differentiation. Consistent with genetic data linking IL23R with autoimmunity, our findings re-emphasize the importance of IL-23 and therefore may have therapeutic implications.
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Affiliation(s)
- Kamran Ghoreschi
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arian Laurence
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiang-Ping Yang
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cristina M. Tato
- Merck Research Laboratories (Schering-Plough Biopharma), Palo Alto, CA 94304, USA
| | - Mandy J. McGeachy
- Merck Research Laboratories (Schering-Plough Biopharma), Palo Alto, CA 94304, USA
| | - Joanne Konkel
- Mucosal Immunology Unit, Oral Infection and Immunity Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haydeé L. Ramos
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lai Wei
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Todd Davidson
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicolas Bouladoux
- Mucosal Immunology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Grainger
- Mucosal Immunology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qian Chen
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuka Kanno
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wendy T. Watford
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gérard Eberl
- Institut Pasteur, Lymphoid Tissue Development Unit, Paris 75724, France
| | - Ethan Shevach
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yasmine Belkaid
- Mucosal Immunology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel J. Cua
- Merck Research Laboratories (Schering-Plough Biopharma), Palo Alto, CA 94304, USA
| | - Wanjun Chen
- Mucosal Immunology Unit, Oral Infection and Immunity Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - John J. O’Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Diveu C, McGeachy MJ, Boniface K, Stumhofer JS, Sathe M, Joyce-Shaikh B, Chen Y, Tato CM, McClanahan TK, de Waal Malefyt R, Hunter CA, Cua DJ, Kastelein RA. IL-27 blocks RORc expression to inhibit lineage commitment of Th17 cells. J Immunol 2009; 182:5748-56. [PMID: 19380822 DOI: 10.4049/jimmunol.0801162] [Citation(s) in RCA: 256] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IL-27 is secreted by APCs in response to inflammatory stimuli and exerts a proinflammatory Th1-enhancing activity but also has significant anti-inflammatory functions. We examined the molecular mechanism by which IL-27 regulates TGFbeta plus IL-6- or IL-23-dependent Th17 development in the mouse and human systems. IL-27 inhibited the production of IL-17A and IL-17F in naive T cells by suppressing, in a STAT1-dependent manner, the expression of the Th17-specific transcription factor RORgamma t. The in vivo significance of the role of IL-27 was addressed in delayed-type hypersensitivity response and experimental autoimmune encephalomyelitis (EAE). By generating mice deficient for the p28 subunit of IL-27, we showed that IL-27 regulated the severity of delayed-type hypersensitivity response and EAE through its effects on Th17 cells. Furthermore, up-regulation of IL-10 in the CNS, which usually occurs late after EAE onset and plays a role in the resolution of the disease, was notably absent in IL-27p28(-/-) mice. These results show that IL-27 acts as a negative regulator of the developing IL-17A response in vivo, suggesting a potential therapeutic role for IL-27 in autoimmune diseases.
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Affiliation(s)
- Caroline Diveu
- Department of Immunology, Schering-Plough Biopharma, Palo Alto, CA 94304, USA
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Abstract
The study of interleukin-23 (IL-23) over the past 8 years has led to the realization that cellular immunity is far more complex than previously appreciated, because it is controlled by additional newly identified players. From the analysis of seemingly straightforward cytokine regulation of autoimmune diseases, many limitations of the established paradigms emerged that required reevaluation of the 'rules' that govern the initiation and maintenance of immune responses. This information led to a major revision of the T-helper 1 (Th1)/Th2 hypothesis and discovery of an unexpected link between transforming growth factor-beta-dependent Th17 and inducible regulatory T cells. The aim of this review is to explore the multiple characteristics of IL-23 with respect to its 'id' in autoimmunity, 'ego' in T-cell help, and 'superego' in defense against mucosal pathogens.
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Affiliation(s)
- Cristina M Tato
- Schering-Plough Biopharma, DNAX Discovery Research, Palo Alto, CA 94304, USA.
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McGeachy MJ, Chen Y, Tato CM, Laurence A, Joyce-Shaikh B, Blumenschein WM, McClanahan TK, O'Shea JJ, Cua DJ. The interleukin 23 receptor is essential for the terminal differentiation of interleukin 17-producing effector T helper cells in vivo. Nat Immunol 2009; 10:314-24. [PMID: 19182808 DOI: 10.1038/ni.1698] [Citation(s) in RCA: 789] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 12/17/2008] [Indexed: 12/11/2022]
Abstract
Interleukin 23 (IL-23) is required for autoimmune inflammation mediated by IL-17-producing helper T cells (T(H)-17 cells) and has been linked to many human immune disorders. Here we restricted deficiency in the IL-23 receptor to defined cell populations in vivo to investigate the requirement for IL-23 signaling in the development and function of T(H)-17 cells in autoimmunity, inflammation and infection. In the absence of IL-23, T(H)-17 development was stalled at the early activation stage. T(H)-17 cells failed to downregulate IL-2 and also failed to maintain IL-17 production or upregulate expression of the IL-7 receptor alpha-chain. These defects were associated with less proliferation; consequently, fewer effector T(H)-17 cells were produced in the lymph nodes and hence available to emigrate to the bloodstream and tissues.
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Takatori H, Kanno Y, Watford WT, Tato CM, Weiss G, Ivanov II, Littman DR, O'Shea JJ. Lymphoid tissue inducer-like cells are an innate source of IL-17 and IL-22. J Exp Med 2009; 206:35-41. [PMID: 19114665 PMCID: PMC2626689 DOI: 10.1084/jem.20072713] [Citation(s) in RCA: 580] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 12/02/2008] [Indexed: 02/06/2023] Open
Abstract
The interleukin (IL) 17 family of cytokines has emerged to be critical for host defense as well as the pathogenesis of autoimmune and autoinflammatory disorders, and serves to link adaptive and innate responses. Recent studies have identified a new subset of T cells that selectively produce IL-17 (Th17 cells; Bettelli, E., T. Korn, and V.K. Kuchroo. 2007. Curr. Opin. Immunol. 19:652-657; Kolls, J.K., and A. Linden. 2004. Immunity. 21:467-476), but the regulation of IL-17 production by innate immune cells is less well understood. We report that in vitro stimulation with IL-23 induced IL-17 production by recombination activating gene (Rag) 2(-/-) splenocytes but not Rag2(-/-) common gamma chain(-/-) splenocytes. We found that a major source of IL-17 was CD4(+)CD3(-)NK1.1(-)CD11b(-)Gr1(-)CD11c(-)B220(-) cells, a phenotype that corresponds to lymphoid tissue inducer-like cells (LTi-like cells), which constitutively expressed the IL-23 receptor, aryl hydrocarbon receptor, and CCR6. In vivo challenge with the yeast cell wall product zymosan rapidly induced IL-17 production in these cells. Genetic deletion of signal transducer and activator of transcription 3 reduced but did not abrogate IL-17 production in LTi-like cells. Thus, it appears that splenic LTi-like cells are a rapid source of IL-17 and IL-22, which might contribute to dynamic organization of secondary lymphoid organ structure or host defense.
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MESH Headings
- Animals
- Antigens, CD/analysis
- CD4 Antigens/analysis
- Cells, Cultured
- DNA-Binding Proteins/genetics
- Flow Cytometry
- Gene Expression/drug effects
- Immune System/cytology
- Immune System/metabolism
- Immunity, Innate/immunology
- Interleukin Receptor Common gamma Subunit/genetics
- Interleukin-17/genetics
- Interleukin-17/immunology
- Interleukin-17/metabolism
- Interleukin-23/pharmacology
- Interleukins/genetics
- Interleukins/immunology
- Interleukins/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Nuclear Receptor Subfamily 1, Group F, Member 3
- Receptors, Aryl Hydrocarbon/genetics
- Receptors, CCR6/genetics
- Receptors, Interleukin/genetics
- Receptors, Retinoic Acid/genetics
- Receptors, Thyroid Hormone/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- STAT3 Transcription Factor/genetics
- Spleen/cytology
- Spleen/metabolism
- Zymosan/pharmacology
- Interleukin-22
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Affiliation(s)
- Hiroaki Takatori
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA.
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Watford WT, Hissong BD, Durant LR, Yamane H, Muul LM, Kanno Y, Tato CM, Ramos HL, Berger AE, Mielke L, Pesu M, Solomon B, Frucht DM, Paul WE, Sher A, Jankovic D, Tsichlis PN, O'Shea JJ. Tpl2 kinase regulates T cell interferon-g production and host resistance to Toxoplasma gondii. J Biophys Biochem Cytol 2008. [DOI: 10.1083/jcb1834oia10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Watford WT, Hissong BD, Durant LR, Yamane H, Muul LM, Kanno Y, Tato CM, Ramos HL, Berger AE, Mielke L, Pesu M, Solomon B, Frucht DM, Paul WE, Sher A, Jankovic D, Tsichlis PN, O'Shea JJ. Tpl2 kinase regulates T cell interferon-gamma production and host resistance to Toxoplasma gondii. ACTA ACUST UNITED AC 2008; 205:2803-12. [PMID: 19001140 PMCID: PMC2585846 DOI: 10.1084/jem.20081461] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Tpl2 (Tumor progression locus 2), also known as Cot/MAP3K8, is a hematopoietically expressed serine-threonine kinase. Tpl2 is known to have critical functions in innate immunity in regulating tumor necrosis factor–α, Toll-like receptor, and G protein–coupled receptor signaling; however, our understanding of its physiological role in T cells is limited. We investigated the potential roles of Tpl2 in T cells and found that it was induced by interleukin-12 in human and mouse T cells in a Stat4-dependent manner. Deficiency of Tpl2 was associated with impaired interferon (IFN)-γ production. Accordingly, Tpl2−/− mice had impaired host defense against Toxoplasma gondii with reduced parasite clearance and decreased IFN-γ production. Furthermore, reconstitution of Rag2−/− mice with Tpl2-deficient T cells followed by T. gondii infection recapitulated the IFN-γ defect seen in the Tpl2-deficient mice, confirming a T cell–intrinsic defect. CD4+ T cells isolated from Tpl2−/− mice showed poor induction of T-bet and failure to up-regulate Stat4 protein, which is associated with impaired TCR-dependent extracellular signal-regulated kinase activation. These data underscore the role of Tpl2 as a regulator of T helper cell lineage decisions and demonstrate that Tpl2 has an important functional role in the regulation of Th1 responses.
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Affiliation(s)
- Wendy T Watford
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Akira S, Anguita J, Anstead GM, Aranow C, Austin HA, Babu S, Baker JR, Baliga CS, Ballow M, Balow JE, Bardana EJ, Becker MD, Belmont JW, Ben-Yehuda D, Berek C, Bieber T, Bijlsma JW, Bleesing JJ, Blutt SE, Borzova E, Boyaka PN, Brockow K, Budd RC, Buttgereit F, Calder VL, Candotti F, Carotta S, Casanova JL, Cascalho M, Chan ES, Chinen J, Cho ME, Christopher-Stine L, Collins HL, Cope AP, Cortese I, Cronstein BN, Custovic A, Dalakas MC, Devlin BH, Diamond B, Dispenzieri A, Drenth JP, Du Clos TW, Dykewicz MS, Eagar TN, Eisenbarth GS, Elson CO, Erkan D, Feinberg M, Fikrig E, Fischer A, Fleisher TA, Fontenot AP, Fortner KA, Frew AJ, Friedman TM, Fujihashi K, Galli SJ, Gatt ME, Gershwin ME, Goronzy JJ, Grattan CE, Greenspan NS, Grubeck-Loebenstein B, Haeberli G, Hall RP, Hamilton RG, Harriman GR, Hassan KM, Helbling A, Hellmann DB, Hernandez-Trujillo V, Hingorani M, Holland SM, Homburger HA, Horne M, Illei G, Imboden J, Ishii KJ, Izraeli S, Jaffe ES, Jalkanen S, June CH, Kahan BD, Kallies A, Kaufmann SH, Kavanaugh AF, Koretzky G, Korngold R, Kovaiou RD, Kuhns DB, Kurlander R, Kyle RA, Lane HC, Laurence A, Le Deist F, Lee SJ, Lemery SJ, Lenardo MJ, Levinson AI, Lewis DB, Lewis DE, Lieberman J, Lieberman P, Lightman SL, Lockshin MD, Lotze MT, Mackay M, Maltzman JS, Manns MP, Mapara MY, Marinho S, Markert ML, Martini A, Masters SL, Mazzolari E, McFarland HF, McGhee JR, McKenna F, Melby PC, Metcalfe DD, Metz M, Mican JM, Miller SD, Mold C, Moller DR, Montanaro A, Mueller SN, Müller UR, Murphy PM, Noel P, Notarangelo LD, Nutman TB, Nutt SL, Bosco de Oliveira J, Oliver SN, Olson CM, O'shea J, Paul ME, Peterson EJ, Picard C, Pichler WJ, Pillemer SR, Pittaluga S, Platt JL, Plotz PH, Radbruch A, Ravelli A, Reveille JD, Rich RR, Rick ME, Risma KA, Rodgers JR, Rosen A, Rosenbaum JT, Rothenberg ME, Rouse BT, Rowley S, Rudelius M, Sakaguchi S, Salmi M, Schaible UE, Schroeder HW, Schwarz MI, Seibel MJ, Selmi C, Shafer WM, Shah PK, Shahbaz-Samavi M, Shaw AR, Shearer WT, Sicherer SH, Siegel R, Jit Singh R, Smith JR, Smith PD, Sneller MC, Steinke JW, Stephens DS, Stone JH, Su HC, Tato CM, Torres RM, Uzel G, van der Hilst JC, van der Meer JW, Varga J, Villadangos JA, Wang SH, Weinberger B, Weller PF, Weyand CM, Wigley FM, Winchester RJ, Wing K, Young LJ, Zuo L. Contributors. Clin Immunol 2008. [DOI: 10.1016/b978-0-323-04404-2.10102-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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McGeachy MJ, Bak-Jensen KS, Chen Y, Tato CM, Blumenschein W, McClanahan T, Cua DJ. TGF-beta and IL-6 drive the production of IL-17 and IL-10 by T cells and restrain T(H)-17 cell-mediated pathology. Nat Immunol 2007; 8:1390-7. [PMID: 17994024 DOI: 10.1038/ni1539] [Citation(s) in RCA: 1187] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 10/16/2007] [Indexed: 11/09/2022]
Abstract
Studies have shown that transforming growth factor-beta (TGF-beta) and interleukin 6 (IL-6) are required for the lineage commitment of pathogenic IL-17-producing T helper cells (T(H)-17 cells). Unexpectedly, here we found that stimulation of myelin-reactive T cells with TGF-beta plus IL-6 completely abrogated their pathogenic function despite upregulation of IL-17 production. Cells stimulated with TGF-beta plus IL-6 were present in the spleen as well as the central nervous system, but they failed to upregulate the proinflammatory chemokines crucial for central nervous system inflammation. In addition, these cells produced IL-10, which has potent anti-inflammatory activities. In contrast, stimulation with IL-23 promoted expression of IL-17 and proinflammatory chemokines but not IL-10. Hence, TGF-beta and IL-6 'drive' initial lineage commitment but also 'restrain' the pathogenic potential of T(H)-17 cells. Our findings suggest that full acquisition of pathogenic function by effector T(H)-17 cells is mediated by IL-23 rather than by TGF-beta and IL-6.
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Abstract
OBJECTIVE Interleukin-17 (IL-17)-producing T helper cells have been proposed to represent a separate lineage of CD4+ cells, designated Th17 cells, which are regulated by the transcription factor retinoic acid-related orphan receptor gammat (RORgammat). However, despite advances in understanding murine Th17 differentiation, a systematic assessment of factors that promote the differentiation of naive human T cells to Th17 cells has not been reported. The present study was undertaken to assess the effects on naive human CD4+ T cells of cytokines known to promote murine Th17 cells. METHODS Human naive and memory CD4+ T cells isolated from peripheral blood were activated and cultured with various cytokines. Cytokine production was measured by enzyme-linked immunosorbent assay and flow cytometry. Messenger RNA was measured by quantitative polymerase chain reaction. RESULTS In response to anti-CD3/anti-CD28 stimulation alone, human memory T cells rapidly produced IL-17, whereas naive T cells expressed low levels. Transforming growth factor beta1 and IL-6 up-regulated RORgammat expression but did not induce Th17 differentiation of naive CD4+ T cells. However, IL-23 up-regulated its own receptor and was an important inducer of IL-17 and IL-22. CONCLUSION The present data demonstrate the differential regulation of IL-17 and RORgammat expression in human CD4+ T cells compared with murine cells. Optimal conditions for the development of IL-17-producing T cells from murine naive precursors are ineffective in human T cells. Conversely, IL-23 promoted the generation of human Th17 cells but was also a very potent inducer of other proinflammatory cytokines. These findings may have important implications in the pathogenesis of human autoimmunity as compared with mouse models.
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Affiliation(s)
- Zhi Chen
- National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Human Genome Research Institute, NIH, Bethesda, Maryland 20892-1820, USA.
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Laurence A, Tato CM, Davidson TS, Kanno Y, Chen Z, Yao Z, Blank RB, Meylan F, Siegel R, Hennighausen L, Shevach EM, O'shea JJ. Interleukin-2 signaling via STAT5 constrains T helper 17 cell generation. Immunity 2007; 26:371-81. [PMID: 17363300 DOI: 10.1016/j.immuni.2007.02.009] [Citation(s) in RCA: 1167] [Impact Index Per Article: 68.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2006] [Revised: 01/23/2007] [Accepted: 02/15/2007] [Indexed: 10/23/2022]
Abstract
Recent work has identified a new subset of effector T cells that produces interleukin (IL)-17 known as T helper 17 (Th17) cells, which is involved in the pathophysiology of inflammatory diseases and is thought to be developmentally related to regulatory T (Treg) cells. Because of its importance for Treg cells, we examined the role of IL-2 in Th17 generation and demonstrate that a previously unrecognized aspect of IL-2 function is to constrain IL-17 production. Genetic deletion or antibody blockade of IL-2 promoted differentiation of the Th17 cell subset. Whereas STAT3 appeared to be a key positive regulator of RORgammat and IL-17 expression, absence of IL-2 or disruption of its signaling by deletion of the transcription factor STAT5 resulted in enhanced Th17 cell development. We conclude that in addition to the promotion of activation-induced cell death of lymphocytes and the generation of Treg cells, inhibition of Th17 polarization appears to be an important function of IL-2.
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Affiliation(s)
- Arian Laurence
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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