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Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM, Thakku SG, Tse MW, Kehe J, Uwera MM, Eversley JS, Bielwaski DA, McGrath G, Braidt J, Johnson J, Cerrato F, Moreno GK, Krasilnikova LA, Petros BA, Gionet GL, King E, Huard RC, Jalbert SK, Cleary ML, Fitzgerald NA, Gabriel SB, Gallagher GR, Smole SC, Madoff LC, Brown CM, Keller MW, Wilson MM, Kirby MK, Barnes JR, Park DJ, Siddle KJ, Happi CT, Hung DT, Springer M, MacInnis BL, Lemieux JE, Rosenberg E, Branda JA, Blainey PC, Sabeti PC, Myhrvold C. Author Correction: Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat Med 2024; 30:307. [PMID: 37946059 PMCID: PMC10803257 DOI: 10.1038/s41591-023-02684-y] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Affiliation(s)
- Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
| | - Meilin Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catherine Hua
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Juliane Weller
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Tien G Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew R Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Bennett M Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sri Gowtham Thakku
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Megan W Tse
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jared Kehe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jacqueline S Eversley
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Derek A Bielwaski
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Graham McGrath
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph Braidt
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Gage K Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lydia A Krasilnikova
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Brittany A Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/Massachusetts Institute of Technology MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Ewa King
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | - Richard C Huard
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | | | - Michael L Cleary
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Sandra C Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | - Matthew W Keller
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Malania M Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marie K Kirby
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Christian T Happi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Springer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Bronwyn L MacInnis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jacob E Lemieux
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - John A Branda
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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Mantena S, Pillai PP, Petros BA, Welch NL, Myhrvold C, Sabeti PC, Metsky HC. Model-directed generation of CRISPR-Cas13a guide RNAs designs artificial sequences that improve nucleic acid detection. bioRxiv 2023:2023.09.20.557569. [PMID: 37786711 PMCID: PMC10541601 DOI: 10.1101/2023.09.20.557569] [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] [Indexed: 10/04/2023]
Abstract
Generating maximally-fit biological sequences has the potential to transform CRISPR guide RNA design as it has other areas of biomedicine. Here, we introduce model-directed exploration algorithms (MEAs) for designing maximally-fit, artificial CRISPR-Cas13a guides-with multiple mismatches to any natural sequence-that are tailored for desired properties around nucleic acid diagnostics. We find that MEA-designed guides offer more sensitive detection of diverse pathogens and discrimination of pathogen variants compared to guides derived directly from natural sequences, and illuminate interpretable design principles that broaden Cas13a targeting.
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Affiliation(s)
- Sreekar Mantena
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | - Brittany A. Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/Massachusetts Institute of Technology, MD-PhD Program, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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3
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Hao L, Zhao RT, Welch NL, Tan EKW, Zhong Q, Harzallah NS, Ngambenjawong C, Ko H, Fleming HE, Sabeti PC, Bhatia SN. CRISPR-Cas-amplified urinary biomarkers for multiplexed and portable cancer diagnostics. Nat Nanotechnol 2023; 18:798-807. [PMID: 37095220 PMCID: PMC10359190 DOI: 10.1038/s41565-023-01372-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
Synthetic biomarkers, bioengineered sensors that generate molecular reporters in diseased microenvironments, represent an emerging paradigm in precision diagnostics. Despite the utility of DNA barcodes as a multiplexing tool, their susceptibility to nucleases in vivo has limited their utility. Here we exploit chemically stabilized nucleic acids to multiplex synthetic biomarkers and produce diagnostic signals in biofluids that can be 'read out' via CRISPR nucleases. The strategy relies on microenvironmental endopeptidase to trigger the release of nucleic acid barcodes and polymerase-amplification-free, CRISPR-Cas-mediated barcode detection in unprocessed urine. Our data suggest that DNA-encoded nanosensors can non-invasively detect and differentiate disease states in transplanted and autochthonous murine cancer models. We also demonstrate that CRISPR-Cas amplification can be harnessed to convert the readout to a point-of-care paper diagnostic tool. Finally, we employ a microfluidic platform for densely multiplexed, CRISPR-mediated DNA barcode readout that can potentially evaluate complex human diseases rapidly and guide therapeutic decisions.
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Affiliation(s)
- Liangliang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Renee T Zhao
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Edward Kah Wei Tan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qian Zhong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nour Saida Harzallah
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chayanon Ngambenjawong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Henry Ko
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Pardis C Sabeti
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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4
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Welch NL, Peterson JA, Adams K. The Price of a Life: Unveiling the Struggle of Living With Hereditary Angioedema. Cureus 2023; 15:e42699. [PMID: 37654956 PMCID: PMC10465713 DOI: 10.7759/cureus.42699] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2023] [Indexed: 09/02/2023] Open
Abstract
Hereditary angioedema (HAE) is a rare, potentially life-threatening genetic condition characterized by recurrent episodes of localized swelling in various body tissues. Despite advancements in the management and prevention of HAE, high costs limit accessibility to these medications and remain a significant hurdle for many patients. This case report illustrates the implications and life-threatening consequences of the affordability crisis associated with HAE medications. To the authors' knowledge, this case also highlights the first reported case of cocaine serving as an HAE trigger.
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Affiliation(s)
- Nicole L Welch
- Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, USA
| | - Joshua A Peterson
- Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, USA
| | - Kaka Adams
- Pediatrics, Texas Tech University Health Sciences Center, Lubbock, USA
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5
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Welch NL, Welch T, Songtanin B. Viral Triggered Celiac Disease: A Case Report. Cureus 2023; 15:e40429. [PMID: 37456501 PMCID: PMC10348803 DOI: 10.7759/cureus.40429] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Celiac disease (CD) is an autoimmune condition presenting with a wide variety of nonspecific gastrointestinal symptoms. It can be difficult to diagnose due to the vagueness of complaints such as diarrhea, anemia due to malabsorption, vitamin or electrolyte deficiencies, and/or failure to thrive. This condition is characterized by a sensitivity to ingested gluten-containing compounds. Blood tests can be used for screening, though confirmatory testing by a small intestine biopsy is needed for diagnosis. Viral infections can trigger autoimmune conditions in individuals. It is possible that viral infections, such as Ebsetein-Barr virus(EBV) or Cytomegalovirus (CMV), can trigger the clinical presentation of celiac disease in certain individuals with genetic predispositions. Early recognition of celiac disease is important to prevent both short and long-term complications and improve the quality of life for the individual. Here, we discuss a case where the patient developed celiac disease only months after a diagnosis of mononucleosis.
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Affiliation(s)
- Nicole L Welch
- Internal Medicine, Texas Tech University Health Sciences Center Lubbock Campus, Lubbock, USA
| | - Tyler Welch
- Family Medicine, Baptist Health-UAMS (University of Arkansas for Medical Sciences), North Little Rock, USA
| | - Busara Songtanin
- Internal Medicine, Texas Tech University Health Sciences Center Lubbock Campus, Lubbock, USA
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6
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Petros BA, Turcinovic J, Welch NL, White LF, Kolaczyk ED, Bauer MR, Cleary M, Dobbins ST, Doucette-Stamm L, Gore M, Nair P, Nguyen TG, Rose S, Taylor BP, Tsang D, Wendlandt E, Hope M, Platt JT, Jacobson KR, Bouton T, Yune S, Auclair JR, Landaverde L, Klapperich CM, Hamer DH, Hanage WP, MacInnis BL, Sabeti PC, Connor JH, Springer M. Early Introduction and Rise of the Omicron Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant in Highly Vaccinated University Populations. Clin Infect Dis 2023; 76:e400-e408. [PMID: 35616119 PMCID: PMC9213864 DOI: 10.1093/cid/ciac413] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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] [Received: 03/21/2022] [Revised: 05/10/2022] [Accepted: 05/19/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible in vaccinated and unvaccinated populations. The dynamics that govern its establishment and propensity toward fixation (reaching 100% frequency in the SARS-CoV-2 population) in communities remain unknown. Here, we describe the dynamics of Omicron at 3 institutions of higher education (IHEs) in the greater Boston area. METHODS We use diagnostic and variant-specifying molecular assays and epidemiological analytical approaches to describe the rapid dominance of Omicron following its introduction into 3 IHEs with asymptomatic surveillance programs. RESULTS We show that the establishment of Omicron at IHEs precedes that of the state and region and that the time to fixation is shorter at IHEs (9.5-12.5 days) than in the state (14.8 days) or region. We show that the trajectory of Omicron fixation among university employees resembles that of students, with a 2- to 3-day delay. Finally, we compare cycle threshold values in Omicron vs Delta variant cases on college campuses and identify lower viral loads among college affiliates who harbor Omicron infections. CONCLUSIONS We document the rapid takeover of the Omicron variant at IHEs, reaching near-fixation within the span of 9.5-12.5 days despite lower viral loads, on average, than the previously dominant Delta variant. These findings highlight the transmissibility of Omicron, its propensity to rapidly dominate small populations, and the ability of robust asymptomatic surveillance programs to offer early insights into the dynamics of pathogen arrival and spread.
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Affiliation(s)
- Brittany A Petros
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.,Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Harvard/Massachusetts Institute of Technology, MD-PhD Program, Boston, Massachusetts, USA
| | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.,Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Laura F White
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts, USA
| | - Eric D Kolaczyk
- Department of Mathematics & Statistics, Boston University, Boston, Massachusetts, USA.,Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston University, Boston, Massachusetts, USA
| | - Matthew R Bauer
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.,Harvard Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Cleary
- Harvard University Clinical Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - Sabrina T Dobbins
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Lynn Doucette-Stamm
- Boston University Clinical Testing Laboratory, Boston University Boston, Massachusetts, USA
| | - Mitch Gore
- Integrated DNA Technologies, Inc, Coralville, Iowa, USA
| | - Parvathy Nair
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Tien G Nguyen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Scott Rose
- Integrated DNA Technologies, Inc, Coralville, Iowa, USA
| | - Bradford P Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Daniel Tsang
- Integrated DNA Technologies, Inc, Coralville, Iowa, USA
| | | | - Michele Hope
- Harvard University Clinical Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - Judy T Platt
- Boston University Student Health Services, Boston, Massachusetts, USA
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Tara Bouton
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Seyho Yune
- Student Affairs, Northeastern University, Boston, Massachusetts, USA
| | - Jared R Auclair
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA.,Life Sciences Testing Center, Northeastern University, Burlington, Massachusetts, USA.,Biopharmaceutical Analysis and Training Laboratory, Burlington, Massachusetts, USA
| | - Lena Landaverde
- Boston University Clinical Testing Laboratory, Boston University Boston, Massachusetts, USA.,Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Catherine M Klapperich
- Boston University Clinical Testing Laboratory, Boston University Boston, Massachusetts, USA.,Boston University Student Health Services, Boston, Massachusetts, USA.,Boston University Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
| | - Davidson H Hamer
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, USA.,Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA.,Boston University Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA.,Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA.,Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Bronwyn L MacInnis
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, Massachusetts, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, Massachusetts, USA.,Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
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7
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Weingarten-Gabbay S, Pearlman LR, Chen DY, Klaeger S, Taylor HB, Welch NL, Keskin DB, Carr SA, Abelin JG, Saeed M, Sabeti PC. HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses. STAR Protoc 2022; 3:101910. [PMID: 36595954 PMCID: PMC9731565 DOI: 10.1016/j.xpro.2022.101910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/12/2022] [Revised: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
Immunopeptidome profiling of infected cells is a powerful technique for detecting viral peptides that are naturally processed and loaded onto class I human leukocyte antigens (HLAs-I). Here, we provide a protocol for preparing samples for immunopeptidome profiling that can inactivate enveloped viruses while still preserving the integrity of the HLA-I complex. We detail steps for lysate preparation of infected cells followed by HLA-I immunoprecipitation and virus inactivation. We further describe peptide purification for mass spectrometry outside a high-containment facility. For complete details on the use and execution of this protocol, please refer to Weingarten-Gabbay et al. (2021).1.
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Affiliation(s)
- Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA,Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA,Corresponding author
| | | | - Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nicole L. Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Derin B. Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA,Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Howard Hughes Medical Institute, Chevy Chase, MD, USA
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8
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Arizti-Sanz J, Bradley A, Zhang YB, Boehm CK, Freije CA, Grunberg ME, Kosoko-Thoroddsen TSF, Welch NL, Pillai PP, Mantena S, Kim G, Uwanibe JN, John OG, Eromon PE, Kocher G, Gross R, Lee JS, Hensley LE, MacInnis BL, Johnson J, Springer M, Happi CT, Sabeti PC, Myhrvold C. Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Nat Biomed Eng 2022; 6:932-943. [PMID: 35637389 PMCID: PMC9398993 DOI: 10.1038/s41551-022-00889-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [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: 10/25/2021] [Accepted: 04/01/2022] [Indexed: 02/03/2023]
Abstract
The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for 'streamlined highlighting of infections to navigate epidemics, version 2'), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.
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Affiliation(s)
- Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
| | - A'Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Yibin B Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Chloe K Boehm
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Catherine A Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Michelle E Grunberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Priya P Pillai
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Sreekar Mantena
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gaeun Kim
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jessica N Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G John
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Gregory Kocher
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Robin Gross
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Justin S Lee
- Biotechnology Cores Facility Branch, Division of Scientific Resources, National Center for Emerging and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Bronwyn L MacInnis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeremy Johnson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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9
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Metsky HC, Welch NL, Pillai PP, Haradhvala NJ, Rumker L, Mantena S, Zhang YB, Yang DK, Ackerman CM, Weller J, Blainey PC, Myhrvold C, Mitzenmacher M, Sabeti PC. Designing sensitive viral diagnostics with machine learning. Nat Biotechnol 2022; 40:1123-1131. [PMID: 35241837 PMCID: PMC9287178 DOI: 10.1038/s41587-022-01213-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 04/25/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022]
Abstract
Design of nucleic acid-based viral diagnostics typically follows heuristic rules and, to contend with viral variation, focuses on a genome's conserved regions. A design process could, instead, directly optimize diagnostic effectiveness using a learned model of sensitivity for targets and their variants. Toward that goal, we screen 19,209 diagnostic-target pairs, concentrated on CRISPR-based diagnostics, and train a deep neural network to accurately predict diagnostic readout. We join this model with combinatorial optimization to maximize sensitivity over the full spectrum of a virus's genomic variation. We introduce Activity-informed Design with All-inclusive Patrolling of Targets (ADAPT), a system for automated design, and use it to design diagnostics for 1,933 vertebrate-infecting viral species within 2 hours for most species and within 24 hours for all but three. We experimentally show that ADAPT's designs are sensitive and specific to the lineage level and permit lower limits of detection, across a virus's variation, than the outputs of standard design techniques. Our strategy could facilitate a proactive resource of assays for detecting pathogens.
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Affiliation(s)
- Hayden C Metsky
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA.
| | - Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Virology Program, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | | | - Nicholas J Haradhvala
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biophysics Program, Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics Program, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sreekar Mantena
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Yibin B Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - David K Yang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | | | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Cameron Myhrvold
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael Mitzenmacher
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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10
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Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM, Thakku SG, Tse MW, Kehe J, Uwera MM, Eversley JS, Bielwaski DA, McGrath G, Braidt J, Johnson J, Cerrato F, Moreno GK, Krasilnikova LA, Petros BA, Gionet GL, King E, Huard RC, Jalbert SK, Cleary ML, Fitzgerald NA, Gabriel SB, Gallagher GR, Smole SC, Madoff LC, Brown CM, Keller MW, Wilson MM, Kirby MK, Barnes JR, Park DJ, Siddle KJ, Happi CT, Hung DT, Springer M, MacInnis BL, Lemieux JE, Rosenberg E, Branda JA, Blainey PC, Sabeti PC, Myhrvold C. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat Med 2022; 28:1083-1094. [PMID: 35130561 PMCID: PMC9117129 DOI: 10.1038/s41591-022-01734-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [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: 11/22/2021] [Accepted: 02/03/2022] [Indexed: 11/23/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.
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Affiliation(s)
- Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
| | - Meilin Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catherine Hua
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Juliane Weller
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Tien G Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew R Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Bennett M Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sri Gowtham Thakku
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Megan W Tse
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jared Kehe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jacqueline S Eversley
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Derek A Bielwaski
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Graham McGrath
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph Braidt
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Gage K Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lydia A Krasilnikova
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Brittany A Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/Massachusetts Institute of Technology MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Ewa King
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | - Richard C Huard
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | | | - Michael L Cleary
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Sandra C Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | - Matthew W Keller
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Malania M Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marie K Kirby
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Christian T Happi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Springer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Bronwyn L MacInnis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jacob E Lemieux
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - John A Branda
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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11
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Arizti-Sanz J, Bradley A, Zhang YB, Boehm CK, Freije CA, Grunberg ME, Kosoko-Thoroddsen TSF, Welch NL, Pillai PP, Mantena S, Kim G, Uwanibe JN, John OG, Eromon PE, Kocher G, Gross R, Lee JS, Hensley LE, Happi CT, Johnson J, Sabeti PC, Myhrvold C. Equipment-free detection of SARS-CoV-2 and Variants of Concern using Cas13. medRxiv 2021:2021.11.01.21265764. [PMID: 34751276 PMCID: PMC8575147 DOI: 10.1101/2021.11.01.21265764] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The COVID-19 pandemic, and the recent rise and widespread transmission of SARS-CoV-2 Variants of Concern (VOCs), have demonstrated the need for ubiquitous nucleic acid testing outside of centralized clinical laboratories. Here, we develop SHINEv2, a Cas13-based nucleic acid diagnostic that combines quick and ambient temperature sample processing and lyophilized reagents to greatly simplify the test procedure and assay distribution. We benchmarked a SHINEv2 assay for SARS-CoV-2 detection against state-of-the-art antigen-capture tests using 96 patient samples, demonstrating 50-fold greater sensitivity and 100% specificity. We designed SHINEv2 assays for discriminating the Alpha, Beta, Gamma and Delta VOCs, which can be read out visually using lateral flow technology. We further demonstrate that our assays can be performed without any equipment in less than 90 minutes. SHINEv2 represents an important advance towards rapid nucleic acid tests that can be performed in any location.
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Affiliation(s)
- Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Program in Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A’Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Yibin B. Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Chloe K. Boehm
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Catherine A. Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Michelle E. Grunberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Nicole L. Welch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Priya P. Pillai
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Sreekar Mantena
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Gaeun Kim
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jessica N. Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G. John
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Philomena E. Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Gregory Kocher
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and infectious diseases, National Institute of Health, Frederick, MD 21702, USA
| | - Robin Gross
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and infectious diseases, National Institute of Health, Frederick, MD 21702, USA
| | - Justin S. Lee
- Biotechnology Cores Facility Branch,Division of Scientific Resources, National Center for Emerging and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lisa E. Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and infectious diseases, National Institute of Health, Frederick, MD 21702, USA
| | - Christian T. Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Jeremy Johnson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- These authors jointly supervised this work: Pardis C. Sabeti, Cameron Myhrvold
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- These authors jointly supervised this work: Pardis C. Sabeti, Cameron Myhrvold
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12
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Starrett GJ, Tisza MJ, Welch NL, Belford AK, Peretti A, Pastrana DV, Buck CB. Adintoviruses: a proposed animal-tropic family of midsize eukaryotic linear dsDNA (MELD) viruses. Virus Evol 2021; 7:veaa055. [PMID: 34646575 PMCID: PMC8502044 DOI: 10.1093/ve/veaa055] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA viruses. This supports the inference that at least some polintons are actually viruses capable of cell-to-cell spread. At present, there are no polinton-associated capsid protein genes annotated in public sequence databases. To rectify this deficiency, we used a data-mining approach to investigate the distribution and gene content of polinton-like elements and related DNA viruses in animal genomic and metagenomic sequence datasets. The results define a discrete family-like clade of viruses with two genus-level divisions. We propose the family name Adintoviridae, connoting similarities to adenovirus virion proteins and the presence of a retrovirus-like integrase gene. Although adintovirus-class PolB sequences were detected in datasets for fungi and various unicellular eukaryotes, sequences resembling adintovirus virion proteins and accessory genes appear to be restricted to animals. Degraded adintovirus sequences are endogenized into the germlines of a wide range of animals, including humans.
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Affiliation(s)
| | - Michael J Tisza
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Nicole L Welch
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Anna K Belford
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Alberto Peretti
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
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13
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Tisza MJ, Pastrana DV, Welch NL, Stewart B, Peretti A, Starrett GJ, Pang YYS, Krishnamurthy SR, Pesavento PA, McDermott DH, Murphy PM, Whited JL, Miller B, Brenchley J, Rosshart SP, Rehermann B, Doorbar J, Ta'ala BA, Pletnikova O, Troncoso JC, Resnick SM, Bolduc B, Sullivan MB, Varsani A, Segall AM, Buck CB. Discovery of several thousand highly diverse circular DNA viruses. eLife 2020; 9:51971. [PMID: 32014111 PMCID: PMC7000223 DOI: 10.7554/elife.51971] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [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] [Received: 09/19/2019] [Accepted: 01/06/2020] [Indexed: 12/18/2022] Open
Abstract
Although millions of distinct virus species likely exist, only approximately 9000 are catalogued in GenBank's RefSeq database. We selectively enriched for the genomes of circular DNA viruses in over 70 animal samples, ranging from nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2500 complete genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these ‘dark matter’ sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere. When scientists hunt for new DNA sequences, sometimes they get a lot more than they bargained for. Such is the case in metagenomic surveys, which analyze not just DNA of a particular organism, but all the DNA in an environment at large. A vexing problem with these surveys is the overwhelming number of DNA sequences detected that are so different from any known microbe that they cannot be classified using traditional approaches. However, some of these “known unknowns” are undoubtedly viral sequences, because only a fraction of the enormous diversity of viruses has been characterized. This “viral dark matter” is a major obstacle for those studying viruses. This led Tisza et al. to attempt to classify some of the unknown viral sequences in their metagenomic surveys. The search, which specifically focused on viruses with circular DNA genomes, detected over 2,500 circular viral genomes. Intensive analysis revealed that many of these genomes had similar makeup to previously discovered viruses, but hundreds of them were totally different from any known virus, based on typical methods of comparison. Computational analysis of genes that were conserved among some of these brand-new circular sequences often revealed virus-like features. Experiments on a few of these genes showed that they encoded proteins capable of forming particles reminiscent of characteristic viral shells, implying that these new sequences are indeed viruses. Tisza et al. have added the 2,500 newly characterized viral sequences to the publicly accessible GenBank database, and the sequences are being considered for the more authoritative RefSeq database, which currently contains around 9,000 complete viral genomes. The expanded databases will hopefully now better equip scientists to explore the enormous diversity of viruses and help medics and veterinarians to detect disease-causing viruses in humans and other animals.
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Affiliation(s)
- Michael J Tisza
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Diana V Pastrana
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Nicole L Welch
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Brittany Stewart
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Alberto Peretti
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Gabriel J Starrett
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Yuk-Ying S Pang
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Patricia A Pesavento
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, Davis, United States
| | - David H McDermott
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Philip M Murphy
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Jessica L Whited
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | - Bess Miller
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jason Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Cambridge, United States
| | - Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Ben Bolduc
- Department of Microbiology, Ohio State University, Columbus, United States
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, United States.,Civil Environmental and Geodetic Engineering, Ohio State University, Columbus, United States
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, United States.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, South Africa
| | - Anca M Segall
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, United States
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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14
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Freije CA, Myhrvold C, Boehm CK, Lin AE, Welch NL, Carter A, Metsky HC, Luo CY, Abudayyeh OO, Gootenberg JS, Yozwiak NL, Zhang F, Sabeti PC. Programmable Inhibition and Detection of RNA Viruses Using Cas13. Mol Cell 2019; 76:826-837.e11. [PMID: 31607545 DOI: 10.1016/j.molcel.2019.09.013] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 12/23/2022]
Abstract
The CRISPR effector Cas13 could be an effective antiviral for single-stranded RNA (ssRNA) viruses because it programmably cleaves RNAs complementary to its CRISPR RNA (crRNA). Here, we computationally identify thousands of potential Cas13 crRNA target sites in hundreds of ssRNA viral species that can potentially infect humans. We experimentally demonstrate Cas13's potent activity against three distinct ssRNA viruses: lymphocytic choriomeningitis virus (LCMV); influenza A virus (IAV); and vesicular stomatitis virus (VSV). Combining this antiviral activity with Cas13-based diagnostics, we develop Cas13-assisted restriction of viral expression and readout (CARVER), an end-to-end platform that uses Cas13 to detect and destroy viral RNA. We further screen hundreds of crRNAs along the LCMV genome to evaluate how conservation and target RNA nucleotide content influence Cas13's antiviral activity. Our results demonstrate that Cas13 can be harnessed to target a wide range of ssRNA viruses and CARVER's potential broad utility for rapid diagnostic and antiviral drug development.
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Affiliation(s)
- Catherine A Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; PhD Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA.
| | - Cameron Myhrvold
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Chloe K Boehm
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Aaron E Lin
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; PhD Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; PhD Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Amber Carter
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Hayden C Metsky
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02142, USA
| | - Cynthia Y Luo
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Omar O Abudayyeh
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA
| | - Jonathan S Gootenberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan L Yozwiak
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Feng Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute (HHMI), Chevy Chase, MD 20815, USA
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA; PhD Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute (HHMI), Chevy Chase, MD 20815, USA; Department of Immunology and Infectious Disease, T.H. Chan Harvard School of Public Health, Boston, MA 02115, USA.
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