A5034268175- SARS-CoV-2 detection and testing
- SARS-CoV-2 and COVID-19 Research
- Biosensors and Analytical Detection
- Advanced biosensing and bioanalysis techniques
- Viral Infections and Outbreaks Research
- Viral gastroenteritis research and epidemiology
- CRISPR and Genetic Engineering
- COVID-19 epidemiological studies
- COVID-19 Clinical Research Studies
- COVID-19 Impact on Reproduction
- Genomics and Chromatin Dynamics
- Cancer Genomics and Diagnostics
- Long-Term Effects of COVID-19
- Molecular Biology Techniques and Applications
- Parvovirus B19 Infection Studies
- Viral Infections and Vectors
- Chromosomal and Genetic Variations
- Adipokines, Inflammation, and Metabolic Diseases
- Plant Virus Research Studies
- Cytomegalovirus and herpesvirus research
- Advanced Biosensing Techniques and Applications
- Respiratory viral infections research
- Data-Driven Disease Surveillance
Broad Institute
2020-2025
Massachusetts Institute of Technology
2020-2025
Université de Montréal
2024
Harvard University
2020
Harvard–MIT Division of Health Sciences and Technology
2020
Howard Hughes Medical Institute
2020
Concord Consortium
2020
Dovetail Genomics (United States)
2018-2019
The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific tool can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions allow RPA-based amplification Cas13-based detection occur in single step, simplifying assay preparation reducing run-time. improve HUDSON rapidly inactivate viruses...
Abstract Recent outbreaks of viral hemorrhagic fevers (VHFs), including Ebola virus disease (EVD) and Lassa fever (LF), highlight the urgent need for sensitive, deployable tests to diagnose these devastating human diseases. Here we develop CRISPR-Cas13a-based (SHERLOCK) diagnostics targeting (EBOV) (LASV), with both fluorescent lateral flow readouts. We demonstrate on laboratory clinical samples sensitivity assays capacity SHERLOCK platform handle virus-specific diagnostic challenges....
Abstract Antibodies serve as biomarkers of infection, but if sustained can confer long-term immunity. Yet, for most clinically approved vaccines, binding antibody titers only a surrogate protection. Instead, the ability vaccine induced antibodies to neutralize or mediate Fc-effector functions is mechanistically linked While evidence has begun point persisting responses among SARS-CoV-2 infected individuals, cases re-infection have emerge, calling protective nature humoral immunity against...
Abstract The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (SHERLOCK and HUDSON Integration to Navigate Epidemics), a sensitive specific integrated tool can detect SARS-CoV-2 RNA from unextracted samples. We combine the steps of SHERLOCK into single-step reaction optimize accelerate viral inactivation in nasopharyngeal swabs saliva. SHINE’s results be visualized with an in-tube fluorescent readout...
Identifying the potential for SARS-CoV-2 reinfection is crucial understanding possible long-term epidemic dynamics. We analysed longitudinal PCR and serological testing data from a prospective cohort of 4,411 United States employees in 4 states between April 2020 February 2021. conducted multivariable logistic regression investigating association baseline status subsequent test result order to calculate an odds ratio reinfection. estimated ranging 0.14 (95% CI: 0.019 0.63) 0.28 0.05 1.1),...
Obesity is a key correlate of severe SARS-CoV-2 outcomes while the role obesity on risk infection, symptom phenotype, and immune response remain poorly defined. We examined data from prospective cohort study to address these questions. Serostatus, body mass index, demographics, comorbidities, prior COVID-19 compatible symptoms were assessed at baseline serostatus monthly thereafter. immunoassays included an IgG ELISA targeting spike RBD, multiarray Luminex 20 viral antigens, pseudovirus...
As public health guidelines throughout the world have relaxed in response to vaccination campaigns against SARS-CoV-2, it is likely that SARS-CoV-2 will remain endemic, fueled by rise of more infectious variants. Moreover, setting waning natural and vaccine immunity, reinfections emerged across globe, even among previously infected vaccinated individuals. such, ability detect reexposure reinfection a key component for global protection this virus and, importantly, potential emergence escape...
The clinical management and therapy of many solid tumor malignancies depends on detection medically actionable or diagnostically relevant genetic variation. However, a principal challenge for assays from tumors is the fragmented chemically damaged state DNA in formalin-fixed, paraffin-embedded (FFPE) samples. From highly RNA there no current technology generating long-range sequence data as required to detect genomic structural variation genotype phasing. We have developed high-throughput...
While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that plays critical role Lassa virus binding and entry. This led us to pursue field work test our hypothesis natural selection acting on LARGE—detected Yoruba population Nigeria—conferred resistance Fever some West African populations. As delved further, conjectured “emerging” nature recently discovered diseases like fever is related newfound capacity for...
Abstract Viral hemorrhagic fevers (VHFs) remain some of the most devastating human diseases, and recent outbreaks Ebola virus disease (EVD) 1,2 Lassa fever (LF) 3,4 highlight urgent need for sensitive, field-deployable tests to diagnose them 5,6 . Here we develop CRISPR-Cas13a-based (SHERLOCK) diagnostics targeting (EBOV) (LASV), with both fluorescent lateral flow readouts. We demonstrate on laboratory clinical samples sensitivity these assays capacity SHERLOCK platform handle virus-specific...
Abstract Obesity is a key correlate of severe SARS-CoV-2 outcomes while the role obesity on risk infection, symptom phenotype, and immune response are poorly defined. We examined data from prospective cohort study to address these questions. Serostatus, body mass index, demographics, comorbidities, prior COVID-19 compatible symptoms were assessed at baseline serostatus monthly thereafter. immunoassays included an IgG ELISA targeting spike RBD, multiarray Luminex 20 viral antigens,...
Estimating the cumulative incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for setting public health policies. We leveraged deidentified Massachusetts newborn screening specimens as an accessible, retrospective source maternal antibodies estimating statewide seroprevalence in a nontest-seeking population.
Abstract CRISPR-based diagnostics have emerged as a promising tool for fast, accurate, and portable pathogen detection. There has been rapid progress in areas such pre-amplification processes CRISPR-related enzymes, but the development of reporter systems reaction platforms lagged behind. In this paper, we develop new bead-based techniques that can help fill both gaps. First, novel split-luciferase system with improved sensitivity compared to standard fluorescence-based design CRISPR...
Abstract Identifying the extent of SARS-CoV-2 reinfection is crucial for understanding possible long-term epidemic dynamics. We analysed longitudinal PCR and serological testing data from a prospective cohort 4411 US employees in four states between April 2020 February 2021. conducted multivariable logistic regression investigating association baseline status subsequent test result order to calculate an odds ratio reinfection. estimated adjusted 0.09 (95% CI: 0.005 – 0.48) reinfection,...
Abstract The clinical management and therapy of many solid tumor malignancies is dependent on detection medically actionable or diagnostically relevant genetic variation. However, a principal challenge for assays from tumors the fragmented chemically damaged state DNA in formalin-fixed paraffin-embedded (FFPE) samples. From highly RNA there no current technology generating long-range sequence data as required to detect genomic structural variation genotype phasing. We have developed...
This protocol describes how to perform a SHINE paper-based assay detect SARS-CoV-2 RNA from self-collected saliva sample. is intended for in-home use. All enzymatic components are provided as single-test freeze-dried pellet shelf-stable storage, and all steps of the performed at ambient temperature. The presented here an improved version method in Arizti-Sanz J*, Freije CA*, et al. Integrated sample inactivation, amplification, Cas13-based detection SARS-CoV-2. bioRxiv (2020).
This protocol describes how to perform a SHINE paper-based assay detect SARS-CoV-2 RNA from self-collected nasopharyngeal sample. is intended for in-home use. All enzymatic components are provided as single-test freeze-dried pellet shelf-stable storage, and all steps of the performed at ambient temperature. The presented here an improved version method in Arizti-Sanz J*, Freije CA*, et al. Integrated sample inactivation, amplification, Cas13-based detection SARS-CoV-2. bioRxiv (2020).
This protocol describes how to perform a SHINE in-tube fluorescent assay detect SARS-CoV-2 RNA from self-collected nasopharyngeal sample. is intended for point-of-care use. All enzymatic components are provided as single-test freeze-dried pellet shelf-stable storage, and all steps of the performed at ambient temperature. The requires transilluminator or another equivalent blue light emitting device. presented here an improved version method in Arizti-Sanz J*, Freije CA*, et al. Integrated...
This protocol describes how to perform a SHINE in-tube fluorescent assay detect SARS-CoV-2 RNA from self-collected nasopharyngeal sample. is intended for point-of-care use. All enzymatic components are provided as single-test freeze-dried pellet shelf-stable storage, and all steps of the performed at ambient temperature. The requires transilluminator or another equivalent blue light emitting device. presented here an improved version method in Arizti-Sanz J*, Freije CA*, et al. Integrated...
Abstract Background Estimating the cumulative incidence of SARS-CoV-2 is essential for setting public health policies. We leveraged de-identified Massachusetts newborn screening specimens to generate an accessible, retrospective source maternal antibodies estimating statewide seroprevalence in a non-test-seeking population. Methods analyzed 72,117 dried blood spots collected from November 2019 through December 2020, representing 337 towns and cities across Massachusetts. Seroprevalence was...