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  1. Article ; Online: Consulting the Oracle of SARS-CoV-2 Infection.

    Lemieux, Jacob E / Luban, Jeremy

    The Journal of infectious diseases

    2021  Volume 225, Issue 7, Page(s) 1115–1117

    MeSH term(s) COVID-19 ; Humans ; Referral and Consultation ; SARS-CoV-2
    Language English
    Publishing date 2021-12-23
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiab623
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  2. Article ; Online: Cerebrospinal fluid metagenomics has greatest added value as a test for Powassan virus among patients in New England with suspected central nervous system infection.

    Klontz, Erik H / Solomon, Isaac H / Turbett, Sarah E / Lemieux, Jacob E / Branda, John A

    Diagnostic microbiology and infectious disease

    2024  Volume 108, Issue 4, Page(s) 116169

    Abstract: Cerebrospinal fluid (CSF) metagenomic next generation sequencing (mNGS) can detect diverse pathogens in patients with central nervous system infection. Due to its high cost and unclear clinical utility, it is typically reserved for patients with ... ...

    Abstract Cerebrospinal fluid (CSF) metagenomic next generation sequencing (mNGS) can detect diverse pathogens in patients with central nervous system infection. Due to its high cost and unclear clinical utility, it is typically reserved for patients with unrevealing routine workups. A multi-center retrospective analysis of real-world CSF mNGS was performed involving orders between 2017 and 2022 at a large New England healthcare system. CSF mNGS was performed 64 times with 17 positive results (27 %). In 11/17 positive samples (65 %), the infectious agent had not been previously detected using routine methods. Arboviruses (n = 8) were the most frequently detected agents, particularly Powassan virus (n = 6). Results changed therapy in 3/64 cases (5 %). Positive results were associated with immunodeficiency (p = 0.06), especially anti-B-cell therapy (p = 0.02), and earlier sample collection (p = 0.06). The association with compromised humoral immunity was stronger in the arbovirus and Powassan virus subgroups (p = 0.001), whose constituents were older than the overall cohort and had higher mortality rates.
    MeSH term(s) Humans ; Central Nervous System Infections ; Encephalitis Viruses, Tick-Borne ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; New England ; Retrospective Studies ; Sensitivity and Specificity
    Language English
    Publishing date 2024-01-04
    Publishing country United States
    Document type Journal Article ; Multicenter Study
    ZDB-ID 604920-5
    ISSN 1879-0070 ; 0732-8893
    ISSN (online) 1879-0070
    ISSN 0732-8893
    DOI 10.1016/j.diagmicrobio.2023.116169
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  3. Article ; Online: Uncovering Ways That Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Lineages May Increase Transmissibility.

    Lemieux, Jacob E / Li, Jonathan Z

    The Journal of infectious diseases

    2020  Volume 223, Issue 10, Page(s) 1663–1665

    Language English
    Publishing date 2020-12-11
    Publishing country United States
    Document type Editorial ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiab083
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  4. Article ; Online: Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection.

    Jankowiak, Martin / Obermeyer, Fritz H / Lemieux, Jacob E

    PLoS genetics

    2022  Volume 18, Issue 12, Page(s) e1010540

    Abstract: ... as pairwise interaction effects, i.e. epistasis. Strikingly, both these analyses point to the pivotal ...

    Abstract The global effort to sequence millions of SARS-CoV-2 genomes has provided an unprecedented view of viral evolution. Characterizing how selection acts on SARS-CoV-2 is critical to developing effective, long-lasting vaccines and other treatments, but the scale and complexity of genomic surveillance data make rigorous analysis challenging. To meet this challenge, we develop Bayesian Viral Allele Selection (BVAS), a principled and scalable probabilistic method for inferring the genetic determinants of differential viral fitness and the relative growth rates of viral lineages, including newly emergent lineages. After demonstrating the accuracy and efficacy of our method through simulation, we apply BVAS to 6.9 million SARS-CoV-2 genomes. We identify numerous mutations that increase fitness, including previously identified mutations in the SARS-CoV-2 Spike and Nucleocapsid proteins, as well as mutations in non-structural proteins whose contribution to fitness is less well characterized. In addition, we extend our baseline model to identify mutations whose fitness exhibits strong dependence on vaccination status as well as pairwise interaction effects, i.e. epistasis. Strikingly, both these analyses point to the pivotal role played by the N501 residue in the Spike protein. Our method, which couples Bayesian variable selection with a diffusion approximation in allele frequency space, lays a foundation for identifying fitness-associated mutations under the assumption that most alleles are neutral.
    Language English
    Publishing date 2022-12-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1010540
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  5. Article: Babesia microti

    Holbrook, Nolan R / Klontz, Erik H / Adams, Gordon C / Schnittman, Samuel R / Issa, Nicolas C / Bond, Sheila A / Branda, John A / Lemieux, Jacob E

    Open forum infectious diseases

    2023  Volume 10, Issue 3, Page(s) ofad097

    Abstract: ... We ... ...

    Abstract We report
    Language English
    Publishing date 2023-02-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2757767-3
    ISSN 2328-8957
    ISSN 2328-8957
    DOI 10.1093/ofid/ofad097
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  6. Article ; Online: Associations between mind-body practice engagement and diet quality: Exploring the mediating roles of eating behaviour traits and regulation styles for eating behaviours in the PREDISE study.

    Lévy-Ndejuru, Julia / Lemieux, Simone / Carbonneau, Élise / Jacob, Raphaëlle / Bégin, Catherine / Desroches, Sophie / Provencher, Véronique

    Appetite

    2023  Volume 184, Page(s) 106495

    Abstract: ... reported whether they currently practice one or more MBP (e.g., yoga or meditation). Canadian Healthy ...

    Abstract While engaging in Mind-Body Practices (MBPs) may be related to better diet quality, its association with eating behaviours is unclear. This cross-sectional study explores whether eating behaviour traits and regulation style of eating behaviours mediate the association between MBP engagement and diet quality. A total of 418 women and 482 men, aged between 18 and 65 years and recruited as part of the PREDISE study cohort, reported whether they currently practice one or more MBP (e.g., yoga or meditation). Canadian Healthy Eating Index (C-HEI) was calculated from three 24h dietary recalls. Intuitive Eating Scale (IES-2), and Regulation of Eating Behaviour Scale were completed online. Mann-Whitney tests were conducted to compare C-HEI scores of individuals who currently engage in MBPs (practitioners) to those who do not (non-practitioners). Multiple regression analyses and bootstrapping were performed to test whether eating behaviours and regulation style of eating behaviours mediate the association between MBPs and diet quality. Overall, 88 women and 43 men were practitioners. They had higher C-HEI scores than non-practitioners (62.9 ± 13.0 vs. 55.6 ± 14.3; p = 0.001). Parallel mediation model showed significant indirect effects of the IES-2 subscale relating to Body-Food Choice Congruence (β = 1.57, SE = 0.41, 95% CI: 0.86, 2.43), self-determined motivation (β = 1.51, SE = 0.39, 95% CI:0.81, 2.32) and non-self-determined motivation (β = 0.39, SE = 0.21, 95% CI: 0.03, 0.85) on the association between practitioner status and C-HEI. These findings suggest that the current practice of MBPs is associated with better diet quality, mainly through practitioners' higher intuitive eating skills and more self-determined regulation of eating behaviours. Further studies should investigate the potential impacts of MBPs on the development and maintenance of positive eating habits.
    MeSH term(s) Male ; Humans ; Female ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Cross-Sectional Studies ; Canada ; Diet ; Feeding Behavior ; Diet, Healthy
    Language English
    Publishing date 2023-02-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1461347-5
    ISSN 1095-8304 ; 0195-6663
    ISSN (online) 1095-8304
    ISSN 0195-6663
    DOI 10.1016/j.appet.2023.106495
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  7. Article ; Online: Development of Cas13a-based assays for

    Allan-Blitz, Lao-Tzu / Shah, Palak / Adams, Gordon / Branda, John A / Klausner, Jeffrey D / Goldstein, Robert / Sabeti, Pardis C / Lemieux, Jacob E

    mSphere

    2023  Volume 8, Issue 5, Page(s) e0041623

    Abstract: Neisseria ... ...

    Abstract Neisseria gonorrhoeae
    MeSH term(s) Infant, Newborn ; Humans ; Neisseria gonorrhoeae/genetics ; Gonorrhea/diagnosis ; Gonorrhea/microbiology ; HIV Infections ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Ciprofloxacin/pharmacology
    Chemical Substances Anti-Bacterial Agents ; Ciprofloxacin (5E8K9I0O4U)
    Language English
    Publishing date 2023-09-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2379-5042
    ISSN (online) 2379-5042
    DOI 10.1128/msphere.00416-23
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  8. Article: Development of Cas13a-based Assays for

    Allan-Blitz, Lao-Tzu / Shah, Palak / Adams, Gordon / Branda, John A / Klausner, Jeffrey D / Goldstein, Robert / Sabeti, Pardis C / Lemieux, Jacob E

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Background: Neisseria gonorrhoeae: Methods and results: We designed and optimized RNA guides and primer-sets for SHERLOCK assays capable of detecting : Conclusion: We report the development of Cas13a-based SHERLOCK assays that ... ...

    Abstract Background: Neisseria gonorrhoeae
    Methods and results: We designed and optimized RNA guides and primer-sets for SHERLOCK assays capable of detecting
    Conclusion: We report the development of Cas13a-based SHERLOCK assays that detect
    Language English
    Publishing date 2023-05-26
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.21.23290304
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  9. Article ; Online: Persistent SARS-CoV-2 infection: significance and implications.

    Machkovech, Heather M / Hahn, Anne M / Garonzik Wang, Jacqueline / Grubaugh, Nathan D / Halfmann, Peter J / Johnson, Marc C / Lemieux, Jacob E / O'Connor, David H / Piantadosi, Anne / Wei, Wanting / Friedrich, Thomas C

    The Lancet. Infectious diseases

    2024  

    Abstract: SARS-CoV-2 causes persistent infections in a subset of individuals, which is a major clinical and public health problem that should be prioritised for further investigation for several reasons. First, persistent SARS-CoV-2 infection often goes ... ...

    Abstract SARS-CoV-2 causes persistent infections in a subset of individuals, which is a major clinical and public health problem that should be prioritised for further investigation for several reasons. First, persistent SARS-CoV-2 infection often goes unrecognised, and therefore might affect a substantial number of people, particularly immunocompromised individuals. Second, the formation of tissue reservoirs (including in non-respiratory tissues) might underlie the pathophysiology of the persistent SARS-CoV-2 infection and require new strategies for diagnosis and treatment. Finally, persistent SARS-CoV-2 replication, particularly in the setting of suboptimal immune responses, is a possible source of new, divergent virus variants that escape pre-existing immunity on the individual and population levels. Defining optimal diagnostic and treatment strategies for patients with persistent virus replication and monitoring viral evolution are therefore urgent medical and public health priorities.
    Language English
    Publishing date 2024-02-07
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2061641-7
    ISSN 1474-4457 ; 1473-3099
    ISSN (online) 1474-4457
    ISSN 1473-3099
    DOI 10.1016/S1473-3099(23)00815-0
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  10. Article: Clinical Performance of Cas13a-based Point-of-Care Lateral Flow Assay for Detecting

    Allan-Blitz, Lao-Tzu / Sanders, Gabriela / Shah, Palak / Adams, Gordon / Jarolimova, Jana / Ard, Kevin / Branda, John A / Klausner, Jeffrey D / Sabeti, Pardis C / Lemieux, Jacob E

    medRxiv : the preprint server for health sciences

    2024  

    Abstract: Background: Diagnosis of : Methods: We collected an additional urine specimen among individuals enrolling in an ongoing clinical trial at the Massachusetts General Hospital Sexual Health Clinic who presented with symptoms of urethritis or cervicitis ( ...

    Abstract Background: Diagnosis of
    Methods: We collected an additional urine specimen among individuals enrolling in an ongoing clinical trial at the Massachusetts General Hospital Sexual Health Clinic who presented with symptoms of urethritis or cervicitis (urethral or vaginal discharge, dysuria, or dyspareunia). We then assessed thermal, detergent, and combination DNA extraction conditions, varying the duration of heat at 95°C and concentration of Triton X. We assessed the efficacy of the various DNA extraction methods by quantitative polymerase chain reaction (qPCR). Once an extraction method was selected, we incubated samples for 90 minutes to permit isothermal recombinase polymerase amplification. We then assessed the performance of lateral flow Cas13a-based detection using our previously designed
    Results: We assessed DNA extraction conditions on 3 clinical urine specimens. There was no consistent significant difference in copies per microliter of DNA obtained using more or less heat. On average, we noted that 0.02% triton combined with 5 minutes of heating to 95°C resulted in the highest DNA yield, however, 0.02% triton alone resulted in a quantity of DNA that was above the previously determined analytic sensitivity of the assay. Given that detergent-based extraction is more easily deployable, we selected that as our method for extraction. We treated 23 clinical specimens with 0.02% triton, which we added to the Cas13a detection system. We ran all lateral flow detections in duplicate. The Cas13a-based assay detected 8 of 8 (100%) positive specimens, and 0 of 15 negative specimens.
    Conclusion: Using point-of-care DNA extraction, isothermal amplification, and Cas13a-based detection, our point-of-care lateral flow
    Language English
    Publishing date 2024-03-04
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.01.24303603
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