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Article ; Online: Label-Free SERS for Rapid Differentiation of SARS-CoV-2-Induced Serum Metabolic Profiles in Non-Hospitalized Adults

Chisanga, Malama / Williams, Hannah / Boudreau, Denis / Pelletier, Joelle N. / Trottier, Sylvie / Masson, Jean-François

Analytical Chemistry. 2023 Feb. 10, v. 95, no. 7 p.3638-3646

2023

Abstract: COVID-19 represents a multi-system infectious disease with broad-spectrum manifestations, including changes in host metabolic processes connected to the disease pathogenesis. Understanding biochemical dysregulation patterns as a consequence of COVID-19 ... ...

Abstract	COVID-19 represents a multi-system infectious disease with broad-spectrum manifestations, including changes in host metabolic processes connected to the disease pathogenesis. Understanding biochemical dysregulation patterns as a consequence of COVID-19 illness promises to be crucial for tracking disease course and clinical outcomes. Surface-enhanced Raman scattering (SERS) has attracted considerable interest in biomedical diagnostics for the sensitive detection of intrinsic profiles of unique fingerprints of serum biomolecules indicative of SARS-CoV-2 infection in a label-free format. Here, we applied label-free SERS and chemometrics for rapid interrogation of temporal metabolic dynamics in longitudinal sera of mildly infected non-hospitalized patients (n = 22), at 4 and 16 weeks post PCR-positive diagnosis, and compared them with negative controls (n = 8). SERS spectral markers revealed distinct metabolic profiles in patient sera that significantly deviated from the healthy metabolic state at the two sampling time intervals. Multivariate and univariate analyses of the spectral data identified abundance dynamics in amino acids, lipids, and protein vibrations as the key spectral features underlying the metabolic differences detected in convalescent samples and perhaps associated with patient recovery progression. A validation study performed using spontaneous Raman spectroscopy yielded spectral data results that corroborated SERS spectral findings and confirmed the detected disease-specific molecular phenotypes in clinical samples. Label-free SERS promises to be a valuable analytical technique for rapid screening of the metabolic phenotype induced by SARS-CoV-2 infection to allow appropriate healthcare intervention.
Keywords	COVID-19 infection ; Raman spectroscopy ; Severe acute respiratory syndrome coronavirus 2 ; biochemical compounds ; blood serum ; chemometrics ; diagnostic techniques ; disease course ; health services ; pathogenesis ; patients ; phenotype ; spectral analysis
Language	English
Dates of publication	2023-0210
Size	p. 3638-3646.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04514
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Label-Free SERS for Rapid Differentiation of SARS-CoV-2-Induced Serum Metabolic Profiles in Non-Hospitalized Adults.

Chisanga, Malama / Williams, Hannah / Boudreau, Denis / Pelletier, Joelle N / Trottier, Sylvie / Masson, Jean-Francois

Analytical chemistry

2023 Volume 95, Issue 7, Page(s) 3638–3646

Abstract	COVID-19 represents a multi-system infectious disease with broad-spectrum manifestations, including changes in host metabolic processes connected to the disease pathogenesis. Understanding biochemical dysregulation patterns as a consequence of COVID-19 illness promises to be crucial for tracking disease course and clinical outcomes. Surface-enhanced Raman scattering (SERS) has attracted considerable interest in biomedical diagnostics for the sensitive detection of intrinsic profiles of unique fingerprints of serum biomolecules indicative of SARS-CoV-2 infection in a label-free format. Here, we applied label-free SERS and chemometrics for rapid interrogation of temporal metabolic dynamics in longitudinal sera of mildly infected non-hospitalized patients (
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/diagnosis ; Proteins ; Spectrum Analysis, Raman/methods ; Metabolome
Chemical Substances	Proteins
Language	English
Publishing date	2023-02-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04514
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Article ; Online: Comparison of rectal swabs and fecal samples for the detection of

Huletsky, Ann / Loo, Vivian G / Longtin, Yves / Longtin, Jean / Trottier, Sylvie / Tremblay, Cécile L / Gilca, Rodica / Lavallée, Christian / Brochu, Éliel / Bérubé, Ève / Bastien, Martine / Bernier, Marthe / Gagnon, Martin / Frenette, Johanne / Bestman-Smith, Julie / Deschênes, Louise / Bergeron, Michel G

Microbiology spectrum

2024 , Page(s) e0022524

Abstract: The detection of : Importance: Clostridioides ... ...

Abstract	The detection of Importance: Clostridioides difficile
Language	English
Publishing date	2024-04-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.00225-24
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Article ; Online: Assessment of the longitudinal humoral response in non-hospitalized SARS-CoV-2-positive individuals at decentralized sites: Outcomes and concordance.

Djaïleb, Abdelhadi / Lavallée, Étienne / Parker, Megan-Faye / Cayer, Marie-Pierre / Desautels, Florence / de Grandmont, Marie Joëlle / Stuible, Matthew / Gervais, Christian / Durocher, Yves / Trottier, Sylvie / Boudreau, Denis / Masson, Jean-Francois / Brouard, Danny / Pelletier, Joelle N

Frontiers in immunology

2023 Volume 13, Page(s) 1052424

Abstract: Introduction: Early in the COVID-19 pandemic, reagent availability was not uniform, and infrastructure had to be urgently adapted to undertake COVID-19 surveillance.: Methods: Before the validation of centralized testing, two enzyme-linked ... ...

Abstract	Introduction: Early in the COVID-19 pandemic, reagent availability was not uniform, and infrastructure had to be urgently adapted to undertake COVID-19 surveillance. Methods: Before the validation of centralized testing, two enzyme-linked immunosorbent assays (ELISA) were established independently at two decentralized sites using different reagents and instrumentation. We compared the results of these assays to assess the longitudinal humoral response of SARS-CoV-2-positive (i.e., PCR-confirmed), non-hospitalized individuals with mild to moderate symptoms, who had contracted SARSCoV-2 prior to the appearance of variants of concern in Québec, Canada. Results: The two assays exhibited a high degree of concordance to identify seropositive individuals, thus validating the robustness of the methods. The results also confirmed that serum immunoglobulins persist ≥ 6 months post-infection among non-hospitalized adults and that the antibodies elicited by infection cross-reacted with the antigens from P.1 (Gamma) and B.1.617.2 (Delta) variants of concern. Discussion: Together, these results demonstrate that immune surveillance assays can be rapidly and reliably established when centralized testing is not available or not yet validated, allowing for robust immune surveillance.
MeSH term(s)	Adult ; Humans ; COVID-19 ; SARS-CoV-2 ; Pandemics ; Antibodies, Viral
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2023-01-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.1052424
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Article ; Online: Longitudinal Study on Seroprevalence and Immune Response to SARS-CoV-2 in a Population of Food and Retail Workers Through Transformation of ELISA Datasets

Djaïleb, Abdelhadi / Parker, Megan-Faye / Lavallée, Étienne / Stuible, Matthew / Durocher, Yves / Thériault, Mathieu / Santerre, Kim / Gilbert, Caroline / Boudreau, Denis / Baz, Mariana / Masson, Jean-Francois / Langlois, Marc-André / Trottier, Sylvie / Quaglia, Daniela / Pelletier, Joelle N.

medRxiv

Abstract: Since the onset of the global pandemic caused by the emergence and spread of SARS-CoV-2 in early 2020, numerous studies have been conducted worldwide to understand our immune response to the virus. This study investigates the humoral response elicited by ...

Abstract	Since the onset of the global pandemic caused by the emergence and spread of SARS-CoV-2 in early 2020, numerous studies have been conducted worldwide to understand our immune response to the virus. This study investigates the humoral response elicited by vaccination and by SARS-CoV-2 infection in the poorly studied food and retail workers in the Quebec City area. The 1.5-year study period spans from early 2021, when vaccination became available in this region, to mid-2022, following waves of virulence due to the emergence of the first Omicron variants. Cross-correlated with data on workplace protective measures, pre-existing conditions, activities and other potentially relevant factors, this longitudinal study applies recently developed ELISA data transformation to our dataset to obtain normal distribution. This unlocked the possibility to use the ANOVA-Welsh method for statistical analysis to obtain a statistical perspective of the serological response. Our work allows the identification of factors contributing to statistically relevant differences in the humoral response of the cohort and strengthens the utility of the use of decentralized approaches to serological analysis.
Keywords	covid19
Language	English
Publishing date	2024-01-29
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2024.01.27.24301877
Database	COVID19

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Article: A Pre-Phase III Efficacy Trial of the Spermicide/Contraceptive Effect of the Invisible Condom, a Non-Hormonal Vaginal Gel, in Women from Canada.

Omar, Rabeea F / Leboeuf, Mathieu / Lemyre, Madeleine / Chabot, Isabelle / Trottier, Sylvie / Ulmann, André / Bergeron, Michel G

Journal of obstetrics and gynaecology Canada : JOGC = Journal d'obstetrique et gynecologie du Canada : JOGC

2021 Volume 44, Issue 2, Page(s) 175–181

Abstract: Objectives: To evaluate the spermicidal efficacy of non-hormonal vaginal gel in vitro and in a post-coital test, and to evaluate its contraceptive efficacy in Canadian women of childbearing age.: Methods: We conducted single-centre trial to assess ... ...

Abstract	Objectives: To evaluate the spermicidal efficacy of non-hormonal vaginal gel in vitro and in a post-coital test, and to evaluate its contraceptive efficacy in Canadian women of childbearing age. Methods: We conducted single-centre trial to assess spermicidal and contraceptive efficacy of vaginal gel. Participants were healthy, sexually active women aged 18-49 years and their regular male sexual partners (30 couples). Measured outcomes included effect of vaginal gel on sperm motility in vitro, its effect on sperm in a post-coital test, and its effect on pregnancy prevention over 3 months. Results: For in vitro spermicidal effect, 98% and 67% of sperm were immotile in the presence of the gel with sodium lauryl sulfate (gel-SLS) and gel alone, respectively. For the post-coital test, 99% and 93% of sperm were immotile in the presence of gel-SLS and gel alone, respectively. In the second part of trial, a total of 410 instances of vaginal intercourse in 95 menstrual cycles were protected (during 3-month period of gel-SLS use before each sexual intercourse with probability of 24 conceptions prevented according to Wilcox's table). Four women became pregnant during the study period; 2 during unprotected vaginal intercourse around the time of ovulation, and 2 attributed to user failure. Conclusion: Based on our results, the vaginal gel demonstrated important spermicidal and contraceptive effect. A larger phase III contraceptive efficacy trial is warranted. The vaginal gel may represent a non-hormonal spermicide/contraceptive option for women.
MeSH term(s)	Adolescent ; Adult ; Canada ; Condoms ; Contraceptive Agents ; Female ; Humans ; Male ; Middle Aged ; Pregnancy ; Sperm Motility ; Vaginal Creams, Foams, and Jellies ; Young Adult
Chemical Substances	Contraceptive Agents ; Vaginal Creams, Foams, and Jellies
Language	English
Publishing date	2021-10-14
Publishing country	Netherlands
Document type	Clinical Trial ; Journal Article
ZDB-ID	2171082-X
ISSN	1701-2163
ISSN	1701-2163
DOI	10.1016/j.jogc.2021.09.018
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Cohort Profile: Prospective Cohort to Study the COVID-19 Immune Response in Retail Workers in Quebec, Canada (CISACOV)

Santerre, Kim / Thériault, Mathieu / Brousseau, Nicholas / Rochette, Samuel / Pelletier, Joelle / Gilbert, Caroline / Masson, Jean-Francois / Baz, Mariana / Boudreau, Denis / Trottier, Sylvie

medRxiv

Abstract: Purpose: Retail workers are an understudied occupational group that may have been at increased risk of contracting SARS-CoV-2 during the COVID-19 pandemic. Therefore, we set up a longitudinal cohort of participants working in this sector to better ... ...

Abstract	Purpose: Retail workers are an understudied occupational group that may have been at increased risk of contracting SARS-CoV-2 during the COVID-19 pandemic. Therefore, we set up a longitudinal cohort of participants working in this sector to better document the incidence of SARS-CoV-2 infection and the immune response to infection and/or vaccination in this group. Participants: A total of 304 participants were recruited between April 20, 2021 and October 22, 2021. They were invited to attend three visits (each separated by ~12 weeks) during which they provided blood samples and information on participant characteristics, COVID-19 symptoms, and vaccination. An extension phase of two additional visits was carried out between March 15th, 2022 and October 3rd, 2022 to document the impact of the Omicron variant among the 198 participants who were still eligible for recruitment. Participants were aged 18 to 75 and worked in grocery stores, hardware stores, bars or restaurants within the Quebec City metropolitan area (Canada). Findings to date: This article describes participants9 demographic, socioeconomic, behavioral, clinical and occupational characteristics, and their COVID-19 symptoms (where applicable). It also describes SARS-CoV-2 vaccination status and any SARS-CoV-2 diagnostic test (i.e., PCR or rapid antigen) performed from the beginning of the pandemic until the last visit. Future plans: The incidence of SARS-CoV-2 infections will be assessed. The immune response (innate and acquired) to SARS-CoV-2 infection or vaccination will be studied using a variety of techniques, including reference and experimental enzyme-linked immunosorbent assays, microneutralization assays with live viruses, experimental pseudoneutralization with an angiotensin-converting enzyme 2-spike assay, peripheral blood mononuclear cells and neutrophil stimulation, and a proliferation assay based on carboxyfluorescein diacetate succinimidyl ester.
Keywords	covid19
Language	English
Publishing date	2023-08-21
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.08.18.23294172
Database	COVID19

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Article ; Online: Cohort Profile: Prospective Cohort to Study the COVID-19 Immune Response in Retail Workers in Québec, Canada (CISACOV)

Santerre, Kim / Thériault, Mathieu / Brousseau, Nicholas / Rochette, Samuel / Pelletier, Joelle N. / Gilbert, Caroline / Masson, Jean-François / Baz, Mariana / Boudreau, Denis / Trottier, Sylvie

medRxiv

Abstract	Purpose: Retail workers are an understudied occupational group that may have been at increased risk of contracting SARS-CoV-2 during the COVID-19 pandemic. Therefore, we set up a longitudinal cohort of participants working in this sector to better document the incidence of SARS-CoV-2 infection and the immune response to infection and/or vaccination in this group. Participants: A total of 304 participants were recruited between April 20, 2021 and October 22, 2021. They were invited to attend three visits (each separated by ~12 weeks) during which they provided blood samples and information on participant characteristics, COVID-19 symptoms, and vaccination. An extension phase of two additional visits was carried out between March 15th, 2022 and October 3rd, 2022 to document the impact of the Omicron variant among the 198 participants who were still eligible for recruitment. Participants were aged 18 to 75 and worked in grocery stores, hardware stores, bars or restaurants within the Quebec City metropolitan area (Canada). Findings to date: This article describes participants9 demographic, socioeconomic, behavioral, clinical and occupational characteristics, and their COVID-19 symptoms (where applicable). It also describes SARS-CoV-2 vaccination status and any SARS-CoV-2 diagnostic test (i.e., PCR or rapid antigen) performed from the beginning of the pandemic until the last visit. Future plans: The incidence of SARS-CoV-2 infections will be assessed. The immune response (innate and acquired) to SARS-CoV-2 infection or vaccination will be studied using a variety of techniques, including reference and experimental enzyme-linked immunosorbent assays, microneutralization assays with live viruses, experimental pseudoneutralization with an angiotensin-converting enzyme 2-spike assay, peripheral blood mononuclear cells and neutrophil stimulation, and a proliferation assay based on carboxyfluorescein diacetate succinimidyl ester.
Keywords	covid19
Language	English
Publishing date	2023-08-21
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.08.18.23294172
Database	COVID19

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Article: Velocity Gradient Separation Reveals a New Extracellular Vesicle Population Enriched in miR-155 and Mitochondrial DNA.

Vaillancourt, Myriam / Hubert, Audrey / Subra, Caroline / Boucher, Julien / Bazié, Wilfried Wenceslas / Vitry, Julien / Berrazouane, Sofiane / Routy, Jean-Pierre / Trottier, Sylvie / Tremblay, Cécile / Jenabian, Mohammad-Ali / Benmoussa, Abderrahim / Provost, Patrick / Tessier, Philippe A / Gilbert, Caroline

Pathogens (Basel, Switzerland)

2021 Volume 10, Issue 5

Abstract: Extracellular vesicles (EVs) and their contents (proteins, lipids, messenger RNA, microRNA, and DNA) are viewed as intercellular signals, cell-transforming agents, and shelters for viruses that allow both diagnostic and therapeutic interventions. EVs ... ...

Abstract	Extracellular vesicles (EVs) and their contents (proteins, lipids, messenger RNA, microRNA, and DNA) are viewed as intercellular signals, cell-transforming agents, and shelters for viruses that allow both diagnostic and therapeutic interventions. EVs circulating in the blood of individuals infected with human immunodeficiency virus (HIV-1) may provide insights into pathogenesis, inflammation, and disease progression. However, distinguishing plasma membrane EVs from exosomes, exomeres, apoptotic bodies, virions, and contaminating proteins remains challenging. We aimed at comparing sucrose and iodixanol density and velocity gradients along with commercial kits as a means of separating EVs from HIV particles and contaminating protein like calprotectin; and thereby evaluating the suitability of current plasma EVs analysis techniques for identifying new biomarkers of HIV-1 immune activation. Multiple analysis have been performed on HIV-1 infected cell lines, plasma from HIV-1 patients, or plasma from HIV-negative individuals spiked with HIV-1. Commercial kits, the differential centrifugation and density or velocity gradients to precipitate and separate HIV, EVs, and proteins such as calprotectin, have been used. EVs, virions, and contaminating proteins were characterized using Western blot, ELISA, RT-PCR, hydrodynamic size measurement, and enzymatic assay. Conversely to iodixanol density or velocity gradient, protein and virions co-sedimented in the same fractions of the sucrose density gradient than AChE-positive EVs. Iodixanol velocity gradient provided the optimal separation of EVs from viruses and free proteins in culture supernatants and plasma samples from a person living with HIV (PLWH) or a control and revealed a new population of large EVs enriched in microRNA miR-155 and mitochondrial DNA. Although EVs and their contents provide helpful information about several key events in HIV-1 pathogenesis, their purification and extensive characterization by velocity gradient must be investigated thoroughly before further use as biomarkers. By revealing a new population of EVs enriched in miR-155 and mitochondrial DNA, this study paves a way to increase our understanding of HIV-1 pathogenesis.
Language	English
Publishing date	2021-04-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens10050526
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Article ; Online: Plasma Extracellular Vesicle Subtypes May be Useful as Potential Biomarkers of Immune Activation in People With HIV.

Bazié, Wilfried Wenceslas / Boucher, Julien / Vitry, Julien / Goyer, Benjamin / Routy, Jean Pierre / Tremblay, Cécile / Trottier, Sylvie / Jenabian, Mohammad-Ali / Provost, Patrick / Alary, Michel / Gilbert, Caroline

Pathogens & immunity

2021 Volume 6, Issue 1, Page(s) 1–28

Abstract: Background: Extracellular vesicles (EVs) are intercellular messengers with epigenetic potential since they can shuttle microRNA (miRNA). EVs and miRNA play a role in human immunodeficiency virus (HIV) infection immunopathogenesis. Chronic immune ... ...

Abstract	Background: Extracellular vesicles (EVs) are intercellular messengers with epigenetic potential since they can shuttle microRNA (miRNA). EVs and miRNA play a role in human immunodeficiency virus (HIV) infection immunopathogenesis. Chronic immune activation and systemic inflammation during HIV infection despite effective antiretroviral therapy (ART) are associated with non-acquired immunodeficiency syndrome (AIDS) comorbidities in people living with HIV (PLWH). Analysis of plasma EVs and their miRNA content may be useful as immune activation or inflammatory biomarkers in PLWH receiving ART. In this study, we hypothesized that the number, size, and miRNA of large and small EVs could reflect immune activation associated with an elevated CD8 T-cell count or a low CD4/CD8 ratio in PLWH. Methods: Plasma EVs subtype purified from PLWH and uninfected controls were sized using dynamic light scattering and quantified using flow cytometry and acetylcholine esterase (AChE) activity. Expression of mature miRNAs miR-92, miR-155, miR-223 was measured by quantitative reverse-transcriptase polymerase chain reaction in EVs and leucocytes. Results: HIV infection induces increased production of small EVs in plasma. EV subtypes were differentially enriched in miR-92, miR-155, and miR-223. Positive correlations between CD8 T-cell count and large EVs abundance and small EVs AChE activity were observed. CD4/CD8 ratio was negatively correlated with small EV AChE activity, and miRNA-155 level per small EV was negatively correlated with CD8 T-cell count. Conclusions: These findings suggest that quantifying large or small EVs and profiling miRNA content per EV might provide new functional biomarkers of immune activation and inflammation.
Language	English
Publishing date	2021-01-14
Publishing country	United States
Document type	Journal Article
ISSN	2469-2964
ISSN (online)	2469-2964
DOI	10.20411/pai.v6i1.384
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