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  1. AU="Matic, Nancy"
  2. AU="Cerqueira, Rui"
  3. AU="Greco, Massimiliano"
  4. AU="Dalton, Michelle"
  5. AU="Letard, Sébastien"
  6. AU="Di Gangi, Iole Maria"
  7. AU="Chen, T T"
  8. AU="Alves, Luiz Felipe M F"
  9. AU="Liao, Jing" AU="Liao, Jing"

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  1. Artikel ; Online: Testing the limits of multiplex respiratory virus assays for SARS-CoV-2 at high cycle threshold values: Comparative performance of cobas 6800/8800 SARS-CoV-2 & Influenza A/B, Xpert Xpress SARS-CoV-2/Flu/RSV, and cobas Liat SARS-CoV-2 & Influenza A/B.

    Matic, Nancy / Lawson, Tanya / Ritchie, Gordon / Lowe, Christopher F / Romney, Marc G

    Journal of the Association of Medical Microbiology and Infectious Disease Canada = Journal officiel de l'Association pour la microbiologie medicale et l'infectiologie Canada

    2024  Band 8, Heft 4, Seite(n) 328–335

    Abstract: Background: Multiplex real-time RT-PCR assays for respiratory pathogens are valuable tools to optimize laboratory workflow and turnaround time. At a time when resurgence of influenza and respiratory syncytial virus (RSV) cases have been widely observed ... ...

    Abstract Background: Multiplex real-time RT-PCR assays for respiratory pathogens are valuable tools to optimize laboratory workflow and turnaround time. At a time when resurgence of influenza and respiratory syncytial virus (RSV) cases have been widely observed along with continued transmission of SARS-CoV-2, timely identification of all circulating respiratory viruses is crucial. This study evaluates the detection of low viral loads of SARS-CoV-2 by four multiplex molecular assays: Roche cobas 6800/8800 SARS-CoV-2 & Influenza A/B Test, Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV, cobas Liat SARS-CoV-2 & Influenza A/B, and a laboratory-developed test (LDT).
    Methods: Retrospective upper respiratory tract specimens positive for various respiratory viruses at a range of cycle threshold (Ct) values (18-40) were tested by four multiplex assays. Positive and negative percent agreement (PPA and NPA) with validated RT-PCR assays were calculated.
    Results: A total of 82 samples were assessed, with discordant results observed in a portion of the samples (10/82, 12.2%) where Ct values were >33. The majority of the discordant results (6/10, 60%) were false negatives. Overall, PPA was 100% (58/58) for cobas 6800, 97.4% (38/39) for GeneXpert, 100% (17/17) for Liat, and 90.5% (57/63) for the LDT. PPA for the LDT increased to 92.1% after manual review of amplification curves.
    Conclusions: Commercial multiplex respiratory virus assays have good performance for samples with medium to high viral loads (Ct values <33). Laboratories should consider appropriate test result review and confirmation protocols to optimize sensitivity, and may consider reporting samples with additional interpretive comments when low viral loads are detected.
    Sprache Englisch
    Erscheinungsdatum 2024-01-16
    Erscheinungsland Canada
    Dokumenttyp Journal Article
    ISSN 2371-0888
    ISSN (online) 2371-0888
    DOI 10.3138/jammi-2022-0039
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  2. Artikel ; Online: Stability of BK polyomavirus DNA in urine over time and analytical evaluation of an automated BKV quantitative nucleic acid test.

    Lowe, Christopher F / Lawson, Tanya / Young, Matthew / Jang, Willson / Ritchie, Gordon / Romney, Marc G / Matic, Nancy

    Journal of medical microbiology

    2024  Band 73, Heft 1

    Abstract: Introduction. ...

    Abstract Introduction.
    Mesh-Begriff(e) Nucleic Acids ; BK Virus ; Prospective Studies ; Reproducibility of Results ; DNA
    Chemische Substanzen Nucleic Acids ; DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2024-01-22
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 218356-0
    ISSN 1473-5644 ; 0022-2615
    ISSN (online) 1473-5644
    ISSN 0022-2615
    DOI 10.1099/jmm.0.001789
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  3. Artikel ; Online: Viral load kinetics and the clinical consequences of cytomegalovirus in kidney transplantation.

    Dobrer, Sabina / Sherwood, Karen R / Hirji, Ishan / Lan, James / Gill, John / Matic, Nancy / Keown, Paul A

    Frontiers in immunology

    2024  Band 14, Seite(n) 1302627

    Abstract: Background: Despite advances in clinical management, cytomegalovirus (CMV) infection remains a serious complication and an important cause of morbidity and mortality following kidney transplantation. Here, we explore the importance of viral load ... ...

    Abstract Background: Despite advances in clinical management, cytomegalovirus (CMV) infection remains a serious complication and an important cause of morbidity and mortality following kidney transplantation. Here, we explore the importance of viral load kinetics as predictors of risk and potential guides to therapy to reduce transplant failure in a large longitudinal Genome Canada Transplant Consortium (GCTC) kidney transplant cohort.
    Methods: We examined the relationship between CMV infection rates and clinical characteristics, CMV viral load kinetics, and graft and patient outcomes in 2510 sequential kidney transplant recipients in the British Columbia Transplant Program. Transplants were performed between January 1, 2008, and December 31, 2018, were managed according to a standard protocol, and were followed until December 31, 2019, representing over 3.4 million days of care.
    Results: Longitudinal CMV testing was performed in 2464 patients, of whom 434 (17.6%) developed a first episode of CMV viremia at a median of 120 (range: 9-3906) days post-transplant. Of these patients, 93 (21.4%) had CMV viremia only and 341 (78.6%) had CMV viremia with clinical complications, of whom 21 (4.8%) had resulting hospitalization. A total of 279 (11.3%) patients died and 177 (7.2%) patients lost their graft during the 12 years of follow-up. Patients with CMV infection were at significantly greater risk of graft loss (p=0.0041) and death (p=0.0056) than those without. Peak viral load ranged from 2.9 to 7.0 (median: 3.5) log
    Conclusion: Viral load kinetics are closely related to CMV severity and to graft loss following kidney transplantation and provide a simple index of risk which may be valuable in guiding trials and treatment to prevent transplant failure.
    Mesh-Begriff(e) Humans ; Cytomegalovirus/genetics ; Kidney Transplantation/adverse effects ; Viral Load ; Viremia/drug therapy ; Cytomegalovirus Infections
    Sprache Englisch
    Erscheinungsdatum 2024-01-31
    Erscheinungsland Switzerland
    Dokumenttyp 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.2023.1302627
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  4. Artikel ; Online: Epidemiology of cytomegalovirus antiviral resistance testing for solid organ and bone marrow transplant patients from 2011 - 2019.

    Li, Lynne / Lowe, Christopher F / McLachlan, Elizabeth / Romney, Marc G / Wright, Alissa / Matic, Nancy

    Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

    2023  Band 166, Seite(n) 105549

    Abstract: Background: CMV reactivation post-transplantation is common, with need for prompt identification of patients most at-risk for CMV antiviral drug resistance (AVDR).: Objectives: This study describes CMV AVDR frequencies, antiviral prescribing ... ...

    Abstract Background: CMV reactivation post-transplantation is common, with need for prompt identification of patients most at-risk for CMV antiviral drug resistance (AVDR).
    Objectives: This study describes CMV AVDR frequencies, antiviral prescribing practices, and AVDR risk factors in patients from 2011 to 2019 in British Columbia, Canada.
    Study design: Retrospective review of demographics, transplant type, viral loads, antiviral exposure duration, and 12-month mortality was conducted for all patients with samples submitted for CMV AVDR testing from 2011 to 2019. Genotyping of AVDR mutations occurred at the national reference laboratory. Mann-Whitney U, T-test or Fisher's exact tests examined differences between patients with and without AVDR.
    Results: Fifty-three plasma and three tissue/fluid specimens successfully underwent CMV AVDR testing; of these samples, 27/56 (48%) had AVDR mutations detected. The commonest AVDR mutations were at UL97 loci A594 (20%), H596 (12%) and L595 (12%). Mutations occurred more frequently in requests from solid organ than hematopoietic stem cell transplant patients (58% vs. 27%, p = 0.05). Previous resistance testing was a significant risk factor for AVDR (p < 0.001). Patients with AVDR had approximately 51 more days of antiviral therapy (p = 0.007) and took 9 days longer to clear viremia (p = 0.23). The median turnaround time from sample send-out to reporting was nine days. However, empiric use of second-line antivirals occurred in most cases (39/53, 74%) before results were available.
    Discussion: Laboratories should strive to provide timely CMV AVDR testing for transplant patients, to minimize unnecessary exposure to second-line antiviral agents. The findings of this study may help guide clinicians when selecting empiric antiviral therapy.
    Mesh-Begriff(e) Humans ; Cytomegalovirus ; Cytomegalovirus Infections ; Bone Marrow Transplantation/adverse effects ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Drug Resistance, Viral
    Chemische Substanzen Antiviral Agents
    Sprache Englisch
    Erscheinungsdatum 2023-07-18
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article
    ZDB-ID 1446080-4
    ISSN 1873-5967 ; 1386-6532
    ISSN (online) 1873-5967
    ISSN 1386-6532
    DOI 10.1016/j.jcv.2023.105549
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  5. Artikel ; Online: Adaptability of single-nucleotide polymorphism-polymerase chain reaction (SNP-PCR) for subtyping SARS-CoV-2 and a new SNP-PCR for XBB, XBB.1.5, and B.Q.1/B.Q.1.1.

    Ritchie, Gordon / Young, Matthew / Prystajecky, Natalie / Romney, Marc G / Lowe, Christopher F / Matic, Nancy

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases

    2023  Band 29, Heft 10, Seite(n) 1339–1341

    Mesh-Begriff(e) Humans ; COVID-19 ; Polymorphism, Single Nucleotide ; SARS-CoV-2/genetics ; COVID-19 Testing
    Sprache Englisch
    Erscheinungsdatum 2023-06-15
    Erscheinungsland England
    Dokumenttyp Letter
    ZDB-ID 1328418-6
    ISSN 1469-0691 ; 1470-9465 ; 1198-743X
    ISSN (online) 1469-0691
    ISSN 1470-9465 ; 1198-743X
    DOI 10.1016/j.cmi.2023.06.014
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  6. Artikel ; Online: Omicron (B.1.1.529) SARS-CoV-2 viral load among nasopharyngeal and oral samples compared to other variants of concern and impact on diagnostic testing strategy.

    Matic, Nancy / Lowe, Christopher F / Ritchie, Gordon / Young, Matthew / Lawson, Tanya / Romney, Marc G

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases

    2022  Band 28, Heft 9, Seite(n) 1302–1303

    Mesh-Begriff(e) COVID-19/diagnosis ; COVID-19 Testing ; Diagnostic Techniques and Procedures ; Humans ; Nasopharynx ; SARS-CoV-2 ; Viral Load
    Sprache Englisch
    Erscheinungsdatum 2022-05-11
    Erscheinungsland England
    Dokumenttyp Letter
    ZDB-ID 1328418-6
    ISSN 1469-0691 ; 1470-9465 ; 1198-743X
    ISSN (online) 1469-0691
    ISSN 1470-9465 ; 1198-743X
    DOI 10.1016/j.cmi.2022.04.022
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  7. Artikel: End-to-End Data Automation for Pooled Sample SARS-CoV-2 Using R and Other Open-Source Tools.

    Mobini, Mahdi / Matic, Nancy / Gugten, J Grace Van Der / Ritchie, Gordon / Lowe, Christopher F / Holmes, Daniel T

    The journal of applied laboratory medicine

    2023  Band 8, Heft 1, Seite(n) 41–52

    Abstract: Background: Due to supply chain shortages of reagents for real-time (RT)-PCR for SARS-CoV-2 and increasing demand on technical staff, an end-to-end data automation strategy for SARS-CoV-2 sample pooling and singleton analysis became necessary in the ... ...

    Abstract Background: Due to supply chain shortages of reagents for real-time (RT)-PCR for SARS-CoV-2 and increasing demand on technical staff, an end-to-end data automation strategy for SARS-CoV-2 sample pooling and singleton analysis became necessary in the summer of 2020.
    Methods: Using entirely open source software tools-Linux, bash, R, RShiny, ShinyProxy, and Docker-we developed a modular software application stack to manage the preanalytical, analytical, and postanalytical processes for singleton and pooled testing in a 5-week time frame.
    Results: Pooling was operationalized for 81 days, during which time 64 pooled runs were performed for a total of 5320 sample pools and approximately 21 280 patient samples in 4:1 format. A total of 17 580 negative pooled results were released in bulk. After pooling was discontinued, the application stack was used for singleton analysis and modified to release all viral RT-PCR results from our laboratory. To date, 236 109 samples have been processed avoiding over 610 000 transcriptions.
    Conclusions: We present an end-to-end data automation strategy connecting 11 devices, one network attached storage, 2 Linux servers, and the laboratory information system.
    Mesh-Begriff(e) Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19 Testing ; Real-Time Polymerase Chain Reaction
    Sprache Englisch
    Erscheinungsdatum 2023-01-06
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2576-9456
    ISSN 2576-9456
    DOI 10.1093/jalm/jfac109
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  8. Artikel ; Online: WGS of a cluster of MDR Shigella sonnei utilizing Oxford Nanopore R10.4.1 long-read sequencing.

    Ritchie, Gordon / Chorlton, Samuel D / Matic, Nancy / Bilawka, Jennifer / Gowland, Leah / Leung, Victor / Stefanovic, Aleksandra / Romney, Marc G / Lowe, Christopher F

    The Journal of antimicrobial chemotherapy

    2023  Band 79, Heft 1, Seite(n) 55–60

    Abstract: Objectives: To utilize long-read nanopore sequencing (R10.4.1 flowcells) for WGS of a cluster of MDR Shigella sonnei, specifically characterizing genetic predictors of antimicrobial resistance (AMR).: Methods: WGS was performed on S. sonnei isolates ... ...

    Abstract Objectives: To utilize long-read nanopore sequencing (R10.4.1 flowcells) for WGS of a cluster of MDR Shigella sonnei, specifically characterizing genetic predictors of antimicrobial resistance (AMR).
    Methods: WGS was performed on S. sonnei isolates identified from stool and blood between September 2021 and October 2022. Bacterial DNA from clinical isolates was extracted on the MagNA Pure 24 and sequenced on the GridION utilizing R10.4.1 flowcells. Phenotypic antimicrobial susceptibility testing was interpreted based on CLSI breakpoints. Sequencing data were processed with BugSeq, and AMR was assessed with BugSplit and ResFinder.
    Results: Fifty-six isolates were sequenced, including 53 related to the cluster of cases. All cluster isolates were identified as S. sonnei by sequencing, with global genotype 3.6.1.1.2 (CipR.MSM5), MLST 152 and PopPUNK cluster 3. Core genome MLST (cgMLST, examining 2513 loci) and reference-based MLST (refMLST, examining 4091 loci) both confirmed the clonality of the isolates. Cluster isolates were resistant to ampicillin (blaTEM-1), trimethoprim/sulfamethoxazole (dfA1, dfrA17; sul1, sul2), azithromycin (ermB, mphA) and ciprofloxacin (gyrA S83L, gyrA D87G, parC S80I). No genomic predictors of resistance to carbapenems were identified.
    Conclusions: WGS with R10.4.1 enabled rapid sequencing and identification of an MDR S. sonnei community cluster. Genetic predictors of AMR were concordant with phenotypic antimicrobial susceptibility testing.
    Mesh-Begriff(e) Humans ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Shigella sonnei/genetics ; Nanopore Sequencing ; Multilocus Sequence Typing ; Nanopores ; Microbial Sensitivity Tests ; Dysentery, Bacillary/microbiology ; Drug Resistance, Bacterial/genetics
    Chemische Substanzen Anti-Bacterial Agents
    Sprache Englisch
    Erscheinungsdatum 2023-11-22
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 191709-2
    ISSN 1460-2091 ; 0305-7453
    ISSN (online) 1460-2091
    ISSN 0305-7453
    DOI 10.1093/jac/dkad346
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  9. Artikel ; Online: Hepatitis B virus genotype surveillance in Canadian blood donors and a referred patient population, 2016-2021.

    Osiowy, Carla / Giles, Elizabeth / Lowe, Christopher F / Matic, Nancy / Murphy, Donald G / Uzicanin, Samra / Drews, Steven J / O'Brien, Sheila F

    Vox sanguinis

    2023  Band 119, Heft 3, Seite(n) 232–241

    Abstract: Background and objectives: Hepatitis B virus (HBV) genotypes (A-H) have a distinct geographic distribution and are highly associated with the country of birth. Canada has experienced increased immigration over the past decade, primarily from regions ... ...

    Abstract Background and objectives: Hepatitis B virus (HBV) genotypes (A-H) have a distinct geographic distribution and are highly associated with the country of birth. Canada has experienced increased immigration over the past decade, primarily from regions where HBV is endemic. This study investigated the proportions and trends of HBV genotypes within blood donor and clinical populations of Canada over the period 2016-2021.
    Materials and methods: Study samples involved two cohorts: (1) Canadian blood donors (n = 246) deferred from donation due to HBV test positivity and (2) chronic HBV patients from across Canada (clinically referred population, n = 3539). Plasma or serum was extracted, and the surface antigen and/or polymerase-coding region was amplified and sequenced to determine genotype by phylogenetic analysis.
    Results: Six (A-E, G) and eight (A-H) HBV genotypes were detected among deferred blood donors and the clinically referred population, respectively. Differences in HBV genotype proportions between the two cohorts were observed across Canada. Males comprised most of the referred population among genotypes A-E (p < 0.0001), except for genotypes B and C. The median age was younger among blood donors (36 years [range 17-72]) compared with the referred population (41 years [range 0-99]). Distinct trends of increasing (E, referred; B, blood donor) and decreasing genotype prevalence were observed over the study period.
    Conclusion: HBV genotypes in Canada are highly diverse, suggesting a large immigrant population. Observed trends in genotype prevalence and proportional differences among cohorts imply shifts among the HBV-infected population of Canada, which warrants continued surveillance.
    Mesh-Begriff(e) Male ; Humans ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Female ; Hepatitis B virus/genetics ; Blood Donors ; Hepatitis B/epidemiology ; Phylogeny ; Canada ; Genotype ; Hepatitis B Surface Antigens ; DNA, Viral
    Chemische Substanzen Hepatitis B Surface Antigens ; DNA, Viral
    Sprache Englisch
    Erscheinungsdatum 2023-12-23
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 80313-3
    ISSN 1423-0410 ; 0042-9007
    ISSN (online) 1423-0410
    ISSN 0042-9007
    DOI 10.1111/vox.13568
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  10. Artikel ; Online: Evaluating in vivo effectiveness of sotrovimab for the treatment of Omicron subvariant BA.2 versus BA.1: a multicentre, retrospective cohort study.

    Lo, Carson K L / Lo, Calvin K F / Komorowski, Adam S / Leung, Victor / Matic, Nancy / McKenna, Susan / Perez-Patrigeon, Santiago / Sheth, Prameet M / Lowe, Christopher F / Chagla, Zain / Bai, Anthony D

    BMC research notes

    2024  Band 17, Heft 1, Seite(n) 37

    Abstract: Background: In vitro data suggested reduced neutralizing capacity of sotrovimab, a monoclonal antibody, against Omicron BA.2 subvariant. However, limited in vivo data exist regarding clinical effectiveness of sotrovimab for coronavirus disease 2019 ( ... ...

    Abstract Background: In vitro data suggested reduced neutralizing capacity of sotrovimab, a monoclonal antibody, against Omicron BA.2 subvariant. However, limited in vivo data exist regarding clinical effectiveness of sotrovimab for coronavirus disease 2019 (COVID-19) due to Omicron BA.2.
    Methods: A multicentre, retrospective cohort study was conducted at three Canadian academic tertiary centres. Electronic medical records were reviewed for patients ≥ 18 years with mild COVID-19 (sequencing-confirmed Omicron BA.1 or BA.2) treated with sotrovimab between February 1 to April 1, 2022. Thirty-day co-primary outcomes included hospitalization due to moderate or severe COVID-19; all-cause intensive care unit (ICU) admission, and all-cause mortality. Risk differences (BA.2 minus BA.1 group) for co-primary outcomes were adjusted with propensity score matching (e.g., age, sex, vaccination, immunocompromised status).
    Results: Eighty-five patients were included (15 BA.2, 70 BA.1) with similar baseline characteristics between groups. Adjusted risk differences were non-statistically significant between groups for 30-day hospitalization (- 14.3%; 95% confidence interval (CI): - 32.6 to 4.0%), ICU admission (- 7.1%; 95%CI: - 20.6 to 6.3%), and mortality (- 7.1%; 95%CI: - 20.6 to 6.3%).
    Conclusions: No differences were demonstrated in hospitalization, ICU admission, or mortality rates within 30 days between sotrovimab-treated patients with BA.1 versus BA.2 infection. More real-world data may be helpful to properly assess sotrovimab's effectiveness against infections due to specific emerging COVID-19 variants.
    Mesh-Begriff(e) Humans ; Retrospective Studies ; Canada ; Antibodies, Monoclonal, Humanized/therapeutic use ; COVID-19 ; Antibodies, Neutralizing
    Chemische Substanzen sotrovimab (1MTK0BPN8V) ; Antibodies, Monoclonal, Humanized ; Antibodies, Neutralizing
    Sprache Englisch
    Erscheinungsdatum 2024-01-24
    Erscheinungsland England
    Dokumenttyp Multicenter Study ; Journal Article
    ZDB-ID 2413336-X
    ISSN 1756-0500 ; 1756-0500
    ISSN (online) 1756-0500
    ISSN 1756-0500
    DOI 10.1186/s13104-024-06695-x
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