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Table of Contents

March 2020; Volume 58,Issue 3

Photo Quiz

  • Photo Quiz: Subcutaneous Infection in an Immunocompetent Patient Handling a Wooden Wheelbarrow
    Photo Quiz
    Photo Quiz: Subcutaneous Infection in an Immunocompetent Patient Handling a Wooden Wheelbarrow
    Ramya Gadde, Linoj Samuel
  • Answer to March 2020 Photo Quiz
    Photo Quiz
    Answer to March 2020 Photo Quiz
    Ramya Gadde, Linoj Samuel

Editorial

  • Free
    The End of Coagulase-Negative Staphylococci? A Micro-Comic Strip
    Editorial
    The End of Coagulase-Negative Staphylococci? A Micro-Comic Strip
    Alexander J. McAdam

The Brief Case

  • Free
    The Brief Case: Cutaneous Fungal Infection in a Pediatric Patient with Newly Diagnosed Acute Lymphocytic Leukemia
    The Brief Case
    The Brief Case: Cutaneous Fungal Infection in a Pediatric Patient with Newly Diagnosed Acute Lymphocytic Leukemia
    Liye Suo, James J. Dunn
  • Free
    Closing the Brief Case: Cutaneous Fungal Infection in a Pediatric Patient with Newly Diagnosed Acute Lymphocytic Leukemia
    The Brief Case
    Closing the Brief Case: Cutaneous Fungal Infection in a Pediatric Patient with Newly Diagnosed Acute Lymphocytic Leukemia
    Liye Suo, James J. Dunn

Biographical Feature

  • Free
    Biographical Feature: Franklin P. Koontz, Ph.D., D(ABMM), F(AAM)
    Biographical Feature
    Biographical Feature: Franklin P. Koontz, Ph.D., D(ABMM), F(AAM)
    Erik Munson

Point-Counterpoint

  • <span hwp:id="article-title-1" class="article-title">Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?</span><span hwp:id="article-title-1" class="sub-article-title inherited-article-title">Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?</span><span hwp:id="article-title-1" class="sub-article-title inherited-article-title">Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?</span><span hwp:id="article-title-1" class="sub-article-title inherited-article-title">Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?</span>
    Point-Counterpoint
    Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?

    With established applications of next-generation sequencing in inherited diseases and oncology, clinical laboratories are evaluating the use of metagenomics for identification of infectious agents directly from patient samples, to aid in the diagnosis of infections. Metagenomic next-generation sequencing for infectious diseases promises an unbiased approach to detection of microbes that does not depend on growth in culture or the...

    Steve Miller, Charles Chiu, Kyle G. Rodino, Melissa B. Miller

Commentary

  • The Clinical and Laboratory Standards Institute Subcommittee on Antimicrobial Susceptibility Testing: Background, Organization, Functions, and Processes
    Commentary
    The Clinical and Laboratory Standards Institute Subcommittee on Antimicrobial Susceptibility Testing: Background, Organization, Functions, and Processes

    The Clinical and Laboratory Standards Institute (CLSI) Subcommittee on Antimicrobial Susceptibility Testing (AST SC) is a volunteer-led, multidisciplinary consensus body that develops and publishes standards and guidelines (among other products) for antimicrobial susceptibility testing (AST) methods and results interpretation in the United States and internationally. The Subcommittee (SC) meets face-to-face twice yearly, and its working...

    Melvin P. Weinstein, James S. Lewis

Bacteriology

  • Comparison of Three Commercial Tools for Metagenomic Shotgun Sequencing Analysis
    Bacteriology
    Comparison of Three Commercial Tools for Metagenomic Shotgun Sequencing Analysis

    Metagenomic shotgun sequencing for the identification of pathogens is being increasingly utilized as a diagnostic method. Interpretation of large and complicated data sets is a significant challenge, for which multiple commercial tools have been developed. Three commercial metagenomic shotgun sequencing tools, CosmosID, One Codex, and IDbyDNA, were compared to determine whether they result in similar interpretations of the same...

    Matthew Thoendel, Patricio Jeraldo, Kerryl E. Greenwood-Quaintance, Janet Yao, Nicholas Chia, Arlen D. Hanssen, Matthew P. Abdel, Robin Patel
  • Method Comparison of the ImmuView <span class="named-content genus-species" id="named-content-1">L. pneumophila</span> and <em>L. longbeachae</em> Urinary Antigen Test with the BinaxNOW <em>Legionella</em> Urinary Antigen Card for Detection of <span class="named-content genus-species" id="named-content-2">Legionella pneumophila</span> Serogroup 1 Antigen in Urine
    Bacteriology
    Method Comparison of the ImmuView L. pneumophila and L. longbeachae Urinary Antigen Test with the BinaxNOW Legionella Urinary Antigen Card for Detection of Legionella pneumophila Serogroup 1 Antigen in Urine

    We compared the clinical performance of the ImmuView L. pneumophila and L. longbeachae urinary antigen test (SSI Diagnostica A/S, Hillerød, Denmark) to that of the BinaxNOW Legionella urinary antigen card (Binax; Abbott, Lake Buff, IL) using urine specimens from patients suspected of having pneumonia. In total, 100 frozen urine samples (derived from...

    Paul Badoux, Lianne Kracht-Kosten, Bjorn Herpers, Sjoerd Euser
  • Phenotypic Detection of Plasmid-Mediated Colistin Resistance in <em>Enterobacteriaceae</em>
    Bacteriology
    Phenotypic Detection of Plasmid-Mediated Colistin Resistance in Enterobacteriaceae

    The aim of this work was to evaluate an easy-to-perform assay based upon inhibition of mobile colistin resistance (MCR) activity by EDTA. We included 92 nonrelated isolates of Enterobacteriaceae (74 Escherichia coli, 17 Klebsiella pneumoniae, and 1...

    Edgar Gonzales Escalante, Katherine Yauri Condor, Jose A. Di Conza, Gabriel O. Gutkind
  • <span class="named-content genus-species" id="named-content-1">Helicobacter pylori</span> Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome Sequencing
    Bacteriology
    Helicobacter pylori Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome Sequencing

    The emergence of drug resistance in Helicobacter pylori has resulted in a greater need for susceptibility-guided treatment. While the alleles associated with resistance to clarithromycin and levofloxacin have been defined, there are limited data regarding the molecular mechanisms underlying resistance to other antimicrobials. Using...

    Rajagopalan Saranathan, Michael H. Levi, Alice R. Wattam, Adel Malek, Emmanuel Asare, Daniel S. Behin, Debra H. Pan, William R. Jacobs, Wendy A. Szymczak
  • Cerebrospinal Fluid Findings Are Poor Predictors of Appropriate FilmArray Meningitis/Encephalitis Panel Utilization in Pediatric Patients
    Bacteriology
    Cerebrospinal Fluid Findings Are Poor Predictors of Appropriate FilmArray Meningitis/Encephalitis Panel Utilization in Pediatric Patients

    Molecular testing of cerebrospinal fluid (CSF) using the BioFire FilmArray meningitis/encephalitis (FA-M/E) panel permits rapid, simultaneous pathogen detection. Due to the broad spectrum of targeted organisms, FA-M/E testing may be restricted to patients with abnormal CSF findings. We sought to determine if restriction is appropriate in our previously healthy and/or immunocompromised pediatric patients.

    Mimi R. Precit, Rebecca Yee, Utsav Pandey, Margil Fahit, Cheryl Pool, Samia N. Naccache, Jennifer Dien Bard
  • Validation of a New Rapid Detection Test for Detection of <span class="named-content genus-species" id="named-content-1">Neisseria meningitidis</span> A/C/W/X/Y Antigens in Cerebrospinal Fluid
    Bacteriology
    Validation of a New Rapid Detection Test for Detection of Neisseria meningitidis A/C/W/X/Y Antigens in Cerebrospinal Fluid

    Meningococcal meningitis remains a life-threatening disease worldwide, with high prevalence in the sub-Saharan meningitis belt. A rapid diagnosis is crucial for implementing adapted antimicrobial treatment. We describe the performances of a new immunochromatographic test (MeningoSpeed, BioSpeedia, France) for detecting and grouping Neisseria meningitidis....

    Cyrille H. Haddar, Aude Terrade, Paul Verhoeven, Berthe-Marie Njanpop-Lafourcade, Mireille Dosso, Fati Sidikou, Ali Elhaj Mahamane, Jean-Pierre Lombart, Aziza Razki, Eva Hong, Alain Agnememel, Evelyne Begaud, Yves Germani, Bruno Pozzetto, Muhamed-Kheir Taha
  • Open Access
    Performance of the QIAstat-Dx Gastrointestinal Panel for Diagnosing Infectious Gastroenteritis
    Bacteriology
    Performance of the QIAstat-Dx Gastrointestinal Panel for Diagnosing Infectious Gastroenteritis

    Detection and identification of enteropathogens that cause infectious gastroenteritis are essential steps for appropriate patient treatment and effective isolation precautions. Several syndrome-based tests have recently become available, with the gastrointestinal panel (GIP) assay on the QIAstat-Dx as the most recent addition to the syndromic testing landscape.

    Stefan A. Boers, Cas J. A. Peters, Els Wessels, Willem J. G. Melchers, Eric C. J. Claas
  • Open Access
    Optimizing DNA Extraction Methods for Nanopore Sequencing of <span class="named-content genus-species" id="named-content-1">Neisseria gonorrhoeae</span> Directly from Urine Samples
    Bacteriology
    Optimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine Samples

    Empirical gonorrhea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance. We investigated if Nanopore sequencing can detect sufficient...

    Teresa L. Street, Leanne Barker, Nicholas D. Sanderson, James Kavanagh, Sarah Hoosdally, Kevin Cole, Robert Newnham, Mathyruban Selvaratnam, Monique Andersson, Martin J. Llewelyn, Justin O’Grady, Derrick W. Crook, David W. Eyre
    and the GonFast Investigators Group
  • Open Access
    Evaluation of the ResistancePlus MG FleXible Assay for Detection of Wild-Type and 23S rRNA-Mutated <span class="named-content genus-species" id="named-content-1">Mycoplasma genitalium</span> Strains
    Bacteriology
    Evaluation of the ResistancePlus MG FleXible Assay for Detection of Wild-Type and 23S rRNA-Mutated Mycoplasma genitalium Strains

    Antibiotic resistance in Mycoplasma genitalium is rising globally, and resistance-guided diagnostics can facilitate targeted and timely treatment. The ResistancePlus MG FleXible (RPMG Flex) assay for the detection of M. genitalium and macrolide resistance-mediating mutations (MRMM) was evaluated for...

    Suhella Tulsiani Drud, Peter Njuguna, Samantha Ebeyan, Simon Erskine, Mette Holm, Susanne Cramer Johansson, Lit Yeen Tan, Jorgen Skov Jensen

Mycology

  • Evaluation of a Rapid Fungal Detection Panel for Identification of Candidemia at an Academic Medical Center
    Mycology
    Evaluation of a Rapid Fungal Detection Panel for Identification of Candidemia at an Academic Medical Center

    This study was conducted to assess the utility of the T2Candida panel across an academic health center and identify potential areas for diagnostic optimization. A retrospective chart review was conducted on patients with a T2Candida panel and mycolytic/fungal (myco/f lytic) blood culture collected simultaneously during hospitalizations from February 2017 to March 2018.

    John P. Bomkamp, Rand Sulaiman, Jennifer L. Hartwell, Armisha Desai, Vera C. Winn, Justin Wrin, Michelle L. Kussin, Jon J. Hiles
  • Human Blastomycosis in South Africa Caused by <em>Blastomyces percursus</em> and <em>Blastomyces emzantsi</em> sp. nov., 1967 to 2014
    Mycology
    Human Blastomycosis in South Africa Caused by Blastomyces percursus and Blastomyces emzantsi sp. nov., 1967 to 2014

    We reevaluated 20 cases of blastomycosis diagnosed in South Africa between 1967 and 2014, with Blastomyces dermatitidis considered to be the etiological agent, in light of newly described species and the use of more advanced technologies. In addition to histopathological and/or culture-based methods, all 20 isolates were phenotypically and genotypically characterized...

    Tsidiso G. Maphanga, Monica Birkhead, José F. Muñoz, Mushal Allam, Thokozile G. Zulu, Christina A. Cuomo, Ilan S. Schwartz, Arshad Ismail, Serisha D. Naicker, Ruth S. Mpembe, Craig Corcoran, Sybren de Hoog, Chris Kenyon, Andrew M. Borman, John A. Frean, Nelesh P. Govender

Parasitology

  • Open Access
    Evaluation of a Novel High-Definition PCR Multiplex Assay for Simultaneous Detection of Tick-Borne Pathogens in Human Clinical Specimens
    Parasitology
    Evaluation of a Novel High-Definition PCR Multiplex Assay for Simultaneous Detection of Tick-Borne Pathogens in Human Clinical Specimens

    The incidence of tick-borne infections in the United States has risen significantly in the past decade. Ticks can transmit a variety of pathogens, including bacteria, protozoa, and viruses, that can cause serious illnesses. Therefore, the use of rapid, sensitive, and specific multiplex tests is important to identify the pathogen(s) in the acute phase and determine appropriate treatment to minimize the severity of the disease.

    ...
    Salika M. Shakir, Christopher R. Mansfield, Elizabeth D. Hays, Marc Roger Couturier, David R. Hillyard

Virology

  • Bayesian Evaluation of Solana HSV 1+2/VZV Assay Compared to Viral Culture and Commercial PCR Assay for Cutaneous or Mucocutaneous Specimens
    Virology
    Bayesian Evaluation of Solana HSV 1+2/VZV Assay Compared to Viral Culture and Commercial PCR Assay for Cutaneous or Mucocutaneous Specimens

    Results from the Solana HSV 1+2/VZV assay for the detection of herpes simplex virus 1 (HSV-1), HSV-2, and varicella-zoster virus (VZV) in cutaneous or mucocutaneous specimens were compared with that of viral culture and a commercial PCR assay (RealStar alpha herpesvirus PCR kit).

    Christine Arsenault, Félix Camirand Lemyre, Philippe Martin, Simon Lévesque
  • Open Access
    Comparison of the ID Now Influenza A &amp; B 2, Cobas Influenza A/B, and Xpert Xpress Flu Point-of-Care Nucleic Acid Amplification Tests for Influenza A/B Virus Detection in Children
    Virology
    Comparison of the ID Now Influenza A & B 2, Cobas Influenza A/B, and Xpert Xpress Flu Point-of-Care Nucleic Acid Amplification Tests for Influenza A/B Virus Detection in Children

    Early diagnosis of influenza (Flu) is critical for patient management and infection control. The ID Now influenza A & B 2 (ID Now) assay (Abbott Laboratories), Cobas influenza A/B nucleic acid test (LIAT; Roche Molecular Systems, Inc.), and Xpert Xpress Flu (Xpert; Cepheid) are rapid, point-of-care molecular assays for Flu virus detection. The study aim was to compare the performances of these three commercially available Clinical...

    Neena Kanwar, Jeffrey Michael, Kathryn Doran, Emily Montgomery, Rangaraj Selvarangan

Immunoassays

  • Diagnostic Value of Galactomannan in Bronchoalveolar Lavage Fluid for Chronic Respiratory Disease with Pulmonary Aspergillosis
    Immunoassays
    Diagnostic Value of Galactomannan in Bronchoalveolar Lavage Fluid for Chronic Respiratory Disease with Pulmonary Aspergillosis

    The objective of this study was to explore the diagnostic value of the bronchoalveolar lavage fluid galactomannan (BALF GM) test for chronic respiratory disease with pulmonary aspergillosis and to establish the optimal cutoff value. Samples from a total of 309 chronic respiratory disease patients seen at the respiratory medicine department of Peking University Shenzhen Hospital from September 2016 to September 2019 were analyzed.

    ...
    Guangbin Lai, Chao Zeng, Jianming Mo, Wei-dong Song, Ping Xu
  • Development and Evaluation of a Novel VHH-Based Immunocapture Assay for High-Sensitivity Detection of Shiga Toxin Type 2 (Stx2) in Stool Samples
    Immunoassays
    Development and Evaluation of a Novel VHH-Based Immunocapture Assay for High-Sensitivity Detection of Shiga Toxin Type 2 (Stx2) in Stool Samples

    Shiga toxin (Stx)-producing Escherichia coli (STEC) is the main cause of postdiarrheal hemolytic-uremic syndrome (HUS), a life-threatening clinical complication characterized by hemolytic anemia, thrombocytopenia, and acute renal failure that mainly affects children. A relevant feature of STEC strains is the production of Stx, and all of them express Stx1 and/or Stx2...

    Luciano J. Melli, Vanesa Zylberman, Yanina Hiriart, Constanza E. Lauche, Ariela Baschkier, Romina Pardo, Elizabeth Miliwebsky, Isabel Chinen, Marta Rivas, Fernando A. Goldbaum, Juan E. Ugalde, Diego J. Comerci, Andrés E. Ciocchini

Clinical Veterinary Microbiology

  • Single-Cell-Based Digital PCR Detection and Association of Shiga Toxin-Producing <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Serogroups and Major Virulence Genes
    Clinical Veterinary Microbiology
    Single-Cell-Based Digital PCR Detection and Association of Shiga Toxin-Producing Escherichia coli Serogroups and Major Virulence Genes

    Escherichia coli serogroups O157, O26, O45, O103, O111, O121, and O145, when carrying major virulence genes, the Shiga toxin genes stx1 and stx2 and the intimin gene eae, are important foodborne pathogens. They are referred to as the “top 7” Shiga toxin-producing...

    Xuming Liu, Lance Noll, Xiaorong Shi, Elizabeth Porter, Yin Wang, Colin Stoy, Nanyan Lu, T. G. Nagaraja, Gary Anderson, Jianfa Bai

Epidemiology

  • Test Accuracy of Human Papillomavirus in Urine for Detection of Cervical Intraepithelial Neoplasia
    Epidemiology
    Test Accuracy of Human Papillomavirus in Urine for Detection of Cervical Intraepithelial Neoplasia

    The objective was to assess the diagnostic test accuracy of high-risk human papillomavirus (hrHPV) testing of self-collected urine and cervicovaginal samples for the detection of cervical intraepithelial neoplasia grade 2 or higher (CIN2+). We recruited a convenience sample of women 25 to 65 years of age who were undergoing clinically indicated colposcopy at two medical centers in North Carolina between November 2016 and January 2019....

    Eliane Rohner, Lisa Rahangdale, Busola Sanusi, Andrea K. Knittel, Laurence Vaughan, Kirsty Chesko, Brian Faherty, Samantha E. Tulenko, John W. Schmitt, LaHoma S. Romocki, Vijay Sivaraman, Julie A. E. Nelson, Jennifer S. Smith
  • Predictors of <span class="named-content genus-species" id="named-content-1">Clostridioides difficile</span> Infection-Related Complications and Treatment Patterns among Nucleic Acid Amplification Test-Positive/Toxin Enzyme Immunoassay-Negative Patients
    Epidemiology
    Predictors of Clostridioides difficile Infection-Related Complications and Treatment Patterns among Nucleic Acid Amplification Test-Positive/Toxin Enzyme Immunoassay-Negative Patients

    The addition of toxin enzyme immunoassay (EIA) to nucleic acid amplification tests, including PCR, creates challenges in the diagnosis and management of Clostridioides difficile infection (CDI). There are limited data in large cohorts, with discordant results, that is, PCR-positive/EIA-negative (PCR+/EIA−) results. We conducted a retrospective...

    Ryan Miller, J. A. Morillas, Kyle D. Brizendine, Thomas G. Fraser

Letters to the Editor

  • Carbapenem-Susceptible <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> and <span class="named-content genus-species" id="named-content-2">Escherichia coli</span> Isolates Carrying a Truncated KPC Carbapenemase: a Challenge for Rapid Molecular Diagnostics
    Letter to the Editor
    Carbapenem-Susceptible Klebsiella pneumoniae and Escherichia coli Isolates Carrying a Truncated KPC Carbapenemase: a Challenge for Rapid Molecular Diagnostics
    Hossein Salimnia, Jennifer Veltman, Pranatharthi H. Chandrasekar, Jason M. Pogue, Ryan Mynatt, Tanaz Salimnia, Steven H. Marshall, Andrea M. Hujer, Robert A. Bonomo
  • Evaluation of the ResistancePlus MG FleXible Cartridge for Near-Point-of-Care Testing of <span class="named-content genus-species" id="named-content-1">Mycoplasma genitalium</span> and Associated Macrolide Resistance Mutations
    Letter to the Editor
    Evaluation of the ResistancePlus MG FleXible Cartridge for Near-Point-of-Care Testing of Mycoplasma genitalium and Associated Macrolide Resistance Mutations
    E. L. Sweeney, L. P. Mhango, S. Ebeyan, L. Y. Tan, C. Bletchly, G. R. Nimmo, D. M. Whiley
  • Simple Processing of Formalin-Fixed Paraffin-Embedded Tissue for Accurate Testing with the Xpert MTB/RIF Assay
    Letter to the Editor
    Simple Processing of Formalin-Fixed Paraffin-Embedded Tissue for Accurate Testing with the Xpert MTB/RIF Assay
    Indre Budvytiene, Niaz Banaei

Erratum

  • Free
    Erratum for Gettings et al., “Antibodies to <em>Borrelia turicatae</em> in Experimentally Infected Dogs Cross-React with <em>Borrelia burgdorferi</em> Serologic Assays”
    Erratum
    Erratum for Gettings et al., “Antibodies to Borrelia turicatae in Experimentally Infected Dogs Cross-React with Borrelia burgdorferi Serologic Assays”
    Jenna R. Gettings, Job E. Lopez, Aparna Krishnavajhala, Brittany A. Armstrong, Alec T. Thompson, Michael J. Yabsley

Retraction

  • Free
    Retraction for Kanabagatte Basavarajappa et al., “Glycoprotein-Based Enzyme-Linked Immunosorbent Assays for Serodiagnosis of Infectious Laryngotracheitis”
    Retraction
    Retraction for Kanabagatte Basavarajappa et al., “Glycoprotein-Based Enzyme-Linked Immunosorbent Assays for Serodiagnosis of Infectious Laryngotracheitis”
    Mallikarjuna Kanabagatte Basavarajappa, Haichen Song, Chinta Lamichhane, Siba K. Samal

Masthead

  • Free
    Editorial Board
    Masthead
    Editorial Board
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Journal of Clinical Microbiology: 58 (3)

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volume 58, issue 3
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  • When To Retest: an Examination of Repeat COVID-19 PCR Patterns in an Ambulatory Population
  • Laboratory Diagnosis of COVID-19: Current Issues and Challenges
  • Performance of Abbott ID Now COVID-19 Rapid Nucleic Acid Amplification Test Using Nasopharyngeal Swabs Transported in Viral Transport Media and Dry Nasal Swabs in a New York City Academic Institution
  • Clinical Evaluation of BD Veritor SARS-CoV-2 Point-of-Care Test Performance Compared to PCR-Based Testing and versus the Sofia 2 SARS Antigen Point-of-Care Test
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