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Article ; Online: Differences in Duration and Degree of Cytomegalovirus DNAemia Observed With Two Standardized Quantitative Nucleic Acid Tests and Implications for Clinical Care.

Meesing, Atibordee / Germer, Jeffrey J / Yao, Joseph D / Gartner, Michelle L / Digmann, Benjamin J / Razonable, Raymund R

The Journal of infectious diseases

2019 Volume 221, Issue 2, Page(s) 251–255

Abstract: Cytomegalovirus (CMV) viral loads overall were 0.29 log IU/mL higher with cobas CMV for use on the cobas 6800/8800 System (cobas CMV) compared with Cobas AmpliPrep/Cobas TaqMan CMV Test (CAP/CTM CMV). Cytomegalovirus DNAemia was detected 11.5 days ... ...

Abstract	Cytomegalovirus (CMV) viral loads overall were 0.29 log IU/mL higher with cobas CMV for use on the cobas 6800/8800 System (cobas CMV) compared with Cobas AmpliPrep/Cobas TaqMan CMV Test (CAP/CTM CMV). Cytomegalovirus DNAemia was detected 11.5 days earlier by cobas CMV, whereas clearance was delayed by 12.8 days. Cytomegalovirus remained detectable by cobas CMV in 44.2% of patients at the time of viral clearance as determined by CAP/CTM CMV. Undetectable viral load by cobas CMV at end of treatment was associated with reduced risk for retreatment (odds ratio, 0.26; 95% confidence interval, 0.04-0.99; P = .05). The use of different quantitative cytomegalovirus nucleic acid tests may affect direct patient care as a result of significant differences in reporting the degree of CMV DNAemia and the time to first detection and clearance of CMV DNAemia.
MeSH term(s)	Cytomegalovirus/genetics ; Cytomegalovirus/isolation & purification ; Cytomegalovirus Infections/diagnosis ; Cytomegalovirus Infections/immunology ; DNA, Viral/blood ; DNA, Viral/genetics ; Female ; Humans ; Male ; Molecular Diagnostic Techniques ; Transplant Recipients ; Viral Load
Chemical Substances	DNA, Viral
Language	English
Publishing date	2019-09-10
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiz452
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Article ; Online: Utility of the Abbott RealTime HCV Genotype Plus RUO assay used in combination with the Abbott RealTime HCV Genotype II assay.

He, Chao / Germer, Jeffrey J / Ptacek, Elizabeth R / Bommersbach, Carl E / Mitchell, P Shawn / Yao, Joseph D C

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

2018 Volume 99-100, Page(s) 97–100

Abstract: Background: Hepatitis virus C (HCV) genotype (GT) determination and subtype (ST) differentiation (1a versus 1b) remain important for the selection of appropriate direct-acting antiviral (DAA) therapy.: Objectives: This study is a retrospective ... ...

Abstract	Background: Hepatitis virus C (HCV) genotype (GT) determination and subtype (ST) differentiation (1a versus 1b) remain important for the selection of appropriate direct-acting antiviral (DAA) therapy. Objectives: This study is a retrospective comparison of HCV GT and ST result distribution when using the Abbott RealTime HCV Genotype II assay (HCVGT II) alone and in combination with the Abbott RealTime HCV Genotype Plus RUO assay (HCVGT Plus) for routine testing of clinical serum specimens at a reference laboratory. Study design: HCVGT II results of specimens tested from June 2014 through January 2016 (period 1) were compared with combined results from HCVGT II and HCVGT Plus (HCVGT II/Plus) performed from January 2016 through January 2017 (period 2). Results: A total of 44,127 and 25,361 specimens were tested during periods 1 and 2, respectively. Use of HCVGT II/Plus significantly reduced the frequency of GT 1 results without ST (0.4%) when compared to preliminary HCVGT II results during period 2 (5.3%; p < 0.01) and final HCVGT II results in period 1 (5.5%; p < 0.01). HCVGT II/Plus also resulted in GT 6 reactivity in 38 specimens with results of "HCV detected" (n = 17) or GT 1 (n = 21) following initial HCVGT II testing during period 2. Conclusions: When compared to the use of HCVGT II alone, HCVGT II/Plus significantly reduced the frequency of GT 1 without ST results observed in a large reference laboratory, while also enabling the identification of HCV GT 6.
MeSH term(s)	5' Untranslated Regions/genetics ; Genotype ; Genotyping Techniques/methods ; Hepacivirus/classification ; Hepacivirus/genetics ; Hepatitis C/diagnosis ; Hepatitis C/virology ; Reagent Kits, Diagnostic ; Real-Time Polymerase Chain Reaction ; Reproducibility of Results ; Retrospective Studies ; Sequence Analysis, DNA ; Serologic Tests ; Viral Core Proteins/genetics ; Viral Load ; Viral Nonstructural Proteins/genetics
Chemical Substances	5' Untranslated Regions ; Reagent Kits, Diagnostic ; Viral Core Proteins ; Viral Nonstructural Proteins ; nucleocapsid protein, Hepatitis C virus ; NS-5 protein, hepatitis C virus (EC 2.7.7.48)
Language	English
Publishing date	2018-01-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2018.01.004
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Article ; Online: HIV-1 subtype diversity among clinical specimens submitted for routine antiviral drug resistance testing in the United States.

Germer, Jeffrey J / Wu, Puqiang / Soderberg, Jason D / Mandrekar, Jayawant N / Yao, Joseph D

Diagnostic microbiology and infectious disease

2015 Volume 83, Issue 3, Page(s) 257–260

Abstract: Diversity of human immunodeficiency virus type 1 (HIV-1) has important implications for the diagnosis, treatment, and management of HIV-1-infected individuals. HIV-1 pol sequences from 3895 clinical plasma specimens collected in the United States over a ... ...

Abstract	Diversity of human immunodeficiency virus type 1 (HIV-1) has important implications for the diagnosis, treatment, and management of HIV-1-infected individuals. HIV-1 pol sequences from 3895 clinical plasma specimens collected in the United States over a 1-year period and submitted for routine HIV-1 genotypic drug resistance testing were retrospectively analyzed for HIV-1 subtype. Of these 3895 HIV-1 sequences, 207 (5.31%) were determined to be non-B subtypes (including recombinant forms). Among individual states, the percentage of non-B subtypes ranged from 0% (12 states) to 28.57% in South Dakota, with 7 states having percentages of >10%. All 4 states with the highest percentages of non-B subtypes were located within the US West North Central region: Minnesota, 11.82%; Iowa, 15.38%; North Dakota, 25.00%; and South Dakota, 28.57%. Reasons for the unexpectedly wide diversity of HIV-1 subtypes present in multiple states located in the West North Central region of the United States remain to be determined.
MeSH term(s)	Drug Resistance, Viral ; Female ; Genotype ; Genotyping Techniques ; HIV Infections/epidemiology ; HIV Infections/virology ; HIV-1/classification ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; Male ; Molecular Epidemiology ; Retrospective Studies ; Sequence Analysis, DNA ; United States/epidemiology ; pol Gene Products, Human Immunodeficiency Virus/genetics
Chemical Substances	pol Gene Products, Human Immunodeficiency Virus
Language	English
Publishing date	2015-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2015.07.014
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Article: Comparison of Standardized Cytomegalovirus (CMV) Viral Load Thresholds in Whole Blood and Plasma of Solid Organ and Hematopoietic Stem Cell Transplant Recipients with CMV Infection and Disease.

Dioverti, M Veronica / Lahr, Brian D / Germer, Jeffrey J / Yao, Joseph D / Gartner, Michelle L / Razonable, Raymund R

Open forum infectious diseases

2017 Volume 4, Issue 3, Page(s) ofx143

Abstract: Background: Quantification of cytomegalovirus (CMV) deoxyribonucleic acid (DNA) has important diagnostic, prognostic, and therapeutic implications in the management of transplant recipients. We aimed to assess a viral load in plasma and whole blood that ...

Abstract	Background: Quantification of cytomegalovirus (CMV) deoxyribonucleic acid (DNA) has important diagnostic, prognostic, and therapeutic implications in the management of transplant recipients. We aimed to assess a viral load in plasma and whole blood that distinguishes CMV disease from asymptomatic infection in a cohort of solid organ and hematopoietic stem cell transplantation. Methods: We prospectively measured and compared CMV viral load in paired plasma and whole blood samples collected from transplant recipients with CMV infection and disease. Cytomegalovirus viral loads were determined by a commercially available US Food and Drug Administration-approved quantitative assay (COBAS AmpliPrep/COBAS TaqMan CMV Test [CAP/CTM CMV]) calibrated to the first World Health Organization International Standard for CMV DNA quantification. Results: Moderate agreement of CMV viral load was observed between plasma and whole blood, with 31% of samples having discordant findings, particularly among samples with low DNA levels. Among the subset of samples where both paired samples had quantifiable levels, we observed a systematic bias that reflected higher viral load in whole blood compared with plasma. Based on receiver operating curve analysis, an initial plasma CMV viral load threshold of 1700 IU/mL in solid organ transplant recipients (sensitivity 80%, specificity 74%) and 1350 IU/mL in allogeneic hematopoietic stem cell transplant recipients (sensitivity 87%, specificity 87%) distinguished CMV disease and asymptomatic infection. Conclusions: This study identifies standardized viral load thresholds that distinguish CMV disease from asymptomatic infection using CAP/CTM CMV assay. We propose these thresholds as potential triggers to be evaluated in prospective studies of preemptive therapy. Plasma was better than whole blood for measuring viral load using the CAP/CTM CMV assay.
Language	English
Publishing date	2017-07-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofx143
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Article ; Online: Hepatitis E Virus (HEV) Detection and Quantification by a Real-Time Reverse Transcription-PCR Assay Calibrated to the World Health Organization Standard for HEV RNA.

Germer, Jeffrey J / Ankoudinova, Irina / Belousov, Yevgeniy S / Mahoney, Walt / Dong, Chen / Meng, Jihong / Mandrekar, Jayawant N / Yao, Joseph D

Journal of clinical microbiology

2017 Volume 55, Issue 5, Page(s) 1478–1487

Abstract: Hepatitis E virus (HEV) has emerged as a cause of chronic hepatitis among immunocompromised patients. Molecular assays have become important tools for the diagnosis and management of these chronically infected patients. A real-time reverse transcription- ... ...

Abstract	Hepatitis E virus (HEV) has emerged as a cause of chronic hepatitis among immunocompromised patients. Molecular assays have become important tools for the diagnosis and management of these chronically infected patients. A real-time reverse transcription-quantitative PCR (RT-qPCR) assay utilizing Pleiades probe chemistry and an RNA internal control for the simultaneous detection and quantification of HEV RNA in human serum was developed based on an adaptation of a previously described and broadly reactive primer set targeting the overlapping open reading frame 2/3 (ORF2/3) nucleotide sequence of HEV. A chimeric bovine viral diarrhea virus construct containing an HEV RNA insert (SynTura HEV) was developed, value assigned with the first World Health Organization (WHO) international standard for HEV RNA (code 6329/10), and used to prepare working assay calibrators and controls, which supported an assay quantification range of 100 to 5,000,000 IU/ml. The analytical sensitivity (95% detection rate) of this assay was 25.2 IU/ml (95% confidence interval [CI], 19.2 to 44.1 IU/ml). The assay successfully amplified 16 different HEV sequences with significant nucleotide mismatching in primer/probe binding regions, while evaluation of a WHO international reference panel for HEV genotypes (code 8578/13) showed viral load results falling within the result ranges generated by WHO collaborative study participants for all panel members (genotypes 1 to 4). Broadly reactive RT-qPCR primers targeting HEV ORF2/3 were successfully adapted for use in an assay based on Pleiades probe chemistry. The availability of secondary standards calibrated to the WHO HEV international standard can improve the standardization and performance of assays for the detection and quantification of HEV RNA.
MeSH term(s)	Hepatitis E/diagnosis ; Hepatitis E/virology ; Hepatitis E virus/genetics ; Hepatitis E virus/isolation & purification ; Humans ; Male ; Middle Aged ; RNA, Viral/blood ; RNA, Viral/genetics ; Real-Time Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Viral Load ; World Health Organization
Chemical Substances	RNA, Viral
Language	English
Publishing date	2017-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.02334-16
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Article ; Online: Cytomegalovirus (CMV) DNA quantification in bronchoalveolar lavage fluid of immunocompromised patients with CMV pneumonia.

Beam, Elena / Germer, Jeffrey J / Lahr, Brian / Yao, Joseph D C / Limper, Andrew Harold / Binnicker, Matthew J / Razonable, Raymund R

Clinical transplantation

2017 Volume 32, Issue 1

Abstract: Cytomegalovirus (CMV) pneumonia causes major morbidity and mortality. Its diagnosis requires demonstration of viral cytopathic changes in tissue, entailing risks of lung biopsy. This study aimed to determine CMV viral load (VL) thresholds in ... ...

Abstract	Cytomegalovirus (CMV) pneumonia causes major morbidity and mortality. Its diagnosis requires demonstration of viral cytopathic changes in tissue, entailing risks of lung biopsy. This study aimed to determine CMV viral load (VL) thresholds in bronchoalveolar lavage fluid (BALF) for diagnosis of CMV pneumonia in immunocompromised patients. CMV VL in BALF was studied in 17 patients (83% transplant recipients) and 21 control subjects with and without CMV pneumonia, respectively, using an FDA-approved PCR assay (Cobas
MeSH term(s)	Adult ; Aged ; Bronchoalveolar Lavage Fluid/virology ; Cytomegalovirus/genetics ; Cytomegalovirus/isolation & purification ; Cytomegalovirus Infections/diagnosis ; Cytomegalovirus Infections/genetics ; Cytomegalovirus Infections/virology ; DNA, Viral/genetics ; Female ; Follow-Up Studies ; Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Immunocompromised Host ; Male ; Middle Aged ; Organ Transplantation/adverse effects ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/genetics ; Pneumonia, Viral/virology ; Prognosis ; Viral Load
Chemical Substances	DNA, Viral
Language	English
Publishing date	2017-12-08
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	639001-8
ISSN	1399-0012 ; 0902-0063
ISSN (online)	1399-0012
ISSN	0902-0063
DOI	10.1111/ctr.13149
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Article ; Online: Evaluation of the Abbott HBV RUO sequencing assay combined with laboratory-modified interpretive software.

Germer, Jeffrey J / Abraham, Priya / Mandrekar, Jayawant N / Yao, Joseph D C

Journal of clinical microbiology

2012 Volume 51, Issue 1, Page(s) 95–100

Abstract: The Abbott HBV RUO Sequencing assay (Abbott Molecular Inc., Des Plaines, IL), which combines automated sample processing, real-time PCR, and bidirectional DNA sequencing, was evaluated for detection of nucleos(t)ide analogue (NA) resistance-associated ... ...

Abstract	The Abbott HBV RUO Sequencing assay (Abbott Molecular Inc., Des Plaines, IL), which combines automated sample processing, real-time PCR, and bidirectional DNA sequencing, was evaluated for detection of nucleos(t)ide analogue (NA) resistance-associated mutations located in the hepatitis B virus (HBV) polymerase (Pol) gene. Interpretive software from the assay manufacturer was modified to allow interrogation of the overlapping HBV surface (S) gene sequence for HBV genotype determination and detection of immune escape mutations. Analytical sensitivity (detection and sequencing) of the assay was determined to be 103.9 IU/ml (95% confidence interval [CI], 80.0 to 173.3) for HBV genotype A. Testing of commercially available HBV genotype panels consisting of 23 individual members yielded complete agreement between expected results and results obtained from the laboratory-developed HBV genotype library. Excellent specificity was observed among clinical specimens with serologic or molecular markers for various unrelated blood-borne viruses (n = 6) and sera obtained from healthy, HBV-negative blood donors (n = 20). Retrospectively selected clinical specimens tested by a commercial reference laboratory HBV sequencing assay (n = 54) or the Trugene HBV Genotyping kit (n = 7) and the Abbott HBV RUO Sequencing assay showed minor differences in detection and reporting of NA resistance-associated mutations in 7 of 61 (11.5%) specimens but complete agreement of genotype results. The Abbott HBV RUO Sequencing assay provided a convenient and efficient assay workflow suitable for routine clinical laboratory use, with the flexibility to be modified for customized detection of NA resistance-associated mutations, HBV genotype determination, and detection of immune escape mutations from a single contiguous HBV sequence.
MeSH term(s)	Automation, Laboratory/methods ; DNA, Viral/chemistry ; DNA, Viral/genetics ; Drug Resistance, Viral ; Hepatitis B/virology ; Hepatitis B virus/drug effects ; Hepatitis B virus/genetics ; Hepatitis B virus/isolation & purification ; Humans ; Molecular Diagnostic Techniques/methods ; Mutation, Missense ; Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; Software ; Virology/methods
Chemical Substances	DNA, Viral
Language	English
Publishing date	2012-10-24
Publishing country	United States
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.02155-12
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Article ; Online: Results of the Abbott RealTime HIV-1 assay for specimens yielding "target not detected" results by the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test.

Babady, N Esther / Germer, Jeffrey J / Yao, Joseph D C

Journal of clinical microbiology

2009 Volume 48, Issue 3, Page(s) 969–971

Abstract: No significantly discordant results were observed between the Abbott RealTime HIV-1 assay and the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test (CTM) among 1,190 unique clinical plasma specimens obtained from laboratories located in 40 states representing all ... ...

Abstract	No significantly discordant results were observed between the Abbott RealTime HIV-1 assay and the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test (CTM) among 1,190 unique clinical plasma specimens obtained from laboratories located in 40 states representing all nine U.S. geographic regions and previously yielding "target not detected" results by CTM.
MeSH term(s)	HIV Infections/diagnosis ; HIV Infections/virology ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; Molecular Diagnostic Techniques/methods ; Sensitivity and Specificity
Language	English
Publishing date	2009-12-30
Publishing country	United States
Document type	Comparative Study ; Evaluation Study ; Journal Article ; Multicenter Study
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.01394-09
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Article: Plasma Load Discrepancies between the Roche Cobas Amplicor Human Immunodeficiency Virus Type 1 (HIV-1) Monitor Version 1.5 and Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 Assays

Yao, Joseph D.C / Germer, Jeffrey J

Journal of clinical microbiology JCM. 2008 Feb., v. 46, no. 2

2008

Language	English
Dates of publication	2008-02
Size	p. 834.
Publishing place	American Society for Microbiology
Document type	Article
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Treatment of acute hepatitis C with interferon alfa-2b.

Patel, Robin / Germer, Jeffrey J

The New England journal of medicine

2002 Volume 346, Issue 14, Page(s) 1091–1092

MeSH term(s)	Acute Disease ; Antiviral Agents/therapeutic use ; Hepacivirus/genetics ; Hepacivirus/isolation & purification ; Hepatitis C/drug therapy ; Hepatitis C, Chronic/prevention & control ; Humans ; Interferon-alpha/therapeutic use ; RNA, Viral/isolation & purification ; Recombinant Proteins
Chemical Substances	Antiviral Agents ; Interferon-alpha ; RNA, Viral ; Recombinant Proteins ; interferon alfa-2b (43K1W2T1M6)
Language	English
Publishing date	2002-04-04
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJM200204043461414
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