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Design and validation of real-time reverse transcription-PCR assays for detection of pandemic (H1N1) 2009 virus.

https://arctichealth.org/en/permalink/ahliterature148750
Source
J Clin Microbiol. 2009 Nov;47(11):3454-60
Publication Type
Article
Date
Nov-2009
Author
Kanti Pabbaraju
Sallene Wong
Anita A Wong
Greg D Appleyard
Linda Chui
Xiao-Li Pang
Stephanie K Yanow
Kevin Fonseca
Bonita E Lee
Julie D Fox
Jutta K Preiksaitis
Author Affiliation
Provincial Laboratory for Public Health (Microbiology), 3030 Hospital Drive, Calgary, Alberta, Canada T2N 4W4. K.Pabbaraju@provlab.ab.ca
Source
J Clin Microbiol. 2009 Nov;47(11):3454-60
Date
Nov-2009
Language
English
Publication Type
Article
Keywords
Alberta
Cross Reactions
Humans
Influenza A Virus, H1N1 Subtype - genetics - isolation & purification
Influenza, Human - diagnosis - virology
RNA, Viral - genetics
Reproducibility of Results
Reverse Transcriptase Polymerase Chain Reaction - methods
Sensitivity and specificity
Sequence Analysis, DNA
Time Factors
Abstract
Tracking novel influenza viruses which have the potential to cause pandemics, such as the pandemic (H1N1) 2009 virus, is a public health priority. Pandemic (H1N1) 2009 virus was first identified in Mexico in April 2009 and spread worldwide over a short period of time. Well-validated diagnostic tools that are rapid, sensitive, and specific for the detection and tracking of this virus are needed. Three real-time reverse transcription PCR (RT-PCR) assays for the amplification and detection of pandemic (H1N1) 2009 virus were developed, and their performance characteristics were compared with those of other published diagnostic assays. Thirty-nine samples confirmed to be positive for pandemic (H1N1) 2009 virus from Alberta, Canada, and six additional samples that were positive for influenza A virus but that were not typeable by using published seasonal influenza H1/H3 virus assays were available for this validation. Amplification and direct sequencing of the products was considered the "gold standard" for case identification. The new assays were sensitive and able to reproducibly detect virus in a 10(-6) dilution of 4 x 10(6) 50% tissue culture infective doses/ml when 5 microl was used as the template. They showed 100% specificity and did not cross-react with other respiratory viruses or seasonal influenza A virus subtypes. The coefficient of variation in crossing cycle threshold values for the detection of different template concentrations of pandemic (H1N1) 2009 virus was
Notes
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PubMed ID
19726603 View in PubMed
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Increased detection of rotavirus using a real time reverse transcription-polymerase chain reaction (RT-PCR) assay in stool specimens from children with diarrhea.

https://arctichealth.org/en/permalink/ahliterature30544
Source
J Med Virol. 2004 Mar;72(3):496-501
Publication Type
Article
Date
Mar-2004
Author
Xiaoli L Pang
Bonita Lee
Nasim Boroumand
Barbara Leblanc
Jutta K Preiksaitis
Charlotte C Yu Ip
Author Affiliation
Provincial Laboratory for Public Health (Microbiology), University Alberta Hospital, Edmonton, Alberta, Canada. x.pang@provlab.ab.ca
Source
J Med Virol. 2004 Mar;72(3):496-501
Date
Mar-2004
Language
English
Publication Type
Article
Keywords
Canada
Child, Preschool
Comparative Study
Diarrhea - virology
Epidemiology, Molecular
Feces - virology
Genes, Viral - genetics
Genotype
Humans
Microscopy, Electron
RNA, Viral - analysis - isolation & purification
Research Support, Non-U.S. Gov't
Reverse Transcriptase Polymerase Chain Reaction
Rotavirus - classification - genetics - isolation & purification
Rotavirus Infections - diagnosis - virology
Sensitivity and specificity
Viral Nonstructural Proteins - genetics
Abstract
Six-hundred and twenty-six stool specimens collected from children with diarrhea over a 12-month period were tested for rotavirus using a real time reverse transcription-polymerase chain reaction (RT-PCR) assay, a conventional nested PCR assay and by electron microscopy (EM). A fragment of 87 bp in a highly-conserved region of non-structural protein 3 (NSP3) in rotavirus genome was amplified by a single-step RT-PCR protocol in a closed-tube system. Rotavirus was detected in 123 samples (20%) with the real time RT-PCR assay, 113 samples (18%) with the nested-PCR assay, and 79 samples (13%) with EM. Using serial diluted nucleic acid extract, we compared the sensitivity of real time RT-PCR with conventional RT-PCR and conventional nested PCR assays. Real time RT-PCR was two to four logs more sensitive than the conventional assays. The reaction time required for the RT-PCR assay is about half the time required for the conventional nested-PCR. The real time RT-PCR assay is both simple and rapid with advantages including enhanced sensitivity and a lower risk for cross-contamination making it a useful tool for the detection of rotavirus in various situations including sporadic gastroenteritis, outbreaks, and environmental investigations. G(1) was the predominant type (89%), followed by G(2) (10%), and G(4) (1%). No rotavirus of G(3), G(8), and G(9) types were found. The peak season for rotavirus infection was January to May in northern Alberta.
PubMed ID
14748075 View in PubMed
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Multiplex real time RT-PCR for the detection and quantitation of norovirus genogroups I and II in patients with acute gastroenteritis.

https://arctichealth.org/en/permalink/ahliterature174671
Source
J Clin Virol. 2005 Jun;33(2):168-71
Publication Type
Article
Date
Jun-2005
Author
Xiaoli L Pang
Jutta K Preiksaitis
Bonita Lee
Author Affiliation
Provincial Laboratory for Public Health (Microbiology), University of Alberta Hospital, WMC 2B2.08, 8440-112 Street, Edmonton, Alta., Canada T6G 2B7. x.pang@provlab.ab.ca
Source
J Clin Virol. 2005 Jun;33(2):168-71
Date
Jun-2005
Language
English
Publication Type
Article
Keywords
Caliciviridae Infections - diagnosis - epidemiology - virology
Canada - epidemiology
Child
Child, Preschool
DNA Primers
Disease Outbreaks
Feces - virology
Gastroenteritis - epidemiology - virology
Humans
Norovirus - classification - genetics - isolation & purification
Reverse Transcriptase Polymerase Chain Reaction - economics - methods
Sensitivity and specificity
Abstract
Conventional reverse transcription-polymerase chain reaction (Con RT-PCR) assay to detect norovirus is a complex multi-step procedure that requires gel electrophoresis as well as hybridization or sequencing to confirm the results.
To develop and evaluate a multiplex real time RT-PCR (Mrt RT-PCR) assay that detect and quantify norovirus GI and GII with a single amplification and detection step.
The primers and TaqMan probes for the Mrt RT-PCR were selected from the ORF1-ORF2 junction region. A total of 97 stools from 41 gastroenteritis outbreaks and 726 stools from children with sporadic diarrhoea were used for this study.
For the 97 outbreak samples, norovirus were detected in 61 of the 69 previously tested positive and 11 of the 28 previously tested negative samples. Eight samples that tested positive for GII by Con RT-PCR but negative by the Mrt RT-PCR also tested negative by a Light Cycler RT-PCR assay. Eighty-two GII and two GI were detected in the 726 sporadic samples. Random primers were more sensitive than specific primers in the cDNA synthesis. The two-step assay using the random primers in RT reaction was 100 times more sensitive than the one-step assay. The Mrt RT-PCR had the same sensitivity as that using two real time RT-PCR for separate detection of GI and GII. A wide dynamic range was obtained with the two-step assay, detecting from 3000 to 3x10(11) of copies RNA/g stool. Very good precision was observed with no cross-reaction with other enteric viruses. The new assay is able to detect both GI and GII in one reaction and brings a cost reduction of approximately 40% compared to separate reactions for GI and GII.
The assay has good precision, sensitivity and specificity and is cost-effective as a routine diagnostic test.
PubMed ID
15911433 View in PubMed
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Nucleic acid testing for west nile virus RNA in plasma enhances rapid diagnosis of acute infection in symptomatic patients.

https://arctichealth.org/en/permalink/ahliterature169754
Source
J Infect Dis. 2006 May 15;193(10):1361-4
Publication Type
Article
Date
May-15-2006
Author
Peter A G Tilley
Julie D Fox
Gayatri C Jayaraman
Jutta K Preiksaitis
Author Affiliation
Provincial Laboratory for Public Health (Microbiology), and Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada. p.tilley@provlab.ab.ca
Source
J Infect Dis. 2006 May 15;193(10):1361-4
Date
May-15-2006
Language
English
Publication Type
Article
Keywords
Acute Disease
Alberta - epidemiology
Diagnostic Tests, Routine
Humans
Immunoglobulin M - immunology
Nucleic Acid Amplification Techniques - standards
Predictive value of tests
RNA, Viral - analysis - blood
Reverse Transcriptase Polymerase Chain Reaction
Sensitivity and specificity
Specimen Handling
Viremia - blood - diagnosis
West Nile Fever - blood - diagnosis - epidemiology
West Nile virus - genetics - immunology - isolation & purification
Abstract
Although nucleic acid amplification testing (NAAT) for West Nile virus (WNV) is useful in screening blood donors, such methods have not been studied in symptomatic patients. For diagnosis of WNV infection, 1.0 mL of plasma was tested by NAAT, and WNV-specific immunoglobulin M was assayed. Of 276 WNV cases, 191 were tested by both serology and NAAT. Of these, 86 (45.0%), 111 (58.1%), and 180 (94.2%) were detected by NAAT, serology, and combined NAAT and serology, respectively. NAAT-based screening was most useful within 8 days of the onset of symptoms. Viremia is common in early symptomatic WNV infection, and NAAT enhances diagnostic yield.
PubMed ID
16619182 View in PubMed
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Rapid HIV tests in acute care settings in an area of low HIV prevalence in Canada.

https://arctichealth.org/en/permalink/ahliterature138212
Source
J Virol Methods. 2011 Mar;172(1-2):66-71
Publication Type
Article
Date
Mar-2011
Author
Bonita E Lee
Sabrina Plitt
Jayne Fenton
Jutta K Preiksaitis
Ameeta E Singh
Author Affiliation
Provincial Laboratory for Public Health, Edmonton, Alberta, Canada.
Source
J Virol Methods. 2011 Mar;172(1-2):66-71
Date
Mar-2011
Language
English
Publication Type
Article
Keywords
Adult
Alberta - epidemiology
Female
HIV Antibodies - blood
HIV Infections - diagnosis - epidemiology
HIV-1
HIV-2
Humans
Immunoassay
Male
Middle Aged
Pilot Projects
Pregnancy
Pregnancy Complications, Infectious - diagnosis
Prevalence
Reagent kits, diagnostic
Sensitivity and specificity
Young Adult
Abstract
Rapid HIV testing has the potential to improve medical care and reduce the transmission of infection. In this study, rapid HIV testing was performed on serum samples in acute care settings in five hospitals from urban and rural regions using the INSTI™ HIV-1/HIV-2 Rapid Antibody Test (bioLytical Laboratories, Richmond, British Columbia). Parallel standard HIV antibody tests were performed at the provincial reference laboratory. Patient demographics, indication for testing and risk behaviours were collected. From April 30, 2007 and November 23, 2009, 1708 individuals were tested: 875 (50.3%) tests in pregnant women, 730 (42%) in source individuals in blood and body fluid exposures and 119 (5.8%) in acutely ill persons. Twenty-five (1.4%) samples were reactive by rapid HIV testing, of which 13 were reactive previously and 1 was a false reactive. Sensitivity of the rapid HIV test compared to standard HIV testing was 100%, specificity was 99.9%, the positive predictive value was 96% and the negative predictive value was 100%. The median time from specimen collection to availability of the rapid HIV result varied by site and ranged from 54 min to 1h 42 min. In this study, the INSTI™ HIV-1 Rapid Antibody test identified reactive and non-reactive samples with similar accuracy to the conventional testing algorithm and provided a reliable way to perform rapid HIV testing in acute care settings.
PubMed ID
21192977 View in PubMed
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Use of quantitative HIV RNA detection for early diagnosis of HIV infection in infants and acute HIV infections in Alberta, Canada.

https://arctichealth.org/en/permalink/ahliterature128897
Source
J Clin Microbiol. 2012 Feb;50(2):502-5
Publication Type
Article
Date
Feb-2012
Author
Bonita E Lee
Sabrina S Plitt
Gayatri C Jayaraman
Linda Chui
Ameeta E Singh
Jutta K Preiksaitis
Author Affiliation
Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada. bonita.lee@albertahealthservices.ca
Source
J Clin Microbiol. 2012 Feb;50(2):502-5
Date
Feb-2012
Language
English
Publication Type
Article
Keywords
Adolescent
Adult
Aged
Aged, 80 and over
Alberta
Child, Preschool
Diagnostic Errors - statistics & numerical data
Early Diagnosis
Female
HIV Infections - diagnosis
Humans
Infant
Infant, Newborn
Male
Middle Aged
RNA, Viral - blood - genetics
Sensitivity and specificity
Viral Load - methods
Young Adult
Abstract
Quantitative HIV RNA viral load (QVL) assays (Roche Diagnostics) were sensitive and specific when used to diagnose HIV infection in (i) HIV-exposed infants (sensitivity of 100% [63.1 to 100%] and specificity of 100% [97.9 to 100%]) and (ii) suspected acute HIV infection patients with a negative/indeterminate Western blot (sensitivity of 97.6% [91.6 to 99.7%] and specificity of 100% [96.1 to 100%]). No false-positive QVL results were identified.
Notes
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PubMed ID
22162550 View in PubMed
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6 records – page 1 of 1.