Kanti Pabbaraju

Provincial Laboratory of Public Health

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Co-Authors

Sallene Wong

Provincial Laboratory of Public Health

Graham Tipples

University of Alberta

Anita Wong

Calgary Laboratory Services

Raymond Tellier

McGill University

Byron M. Berenger

University of Calgary

Julie D. Fox

Leicester City Council

Kevin Fonseca

Provincial Laboratory of Public Health

Nathan Zelyas

Alberta Hospital Edmonton

Kara Gill

Calgary Laboratory Services

Steven J. Drews

Canadian Blood Services

Cooperative Institutions

Communities In Schools of Orange County

188

New York Proton Center

188

Oregon Medical Research Center

180

Lindsay Unified School District

177

Manhattan Institute for Policy Research

173

University of Pittsburgh

163

University of Alberta

129

University of Calgary

110

Alberta Health Services

Provincial Laboratory of Public Health

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Distribution and Phylogenetic Comparisons of a Novel Mosquito Flavivirus Sequence Present in Culex tarsalis Mosquitoes from Western Canada with Viruses Isolated in California and Colorado

American Journal of Tropical Medicine and Hygiene (2011)

Shaun Tyler Bethany G. Bolling Carol D. Blair Aaron C. Brault Kanti Pabbaraju

In a previous study, a new flavivirus genome sequence was identified in Culex tarsalis mosquitoes obtained in Alberta, Canada and was shown to be genetically related to but distinct from members of the insect-specific flaviviruses. Nonstructural protein 5–encoding sequences amplified from Cx. tarsalis pools from western Canada have shown a high similarity to genome sequences of novel flaviviruses isolated from mosquitoes in California and Colorado. Despite wide distribution of this virus, designated Calbertado virus, strains demonstrate a high degree of nonstructural protein 5 nucleotide (> 90%) and amino acid (> 97%) identity. The ecology and geographic range of Calbertado virus warrants further study because it may potentially influence transmission of mosquito-borne flaviviruses, including important human pathogens such as West Nile and Saint Louis encephalitis viruses.

Flavivirus

Sequence (biology)

10.4269/ajtmh.2011.10-0469

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Citations (43)

Evolving strategy for an evolving virus: Development of real-time PCR assays for detecting all SARS-CoV-2 variants of concern

Journal of Virological Methods (2022)

Kanti Pabbaraju Nathan Zelyas Anita Wong Matthew A. Croxen Tarah Lynch

Duplex (building)

10.1016/j.jviromet.2022.114553

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Citations (10)

Diagnosis and epidemiological studies of human metapneumovirus using real-time PCR

Journal of Clinical Virology (2007)

Kanti Pabbaraju Sallene Wong T. M. McMillan Bonita E. Lee Julie D. Fox

Metapneumovirus

Etiology

10.1016/j.jcv.2007.08.004

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Citations (41)

Comparison of the Hybrid Capture 2 and cobas 4800 Tests for Detection of High-Risk Human Papillomavirus in Specimens Collected in PreservCyt Medium

Journal of Clinical Microbiology (2011)

Anita Wong Jeff Fuller Kanti Pabbaraju Sallene Wong George Zahariadis

ABSTRACT Clinical cervical cytology specimens ( n = 466) collected in PreservCyt (Hologic Inc.) were used to evaluate the agreement between Hybrid Capture 2 (hc2; Qiagen) and cobas 4800 (c4800; Roche Molecular Diagnostics) for the detection of high-risk human papillomavirus (HR HPV) genotype infections. The agreement between the two assays was 93.8% (kappa = 0.87; 95% confidence interval, 0.828 to 0.918), with 186 and 251 concordant positive and negative results, respectively. All 186 concordant positives were confirmed using the Linear Array (LA; Roche Molecular Diagnostics) genotyping test. Of the 29 samples with discordant results (6.2%), 18 were hc2 positive and LA verified 17 as positive for HR HPV. Eleven discordant specimens were c4800 positive, and LA confirmed 5 as positive for HR HPV. As of October 2009, practice guidelines in Alberta, Canada, recommend reflex HPV testing for women over 30 years old with atypical squamous cells of undetermined significance (ASCUS) and for women over 50 years old with low-grade squamous intraepithelial lesions (LSIL) to help prioritize those who should undergo further evaluation. In this study, agreement between hc2 and c4800 results for samples from women over 30 years old with ASCUS cytology was 92.3% ( n = 13), while no samples from women over 50 years old with LSIL cytology were identified for analysis.

Ascus (bryozoa)

Hybrid capture

Kappa

Papillomaviridae

Roche Diagnostics

Squamous intraepithelial lesion

10.1128/jcm.05400-11

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Citations (42)

Development and validation of a multiplex reverse transcriptase-PCR assay for simultaneous testing of influenza A, influenza B and SARS-CoV-2

Journal of Virological Methods (2021)

Kanti Pabbaraju Anita Wong Raymond Ma Nathan Zelyas Graham Tipples

Multiplex

Pandemic

Coronavirus

10.1016/j.jviromet.2021.114151

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Citations (25)

O52 Identification and characterization of West Nile virus genetic variants collected from Canadian samples 2006–2008

International Journal of Antimicrobial Agents (2009)

K Holloway Margaret Fearon Vito Scalia Magdy Dawood Hiroshi Mamiya

West Nile virus

Identification

10.1016/s0924-8579(09)70199-2

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Citations (2)

Detection of influenza C virus by a real‐time RT‐PCR assay

Influenza and Other Respiratory Viruses (2013)

Kanti Pabbaraju Sallene Wong Anita Wong Jennifer May‐Hadford Raymond Tellier

Background Influenza C virus can cause both upper and lower respiratory tract infections and has been reported to be prevalent in children. However, these infections have been under‐diagnosed, and epidemiological data available are limited due to the lack of convenient detection assays. Objective Design and validate a real‐time reverse‐transcriptase PCR (rt RT ‐ PCR ) assay for the detection of influenza C. Study design Respiratory samples from two primary settings, namely, children who were hospitalized or seen in the emergency department, and respiratory outbreaks for which no other viral etiology was found were used for the detection of influenza C. Results and Conclusions The assay was sensitive and specific for the detection of influenza C. Eleven of 474 (2·32%) patients, all less than 10 years of age, were positive for influenza C. The strains clustered into two lineages, namely C/Kanagawa and C/Sao Paulo, based upon sequencing of the hemagglutinin‐esterase gene. Epidemiological data showed that a higher proportion of influenza C infections occur in younger children and during the winter months. This is the first report of the detection of influenza C in Alberta, Canada, and suggests that the detection of this virus should be included in respiratory virus testing panels.

10.1111/irv.12099

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Citations (29)

The need for a sequencing-based assay to supplement the Abbott m2000 RealTime HCV Genotype II assay: A 1 year analysis

Journal of Clinical Virology (2014)

Marlin Benedet Dena Adachi Anita Wong Sallene Wong Kanti Pabbaraju

NS5B

10.1016/j.jcv.2014.04.005

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Citations (34)

Validating and optimizing the method for molecular detection and quantification of SARS-CoV-2 in wastewater

The Science of The Total Environment (2021)

Yuanyuan Qiu Jiaao Yu Kanti Pabbaraju Bonita E. Lee Tiejun Gao

Wastewater surveillance of SARS-CoV-2 has become a promising tool to estimate population-level changes in community infections and the prevalence of COVID-19 disease. Although many studies have reported the detection and quantification of SARS-CoV-2 in wastewater, remarkable variation remains in the methodology. In this study, we validated a molecular testing method by concentrating viruses from wastewater using ultrafiltration and detecting SARS-CoV-2 using one-step RT-qPCR assay. The following parameters were optimized including sample storage condition, wastewater pH, RNA extraction and RT-qPCR assay by quantification of SARS-CoV-2 or spiked human coronavirus strain 229E (hCoV-229E). Wastewater samples stored at 4 °C after collection showed significantly enhanced detection of SARS-CoV-2 with approximately 2–3 PCR-cycle threshold (Ct) values less when compared to samples stored at −20 °C. Pre-adjustment of the wastewater pH to 9.6 to aid virus desorption followed by pH readjustment to neutral after solid removal significantly increased the recovery of spiked hCoV-229E. Of the five commercially available RNA isolation kits evaluated, the MagMAX-96 viral RNA isolation kit showed the best recovery of hCoV-229E (50.1 ± 20.1%). Compared with two-step RT-qPCR, one-step RT-qPCR improved sensitivity for SARS-CoV-2 detection. Salmon DNA was included for monitoring PCR inhibition and pepper mild mottle virus (PMMoV), a fecal indicator indigenous to wastewater, was used to normalize SARS-CoV-2 levels in wastewater. Our method for molecular detection of SARS-CoV-2 in wastewater provides a useful tool for public health surveillance of COVID-19.

Solid phase extraction

10.1016/j.scitotenv.2021.151434

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Citations (44)

O.7.6 Enhanced etiological diagnosis of respiratory virus infections and outbreaks using nucleic acid amplification testing against an expanded range of targets

Journal of Clinical Virology (2008)

Julie D. Fox Sallene Wong V. Khurana Kara L. Tokaryk Kanti Pabbaraju

Etiology

10.1016/s1386-6532(08)70061-1

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Citations (0)