Dataset Information

Single vs replicate Real-Time PCR SARS-CoV-2 testing: Lessons learned for effective pandemic management.

ABSTRACT: Coronavirus Disease 19 (COVID-19) caused by the SARS-CoV-2 virus remains a global pandemic having a serious impact on national economies and healthcare infrastructure. Accurate infection detection protocols are key to policy guidance and decision making. In this pilot study, we compared single versus replicate PCR testing for effective and accurate SARS-CoV-2 infection detection. One-Step Real-Time RT-PCR was employed for the detection of SARS-CoV-2 RNA isolated from individual nasopharyngeal swabs. A total of 10,014 swabs, sampled from the general public (hospital admissions, A&E, elective surgeries, cancer patients, care home residents and healthcare staff), were tested using standard replicate testing. Our analysis demonstrates that approximately 19% of SARS-CoV-2 infected individuals would have been reported as false negative if single sample Real-Time PCR testing was used. Therefore, two replicate tests can substantially decrease the risk of false negative reporting and reduce hospital and community infection rates. As the number of variants of concern increases, we believe that replicate testing is an essential consideration for effective SARS-CoV-2 infection detection and prevention of further outbreaks. A strategic approach limiting the number of missed infections is crucial in controlling the rise of new SARS-CoV-2 variants as well as the management of future pandemics.

SUBMITTER: Webb WR

PROVIDER: S-EPMC9282535 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Single vs replicate Real-Time PCR SARS-CoV-2 testing: Lessons learned for effective pandemic management.

Webb William R WR Thapa Gauri G Tirnoveanu Alice A Kallu Sabrina S Loo Jin Yi Charlene C Shah Nirali N Macari Joseph J Mitchell Sadie S Fagg Graham J GJ Jeremiah Rachael N RN Theminimulle Sandiya S Vuono Romina R Mylona Athina A

PloS one 20220714 7

Coronavirus Disease 19 (COVID-19) caused by the SARS-CoV-2 virus remains a global pandemic having a serious impact on national economies and healthcare infrastructure. Accurate infection detection protocols are key to policy guidance and decision making. In this pilot study, we compared single versus replicate PCR testing for effective and accurate SARS-CoV-2 infection detection. One-Step Real-Time RT-PCR was employed for the detection of SARS-CoV-2 RNA isolated from individual nasopharyngeal sw ...[more]

PMID: 35834476

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Project description:2018 marks the 100-year anniversary of the 1918 influenza pandemic, which killed ~50 million people worldwide. The severity of this pandemic resulted from a complex interplay between viral, host, and societal factors. Here, we review the viral, genetic and immune factors that contributed to the severity of the 1918 pandemic and discuss the implications for modern pandemic preparedness. We address unresolved questions of why the 1918 influenza H1N1 virus was more virulent than other influenza pandemics and why some people survived the 1918 pandemic and others succumbed to the infection. While current studies suggest that viral factors such as haemagglutinin and polymerase gene segments most likely contributed to a potent, dysregulated pro-inflammatory cytokine storm in victims of the pandemic, a shift in case-fatality for the 1918 pandemic toward young adults was most likely associated with the host's immune status. Lack of pre-existing virus-specific and/or cross-reactive antibodies and cellular immunity in children and young adults likely contributed to the high attack rate and rapid spread of the 1918 H1N1 virus. In contrast, lower mortality rate in in the older (>30 years) adult population points toward the beneficial effects of pre-existing cross-reactive immunity. In addition to the role of humoral and cellular immunity, there is a growing body of evidence to suggest that individual genetic differences, especially involving single-nucleotide polymorphisms (SNPs), contribute to differences in the severity of influenza virus infections. Co-infections with bacterial pathogens, and possibly measles and malaria, co-morbidities, malnutrition or obesity are also known to affect the severity of influenza disease, and likely influenced 1918 H1N1 disease severity and outcomes. Additionally, we also discuss the new challenges, such as changing population demographics, antibiotic resistance and climate change, which we will face in the context of any future influenza virus pandemic. In the last decade there has been a dramatic increase in the number of severe influenza virus strains entering the human population from animal reservoirs (including highly pathogenic H7N9 and H5N1 viruses). An understanding of past influenza virus pandemics and the lessons that we have learnt from them has therefore never been more pertinent.

Project description:BackgroundDuring the Coronavirus disease (COVID-19) pandemic, countries implemented border control and quarantine measures to reduce transmission. The Alberta Border Testing Pilot Program (ABTPP) allowed international travellers entering Alberta to reduce their quarantine period following two negative COVID-19 tests. We evaluated participant experiences with the ABTPP and implementation.MethodWe used a parallel convergent mixed-methods design to explore participant experiences through electronic web-based questionnaires (n = 21,089; n = 13,839) and semi-structured telephone interviews (n = 30). We evaluated implementation through three staff focus groups (n = 11). We analysed questionnaires using descriptive statistics and analysed interviews using inductive and deductive thematic analysis. We deductively coded focus group data using the 2009 Consolidated Framework for Implementation Research (CFIR).ResultsQuestionnaires indicated minimal issues with registration forms (91.7%), symptom reports (95.5%), and COVID-19 testing (95.7%). Most respondents (95.1%) expressed willingness to participate in the ABTPP again. Interviews revealed three themes related to participant experience: program efficiency, clarity of information, and requisite effort. Focus groups identified key implementation facilitators including the single health information system, strong stakeholder partnerships, and good communication across partnerships. Barriers included program complexity, implementation timeline, and evolving external context.DiscussionParticipants reported high satisfaction with the ABTPP. Border testing programs should have high efficiency, require low effort, and use messaging that is clear and consistent. The effective implementation of border testing programs may be facilitated by strong leadership, adaptability, automated components, good communication, and simple technology. Learnings from participants and staff may help improve the implementation of border control programs for future pandemics or other emergencies.ConclusionsThe ABTTP was a novel border control measure during the COVID-19 pandemic. Our evaluation of both participant and staff experiences demonstrated high levels of traveller satisfaction and identified areas for improvement that can inform the development of future border control measures.

Dataset Information

Single vs replicate Real-Time PCR SARS-CoV-2 testing: Lessons learned for effective pandemic management.

Publications

Single vs replicate Real-Time PCR SARS-CoV-2 testing: Lessons learned for effective pandemic management.

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