The impact of the COVID-19 pandemic on influenza, respiratory syncytial virus, and other seasonal respiratory virus circulation in Canada

BackgroundThe ongoing coronavirus disease 2019 (COVID-19) pandemic has resulted in implementation of public health measures worldwide to mitigate disease spread, including; travel restrictions, lockdowns, messaging on handwashing, use of face coverings and physical distancing. As the pandemic progresses, exceptional decreases in seasonal respiratory viruses are increasingly reported. We aimed to evaluate the impact of the pandemic on circulation of influenza, respiratory syncytial virus and other seasonal respiratory viruses in Canada. MethodsEpidemiologic data were obtained from the Canadian Respiratory Virus Detection Surveillance System. Weekly data from the week ending 30th August 2014 until the week ending the 13th February 2021 were analysed. We compared trends in laboratory detection and test volumes during the 2020/2021 influenza season with baseline pre-pandemic seasons from 2014 to 2019. FindingsWe observed a dramatically lower percentage of tests positive for all seasonal respiratory viruses during 2020-2021 compared to baseline. For influenza A and B the percent positive decreased to 0{middle dot}0017 and 0{middle dot}0061 times that of baseline respectively and for RSV, the percent positive dropped to 0{middle dot}0145 times that of baseline. Ongoing detection of enterovirus/rhinovirus occurred, with regional variation in the epidemic patterns and intensity. InterpretationWe report an effective absence of the annual seasonal epidemic of most seasonal respiratory viruses in 2020/2021. This dramatic decrease is likely related to implementation of multi-layered public health measures during the pandemic. The impact of such measures may have relevance for public health practice in mitigating seasonal respiratory virus epidemics and for informing responses to future respiratory virus pandemics. FundingNo additional funding source was required for this study. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, preprint servers and country-specific public health rapid communications to identify surveillance and epidemiological studies on influenza, respiratory syncytial virus and other seasonal respiratory virus detection during the COVID-19 pandemic. A number of regional and national studies were identified worldwide. The majority of these studies focus on influenza epidemiology and all studies show consistent decreases in circulation of seasonal non-SARS-CoV-2 respiratory viruses. One previous study on the impact of non-pharmaceutical interventions on laboratory detections of influenza A and B in Canada included data for the 2019/2020 influenza season. Another recent study examined the effect of seasonal respiratory virus transmission on COVID-19 syndromic surveillance in the province of Ontario, Canada. No previous Canada-wide study has described the epidemiology of influenza, respiratory syncytial virus and other seasonal respiratory virus detection during the 2020/2021 influenza season. Added value of this studyThe Canadian Respiratory Virus Detection Surveillance System provides weekly respiratory virus detection reports from sentinel laboratories across Canada for influenza, respiratory syncytial virus, parainfluenza viruses, adenovirus, human metapneumovirus, enterovirus/rhinovirus and seasonal coronaviruses. Data have been collected continuously since 2004. Analysis of this dataset provides a comprehensive assessment of the impact of the COVID-19 pandemic on circulation of seasonal respiratory viruses in Canada and analysis of data from the Canadian Public Health Infobase on COVID-19 allowed comparison of SARS-CoV-2 epidemiology. This is the first country-wide study in the Northern hemisphere to describe the concurrent epidemiology of all major seasonal respiratory viruses and SARS-CoV-2 during the 2020/2021 influenza season. Implications of all the available evidenceThe effective absence of the annual seasonal epidemic for most non-SARS-CoV-2 respiratory viruses in 2020/2021 has important public health implications for informing ongoing and future responses to respiratory virus epidemics and pandemics.

Characteristics of SARS-CoV-2 Testing for Rapid Diagnosis of COVID-19 during the Initial Stages of a Global Pandemic

Accurate SARS-CoV-2 diagnosis is essential to guide prevention and control of COVID-19. From January 11 - April 22, 2020, Public Health Ontario conducted SARS-CoV-2 testing of 86,942 specimens collected from 80,354 individuals, primarily using real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods. We analyzed test results across specimen types and for individuals with multiple same-day and multi-day collected specimens. Nasopharyngeal compared to throat swabs had a higher positivity (8.8% vs. 4.8%) and an adjusted estimate 2.9 Ct lower (SE=0.5, p<0.001). Same-day specimens showed high concordance (98.8%), and the median Ct of multi-day specimens increased over time. Symptomatic cases had rRT-PCR results with an adjusted estimate 3.0 Ct (SE=0.5, p<0.001) lower than asymptomatic/pre-symptomatic cases. Overall test sensitivity was 84.6%, with a negative predictive value of 95.5%. Molecular testing is the mainstay of SARS-CoV-2 diagnosis and testing protocols will continue to be dynamic and iteratively modified as more is learned about this emerging pathogen.