The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 Surveillance How concurrent epidemics may introduce bias and decrease the observed SARS-CoV-2 percent positivity

Abstract Background Circulation of seasonal non-SARS-CoV-2 respiratory viruses with syndromic overlap during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Methods Using a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory virus, we assess how an outbreak of secondary virus may affect two COVID-19 surveillance indicators: testing demand and positivity. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can help correct of the observed SARS-CoV-2 percent positivity and improve surveillance quality. Results We find that a non-SARS-CoV-2 epidemic strongly increases SARS-CoV-2 daily testing demand and artificially reduces the observed SARS-CoV-2 percent positivity for the duration of the outbreak. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positivity. Conclusions This study highlights that co-circulating respiratory viruses can distort SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR tests, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.

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The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 surveillance. How concurrent epidemics may decrease true SARS-CoV-2 percent positivity.

10.1101/2021.06.08.21258533 ◽

2021 ◽

Author(s):

Aleksandra Kovacevic ◽

Rosalind M Eggo ◽

Marc Baguelin ◽

Matthieu Domenech de Cellès ◽

Lulla Opatowski

Keyword(s):

Multiplex Pcr ◽

Respiratory Viruses ◽

Surveillance Data ◽

Control Measures ◽

Transmission Model ◽

Time Analysis ◽

Real Time Analysis ◽

Percent Positivity ◽

The Impact

Background: Circulation of non-SARS-CoV-2 respiratory viruses during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Here, we assess the impact of an increased circulation of other respiratory viruses on the monitoring of positivity rates of SARS-CoV-2 and interpretation of surveillance data. Methods: Using a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory we assess how an outbreak of secondary virus may inflate the number of SARS-CoV-2 tests and affect the interpretation of COVID-19 surveillance data. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can support correction of the observed SARS-CoV-2 percent positive during other virus outbreaks and improve surveillance quality. Results: Model simulations demonstrated that a non-SARS-CoV-2 epidemic creates an artificial decrease in the observed percent positivity of SARS-CoV-2, with stronger effect during the growth phase, until the peak is reached. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positive. Conclusions: This study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.

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Optimal number of samples to test for institutional respiratory infection outbreaks in Ontario

Epidemiology and Infection ◽

10.1017/s0950268812002531 ◽

2012 ◽

Vol 141 (8) ◽

pp. 1781-1785 ◽

Cited By ~ 1

Author(s):

A. PECI ◽

A. MARCHAND-AUSTIN ◽

A-J. WINTER ◽

J. B. GUBBAY

Keyword(s):

Multiplex Pcr ◽

Respiratory Infection ◽

Respiratory Virus ◽

Respiratory Viruses ◽

Optimal Number ◽

Chronological Order ◽

Percent Positivity ◽

Outbreak Investigations ◽

Fourth Sample ◽

Minimal Benefit

SUMMARYThe objective of this study was to determine the optimal number of respiratory samples per outbreak to be tested for institutional respiratory outbreaks in Ontario. We reviewed respiratory samples tested for respiratory viruses by multiplex PCR as part of outbreak investigations. We documented outbreaks that were positive for any respiratory viruses and for influenza alone. At least one virus was detected in 1454 (85·2%) outbreaks. The ability to detect influenza or any respiratory virus increased as the number of samples tested increased. When analysed by chronological order of when samples were received at the laboratory, percent positivity of outbreaks testing positive for any respiratory virus including influenza increased with the number of samples tested up to the ninth sample, with minimal benefit beyond the fourth sample tested. Testing up to four respiratory samples per outbreak was sufficient to detect viral organisms and resulted in significant savings for outbreak investigations.

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Understanding contributors to quality of care in long-term care and changes under COVID-19

Innovation in Aging ◽

10.1093/geroni/igaa057.3509 ◽

2020 ◽

Vol 4 (Supplement_1) ◽

pp. 960-960

Author(s):

Sara Luck ◽

Katie Aubrecht

Keyword(s):

Quality Of Care ◽

Long Term Care ◽

The United States ◽

Control Measures ◽

Qualitative Description ◽

Care Staff ◽

Term Care ◽

The Impact

Abstract Nursing home facilities are responsible for providing care for some of the most vulnerable groups in society, including the elderly and those with chronic medical conditions. In times of crisis, such as COVID-19 or other pandemics, the delivery of ‘regular’ care can be significantly impacted. In relation to COVID-19, there is an insufficient supply of personal protective equipment (PPE) to care for residents, as PPE not only protects care staff but also residents. Nursing homes across the United States and Canada have also taken protective measures to maximize the safety of residents by banning visitors, stopping all group activities, and increasing infection control measures. This presentation shares a research protocol and early findings from a study investigating the impact of COVID-19 on quality of care in residential long-term care (LTC) in the Canadian province of New Brunswick. This study used a qualitative description design to explore what contributes to quality of care for residents living in long-term care, and how this could change in times of crisis from the perspective of long-term care staff. Interviews were conducted with a broad range of staff at one LTC home. A semi-structured interview guide and approach to thematic analysis was framed by a social ecological perspective, making it possible to include the individual and proximal social influences as well as community, organizations, and policy influencers. Insights gained will improve the understanding of quality of care, as well as potential barriers and facilitators to care during times of crisis.

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Rapid disappearance of influenza following the implementation of COVID-19 mitigation measures in Hamilton, Ontario

Canada Communicable Disease Report ◽

10.14745/ccdr.v47i04a04 ◽

2021 ◽

Vol 47 (04) ◽

pp. 202-208

Author(s):

Kevin Zhang ◽

Avika Misra ◽

Patrick J Kim ◽

Seyed M Moghadas ◽

Joanne M Langley ◽

...

Keyword(s):

Public Health ◽

Influenza A ◽

Respiratory Virus ◽

Respiratory Viruses ◽

Mitigation Measures ◽

Nasopharyngeal Swab ◽

Health Measures ◽

Bayesian Linear Regression ◽

Syncytial Virus ◽

The Impact

Background: Public health measures, such as physical distancing and closure of schools and non-essential services, were rapidly implemented in Canada to interrupt the spread of the coronavirus disease 2019 (COVID-19). We sought to investigate the impact of mitigation measures during the spring wave of COVID-19 on the incidence of other laboratory-confirmed respiratory viruses in Hamilton, Ontario. Methods: All nasopharyngeal swab specimens (n=57,503) submitted for routine respiratory virus testing at a regional laboratory serving all acute-care hospitals in Hamilton between January 2010 and June 2020 were reviewed. Testing for influenza A and B, respiratory syncytial virus, human metapneumovirus, parainfluenza I–III, adenovirus, and rhinovirus/enterovirus was done routinely using a laboratory-developed polymerase chain reaction multiplex respiratory viral panel. A Bayesian linear regression model was used to determine the trend of positivity rates of all influenza samples for the first 26 weeks of each year from 2010 to 2019. The mean positivity rate of Bayesian inference was compared with the weekly reported positivity rate of influenza samples in 2020. Results: The positivity rate of influenza in 2020 diminished sharply following the population-wide implementation of COVID-19 interventions. Weeks 12–26 reported 0% positivity for influenza, with the exception of 0.1% reported in week 13. Conclusion: Public health measures implemented during the COVID-19 pandemic were associated with a reduced incidence of other respiratory viruses and should be considered to mitigate severe seasonal influenza and other respiratory virus pandemics.

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Modelling control measures to reduce the impact of pandemic influenza among schoolchildren

Epidemiology and Infection ◽

10.1017/s0950268807009284 ◽

2007 ◽

Vol 136 (8) ◽

pp. 1035-1045 ◽

Cited By ~ 32

Author(s):

S.-C. CHEN ◽

C.-M. LIAO

Keyword(s):

Elementary School ◽

Pandemic Influenza ◽

Age Groups ◽

Integrated Approach ◽

Control Measures ◽

Transmission Model ◽

Transmission Potential ◽

Vaccination Coverage Rate ◽

Control Programmes ◽

The Impact

SUMMARYWe coupled the Wells–Riley equation and the susceptible–exposed–infected–recovery (SEIR) model to quantify the impact of the combination of indoor air-based control measures of enhanced ventilation and respiratory masking in containing pandemic influenza within an elementary school. We integrated indoor environmental factors of a real elementary school and aetiological characteristics of influenza to estimate the age-specific risk of infection (P) and basic reproduction number (R0). We combined the enhanced ventilation rates of 0·5, 1, 1·5, and 2/h and respiratory masking with 60%, 70%, 80%, and 95% efficacies, respectively, to predict the reducing level of R0. We also took into account the critical vaccination coverage rate among schoolchildren. Age-specific P and R0 were estimated respectively to be 0·29 and 16·90; 0·56 and 16·11; 0·59 and 12·88; 0·64 and 16·09; and 0·07 and 2·80 for five age groups 4–6, 7–8, 9–10, 11–12, and 25–45 years, indicating pre-schoolchildren have the highest transmission potential. We conclude that our integrated approach, employing the mechanism of transmission of indoor respiratory infection, population-dynamic transmission model, and the impact of infectious control programmes, is a powerful tool for risk profiling prediction of pandemic influenza among schoolchildren.

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From Intended Strategies to Unintended Outcomes: The Impact of Change Recipient Sensemaking

Organization Studies ◽

10.1177/0170840605054624 ◽

2005 ◽

Vol 26 (11) ◽

pp. 1573-1601 ◽

Cited By ~ 321

Author(s):

Julia Balogun ◽

Gerry Johnson

Keyword(s):

Middle Managers ◽

Strategic Change ◽

Social Processes ◽

Unintended Consequences ◽

Planned Change ◽

Change Implementation ◽

Time Analysis ◽

Real Time Analysis ◽

The Social ◽

The Impact

The tendency for intended strategies to lead to unintended consequences is well documented. This longitudinal, real-time analysis of planned change implementation provides an explanation for this phenomenon. We focus on the social processes of interaction between middle managers as change recipients as they try to make sense of the change interventions. We show the extent to which lateral, informal processes of inter-recipient sensemaking contribute to both intended and unintended change outcomes, and therefore the unpredictable, emergent nature of strategic change. The findings raise the issue of the extent to which it is possible to manage evolving recipient interpretations during change implementation.

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Presence of atopy increases the risk of asthma relapse

Archives of Disease in Childhood ◽

10.1136/archdischild-2017-312982 ◽

2017 ◽

Vol 103 (4) ◽

pp. 346-351 ◽

Cited By ~ 4

Author(s):

Laurel Teoh ◽

Ian M Mackay ◽

Peter P Van Asperen ◽

Jason P Acworth ◽

Mark Hurwitz ◽

...

Keyword(s):

Emergency Departments ◽

Acute Asthma ◽

Respiratory Viruses ◽

Prick Test ◽

Asthma Exacerbations ◽

A Prospective Study ◽

Micro Organisms ◽

The Impact ◽

Atypical Bacteria

ObjectivesTo describe the point prevalence of respiratory viruses/atypical bacteria using PCR and evaluate the impact of respiratory viruses/atypical bacteria and atopy on acute severity and clinical recovery in children with hospitalised and non-hospitalised asthma exacerbations.DesignThis was a prospective study performed during 2009–2011.SettingThe study was performed in the emergency departments of two hospitals.Patients244 children aged 2–16 years presenting with acute asthma to the emergency departments were recruited. A nasopharyngeal aspirate and allergen skin prick test were performed.Main outcome measuresThe outcomes were divided into (1) acute severity outcomes (Australian National Asthma Council assessment, hospitalisation, Functional Severity Scale, Acute Asthma Score, asthma quality of life questionnaires for parents (PACQLQ) on presentation, asthma diary scores (ADS) on presentation and length of hospitalisation) and (2) recovery outcomes (PACQLQ for 21 days, ADS for 14 days and representation for asthma for 21 days).ResultsPCR for viruses/atypical bacteria was positive in 81.7% of children (75.1% human rhinovirus, codetection in 14.2%). Mycoplasma pneumoniae and Chlamydophila pneumoniae were rarely detected. The presence of micro-organisms had little impact on acute asthma or recovery outcomes. Children with atopy were significantly more likely to relapse and represent for medical care by day 14 (OR 1.11, 95% CI 1.00 to 1.23).ConclusionsThe presence of any viruses is associated with asthma exacerbations but does not appear to influence asthma recovery. In contrast, atopy is associated with asthma relapse. M. pneumoniae and C. pneumoniae are rare triggers of acute asthma in young children.

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Image Quality Evaluation of Sanda Sports Video Based on BP Neural Network Perception

Computational Intelligence and Neuroscience ◽

10.1155/2021/5904400 ◽

2021 ◽

Vol 2021 ◽

pp. 1-8

Author(s):

Kai Fan ◽

Xiaoye Gu

Keyword(s):

Neural Network ◽

Image Quality ◽

Evaluation Method ◽

Video Image ◽

Time Analysis ◽

Sports Video ◽

Real Time Analysis ◽

Video Images ◽

Motion Video

In the special sports camera, there are subframes. A lens is composed of multiple frames. It will be unclear if a frame is cut out. The definition of video screenshots lies in the quality of video. To get clear screenshots, we need to find clear video. The purpose of this paper is to analyze and evaluate the quality of sports video images. Through the semantic analysis and program design of video using computer language, the video images are matched with the data model constructed by research, and the real-time analysis of sports video images is formed, so as to achieve the real-time analysis effect of sports techniques and tactics. In view of the defects of rough image segmentation and high spatial distortion rate in current sports video image evaluation methods, this paper proposes a sports video image evaluation method based on BP neural network perception. The results show that the optimized algorithm can overcome the slow convergence of weights of traditional algorithm and the oscillation in error convergence of variable step size algorithm. The optimized algorithm will significantly reduce the learning error of neural network and the overall error of network quality classification and greatly improve the accuracy of evaluation. Sanda motion video image quality evaluation method based on BP (back propagation) neural network perception has high spatial accuracy, good noise iteration performance, and low spatial distortion rate, so it can accurately evaluate Sanda motion video image quality.

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Impact of the COVID-19 pandemic on other respiratory virus outbreaks

10.21203/rs.3.rs-110941/v1 ◽

2020 ◽

Author(s):

Sujin Yum ◽

Kwan Hong ◽

Jeehyun Kim ◽

Byung Chul Chun

Keyword(s):

Respiratory Virus ◽

Preventive Measures ◽

Respiratory Viruses ◽

Control Measures ◽

Management Policy ◽

Human Bocavirus ◽

The Past ◽

Positive Rate ◽

The Mean ◽

Syncytial Virus

Abstract The preventive measures to control the coronavirus disease (COVID-19) pandemic could affect other virus outbreaks. However, any changes in their incidence have not been evaluated. This study aimed to determine how the COVID-19 management policy has influenced the positive rates of other respiratory viruses. We collected data from the weekly reports of Korea Influenza and Respiratory Viruses Surveillance System on eight targeted viruses—adenovirus, human bocavirus, human coronavirus, human metapneumovirus, human rhinovirus, influenza virus, parainfluenza virus, and respiratory syncytial virus—from weeks 1 to 18 per year for the past 10 years. We compared the mean of each week in 2020 with the past 10 years using paired t-test. The study period was divided based on the date of the first COVID-19 case in South Korea (before: weeks 1–4; after: weeks 5–18). The overall positive rate of the respiratory viral infection was 38.7% in 2020 and 62.0% in 2010–2019. The positive rates of respiratory viruses with seasonality—hRV, IFV, and PIV—decreased during the COVID-19 pandemic. Although the positive rate of RSV increased significantly in the early weeks, the changes after week 5 were not significant. This phenomenon may be attributed to the strict COVID-19 control measures.

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