Model-based evaluation of alternative reactive class closure strategies against COVID-19

There are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, here we develop a data-driven computational model of SARS-CoV-2 transmission to investigate mechanistically the effect on COVID-19 outbreaks of school closure strategies based on syndromic surveillance and antigen screening of students. We found that by reactively closing classes based on syndromic surveillance, SARS-CoV-2 infections are reduced by no more than 13.1% (95%CI: 8.6%-20.2 %), due to the low probability of timely symptomatic case identification among the young population. We thus investigated an alternative triggering mechanism based on repeated screening of students using antigen tests. Should population-level social distancing measures unrelated to schools enable maintaining the reproduction number (R) at 1.3 or lower, an antigen-based screening strategy is estimated to fully prevent COVID-19 outbreaks in the general population. Depending on the contribution of schools to transmission, this strategy can either prevent COVID-19 outbreaks for R up to 1.9 or to at least greatly reduce outbreak size in very conservative scenarios about school contribution to transmission. Moving forward, the adoption of antigen-based screenings in schools could be instrumental to limit COVID-19 burden while vaccines continue to roll out through 2021, especially in light of possible continued emergence of SARS-CoV-2 variants.

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Model-based evaluation of alternative reactive class closure strategies against COVID-19

Nature Communications ◽

10.1038/s41467-021-27939-5 ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

Quan-Hui Liu ◽

Juanjuan Zhang ◽

Cheng Peng ◽

Maria Litvinova ◽

Shudong Huang ◽

...

Keyword(s):

Computational Model ◽

Syndromic Surveillance ◽

School Closure ◽

Data Driven ◽

Young Population ◽

Triggering Mechanism ◽

Model Based ◽

Low Probability ◽

Antigen Tests ◽

Shed Light

AbstractThere are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, we developed a data-driven computational model of SARS-CoV-2 transmission. We found that by reactively closing classes based on syndromic surveillance, SARS-CoV-2 infections are reduced by no more than 17.3% (95%CI: 8.0–26.8%), due to the low probability of timely identification of infections in the young population. We thus investigated an alternative triggering mechanism based on repeated screening of students using antigen tests. Depending on the contribution of schools to transmission, this strategy can greatly reduce COVID-19 burden even when school contribution to transmission and immunity in the population is low. Moving forward, the adoption of antigen-based screenings in schools could be instrumental to limit COVID-19 burden while vaccines continue to be rolled out.

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Safely return to schools and offices: early and frequent screening with high sensitivity antigen tests effectively identifies COVID-19 patients

10.1101/2021.10.08.21264782 ◽

2021 ◽

Author(s):

Yong Dam Jeong ◽

Keisuke Ejima ◽

Kwang Su Kim ◽

Shoya Iwanami ◽

Shingo Iwami ◽

...

Keyword(s):

Infected Individual ◽

High Sensitivity ◽

Population Level ◽

Epidemiological Data ◽

Compartment Model ◽

Screening Strategy ◽

Model Parameters ◽

Economic Activities ◽

Screening Strategies ◽

Antigen Tests

AbstractBackgroundIn-person interaction at school and offices offers invaluable experience to students and benefits to companies. In the midst of the pandemic, ways to safely go back to schools and offices have been argued. Centers for Disease Control and Prevention (CDC) recommends taking all precautions such as vaccination and universal indoor masking. However, even if all the precautions are implemented and transmission is perfectly prevented in the facilities, they may be infected outside of the facilities, which would be a source of transmission in the facilities. Therefore, identifying those infected outside of the facility through screening is essential to safely go back to schools or offices. However, studies investigating the effectiveness of screening are limited. Further, it is not well clarified now which screening strategy (e.g., low or high sensitivity antigen tests, intervals and the number of tests) effectively identify infected and infectious individuals to avoid transmission in facilitiesMethodsWe assessed the effectiveness of various screening strategies in schools and offices through quantitative simulation. The effectiveness was assessed by the proportion of identified infected and infectious participants. Infection dynamics in the facility is governed by transmission dynamics of the population they belong to, and the screening is initiated at different epidemic phases: growth, peak, and declining phases. The viral load trajectory over time for each infected individual was modelled by the viral dynamics model, and the transmission process at the population level was modelled by a deterministic compartment model. The model parameters were estimated from clinical and epidemiological data. Screening strategies were varied by antigen tests with different sensitivity and schedules of screening over 10 days.ResultsUnder the daily screening, we found high sensitivity antigen tests (the detection limit: 6.3 × 104 copies/mL) yielded 88% (95%CI 86-89) of effectiveness by the end of 10 days screening period, which is about 20% higher than that with low sensitivity antigen tests (2.0 × 106 copies/mL). Comparing screening scenarios with different schedules, we found early and frequent screening is the key to maximize the effectiveness. Sensitivity analysis revealed that less frequent tests might be an option when the number of antigen tests is limited especially when the screening is performed at the growth phase.DiscussionHigh sensitivity antigen tests, high frequency screening, and immediate initiation of screening are the key to safely restart educational and economic activities allowing in-person interactions. Our computational framework is useful in assessment of screening strategies by incorporating additional factors for specific situations.

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A Novel Olfactory Self-Test Effectively Screens for COVID-19

10.1101/2021.02.18.21251422 ◽

2021 ◽

Author(s):

kobi snitz ◽

Danielle Honigstein ◽

Reut Weisgross ◽

Aharon Ravia ◽

Eva Mishor ◽

...

Keyword(s):

Population Level ◽

Individual Level ◽

Olfactory Test ◽

Testing Strategies ◽

Olfactory Testing ◽

Wide Scale ◽

Olfactory Impairment ◽

Self Test ◽

Antigen Tests ◽

The Individual

Key to curtailing the COVID-19 pandemic are wide-scale testing strategies 1,2 . An ideal test is one that would not rely on transporting, distributing, and collecting physical specimens. Given the olfactory impairment associated with COVID-19 3-7 , we developed a novel measure of olfactory perception that relies on smelling household odorants and rating them online. We tested the performance of this real-time tool in 12,020 participants from 134 countries who provided 171,500 perceptual ratings of 60 different household odorants. We observed that olfactory ratings were indicative of COVID-19 status in a country, significantly correlating with national infection rates over time. More importantly, we observed remarkable indicative power at the individual level (90% sensitivity and 80% specificity). Critically, olfactory testing remained highly effective in participants with COVID-19 but without symptoms, and in participants with symptoms but without COVID-19. In this, the current odorant-based olfactory test stands apart from symptom-checkers (including olfactory symptom-checkers) 3 , and even from antigen tests 8 , to potentially provide a first line of screening that can help halt disease progression at the population level.

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Revisiting early-stage COVID-19 strategy options

F1000Research ◽

10.12688/f1000research.23524.3 ◽

2021 ◽

Vol 9 ◽

pp. 327

Author(s):

Philip Machanick

Keyword(s):

Early Stage ◽

Asymptomatic Infection ◽

Interesting Case ◽

Precise Analysis ◽

Two Factors ◽

The Difference ◽

Nonpharmaceutical Interventions ◽

Shed Light ◽

Roll Out

Background: Early-stage interventions in a potential pandemic are important to understand as they can make the difference between runaway exponential growth that is hard to turn back and stopping the spread before it gets that far. COVID19 is an interesting case study because there have been very different outcomes in different localities. These variations are best studied after the fact if precision is the goal; while a pandemic is still unfolding less precise analysis is of value in attempting to guide localities to learn lessons of those that preceded them. Methods: I examine two factors that could differentiate strategy: asymptomatic spread and the risks of basing strategy on untested claims, such as potential protective value of the Bacillus Calmette-Guerin (BCG) tuberculosis vaccine. Results: Differences in disease progression as well as the possibility of alternative strategies to prevent COVID-19 from entering the runaway phase or damping it down later can be elucidated by a study of asymptomatic infection. An early study to demonstrate not only what fraction are asymptomatic but how contagious they are would have informed policy on nonpharmaceutical interventions but could still be of value to understand containment during vaccine roll out. Conclusions: When a COVID-19 outbreak is at a level that makes accurate trace-and test possible, investigation of asymptomatic transmission is viable and should be attempted to enhance understanding of spread and variability in the disease as well as policy options for slowing the spread. Understanding mild cases could shed light on the disease in the longer term, including whether vaccines prevent contagiousness.

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Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2

PeerJ ◽

10.7717/peerj.9576 ◽

2020 ◽

Vol 8 ◽

pp. e9576

Author(s):

Arohi Parlikar ◽

Kishan Kalia ◽

Shruti Sinha ◽

Sucheta Patnaik ◽

Neeraj Sharma ◽

...

Keyword(s):

Genomic Diversity ◽

Whole Genome Sequence ◽

The Novel ◽

Origin And Evolution ◽

Pan Genome ◽

Mutational Hotspots ◽

Evolutionary Studies ◽

Low Probability ◽

Shed Light ◽

Country Specific

Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment.

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Trend analysis of tuberculosis case notifications with scale-up of antiretroviral therapy and roll-out of isoniazid preventive therapy in Zimbabwe, 2000–2018

BMJ Open ◽

10.1136/bmjopen-2019-034721 ◽

2020 ◽

Vol 10 (4) ◽

pp. e034721

Author(s):

Kudakwashe C Takarinda ◽

Anthony D Harries ◽

Tsitsi Mutasa-Apollo ◽

Charles Sandy ◽

Regis C Choto ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Scale Up ◽

Population Level ◽

Preventive Therapy ◽

Isoniazid Preventive Therapy ◽

People Living With Hiv ◽

National Data ◽

Tuberculosis Case ◽

Case Notification ◽

Roll Out

ObjectivesAntiretroviral therapy (ART) and isoniazid preventive therapy (IPT) are known to have a tuberculosis (TB) protective effect at the individual level among people living with HIV (PLHIV). In Zimbabwe where TB is driven by HIV infection, we have assessed whether there is a population-level association between IPT and ART scale-up and annual TB case notification rates (CNRs) from 2000 to 2018.DesignEcological study using aggregate national data.SettingAnnual aggregate national data on TB case notification rates (stratified by TB category and type of disease), numbers (and proportions) of PLHIV in ART care and of these, numbers (and proportions) ever commenced on IPT.ResultsART coverage in the public sector increased from <1% (8400 PLHIV) in 2004 to ~88% (>1.1 million PLHIV patients) by December 2018, while IPT coverage among PLHIV in ART care increased from <1% (98 PLHIV) in 2012 to ~33% (373 917 PLHIV) by December 2018. These HIV-related interventions were associated with significant declines in TB CNRs: between the highest CNR prior to national roll-out of ART (in 2004) to the lowest recorded CNR after national IPT roll-out from 2012, these were (1) for all TB case (510 to 173 cases/100 000 population; 66% decline, p<0.001); (2) for those with new TB (501 to 159 cases/100 000 population; 68% decline, p<0.001) and (3) for those with new clinically diagnosed PTB (284 to 63 cases/100 000 population; 77.8% decline, p<0.001).ConclusionsThis study shows the population-level impact of the continued scale-up of ART among PLHIV and the national roll-out of IPT among those in ART care in reducing TB, particularly clinically diagnosed TB which is largely associated with HIV. There are further opportunities for continued mitigation of TB with increasing coverage of ART and in particular IPT which still has a low coverage.

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A difference that matters: comparisons of structured and semi-structured psychiatric diagnostic interviews in the general population

Psychological Medicine ◽

10.1017/s0033291799008880 ◽

1999 ◽

Vol 29 (5) ◽

pp. 1013-1020 ◽

Cited By ~ 77

Author(s):

T. S. BRUGHA ◽

P. E. BEBBINGTON ◽

R. JENKINS

Keyword(s):

General Population ◽

Psychiatric Disorders ◽

Large Scale ◽

Population Level ◽

Individual Level ◽

Case Identification ◽

Diagnostic Interviews ◽

Health Project ◽

The Individual ◽

General Populations

Psychiatric case-identification in general populations allows us to study both individuals with functional psychiatric disorders and the populations from which they come. The individual level of analysis permits disorders to be related to factors of potential aetiological significance and the study of attributes of the disorders that need to be assessed in non-referred populations (an initially scientific endeavour). At the population level valid case identification can be used to evaluate needs for treatment and the utilization of service resources (a public health project). Thus, prevalence is of interest both to scientists and to those responsible for commissioning and planning services (Brugha et al. 1997; Regier et al. 1998). The quality of case identification techniques and of estimates of prevalence is thus of general concern (Bartlett & Coles, 1998).Structured diagnostic interviews were introduced into general population surveys in the 1970s as a method ‘to enable interviewers to obtain psychiatric diagnoses comparable to those a psychiatrist would obtain’ (Robins et al. 1981). The need to develop reliable standardized measures was partly driven by an earlier generation of prevalence surveys showing rates ranging widely from 10·9% (Pasamanick et al. 1956) to 55% (Leighton et al. 1963) in urban and rural North American communities respectively. If the success of large scale psychiatric epidemiological enquiries using structured diagnostic interviews and standardized classifications is measured in terms of citation rates it would seem difficult to question. But the development of standardized interviews of functional psychiatric disorders has not solved this problem of variability: the current generation of large scale surveys, using structured diagnostic interviews and serving strictly defined classification rules, have generated, for example, 12-month prevalence rates of major depression in the US of 4·2% (Robins & Regier, 1991) and 10·1% (Kessler et al. 1994). This calls into question the validity of the assessments, such that we must reopen the question of what they should be measuring and how they should do it.

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Prediabetes: lifestyle, pharmacotherapy or regulation?

Therapeutic Advances in Endocrinology and Metabolism ◽

10.1177/2042018819863020 ◽

2019 ◽

Vol 10 ◽

pp. 204201881986302 ◽

Cited By ~ 2

Author(s):

Jonathan E. Shaw

Keyword(s):

Clinical Trials ◽

Fasting Glucose ◽

Effective Means ◽

Population Level ◽

Lifestyle Interventions ◽

Sugar Sweetened Beverage ◽

Population Prevalence ◽

Clinical Consequences ◽

Roll Out

The rapidly rising number of people with diabetes worldwide has led to multiple attempts to identify effective means of preventing type 2 diabetes. Lifestyle interventions have shown impressive efficacy in multiple clinical trials of people with impaired glucose tolerance, but, as currently formulated, appear to have very little impact on impaired fasting glucose. Attempts to roll out lifestyle interventions beyond clinical trials have generally recruited too few people to have a chance of influencing the population prevalence of diabetes. Several drugs have also been shown to reduce the incidence of diabetes, but until such drugs can be shown to prevent the clinical consequences of diabetes, it is unlikely that guidelines will recommend their widespread use for diabetes prevention. Population-level interventions, including education and regulation, are attractive, as they have the potential to influence a high proportion of the population. Favourable effects of a sugar sweetened beverage tax on consumption are encouraging, but data on its influence on diabetes are not yet available.

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Southern sustainability initiatives in agricultural value chains: a question of enhanced inclusiveness? The case of Trustea in India

Agriculture and Human Values ◽

10.1007/s10460-020-10151-4 ◽

2020 ◽

Author(s):

Verena Bitzer ◽

Alessia Marazzi

Keyword(s):

Theoretical Perspective ◽

Value Chains ◽

Small Scale ◽

Decision Making Processes ◽

Tea Production ◽

Sustainability Initiatives ◽

Multi Stakeholder ◽

Indian Tea ◽

Shed Light ◽

Roll Out

Abstract Recent studies have shed light on the emergence of Southern sustainability initiatives in commodity-based value chains. These initiatives position themselves as countering the exclusionary nature of many global multi-stakeholder initiatives (MSIs), as critically analysed by previous studies. However, a common theoretical perspective on the inclusiveness of MSIs is still lacking. By drawing on the theory of regimes of engagement, we develop a theoretical framework which helps understanding the overt and subtle practices of including or excluding different stakeholders in MSIs. We apply this framework to ‘Trustea’, an Indian MSI for sustainable tea production, to further investigate the ‘inclusiveness paradigm’ of Southern sustainability initiatives. Our findings highlight the complexity of stakeholder engagement across the different phases of Trustea’s development, from initiation and code development to formal launch and roll-out. We find that different types of engagement can exist in parallel. Justifiable engagement is expressed in the participating organisations’ reference to a shared common goal of Trustea, whereas familiar engagement is linked to the rootedness of the individuals involved in the Indian tea industry. Strategic engagement, in turn, comes to the fore through the strong emphasis on developing an Indian code for sustainable tea production and promoting adoption among tea growers. The importance of reaching this objective has led to the replication of exclusionary patterns also noted for global MSIs, as small-scale producers and other weak actors have been largely excluded from decision-making processes, despite informal efforts aimed at substitution of representation.

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