Estimating COVID Risk During a Period of Pandemic Decline

Background: Many parts of the world that succeeded in suppressing epidemic coronavirus spread in 2020 have been caught out by recent changes in the transmission dynamics of SARS-CoV-2. Australia's early success in suppressing COVID-19 resulted in lengthy periods without community transmission. However, a slow vaccine rollout leaves this geographically isolated population vulnerable to leakage of new variants from quarantine, which requires internal travel restrictions, disruptive lockdowns, contact tracing and testing surges.Methods: To assist long term sustainment of limited public health resources, we sought a method of continuous, real-time COVID-19 risk monitoring that could be used to alert non-specialists to the level of epidemic risk on a sub-national scale. After an exploratory data assessment, we selected four COVID-19 metrics used by public health in their periodic threat assessments, applied a business continuity matrix and derived a numeric indicator; the COVID-19 Risk Estimate (CRE), to generate a daily spot CRE, a 3 day net rise and a seven day rolling average. We used open source data updated daily from all Australian states and territories to monitor the CRE for over a year.Results: Upper and lower CRE thresholds were established for the CRE seven day rolling average, corresponding to risk of sustained and potential outbreak propagation, respectively. These CRE thresholds were used in a real-time map of Australian COVID-19 risk estimate distribution by state and territory.Conclusions: The CRE toolkit we developed complements other COVID-19 risk management techniques and provides an early indication of emerging threats to business continuity.

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Likely community transmission of COVID-19 infections between neighboring, persistent hotspots in Ontario, Canada

F1000Research ◽

10.12688/f1000research.75891.1 ◽

2021 ◽

Vol 10 ◽

pp. 1312

Author(s):

Eliseos J. Mucaki ◽

Ben C. Shirley ◽

Peter K. Rogan

Keyword(s):

Public Health ◽

Real Time ◽

Disease Transmission ◽

Time Integration ◽

Community Level ◽

Moran’S I ◽

Contact Tracing ◽

Term Care ◽

Moran's I ◽

Community Transmission

Introduction: This study aimed to produce community-level geo-spatial mapping of confirmed COVID-19 cases in Ontario Canada in near real-time to support decision-making. This was accomplished by area-to-area geostatistical analysis, space-time integration, and spatial interpolation of COVID-19 positive individuals. Methods: COVID-19 cases and locations were curated for geostatistical analyses from March 2020 through June 2021, corresponding to the first, second, and third waves of infections. Daily cases were aggregated according to designated forward sortation area (FSA), and postal codes (PC) in municipal regions Hamilton, Kitchener/Waterloo, London, Ottawa, Toronto, and Windsor/Essex county. Hotspots were identified with area-to-area tests including Getis-Ord Gi*, Global Moran’s I spatial autocorrelation, and Local Moran’s I asymmetric clustering and outlier analyses. Case counts were also interpolated across geographic regions by Empirical Bayesian Kriging, which localizes high concentrations of COVID-19 positive tests, independent of FSA or PC boundaries. The Geostatistical Disease Epidemiology Toolbox, which is freely-available software, automates the identification of these regions and produces digital maps for public health professionals to assist in pandemic management of contact tracing and distribution of other resources. Results: This study provided indicators in real-time of likely, community-level disease transmission through innovative geospatial analyses of COVID-19 incidence data. Municipal and provincial results were validated by comparisons with known outbreaks at long-term care and other high density residences and on farms. PC-level analyses revealed hotspots at higher geospatial resolution than public reports of FSAs, and often sooner. Results of different tests and kriging were compared to determine consistency among hotspot assignments. Concurrent or consecutive hotspots in close proximity suggested potential community transmission of COVID-19 from cluster and outlier analysis of neighboring PCs and by kriging. Results were also stratified by population based-categories (sex, age, and presence/absence of comorbidities). Conclusions: Earlier recognition of hotspots could reduce public health burdens of COVID-19 and expedite contact tracing.

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Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence

10.1101/2020.06.08.20124834 ◽

2020 ◽

Cited By ~ 7

Author(s):

Ana da Silva Filipe ◽

James Shepherd ◽

Thomas Williams ◽

Joseph Hughes ◽

Elihu Aranday-Cortes ◽

...

Keyword(s):

Real Time ◽

Hospital Admissions ◽

International Travel ◽

European Countries ◽

Added Value ◽

Contact Tracing ◽

Genomic Epidemiology ◽

First Case ◽

Travel Restrictions ◽

Community Transmission

AbstractSARS-CoV-2, the causative agent of COVID-19, emerged in Wuhan, China in December 2019 and spread rapidly throughout the world. Understanding the introductions of this new coronavirus in different settings may assist control efforts and the establishment of frameworks to support rapid response in future infectious disease outbreaks.We investigated the first four weeks of emergence of the SARS-CoV-2 virus in Scotland after the first case reported on the 1st March 2020. We obtained full genome sequences from 452 individuals with a laboratory-confirmed diagnosis of COVID-19, representing 20% of all cases until 1st April 2020 (n=2310). This permitted a genomic epidemiology approach to study the introductions and spread of the SARS-2 virus in Scotland.From combined phylogenetic and epidemiological analysis, we estimated at least 113 introductions of SARS-CoV-2 into Scotland during this period. Clusters containing multiple sequences suggestive of onward transmission occurred in 48/86 (56%). 42/86 (51%) clusters had no known international travel history indicating undetected introductions.The majority of viral sequences were most closely related to those circulating in other European countries, including Italy, Austria and Spain. Travel-associated introductions of SARS-CoV-2 into Scotland predated travel restrictions in the UK and other European countries. The first local transmission occurred three days after the first case. A shift from travel-associated to sustained community transmission was apparent after only 11 days. Undetected introductions occurred prior to the first known case of COVID-19. Earlier travel restrictions and quarantine measures might have resulted in fewer introductions into Scotland, thereby reducing the number of cases and the subsequent burden on health services. The high number of introductions and transmission rates were likely to have impacted on national contact tracing efforts. Our results also demonstrate that local real-time genomic epidemiology can be used to monitor transmission clusters and facilitate control efforts to restrict the spread of COVID-19.FundingMRC (MC UU 1201412), UKRI/Wellcome (COG-UK), Wellcome Trust Collaborator Award (206298/Z/17/Z – ARTIC Network; TCW Wellcome Trust Award 204802/Z/16/ZResearch in contextEvidence before this studyCoronavirus disease-2019 (COVID-19) was first diagnosed in Scotland on the 1st of March 2020 following the emergence of the causative severe acute respiratory system coronavirus 2 (SARS-CoV-2) virus in China in December 2019. During the first month of the outbreak in Scotland, 2310 positive cases of COVID-19 were detected, associated with 1832 hospital admissions, 207 intensive care admissions and 126 deaths. The number of introductions into Scotland and the source of those introductions was not known prior to this study.Added value of this studyUsing a combined phylogenetic and epidemiological approach following real-time next generation sequencing of 452 SARS-CoV-2 samples, it was estimated that the virus was introduced to Scotland on at least 113 occasions, mostly from other European countries, including Italy, Austria and Spain. Localised outbreaks occurred in the community across multiple Scottish health boards, within healthcare facilities and an international conference and community transmission was established rapidly, before local and international lockdown measures were introduced.

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Likely community transmission of COVID-19 infections between neighboring, persistent hotspots in Ontario, Canada

10.1101/2021.12.06.21267360 ◽

2021 ◽

Author(s):

Eliseos J. Mucaki ◽

Ben C. Shirley ◽

Peter K. Rogan

Keyword(s):

Public Health ◽

Real Time ◽

Disease Transmission ◽

Time Integration ◽

Community Level ◽

Moran’S I ◽

Contact Tracing ◽

Term Care ◽

Moran's I ◽

Community Transmission

AbstractIntroductionThis study aimed to produce community-level geo-spatial mapping of confirmed COVID-19 cases in Ontario, Canada in near real-time to support decision-making. This was accomplished by area-to-area geostatistical analysis, space-time integration, and spatial interpolation of COVID-19 positive individuals.MethodsCOVID-19 cases and locations were curated for geostatistical analyses from March 2020 through June 2021, corresponding to the first, second, and third waves of infections. Daily cases were aggregated according to designated forward sortation area [FSA], and postal codes [PC] in municipal regions covering Hamilton, Kitchener/Waterloo, London, Ottawa, Toronto, and Windsor/Essex county. Hotspots were identified with area-to-area tests including Getis-Ord Gi*, Global Moran’s I spatial autocorrelation, and Local Moran’s I asymmetric clustering and outlier analyses. Case counts were also interpolated across geographic regions by Empirical Bayesian Kriging, which localizes high concentrations of COVID-19 positive tests, independent of FSA or PC boundaries. The Geostatistical Disease Epidemiology Toolbox, which is freely-available software, automates the identification of these regions and produces digital maps for public health professionals to assist in pandemic management of contact tracing and distribution of other resources.Results/DiscussionThis study provided indicators in real-time of likely, community-level disease transmission through innovative geospatial analyses of COVID-19 incidence data. Municipal and provincial results were validated by comparisons with known outbreaks at long-term care and other high density residences and on farms. PC-level analyses revealed hotspots at higher geospatial resolution than public reports of FSAs, and often sooner. Results of different tests and kriging were compared to determine consistency among hotspot assignments. Concurrent or consecutive hotspots in close proximity suggested potential community transmission of COVID-19 from cluster and outlier analysis of neighboring PCs and by kriging. Results were also stratified by population based-categories (sex, age, and presence/absence of comorbidities). Earlier recognition of hotspots could reduce public health burdens of COVID-19 and expedite contact tracing.

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COVID-19 crisis risks deeper European rifts on privacy

Emerald Expert Briefings ◽

10.1108/oxan-db252185 ◽

2020 ◽

Keyword(s):

Public Health ◽

Public Participation ◽

Contact Tracing ◽

Health Crisis ◽

Content Type ◽

Public Health Crisis ◽

Travel Restrictions ◽

Digital Strategy ◽

Mass Surveillance ◽

The Eu

Subject New privacy guidelines. Significance The EU wants contact tracing apps for tackling COVID-19 to be effective, secure and privacy-compliant. Its efforts have exposed how its existing rules on data are adapting (or not) to the extraordinary public health crisis. Impacts Fear of mass surveillance and data breaches will reduce public participation in tracer apps, casting doubts over their effectiveness. The EU’s digital strategy, notably in terms of reviewing the effectiveness of GDPR, may be rethought in response to the COVID-19 crisis. If tracer apps are not inter-operable across national borders, lifting intra-EU travel restrictions will become harder.

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Impact of public health interventions on the COVID-19 epidemic: a stochastic model based on data from an African island

10.1101/2020.06.22.20134130 ◽

2020 ◽

Author(s):

D. C. Nuckchady

Keyword(s):

Stochastic Model ◽

Population Surveillance ◽

Health Interventions ◽

Contact Tracing ◽

Point Of Entry ◽

Highly Sensitive ◽

Travel Restrictions ◽

Community Transmission ◽

The Impact ◽

Key Interventions

AbstractA stochastic model was created to simulate the impact of various healthcare measures on the COVID-19 epidemic. Travel restrictions and point of entry or exit screening help to delay the onset of the outbreak by a few weeks. Population surveillance is critical to detect the start of community transmission early and to avoid a surge in cases. Contact reduction and contact tracing are key interventions that can help to control the outbreak. To promptly curb the number of new cases, countries should diagnose patients using a highly sensitive test.

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Containing SARS-CoV-2 in Belize

Caribbean Medical Journal ◽

10.48107/cmj.2020.08.002 ◽

2020 ◽

Author(s):

Kyle Habet ◽

Diomne Habet ◽

Gliselle Marin

Keyword(s):

Public Health ◽

Early Intervention ◽

Population Density ◽

Central America ◽

National Level ◽

Contact Tracing ◽

Limited Resources ◽

Global Pandemic ◽

Caribbean Country ◽

Community Transmission

Belize is a small Caribbean country in Central America with limited resources in public health. Amidst a global pandemic, urgent attention was given to mitigating the spread of SARS-CoV-2 (COVID-19) in order to prevent a public health catastrophe. Early intervention on a national level was key to preventing the importation of cases and subsequent community transmission. Limiting the conglomeration of people, implementation of curfews, closures of school and universities, government-mandated social distancing, and extensive contact tracing may have mitigated the exponential spread of COVID-19. Mandatory mask-wearing in public may have helped to prevent spread between asymptomatic carriers to susceptible individuals. A low population density may have also contributed to containing the virus.

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Impact of lockdown measures in abating the COVID-19 pandemic: Lessons from India’s phased approach

European Journal of Public Health ◽

10.1093/eurpub/ckaa165.430 ◽

2020 ◽

Vol 30 (Supplement_5) ◽

Author(s):

R Singh ◽

K Sharma

Keyword(s):

Public Health ◽

World Health ◽

The Public ◽

Daily Data ◽

Travel Restrictions ◽

Community Transmission ◽

The Government ◽

Novel Coronavirus ◽

Health Organization ◽

The Impact

Abstract Background World Health Organization (WHO) declared that the outbreak of novel coronavirus (2019-nCoV) constituted a Public Health Emergency of International Concern (PHEIC) on 30 January 2020 and characterized the novel coronavirus disease (COVID-19) as a pandemic on 11 March 2020. India enacted such measures early on for effective mitigation and suppression to reduce community transmission, including an onerous national lockdown. The impact of the health system governance is quite apparent among all stakeholders including the public in such emergency contexts. Methods We compiled the daily data on the number of COVID-19 cases, recoveries and deaths from January 30th until June 16th, 2020. Different stages were categorized from post PHEIC declaration (pre-lockdown) phase to lockdown phases and unlocking phase as implemented. The several measures adopted by the national government were structured in four broad categories as Governance and socioeconomic, travel restrictions, lockdown and public health measures. These measures were compared during each phase. Results It was revealed that while the cases are rising the phased restrictions has helped in delaying the peak and remarkably interrupted the rate of transmission. The national average doubling rate was 3 days at the beginning which improved to 22 days. The basic reproduction number remained close to 1 during the last week of lockdown. However, the initial interruption of needed aid and technical support had negative social and economic impacts on the affected population. Conclusions As the situation abates following the measures adopted by the government, an articulate strategy of unlocking through increased testing and prompt isolation needs to be developed for more effective reduction and protecting the livelihoods allowing to further relax the lockdown measures. Key messages There is need for the local government to consider a strategic easing of the lockdown for protecting the rights of the most affected population. As the transmission rates are low, the easing of lockdown can be benefited from improved testing and prompt isolation.

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The Ontario Universal Typing of Tuberculosis (OUT-TB) Surveillance Program – What It Means to You

Canadian Respiratory Journal ◽

10.1155/2010/715202 ◽

2010 ◽

Vol 17 (3) ◽

pp. e51-e54 ◽

Cited By ~ 4

Author(s):

Shelly Bolotin ◽

David C Alexander ◽

Jennifer L Guthrie ◽

Steven J Drews ◽

Frances Jamieson

Keyword(s):

Public Health ◽

Disease Control ◽

Variable Number Tandem Repeat ◽

Health Resources ◽

Molecular Methods ◽

Contact Tracing ◽

Surveillance Program ◽

Polymorphism Analysis ◽

Outbreak Management ◽

Investigation Methods

BACKGROUND: Tuberculosis (TB) is a serious disease that is transmitted primarily by the airborne route. Effective disease control and outbreak management requires the timely diagnosis, isolation and treatment of infected individuals with active disease; contact tracing to identify secondary cases likely to benefit from treatment of latent infection; and laboratory identification or confirmation of epidemiologically linked cases. TB genotyping enables the comparison ofMycobacterium tuberculosiscomplex (MTBC) strains and the identification of cases that may or may not be linked. The increased availability of molecular methods for genotyping has allowed for greater discrimination of MTBC strains and greatly enhanced understanding of TB transmission patterns.OBJECTIVE: To improve TB surveillance and control in Ontario, the Public Health Laboratories of the Ontario Agency for Health Protection and Promotion has introduced the Ontario Universal Typing of Tuberculosis (OUT-TB) Surveillance Program.METHODS: The first isolate from every new TB case will be genotyped with two rapid molecular methods: spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat typing. MTBC isolates with nonunique genotypes and, thus, potentially linked to other TB cases, will also be genotyped by IS6110restriction fragment length polymorphism analysis.CONCLUSION: By providing TB control programs using these new genotyping tools, and using traditional and new case investigation methods (eg, social network analysis), this new program will provide a clearer picture of TB in Ontario, and permit more effective use of public health resources and improve disease control.

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A Model Based Analysis for COVID-19 Pandemic in India: Implications for Health Systems and Policy for Low- and Middle-Income Countries

10.1101/2020.06.11.20128231 ◽

2020 ◽

Author(s):

Shankar Prinja ◽

Pankaj Bahuguna ◽

Yashika Chugh ◽

Anna Vassall ◽

Arvind Pandey ◽

...

Keyword(s):

Public Health ◽

Health System ◽

Air Travel ◽

Contact Tracing ◽

System Response ◽

Middle Income ◽

Middle Income Countries ◽

Health Measures ◽

Travel Restrictions ◽

The Impact

AbstractBackgroundOur analysis aims to model COVID-19 pandemic in India, potential impact of various measures, along with assessment of health system preparedness and cost to manage the epidemic.MethodsWe developed a susceptible-exposed-infectious-recovered (SEIR) mathematical model to predict the health outcomes under an unmitigated scenario which comprises of air travel restrictions alone, and the current scenario consisting of air travel restrictions along with 8-week lockdown. In addition, we also evaluate the effectiveness of 8-week lockdown along with intensified public health measures at varying level of effectiveness. We assessed the impact of these interventions on COVID-19 related health outcomes in comparison to the unmitigated scenario. Next, we ascertain the need for augmenting infrastructure and the costs of COVID-19 management in India.FindingsIn the event of a lockdown for 8 weeks, the peak of the epidemic shifts by 34-76 days, and the number of cases at the end of 8-week lockdown reduces by 69% to 97% with varying effectiveness of lockdown. However, the cumulative long-term cases remain the same. Intensification of public health surveillance measures with 60% effectiveness is estimated to reduce the cases at peak and cumulative number of infections by 70% and 26.6% respectively. The requirement of ICU beds and ventilators would reduce by 83% with intensified public health measures. The cost of managing COVID-19 in India is nearly 4.5% of the gross domestic product (GDP) in the absence of any intervention which increases to 6.2% with intensified public health measures for COVID-19 response.ConclusionLockdown measures delay the onset of peak, and give much needed time to health system to prepare. Strengthening the public health system response in terms of testing, isolation treatment of cases, and contact tracing needs would lead to significant gains in terms of case load, and meeting health system needs.SummaryWhat is already known?A few studies have been carried out in Indian context to model the epidemic. These models explored the impact of lockdowns and social distancing measures focusing more on the course of the epidemic but none of these evaluated the impact on health system’s response needed as well as the economic impact of COVID-19 management in India. The findings from these studies are limited in a sense that either these studies evaluated the hypothetical scenarios of strategies implemented or focusing to smaller geographical regions in India.What are the new findings?Evidence pertaining to health economic impact of COVID-19 management, in context to Low- and Middle-Income countries, is very limited. To address this, we used the susceptible-exposed-infectious-recovered (SEIR) model to assess:the health system preparedness challenge in terms of hospital beds for isolation, intensive care and ventilators which would be required to manage the epidemic and the economic implications of managing the COVID-19 pandemic in India.the incremental cost of intensified public health measures per infection and per death averted.What do the new finding imply?In India, measures such as lockdowns would certainly delays the onset of peak of COVID-19 epidemic. This would help delay the surge of cases, which would buy time for the health system to prepare. Strengthening the health system response in terms of enhanced testing, isolation of cases, treatment and contact tracing, as is being done currently, would have to be the mainstay to reduce the impact of the pandemic in terms of reduction in infected population and COID-19 deaths in India until vaccine becomes available.

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COVID-19: Facts, Cultural Considerations, and Risk of Stigmatization

Journal of Transcultural Nursing ◽

10.1177/1043659620917724 ◽

2020 ◽

Vol 31 (4) ◽

pp. 326-332 ◽

Cited By ~ 28

Author(s):

Debra Pettit Bruns ◽

Nina Vanessa Kraguljac ◽

Thomas R. Bruns

Keyword(s):

Public Health ◽

General Education ◽

Health Care Providers ◽

Contact Tracing ◽

Care Providers ◽

Negative Effects ◽

Cultural Considerations ◽

Cultural Implications ◽

Travel Restrictions ◽

Public Health Information

Data on COVID-19 supports targeted social distancing could be an effective way to reduce morbidity and mortality, but could inadvertently increase stigma for affected populations. As health care providers we must be aware of the facts of COVID-19, cultural implications, and potential for stigmatization of populations affected by COVID-2019. It is important to consider the real economic impact related to lost workdays due to quarantine and social isolation efforts as well as travel restrictions that may negatively impact access to care and ability to pay for care. Efforts geared towards general education about the disease and the rationale for quarantine and public health information provided to the general public can reduce stigmatization. Countries who are successful at aggressive screening, early identification, patient isolation, contact tracing, quarantine, and infection control methods should also address the risk of stigmatization among populations and the negative effects which could occur. The cases of COVID-19 will continue to rise and the virus will be sustainable for future infections. Timely and appropriate public health interventions addressing cultural impact and risk for stigmatization along with proper screening, treatment, and follow up for affected individuals and close contacts can reduce the number of infections, serious illness, and deaths.

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