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Ma L, Qiu Z, Van Mieghem P, Kitsak M. Reporting delays: A widely neglected impact factor in COVID-19 forecasts. PNAS NEXUS 2024; 3:pgae204. [PMID: 38846778 PMCID: PMC11156234 DOI: 10.1093/pnasnexus/pgae204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 05/13/2024] [Indexed: 06/09/2024]
Abstract
Epidemic forecasts are only as good as the accuracy of epidemic measurements. Is epidemic data, particularly COVID-19 epidemic data, clean, and devoid of noise? The complexity and variability inherent in data collection and reporting suggest otherwise. While we cannot evaluate the integrity of the COVID-19 epidemic data in a holistic fashion, we can assess the data for the presence of reporting delays. In our work, through the analysis of the first COVID-19 wave, we find substantial reporting delays in the published epidemic data. Motivated by the desire to enhance epidemic forecasts, we develop a statistical framework to detect, uncover, and remove reporting delays in the infectious, recovered, and deceased epidemic time series. Using our framework, we expose and analyze reporting delays in eight regions significantly affected by the first COVID-19 wave. Further, we demonstrate that removing reporting delays from epidemic data by using our statistical framework may decrease the error in epidemic forecasts. While our statistical framework can be used in combination with any epidemic forecast method that intakes infectious, recovered, and deceased data, to make a basic assessment, we employed the classical SIRD epidemic model. Our results indicate that the removal of reporting delays from the epidemic data may decrease the forecast error by up to 50%. We anticipate that our framework will be indispensable in the analysis of novel COVID-19 strains and other existing or novel infectious diseases.
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Affiliation(s)
- Long Ma
- Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, GA 2600, The Netherlands
| | - Zhihao Qiu
- Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, GA 2600, The Netherlands
| | - Piet Van Mieghem
- Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, GA 2600, The Netherlands
| | - Maksim Kitsak
- Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, GA 2600, The Netherlands
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2
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Dai P, Qi L, Jia M, Li T, Ran H, Jiang M, Tang W, Yan C, Yang W, Ren Y, Feng L. Healthcare-seeking behaviours of patients with acute respiratory infection: a cross-sectional survey in a rural area of southwest China. BMJ Open 2024; 14:e077224. [PMID: 38365288 PMCID: PMC10875477 DOI: 10.1136/bmjopen-2023-077224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
OBJECTIVES This study aimed to assess the healthcare-seeking behaviour and related factors of people with acute respiratory symptoms in the rural areas of central and western China to estimate the disease burden of influenza more accurately. DESIGN Cross-sectional survey. SETTINGS Fifty-two communities/villages in the Wanzhou District, Chongqing, China, a rural area in southwest China, from May 2022 to July 2022. PARTICIPANTS The participants were those who had been living in Wanzhou District continuously for more than 6 months and consented to participate. OUTCOME MEASURES A semistructured questionnaire was used to determine the healthcare-seeking behaviour of participants, and the dichotomous response of 'yes' or 'no' was used to assess whether participants had acute respiratory symptoms and their healthcare-seeking behaviour. RESULTS Only 50.92% (360 of 707) of the patients with acute respiratory infection visited medical and health institutions for treatment, whereas 49.08% (347 of 707) avoided treatment or opted for self-medication. The primary reason for not seeing a doctor was that patients felt their condition was not serious and visiting a medical facility for treatment was unnecessary. Short distance (87.54%) and reasonable charges (49.48%) were ranked as the most important reasons for choosing treatment at primary medical and health facilities (80.27%). The primary reasons for which patients visited secondary and tertiary hospitals (7.78% and 8.61%, respectively) were that doctors in such facilities were better at diagnosis (57.14%) and at treatment (87.10%). CONCLUSION The findings provided in this study indicated that regular healthcare-seeking behaviour investigations should be conducted. The disease burden of influenza can be calculated more accurately when healthcare-seeking behaviour investigations are combined with surveillance in the hospitals.
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Affiliation(s)
- Peixi Dai
- Division of Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Qi
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, China
| | - Mengmeng Jia
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tingting Li
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, China
| | - Hua Ran
- Wanzhou District Center for Disease Control and Prevention, Wanzhou District, Chongqing, China
| | - Mingyue Jiang
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wenge Tang
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, China
| | - Chaoyang Yan
- Wanzhou District Center for Disease Control and Prevention, Wanzhou District, Chongqing, China
| | - Weizhong Yang
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yuhua Ren
- Wanzhou District Center for Disease Control and Prevention, Wanzhou District, Chongqing, China
| | - Luzhao Feng
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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3
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Eales O, Plank MJ, Cowling BJ, Howden BP, Kucharski AJ, Sullivan SG, Vandemaele K, Viboud C, Riley S, McCaw JM, Shearer FM. Key Challenges for Respiratory Virus Surveillance while Transitioning out of Acute Phase of COVID-19 Pandemic. Emerg Infect Dis 2024; 30:e230768. [PMID: 38190760 PMCID: PMC10826770 DOI: 10.3201/eid3002.230768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
To support the ongoing management of viral respiratory diseases while transitioning out of the acute phase of the COVID-19 pandemic, many countries are moving toward an integrated model of surveillance for SARS-CoV-2, influenza virus, and other respiratory pathogens. Although many surveillance approaches catalyzed by the COVID-19 pandemic provide novel epidemiologic insight, continuing them as implemented during the pandemic is unlikely to be feasible for nonemergency surveillance, and many have already been scaled back. Furthermore, given anticipated cocirculation of SARS-CoV-2 and influenza virus, surveillance activities in place before the pandemic require review and adjustment to ensure their ongoing value for public health. In this report, we highlight key challenges for the development of integrated models of surveillance. We discuss the relative strengths and limitations of different surveillance practices and studies as well as their contribution to epidemiologic assessment, forecasting, and public health decision-making.
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Plank MJ, Watson L, Maclaren OJ. Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand. PLoS Comput Biol 2024; 20:e1011752. [PMID: 38190380 PMCID: PMC10798620 DOI: 10.1371/journal.pcbi.1011752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/19/2024] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
Near-term forecasting of infectious disease incidence and consequent demand for acute healthcare services can support capacity planning and public health responses. Despite well-developed scenario modelling to support the Covid-19 response, Aotearoa New Zealand lacks advanced infectious disease forecasting capacity. We develop a model using Aotearoa New Zealand's unique Covid-19 data streams to predict reported Covid-19 cases, hospital admissions and hospital occupancy. The method combines a semi-mechanistic model for disease transmission to predict cases with Gaussian process regression models to predict the fraction of reported cases that will require hospital treatment. We evaluate forecast performance against out-of-sample data over the period from 2 October 2022 to 23 July 2023. Our results show that forecast performance is reasonably good over a 1-3 week time horizon, although generally deteriorates as the time horizon is lengthened. The model has been operationalised to provide weekly national and regional forecasts in real-time. This study is an important step towards development of more sophisticated situational awareness and infectious disease forecasting tools in Aotearoa New Zealand.
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Affiliation(s)
- Michael J. Plank
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | - Leighton Watson
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | - Oliver J. Maclaren
- Department of Engineering Science, University of Auckland, Auckland, New Zealand
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5
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Pendrey CG, Strachan J, Peck H, Aziz A, Moselen J, Moss R, Rahaman MR, Barr IG, Subbarao K, Sullivan SG. The re-emergence of influenza following the COVID-19 pandemic in Victoria, Australia, 2021 to 2022. Euro Surveill 2023; 28:2300118. [PMID: 37707981 PMCID: PMC10687983 DOI: 10.2807/1560-7917.es.2023.28.37.2300118] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/28/2023] [Indexed: 09/16/2023] Open
Abstract
BackgroundCOVID-19 pandemic mitigation measures, including travel restrictions, limited global circulation of influenza viruses. In Australia, travel bans for non-residents and quarantine requirements for returned travellers were eased in November 2021, providing pathways for influenza viruses to be re-introduced.AimWe aimed to describe the epidemiological and virological characteristics of the re-emergence of influenza in Victoria, Australia to inform public health interventions.MethodsFrom 1 November 2021 to 30 April 2022, we conducted an epidemiological study analysing case notification data from the Victorian Department of Health to describe case demographics, interviewed the first 200 cases to establish probable routes of virus reintroduction and examined phylogenetic and antigenic data to understand virus diversity and susceptibility to current vaccines.ResultsOverall, 1,598 notifications and 1,064 positive specimens were analysed. The majority of cases (61.4%) occurred in the 15-34 years age group. Interviews revealed a higher incidence of international travel exposure during the first month of case detections, and high levels of transmission in university residential colleges were associated with return to campus. Influenza A(H3N2) was the predominant subtype, with a single lineage predominating despite multiple importations.ConclusionEnhanced testing for respiratory viruses during the COVID-19 pandemic provided a more complete picture of influenza virus transmission compared with previous seasons. Returned international travellers were important drivers of influenza reemergence, as were young adults, a group whose role has previously been under-recognised in the establishment of seasonal influenza epidemics. Targeting interventions, including vaccination, to these groups could reduce future influenza transmission.
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Affiliation(s)
- Catherine Ga Pendrey
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
- Communicable Diseases, Health Protection Branch, Public Health Division, Department of Health, Victoria, Melbourne, Australia
| | - Janet Strachan
- Communicable Diseases, Health Protection Branch, Public Health Division, Department of Health, Victoria, Melbourne, Australia
| | - Heidi Peck
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ammar Aziz
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jean Moselen
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Rob Moss
- School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Md Rezanur Rahaman
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Immunology and Microbiology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Immunology and Microbiology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Communicable Diseases, Health Protection Branch, Public Health Division, Department of Health, Victoria, Melbourne, Australia
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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6
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Moss R, Price DJ, Golding N, Dawson P, McVernon J, Hyndman RJ, Shearer FM, McCaw JM. Forecasting COVID-19 activity in Australia to support pandemic response: May to October 2020. Sci Rep 2023; 13:8763. [PMID: 37253758 DOI: 10.1038/s41598-023-35668-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/19/2023] [Indexed: 06/01/2023] Open
Abstract
As of January 2021, Australia had effectively controlled local transmission of COVID-19 despite a steady influx of imported cases and several local, but contained, outbreaks in 2020. Throughout 2020, state and territory public health responses were informed by weekly situational reports that included an ensemble forecast of daily COVID-19 cases for each jurisdiction. We present here an analysis of one forecasting model included in this ensemble across the variety of scenarios experienced by each jurisdiction from May to October 2020. We examine how successfully the forecasts characterised future case incidence, subject to variations in data timeliness and completeness, showcase how we adapted these forecasts to support decisions of public health priority in rapidly-evolving situations, evaluate the impact of key model features on forecast skill, and demonstrate how to assess forecast skill in real-time before the ground truth is known. Conditioning the model on the most recent, but incomplete, data improved the forecast skill, emphasising the importance of developing strong quantitative models of surveillance system characteristics, such as ascertainment delay distributions. Forecast skill was highest when there were at least 10 reported cases per day, the circumstances in which authorities were most in need of forecasts to aid in planning and response.
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Affiliation(s)
- Robert Moss
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia.
| | - David J Price
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Department of Infectious Diseases, Melbourne Medical School, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nick Golding
- Telethon Kids Institute, Perth, WA, Australia
- Curtin School of Population Health, Curtin University, Perth, WA, Australia
| | - Peter Dawson
- Defence Science and Technology Group, Melbourne, VIC, Australia
| | - Jodie McVernon
- Department of Infectious Diseases, Melbourne Medical School, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Victorian Infectious Diseases Reference Laboratory Epidemiology Unit, Royal Melbourne Hospital, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Rob J Hyndman
- Department of Econometrics and Business Statistics, Monash University, Melbourne, VIC, Australia
| | - Freya M Shearer
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Telethon Kids Institute, Perth, WA, Australia
| | - James M McCaw
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, Australia
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7
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Toh KB, Runge M, Richardson RA, Hladish TJ, Gerardin J. Design of effective outpatient sentinel surveillance for COVID-19 decision-making: a modeling study. BMC Infect Dis 2023; 23:287. [PMID: 37142984 PMCID: PMC10158704 DOI: 10.1186/s12879-023-08261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/17/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Decision-makers impose COVID-19 mitigations based on public health indicators such as reported cases, which are sensitive to fluctuations in supply and demand for diagnostic testing, and hospital admissions, which lag infections by up to two weeks. Imposing mitigations too early has unnecessary economic costs while imposing too late leads to uncontrolled epidemics with unnecessary cases and deaths. Sentinel surveillance of recently-symptomatic individuals in outpatient testing sites may overcome biases and lags in conventional indicators, but the minimal outpatient sentinel surveillance system needed for reliable trend estimation remains unknown. METHODS We used a stochastic, compartmental transmission model to evaluate the performance of various surveillance indicators at reliably triggering an alarm in response to, but not before, a step increase in transmission of SARS-CoV-2. The surveillance indicators included hospital admissions, hospital occupancy, and sentinel cases with varying levels of sampling effort capturing 5, 10, 20, 50, or 100% of incident mild cases. We tested 3 levels of transmission increase, 3 population sizes, and conditions of either simultaneous transmission increase or lagged increase in the older population. We compared the indicators' performance at triggering alarm soon after, but not prior, to the transmission increase. RESULTS Compared to surveillance based on hospital admissions, outpatient sentinel surveillance that captured at least 20% of incident mild cases could trigger an alarm 2 to 5 days earlier for a mild increase in transmission and 6 days earlier for a moderate or strong increase. Sentinel surveillance triggered fewer false alarms and averted more deaths per day spent in mitigation. When transmission increase in older populations lagged the increase in younger populations by 14 days, sentinel surveillance extended its lead time over hospital admissions by an additional 2 days. CONCLUSIONS Sentinel surveillance of mild symptomatic cases can provide more timely and reliable information on changes in transmission to inform decision-makers in an epidemic like COVID-19.
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Affiliation(s)
- Kok Ben Toh
- Department of Preventive Medicine, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Manuela Runge
- Department of Preventive Medicine, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Reese Ak Richardson
- Department of Chemical and Biological Engineering, Northwestern University, Chicago, IL, USA
| | - Thomas J Hladish
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogen Institute, University of Florida, Gainesville, FL, USA
| | - Jaline Gerardin
- Department of Preventive Medicine, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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8
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Kim Y, Donnelly CA, Nouvellet P. Drivers of SARS-CoV-2 testing behaviour: a modelling study using nationwide testing data in England. Nat Commun 2023; 14:2148. [PMID: 37059861 PMCID: PMC10103662 DOI: 10.1038/s41467-023-37813-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
During the COVID-19 pandemic, national testing programmes were conducted worldwide on unprecedented scales. While testing behaviour is generally recognised as dynamic and complex, current literature demonstrating and quantifying such relationships is scarce, despite its importance for infectious disease surveillance and control. Here, we characterise the impacts of SARS-CoV-2 transmission, disease susceptibility/severity, risk perception, and public health measures on SARS-CoV-2 PCR testing behaviour in England over 20 months of the pandemic, by linking testing trends to underlying epidemic trends and contextual meta-data within a systematic conceptual framework. The best-fitting model describing SARS-CoV-2 PCR testing behaviour explained close to 80% of the total deviance in NHS test data. Testing behaviour showed complex associations with factors reflecting transmission level, disease susceptibility/severity (e.g. age, dominant variant, and vaccination), public health measures (e.g. testing strategies and lockdown), and associated changes in risk perception, varying throughout the pandemic and differing between infected and non-infected people.
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Affiliation(s)
- Younjung Kim
- Department of Evolution, Behaviour, and Environment, School of Life Sciences, University of Sussex, Brighton, UK
| | - Christl A Donnelly
- Department of Statistics, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Pierre Nouvellet
- Department of Evolution, Behaviour, and Environment, School of Life Sciences, University of Sussex, Brighton, UK.
- MRC Centre for Global Infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK.
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9
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Yoo S, Gulbransen-Diaz N, Parker C, Wang AP. Designing Digital COVID-19 Screening: Insights and Deliberations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3899. [PMID: 36900909 PMCID: PMC10001447 DOI: 10.3390/ijerph20053899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Due to the global COVID-19 pandemic, public health control and screening measures have been introduced at healthcare facilities, including those housing our most vulnerable populations. These warning measures situated at hospital entrances are presently labour-intensive, requiring additional staff to conduct manual temperature checks and risk-assessment questionnaires of every individual entering the premises. To make this process more efficient, we present eGate, a digital COVID-19 health-screening smart Internet of Things system deployed at multiple entry points around a children's hospital. This paper reports on design insights based on the experiences of concierge screening staff stationed alongside the eGate system. Our work contributes towards social-technical deliberations on how to improve design and deploy of digital health-screening systems in hospitals. It specifically outlines a series of design recommendations for future health screening interventions, key considerations relevant to digital screening control systems and their implementation, and the plausible effects on the staff who work alongside them.
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Affiliation(s)
- Soojeong Yoo
- Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS), University College London, London W1W 7TY, UK
| | - Natalia Gulbransen-Diaz
- School of Architecture, Planning and Design, The University of Sydney, Sydney, NSW 2006, Australia
| | - Callum Parker
- School of Architecture, Planning and Design, The University of Sydney, Sydney, NSW 2006, Australia
| | - Audrey P. Wang
- Biomedical Informatics and Digital Health, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- DHI Laboratory, Research Education Network, Western Sydney Local Health District, Westmead Health Precinct, Westmead, NSW 2145, Australia
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10
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Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA. Nat Commun 2022; 13:5547. [PMID: 36138039 PMCID: PMC9499975 DOI: 10.1038/s41467-022-33317-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/12/2022] [Indexed: 01/08/2023] Open
Abstract
Public health indicators typically used for COVID-19 surveillance can be biased or lag changing community transmission patterns. In this study, we investigate whether sentinel surveillance of recently symptomatic individuals receiving outpatient diagnostic testing for SARS-CoV-2 could accurately assess the instantaneous reproductive number R(t) and provide early warning of changes in transmission. We use data from community-based diagnostic testing sites in the United States city of Chicago. Patients tested at community-based diagnostic testing sites between September 2020 and June 2021, and reporting symptom onset within four days preceding their test, formed the sentinel population. R(t) calculated from sentinel cases agreed well with R(t) from other indicators. Retrospectively, trends in sentinel cases did not precede trends in COVID-19 hospital admissions by any identifiable lead time. In deployment, sentinel surveillance held an operational recency advantage of nine days over hospital admissions. The promising performance of opportunistic sentinel surveillance suggests that deliberately designed outpatient sentinel surveillance would provide robust early warning of increasing transmission.
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11
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Moss R. Commentary on "Transparent modeling of influenza incidence": Because the model said so. INTERNATIONAL JOURNAL OF FORECASTING 2022; 38:620-621. [PMID: 35185231 PMCID: PMC8846926 DOI: 10.1016/j.ijforecast.2021.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Robert Moss
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville 3052, Australia
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12
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Zarebski AE, du Plessis L, Parag KV, Pybus OG. A computationally tractable birth-death model that combines phylogenetic and epidemiological data. PLoS Comput Biol 2022; 18:e1009805. [PMID: 35148311 PMCID: PMC8903285 DOI: 10.1371/journal.pcbi.1009805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 03/08/2022] [Accepted: 01/05/2022] [Indexed: 11/19/2022] Open
Abstract
Inferring the dynamics of pathogen transmission during an outbreak is an important problem in infectious disease epidemiology. In mathematical epidemiology, estimates are often informed by time series of confirmed cases, while in phylodynamics genetic sequences of the pathogen, sampled through time, are the primary data source. Each type of data provides different, and potentially complementary, insight. Recent studies have recognised that combining data sources can improve estimates of the transmission rate and the number of infected individuals. However, inference methods are typically highly specialised and field-specific and are either computationally prohibitive or require intensive simulation, limiting their real-time utility. We present a novel birth-death phylogenetic model and derive a tractable analytic approximation of its likelihood, the computational complexity of which is linear in the size of the dataset. This approach combines epidemiological and phylodynamic data to produce estimates of key parameters of transmission dynamics and the unobserved prevalence. Using simulated data, we show (a) that the approximation agrees well with existing methods, (b) validate the claim of linear complexity and (c) explore robustness to model misspecification. This approximation facilitates inference on large datasets, which is increasingly important as large genomic sequence datasets become commonplace.
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Affiliation(s)
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kris Varun Parag
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
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13
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Riley S, Ainslie KEC, Eales O, Walters CE, Wang H, Atchison C, Fronterre C, Diggle PJ, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P. Resurgence of SARS-CoV-2: Detection by community viral surveillance. Science 2021; 372:990-995. [PMID: 33893241 PMCID: PMC8158959 DOI: 10.1126/science.abf0874] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/20/2021] [Indexed: 12/14/2022]
Abstract
Surveillance of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has mainly relied on case reporting, which is biased by health service performance, test availability, and test-seeking behaviors. We report a community-wide national representative surveillance program in England based on self-administered swab results from ~594,000 individuals tested for SARS-CoV-2, regardless of symptoms, between May and the beginning of September 2020. The epidemic declined between May and July 2020 but then increased gradually from mid-August, accelerating into early September 2020 at the start of the second wave. When compared with cases detected through routine surveillance, we report here a longer period of decline and a younger age distribution. Representative community sampling for SARS-CoV-2 can substantially improve situational awareness and feed into the public health response even at low prevalence.
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Affiliation(s)
- Steven Riley
- School of Public Health, Imperial College London, London, UK.
- MRC Centre for Global Infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Kylie E C Ainslie
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Oliver Eales
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Caroline E Walters
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Haowei Wang
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | | | - Claudio Fronterre
- Centre for Health Informatics, Computing, and Statistics (CHICAS), Lancaster Medical School, Lancaster University, Lancaster, UK
- Health Data Research UK, London, UK
| | - Peter J Diggle
- Centre for Health Informatics, Computing, and Statistics (CHICAS), Lancaster Medical School, Lancaster University, Lancaster, UK
- Health Data Research UK, London, UK
| | - Deborah Ashby
- School of Public Health, Imperial College London, London, UK
| | - Christl A Donnelly
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Helen Ward
- School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Ara Darzi
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- Institute of Global Health Innovation, Imperial College London, London, UK
| | - Paul Elliott
- School of Public Health, Imperial College London, London, UK.
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
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14
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De la Puente-León M, Levy MZ, Toledo AM, Recuenco S, Shinnick J, Castillo-Neyra R. Spatial Inequality Hides the Burden of Dog Bites and the Risk of Dog-Mediated Human Rabies. Am J Trop Med Hyg 2020; 103:1247-1257. [PMID: 32662391 PMCID: PMC7470517 DOI: 10.4269/ajtmh.20-0180] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/25/2020] [Indexed: 12/21/2022] Open
Abstract
Since its reintroduction in 2015, rabies has been established as an enzootic disease among the dog population of Arequipa, Peru. Given the unknown rate of dog bites, the risk of human rabies transmission is concerning. Our objective was to estimate the rate of dog bites in the city and to identify factors associated with seeking health care in a medical facility for wound care and rabies prevention follow-up. To this end, we conducted a door-to-door survey with 4,370 adults in 21 urban and 21 peri-urban communities. We then analyzed associations between seeking health care following dog bites and various socioeconomic factors, stratifying by urban and peri-urban localities. We found a high annual rate of dog bites in peri-urban communities (12.4%), which was 2.6 times higher than that in urban areas (4.8%). Among those who were bitten, the percentage of people who sought medical treatment was almost twice as high in urban areas (39.1%) as in peri-urban areas (21.4%).
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Affiliation(s)
- Micaela De la Puente-León
- Zoonotic Disease Research Laboratory, One Health Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Arequipa, Perú
| | - Michael Z. Levy
- Zoonotic Disease Research Laboratory, One Health Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Arequipa, Perú
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amparo M. Toledo
- Zoonotic Disease Research Laboratory, One Health Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Arequipa, Perú
| | - Sergio Recuenco
- Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Julianna Shinnick
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ricardo Castillo-Neyra
- Zoonotic Disease Research Laboratory, One Health Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Arequipa, Perú
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
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15
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Price DJ, Shearer FM, Meehan MT, McBryde E, Moss R, Golding N, Conway EJ, Dawson P, Cromer D, Wood J, Abbott S, McVernon J, McCaw JM. Early analysis of the Australian COVID-19 epidemic. eLife 2020; 9:e58785. [PMID: 32788039 PMCID: PMC7449695 DOI: 10.7554/elife.58785] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/12/2020] [Indexed: 01/15/2023] Open
Abstract
As of 1 May 2020, there had been 6808 confirmed cases of COVID-19 in Australia. Of these, 98 had died from the disease. The epidemic had been in decline since mid-March, with 308 cases confirmed nationally since 14 April. This suggests that the collective actions of the Australian public and government authorities in response to COVID-19 were sufficiently early and assiduous to avert a public health crisis - for now. Analysing factors that contribute to individual country experiences of COVID-19, such as the intensity and timing of public health interventions, will assist in the next stage of response planning globally. We describe how the epidemic and public health response unfolded in Australia up to 13 April. We estimate that the effective reproduction number was likely below one in each Australian state since mid-March and forecast that clinical demand would remain below capacity thresholds over the forecast period (from mid-to-late April).
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Affiliation(s)
- David J Price
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of MelbourneMelbourneAustralia
- Victorian Infectious Diseases Reference Laboratory Epidemiology Unit at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne HospitalMelbourneAustralia
| | - Freya M Shearer
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of MelbourneMelbourneAustralia
| | - Michael T Meehan
- Australian Institute of Tropical Health and Medicine, James Cook UniversityTownsvilleAustralia
| | - Emma McBryde
- Australian Institute of Tropical Health and Medicine, James Cook UniversityTownsvilleAustralia
| | - Robert Moss
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of MelbourneMelbourneAustralia
| | - Nick Golding
- Telethon Kids Institute and Curtin UniversityPerthAustralia
| | - Eamon J Conway
- Victorian Infectious Diseases Reference Laboratory Epidemiology Unit at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne HospitalMelbourneAustralia
| | - Peter Dawson
- Defence Science and Technology, Department of DefenceCanberraAustralia
| | - Deborah Cromer
- Kirby Institute for Infection and Immunity, University of New South WalesSydneyAustralia
- School of Mathematics and Statistics, University of New South WalesSydneyAustralia
| | - James Wood
- School of Public Health and Community Medicine, University of New South WalesSydneyAustralia
| | - Sam Abbott
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Jodie McVernon
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of MelbourneMelbourneAustralia
- Victorian Infectious Diseases Reference Laboratory Epidemiology Unit at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne HospitalMelbourneAustralia
- Infection and Immunity Theme, Murdoch Children’s Research Institute, The Royal Children’s HospitalMelbourneAustralia
| | - James M McCaw
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of MelbourneMelbourneAustralia
- Victorian Infectious Diseases Reference Laboratory Epidemiology Unit at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne HospitalMelbourneAustralia
- School of Mathematics and Statistics, The University of MelbourneMelbourneAustralia
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16
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Hemanth DJ. Artificial Intelligence Applications in Tracking Health Behaviors During Disease Epidemics. HUMAN BEHAVIOUR ANALYSIS USING INTELLIGENT SYSTEMS 2020. [PMCID: PMC7123557 DOI: 10.1007/978-3-030-35139-7_7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The threat of emerging and re-emerging infectious diseases to global population health remains significantly enormous, and the pandemic preparedness capabilities necessary to confront such threats must be of greater potency. Artificial Intelligence (AI) offers new hope in not only effectively pre-empting, preventing and combating the threats of infectious disease epidemics, but also facilitating the understanding of health-seeking behaviors and public emotions during epidemics. From a systems-thinking perspective, and in today’s world of seamless boundaries and global interconnectivity, AI offers enormous potential for public health practitioners and policy makers to revolutionize healthcare and population health through focussed, context-specific interventions that promote cost-savings on therapeutic care, expand access to health information and services, and enhance individual responsibility for their health and well-being. This chapter systematically appraises the dawn of AI technology towards empowering population health to combat the rise of infectious disease epidemics.
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Affiliation(s)
- D. Jude Hemanth
- Department of Electronics and Communication Engineering, Karunya University, Coimbatore, Tamil Nadu India
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