Monitoring Of Infectious Diseases Research Articles

Dynamic SARS-CoV-2 surveillance model combining seroprevalence and wastewater concentrations for post-vaccine disease burden estimates

BackgroundDespite wide scale assessments, it remains unclear how large-scale severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination affected the wastewater concentration of the virus or the overall disease burden as measured by hospitalization rates.MethodsWe used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and linked vaccination and hospitalization data, from April 2021–August 2021 in Jefferson County, Kentucky (USA). Our susceptible (S\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$S$$\\end{document}), vaccinated (V\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$V$$\\end{document}), variant-specific infected (I1\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${I}_{1}$$\\end{document} and I2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${I}_{2}$$\\end{document}), recovered (R\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$R$$\\end{document}), and seropositive (T\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$T$$\\end{document}) model (SVI2RT\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${SV}{I}_{2}{RT}$$\\end{document}) tracked prevalence longitudinally. This was related to wastewater concentration.ResultsHere we show the 64% county vaccination rate translate into about a 61% decrease in SARS-CoV-2 incidence. The estimated effect of SARS-CoV-2 Delta variant emergence is a 24-fold increase of infection counts, which correspond to an over 9-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration have the strongest correlation (r = 0.95) at 1 week lag.ConclusionsOur study underscores the importance of continuing environmental surveillance post-vaccine and provides a proof-of-concept for environmental epidemiology monitoring of infectious disease for future pandemic preparedness.

Molecular Imaging Techniques in the Diagnosis and Monitoring of Infectious Diseases

Molecular Imaging Techniques in the Diagnosis and Monitoring of Infectious Diseases

Identification of Early Warning Signals of Infectious Diseases in Hospitals by Integrating Clinical Treatment and Disease Prevention.

The global incidence of infectious diseases has increased in recent years, posing a significant threat to human health. Hospitals typically serve as frontline institutions for detecting infectious diseases. However, accurately identifying warning signals of infectious diseases in a timely manner, especially emerging infectious diseases, can be challenging. Consequently, there is a pressing need to integrate treatment and disease prevention data to conduct comprehensive analyses aimed at preventing and controlling infectious diseases within hospitals. This paper examines the role of medical data in the early identification of infectious diseases, explores early warning technologies for infectious disease recognition, and assesses monitoring and early warning mechanisms for infectious diseases. We propose that hospitals adopt novel multidimensional early warning technologies to mine and analyze medical data from various systems, in compliance with national strategies to integrate clinical treatment and disease prevention. Furthermore, hospitals should establish institution-specific, clinical-based early warning models for infectious diseases to actively monitor early signals and enhance preparedness for infectious disease prevention and control.

Large-volume RT-LAMP enables extraction-free amplification of HIV RNA from fingerstick plasma

BackgroundPoint-of-care (POC) nucleic acid amplification tests (NAAT) can significantly expand testing coverage, which is critical for infectious disease diagnostics and monitoring. The development of various isothermal amplification techniques greatly simplifies NAATs, but the cumbersome nucleic acid extraction step remains a bottleneck for the POC. Alternatively, extraction-free amplification, where crude samples are directly added into the assay, substantially simplifies the workflow. However, sample dilution is often needed in extraction-free amplification to reduce assay inhibition from sample matrices. Since NAATs are typically run at small volumes around 20 μL, the input sample quantity is therefore limited, resulting in an inevitable sensitivity loss. ResultsHere we explore the potential to perform isothermal amplification in larger reaction volumes to accommodate larger sample quantities, thereby improving sensitivity in extraction-free amplification. We demonstrated the approach by developing large-volume reverse transcription loop-mediated isothermal amplification (RT-LAMP) for HIV RNA detection from fingerstick plasma. We found that LAMP at reaction volumes up to 1 mL maintained the same performance. We then identified plasma dilution conditions needed to maintain the limit of detection in RT-LAMP. Subsequently, using inactivated HIV virus, we showed the successful detection of 24 HIV RNA copies in a 500 μL RT-LAMP reaction in the presence of 20 μL plasma (fingerstick volumes), translating to a viral load of 1200 copies per mL. To reduce the increased reagent cost with expanded reaction volumes, we further identified lower-cost reagents with maintained assay performance. Moreover, we showed that large-volume LAMP, compared to 20 μL reactions, could tolerate higher concentrations of various inhibitors in the sample, such as albumin and GuSCN. Significance and noveltyNAATs are conventionally conducted at small reaction volumes. Here we demonstrated that LAMP can be run at large reaction volumes (over 100 μL) with maintained assay performance, allowing sample inhibition to be mitigated while accommodating larger sample quantities. The same strategy of expanding reaction volumes could be applied to other isothermal amplification methods and various POC applications, to streamline test workflows and/or improve assay sensitivity.

Application of genomic studies in epidemiological surveillance: A mini-overview

The 21st century has already seen the emergence of several pandemics both in developed and developing nations, including the recent Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. The recent upsurge in certain diseases clearly indicates the need for continuous epidemiological surveillance and real-time monitoring of infectious diseases. Interestingly, genomics has found extensive application in monitoring infectious diseases through the sequencing of bacteria, parasites, and virus genomes. The continual scrutiny of pathogens and the examination of their genetic similarities and distinctions constitute genomic surveillance. The potential of genomic sequencing lies in its ability to offer a significantly more detailed depiction of the evolution and transmission of antimicrobial resistance (AMR), thus initiating a transformative impact on how public health surveillance networks address bacterial AMR. The utilization of whole-genome sequencing (WGS) stands as a prevalent technique for identifying and tracking pathogens, establishing transmission routes, and managing outbreaks. However, despite several decades of advancements, the seamless integration of genomics into surveillance pipelines faces substantial barriers that necessitate overcoming. Recent advances in genomics and next-generation sequencing approaches provide new paradigms for monitoring transmission pipelines and reducing overall morbidity and mortality. In this mini-review, we highlight the advances in genomics, how they have been critical in epidemiological surveillance and monitoring outbreaks, and how they can help predict and monitor possible future outbreaks.

Web search volume as a near-real-time complementary surveillance tool of tick-borne encephalitis (TBE) in Italy

The Internet is an important gateway for accessing health-related information, and data generated through web queries have been increasingly used as a complementary source for monitoring and forecasting of infectious diseases and they may partially address the issue of underreporting. In this study, we assessed whether tick-borne encephalitis (TBE)-related Internet search volume may be useful as a complementary tool for TBE surveillance in Italy. Monthly Google Trends (GT) data for TBE-related information were extracted for the period between January 2017 and September 2022, corresponding to the available time series of TBE notifications in Italy. Time series modeling was performed by applying seasonal autoregressive integrated moving average (SARIMA) models with or without GT data. The search terms relative to tick bites reflected best the observed temporal distribution of TBE cases, showing a correlation coefficient of 0.81 (95 % CI: 0.71–0.88). Particularly, both the reported number of TBE cases and GT searches occurred mainly during the summer. The peak of disease notifications coincided with that of Google searches in 4 of 6 years. Once calibrated, SARIMA models with or without GT data were applied to a validation set. Retrospective forecast made by the model with GT data was associated with a lower prediction error and accurately predicted the peak timing. By contrast, the traditional SARIMA model underestimated the actual number of TBE notifications by 65 %. Timeliness, easy availability, low cost and transparency make monitoring of the TBE-related Internet search queries a promising addition to the traditional methods of TBE surveillance in Italy.

Infection Prevention Measures for Service Recipients in Postpartum Care Homes

<p>產後護理之家服務對象，包括產後未滿二個月產婦及出生未滿二個月嬰兒。又嬰兒出生後來自母親的抗體逐漸消退，且免疫力尚未達到成熟階段，感染疾病風險高及可能嚴重併發症，因此對於服務對象入住機構內健康管理、包括疾病監測、疑似感染及適當隔離等，防範於未然及有效感染控制措施至為重要，各項感染管制訂定如：陪住家屬及訪客管理，遵守政府規範防疫政策；服務對象之配膳、飲食衛生、哺餵、哺育器材清消，飲用水衛生安全、供水設施等措施並落實執行，維護產婦、嬰兒及工作人員等之健康，建構優質安全環境，提升照護品質。機構管理者及工作人員應瞭解基本的感染預防及管制策略，確實執行應用，避免機構內感染及群聚事件，且配合衛生主管機關評鑑及感染管制查核督導，強化各項感染管制措施，共築完善防疫網。</p> <p> </p><p>Postpartum care homes provide services to mothers and infants in the first 2 months after birth. During this time, antibodies from the mother gradually diminish in infants, whose immunity is insufficiently mature, placing them at high risk of contracting diseases and developing serious complications. Therefore, adhering to and implementing strict infection control measures is crucial. For service recipients of health management in postpartum homes, infectious disease monitoring, isolation precautions, rules for managing family members and visitors, disease control regulations, meal preparation and feeding hygiene, access to cleaning and disinfection equipment, and regular cleaning and disinfection of water supplies are all critical measures for improving service quality and creating a high-quality and safe care environment. Institutional managers and staff must understand basic infection prevention and control strategies and carefully implement them to avoid infections and cluster incidents in postpartum homes. They must also cooperate with health authorities for institution accreditation, infection control inspection, and supervision to strengthen infection control measures and create comprehensive epidemic prevention strategies.</p> <p> </p>

Thai COVID-19 patient clustering for monitoring and prevention: data mining techniques

<span lang="EN-US">This research aims to optimize emerging infectious disease monitoring techniques in Thailand, which will be extremely valuable to the government, doctors, police, and others involved in understanding the seriousness of the spread of novel coronavirus to improve government policies, decisions, medical facilities, treatment. The data mining techniques included cluster analysis using K-means clustering. The infection data were obtained from the open data of the digital government development agency, Thailand. The dataset consisted of 1,893,941 cumulative cases from January 2020 to October 2021 of the outbreak. The results from clustering consisted of 8 groups. Clustering results determined the three largest, three medium-sized, and the two most minor numbers of infected people, respectively. These clusters represent their activities, namely touching an infected person and checking themselves. The components of emerging diseases in Thailand are closely related to waves, gender, age, nationality, career, behavioral risk, and region. The province of onset was mainly in Bangkok and its vicinity or central Thailand, as well as industrial areas. Adult workers aged 19 to 27 years and 43 to 54 years or over were seeds of new infection sources.</span>

Wastewater Surveillance of SARS-CoV-2 in Minnesota

Wastewater-based epidemiology provides an approach for assessing the prevalence of COVID-19 in a sewer service area. In this study, SARS-CoV-2 RNA was measured in 44 wastewater-treatment plants of varying sizes that sampled approximately 67% of the population of Minnesota, from September 2020 through December 2022. Various linear regression models were investigated to predict the weekly case count from SARS-CoV-2 RNA concentrations under various transformation and normalization methods which we validated via cross-validation averaged across all treatment plants. We find that the relationship between COVID-19 incidence and SARS-CoV-2 RNA in wastewater may be treatment plant-specific. We study storage and time-to-analysis for RNA wastewater data and find large effects of storage temperature, indicating that collection methods may have an important effect on the utility and validity of wastewater data for infectious disease monitoring. Our findings are important for any large-scale wastewater surveillance program.

Combination-Lock SlipChip Integrating Nucleic Acid Sample Preparation and Isothermal LAMP Amplification for the Detection of SARS-CoV-2.

Nucleic acid analysis with an easy-to-use workflow, high specificity and sensitivity, independence of sophisticated instruments, and accessibility outside of the laboratory is highly desirable for the detection and monitoring of infectious diseases. Integration of laboratory-quality sample preparation on a hand-held system is critical for performance. A SlipChip device inspired by the combination lock can perform magnetic bead-based nucleic acid extraction with several clockwise and counterclockwise rotations. A palm-sized base station was developed to assist sample preparation and provide thermal control of isothermal nucleic acid amplification without plug-in power. The loop-mediated isothermal amplification reaction can be performed with a colorimetric method and directly analyzed by the naked eye or with a mobile phone app. This system achieves good bead recovery during the sample preparation workflow and has minimal residue carryover from the lysis and elution buffers. Its performance is comparable to that of the standard laboratory protocol with real-time qPCR amplification methods. The entire workflow is completed in less than 35 min and the device can achieve 500 copies/mL sensitivity. Thirty clinical nasal swab samples were collected and tested with a sensitivity of 95% and a specificity of 100% for SARS-CoV-2. This combination-lock SlipChip provides a promising fast, easy-to-use nucleic acid test with bead-based sample preparation that produces laboratory-quality results for point-of-care settings, especially in home use applications.

Accuracy of Saliva as a Diagnostic Medium for Hepatitis B Virus Infection: A Quantitative ELISA Analysis

Context: Diagnosis of hepatitis B virus infection (HBV) has been traditionally serum-based with its attendant risks and invasive procedure. Massive research interests are being directed to the use of saliva for screening, diagnosis, and monitoring of several infectious diseases, including HBV. Various reports suggest that saliva contains biomarkers that are comparable with that of sera. It can also be obtained with minimal risk to the clinician and patient as well. Aim: To determine the diagnostic accuracy of saliva in quantitative detection of hepatitis B surface antigen (HBsAg) using enzyme-linked immunosorbent assay (ELISA). Settings and Design: This cross-sectional analytical study was performed on HBV seropositive patients at the Gastroenterology clinic of the University of Benin Teaching Hospital, Benin City, Edo State. Materials and Methods: Under standardized conditions, equal amounts of blood and saliva samples of 43 HBsAg seropositive patients were analyzed using ELISA to quantitatively detect the concentration of HBsAg. Statistical Analysis Used: The analysis relied on Spearman’s correlation coefficient, linear regression analysis, and Bland–Altman plots to describe the correlational, predictive, and agreements between measurements of HBsAg in sera and saliva. The statistical significance was set at P < 0.05, while a 95% confidence level was used to construct intervals. Results: All participants had detectable levels of HBsAg in both saliva and serum with mean titers of 1.70 ± 0.35 ng/ml and 2.80 ± 0.77 ng/ml, respectively. Correlational and linear regression showed poor fit and predictive relationships of the HBsAg levels. Bland–Altman analysis showed good agreement and no significant bias in their diagnostic agreements. Conclusion: Saliva can be reliably used in screening and diagnosis of HBV infection. There was agreement in their levels independently and within their averages. It may be premature to rely on saliva for quantitative assay of HBsAg in treatment monitoring.

Virus adsorption and elution using cationic polymer brushes: potential applications for passive sampling in wastewater-based epidemiology

Efficient virus adsorption and selective elution of a nonenveloped virus are demonstrated by using cationic polymer brushes. These materials may have potential for passive sampling in wastewater-based epidemiology.

Innovations in Global Health: Leveraging Technology for Disease Surveillance and Pandemic Preparedness

The emergence of infectious diseases and global pandemics necessitates continuous advancements in health surveillance and preparedness strategies. This article explores the innovations in global health that leverage technology to enhance disease surveillance and improve pandemic preparedness. The study investigates the role of various technological solutions, including artificial intelligence, data analytics, mobile applications, and digital communication platforms, in strengthening global health systems.
 The article reviews recent case studies and initiatives where technology has been successfully employed for disease surveillance, early detection of outbreaks, and rapid response to emerging health threats. It examines how digital tools facilitate real-time data collection, analysis, and dissemination, enabling more effective monitoring of infectious diseases globally. Additionally, the article discusses the integration of wearable devices, telemedicine, and other remote health technologies in enhancing the resilience of health systems during pandemics.
 Furthermore, the challenges and ethical considerations associated with the implementation of technological innovations in global health are critically assessed. Privacy concerns, data security, and the need for global collaboration are addressed to ensure the responsible and ethical use of technology in disease surveillance.
 The article concludes by highlighting the potential of technology to revolutionize global health practices, emphasizing the importance of collaborative efforts among governments, international organizations, and the private sector. As the world faces ongoing and emerging health threats, the adoption of innovative technological solutions becomes paramount for building robust disease surveillance systems and improving overall pandemic preparedness on a global scale.

Medical support for major international sports events: a literature rewiew

Introduction. The article carries out a critical review of the literature and updates the emphasis in organizing the preparation and holding of major sporting events from the point of view of a healthcare organizer.Target: to identify areas of activity that require further improvement and development in the organization of medical support for major sporting events.Materials and methods. An analysis of the available literary sources of databases was carried out: RSCI, RusMed, Pubmed, Web of Science.Results. The most pressing groups of issues for further study and solution have been identified: the uniqueness, significance and complexity of sporting events; statistics and structure of diseases and injuries; features of the structure and course of medical conditions at sports facilities and events; organizing interaction between different services within the healthcare system and interdepartmental interaction; prevention and monitoring of infectious diseases; features of training of medical personnel.Conclusion. The holding of major sporting events, in turn, is a driver for the development of the healthcare system in the host city and country. Preparing for such an event requires the creation of a vision, operational plans, targeted training of personnel and infrastructure.

Possibilities of a biobank for serological monitoring of infectious morbidity

Currently, monitoring infectious morbidity, control and forecasting the epidemic process is a topical health problem.Aim. To analyze the capabilities of the biobank for serological monitoring of infectious diseases using the Epstein- Barr virus (EBV), which is associated with infectious mononucleosis, as well as somatic pathology, including cancer.Material and methods. Using the quantitative enzyme- linked immunosorbent assay for specific antibodies to various EBV proteins, we studied blood serum samples from healthy individuals (2010, 2016, 2019, 2020, 2021 and 2022) from the collection of the N. F. Gamaleya National Center of Epidemiology and Microbiology.Results. For the first time, the intensity of EBV epidemic process among apparently healthy adult residents of the capital was assessed using samples of biological material and a biobank information database. At the time of examination, 0,8% of individuals were not infected with EBV, and 9,4% suffered reactivation of a chronic infection. There were no significant changes in detection rate of markers over the years.Conclusion. Certified collections of blood sera can be effectively used to study population immunity, the prevalence of individual infections, population protection nationwide, etc.

A Survey on Core Flow Cytometry Facilities: Instrument Maintenance, Usage, and Funding.

Flow cytometry is a powerful tool that finds applications in various fields such as immunology, molecular biology, cancer biology, virology, and infectious disease monitoring. A significant portion of the research in these disciplines is supported by flow cytometry shared resource laboratories (SRLs). There are several types of flow cytometers available for use in SRLs, including analyzers, sorters, imaging flow cytometers, and mass cytometers. Each type has different challenges when it comes to maintenance and life expectancy. An independent online survey was conducted to better understand instrument maintenance and turnover in flow cytometry SRLs. Questions regarding instrument uptime (availability), its usage, routine maintenance, and cost associated with it were addressed. The respondents also answered questions pertaining to the frequency of deep cleaning of the instrument and quality control. In addition, the survey queried about the source of funding used to purchase the instruments and possible reasons for a replacement. Presented herein are the results compiled from 146 core facilities that provide a look at the operation within a typical SRL, with the responses reflecting researchers' experiences with handling flow cytometers.

Climate change and infectious disease surveillance in Nepal: qualitative study exploring social, cultural, political and institutional factors influencing disease surveillance.

To explore the impacts of contextual issues encompassing social, cultural, political and institutional elements, on the operation of public health surveillance systems in Nepal concerning the monitoring of infectious diseases in the face of a changing climate. Semi-structured interviews (n=16) were conducted amongst key informants from the Department of Health Services, Health Information Management System, Department of Hydrology and Meteorology, World Health Organization, and experts working on infectious disease and climate change in Nepal, and data were analysed using thematic analysis technique. Analysis explicates how climate change is constructed as a contingent risk for infectious diseases transmission and public health systems, and treated less seriously than other 'salient' public health risks, having implications for how resources are allocated. Further, analysis suggests a weak alliance among different stakeholders, particularly policy makers and evidence generators, resulting in the continuation of traditional practices of infectious diseases surveillance without consideration of the impacts of climate change. We argue that along with strengthening systemic issues (epidemiological capacity, data quality and inter-sectoral collaboration), it is necessary to build a stronger political commitment to urgently address the influence of climate change as a present and exponential risk factor in the spread of infectious disease in Nepal.

A web-based analytical framework for the detection and visualization space-time clusters of COVID-19

ABSTRACT The COVID-19 pandemic has had a profound impact worldwide and continues to spread due to various mutations of the virus. Many governmental and nonprofit agencies at different levels have quickly developed COVID-19 dashboards to disseminate information on the pandemic to the public. However, most of these systems have mainly distributed “plain” information (e.g. cases, death counts, vaccination), and rarely provided insights that can be gained from spatiotemporal analyses, such as the detection of emerging clusters. The results from these analyses hold tremendous potential for health policymakers as they try to identify ways to slow down transmission. We present a web-based geographic framework to detect and visualize space-time clusters of COVID-19. Our tightly coupled framework integrates the prospective space-time scan statistics and local indicators of spatial association (LISA) with novel 2D and 3D interactive visuals in a cyber environment (http://159.223.164.41/app/). We illustrate the applicability of our approach using COVID-19 data for the continental US. Our framework is portable to other regions that may experience infectious diseases but is also flexible to handle data of different spatial and temporal granularities. This paper fits within an effort to integrate space-time analytics for the monitoring of infectious diseases in web environment, ultimately improving health surveillance systems.

Data-driven adaptive testing resource allocation strategies for real-time monitoring of infectious diseases

Since 2002, with the SARS outbreak, infectious diseases, including the ongoing COVID-19 pandemic, have continued to be a major global public health threat. It is critical to develop effective data science methods to quickly detect disease outbreaks and contain their rapid globalized spread. However, in practice, limited testing availability, and thus insufficient testing data poses significant challenges in effective analysis and real-time monitoring of infectious diseases, especially during early stages of a novel disease outbreak. To tackle these challenges, this article proposes adaptive testing resource allocation strategies integrated with a physics-informed model to dynamically allocate limited testing resources across different communities. The physics-informed model accounts for transmission dynamics and health disparities, enabling effective health risk assessment despite limited data. By integrating nonstationary Multi-Armed Bandit techniques that strike superior balance between exploring the communities with high uncertain risks and exploiting those with high risk levels, the proposed methodology facilitates test allocation to collect high-quality testing data for early outbreak detection. Theoretical analysis is carried out to evaluate the performance of the proposed allocation strategies, ensuring either sublinear or linear dynamic pseudo-regret under regularity assumptions. A comprehensive simulation study is conducted under three transmission scenarios to thoroughly evaluate the proposed methodology.

Cycle Threshold Values as Indication of Increasing SARS-CoV-2 New Variants, England, 2020-2022.

Early detection of increased infections or new variants of SARS-CoV-2 is critical for public health response. To determine whether cycle threshold (Ct) data from PCR tests for SARS-CoV-2 could serve as an early indicator of epidemic growth, we analyzed daily mean Ct values in England, UK, by gene target and used iterative sequential regression to detect break points in mean Ct values (and positive test counts). To monitor the epidemic in England, we continued those analyses in real time. During September 2020-January 2022, a total of 7,611,153 positive SARS-CoV-2 PCR test results with Ct data were reported. Spike (S) gene target (S+/S-)-specific mean Ct values decreased 6-29 days before positive test counts increased, and S-gene Ct values provided early indication of increasing new variants (Delta and Omicron). Our approach was beneficial in the context of the first waves of the COVID-19 pandemic and can be used to support future infectious disease monitoring.