Contact Tracing Research Articles

Considering best practice standards for routine whole-genome sequencing for TB care and control.

TB is a priority pathogen for the application of whole-genome sequencing (WGS) into routine public health practice. In low-incidence settings, a growing number of services have begun to incorporate routine WGS into standard practice. The increasing availability of real-time genomic information supports a variety of aspects of the public health response, including the detection of drug resistance, monitoring of laboratory and clinical practices, contact tracing investigations and active case finding. Optimal structures and approaches are needed to support the rapid translation of genomic information into practice and to evaluate outcomes and impact. In this consensus paper, we outline the elements needed to systemically incorporate routine WGS into the TB public health response, including the sustainability of services, multidisciplinary team models and monitoring and evaluation frameworks. If integrated in an efficient and thoughtful manner, routine WGS has the potential to significantly improve clinical TB care for individuals and the overall public health response.

Tuberculosis in Solomon Islands: why declining case notifications may not reflect true incidence.

Interpretation of tuberculosis (TB) surveillance data in Solomon Islands between 2016 and 2022 should be informed by local conditions, including pandemic disruptions in contact tracing. The TB surveillance data recently reported by Yanagawa et al. has features indicative of underdiagnosis. We thus advise caution in the interpretation of this data.

Role of mothers in preventing tuberculosis in children: A scoping review

Tuberculosis (TB) remains a significant global health challenge, especially for children. The aim of this scoping review was to investigate the role of mothers in preventing childhood TB transmission and highlight effective strategies and associated barriers. A systematic literature search was conducted using PubMed, Web of Science, and Scopus, covering articles up to January 17, 2024. The search included keywords like “mother,” “parents,” “care,” “prevention,” and “tuberculosis.” Eligibility criteria included peer-reviewed articles on maternal health interventions for TB prevention in children and published in English. The study selection process involved screening titles and abstracts, followed by full-text reviews by Rayyan Artificial Intelligence (AI). Eighteen studies were analyzed, revealing the crucial roles of mothers and healthcare workers in TB prevention. The results indicated that in South Africa, only 47% of eligible pregnant women underwent Mantoux testing, with lower rates in rural areas. The isoniazid preventive therapy (IPT) uptake rate was 79%, with geographical variations. Barriers included insufficient patient information, inadequate screening facilities, and healthcare providers' knowledge gaps. Parental involvement, particularly by mothers, is vital for adherence to TB preventive measures. Challenges in integrating TB case-finding with antenatal care and prevention of mother-to-child transmission (PMTCT) services included inconsistent screening and healthcare worker shortages. Enhancing health services, reducing stigma, and integrating TB prevention into existing programs are essential. In conclusion, this review underscores that effective childhood TB prevention requires a coordinated approach that incorporates the efforts of the mother and healthcare worker. Addressing barriers such as contact tracing gaps and diagnostic delays, alongside enhancing maternal health education and support, is essential for improving TB prevention and management. Targeted interventions and collaborative efforts are needed to reduce transmission and improve health outcomes, particularly in bridging rural-urban disparities.

Modeling the Two-Strain Dynamics of COVID-19 in Ghana Using a Logistic Growth Model

Through mutation, viruses constantly change, bringing into existence new variants; SARS-CoV-2 is no different. In December 2020, variants with different characteristics that could affect transmissibility and death emerged around the world of which Ghana is not an exception. To address this new phenomenon, a two-strain mathematical model of SARS-CoV-2 was formulatedto analyzed thetransmission dynamicsin Ghana. Thedisease-free equilibriumwas calculated. The basicreproduction number, <I>R</I><sub>0</sub>= max{<I>R</I><sub>0A</sub>, <I>R</I><sub>0B</sub>} = max(0.9957945674, 1.109170840), associated with the model is computed using the next generation matrix operator. The disease-free equilibrium is found to be locally asymptotically stable when both <I>R</I><sub>0<I>A</I></sub>, <I>R</I><sub>0<I>B</sub> <sub></I></sub>< 1, but unstable otherwise. In addition to the disease-free, the boundary equilibrium for strain <I>A</I> and strain <I>B</I> was also calculated. Using the Gershgorin’s circle theorem, it was shown that the boundary equilibrium is locally asymptotically stable when both <I>R</I><sub>0<I>A</I></sub>, <I>R</I><sub>0<I>B</sub> <sub></I></sub>> 1, but unstable when otherwise. Simulations of the model were carried out. Results indicate that the government should intensify its efforts to vaccinate a larger proportion of the population and also recommends implementing comprehensive control measures, such as the use of face masks, social distancing, and contact tracing, to mitigate the spread of the disease.

End of the Pandemic - Beginning of Digitalization in the Public Health Service? The German National Funding Program

The data-related desolate state of the health authorities became evident at the latest with the onset of the Covid-19 pandemic. The lack of interoperability and networking among health authorities quickly developed into blockages in contact tracing and pandemic control. As a basis for the study, key figures and funding volumes from the Pact-Public Health Service (Pakt-ÖGD) were evaluated and analyzed using descriptive parameters. In addition, a literature review on the Pakt-ÖGD and related terms was carried out. The Pakt-ÖGD represents the largest financing offensive for the Public Health Service to date. Despite the digitalization pact and the first distributions of funds, there is no consensus on the goals of digitalization such as the ISCODE, Findability, Accessibility, Interoperability und Reuse (FAIR concept). The RKI is currently presenting a new electronic reporting and information system for health authorities (EMIGA), which is to be introduced parallel to DEMIS as a nationwide core application for infection protection. In analogy to health literacy, the public health service needs increased digital literacy to strengthen competence in order to agree on common goals of ISCODE and the FAIR concept, i.e. what digitalization should create or not. A sustainable public health service requires an open and connectable network that goes beyond infection protection (pandemic prevention, preparedness and response - PPPR) to a global One-Health platform.

Incubation Periods of SARS-CoV-2 Wild-Type, Delta, and Omicron Variants–Dominant Periods in Singapore

This study in Singapore analysed the incubation periods of the following SARS-CoV-2 variants: Wuhan-Hu-1, Delta, and Omicron. Three pandemic waves were examined: Wuhan-Hu-1 (January 2020–March 2021), Delta (May–October 2021), and Omicron (January–June 2022). Data from the SingHealth COVID-19 registry, covering patients from 23 January 2020 to 10 June 2022, were used to calculate incubation periods during the three time periods. The study found median incubation periods of 11 days for Wuhan-Hu-1, 3 days for Delta, and 3 days for Omicron (p-value: <0.001). This study highlighted the impact of different containment measures and the importance of robust EMR systems for tracking and managing infectious diseases. Key challenges included accurate contact tracing and IT infrastructure capabilities. The findings support the use of EMR data for future infectious disease preparedness in Singapore.

Turkey’s Contact Tracing Infrastructure From Security and Privacy Perspective

Contact tracing applications may lead to security and privacy concerns. Turkey’s contact tracing application (Hayat Eve Sığar, abbreviated as HES), which is introduced during COVID-19 pandemic, have not been covered yet for its security and privacy features. Comparison of HES with the existing cutting-edge contact tracing approaches could be used to analyse and determine the features of HES. Comparison indicated the undocumented security and privacy features of HES and revealed a set of vulnerabilities that could cause serious attacks. Mitigation techniques against vulnerabilities are proposed but current HES application includes serious attacks that could be performed by an insider or an outsider. The analysis emphasized to be considered in the design of similar applications that will emerge in the future.

SARS-CoV-2 Quarantine Mandated by Contact Tracing: Burden and Infection Rate Among Close Contacts in Zurich, Switzerland, 2020-2021.

Before vaccines and effective treatments were available, quarantine of close contacts was important to limit the spread of SARS-CoV-2. To evaluate potential benefits and harms of quarantine, we aimed to estimate infection rates and describe experiences and mental health among persons in mandated quarantine during the early SARS-CoV-2 pandemic. We invited adults in mandated quarantine after an exposure to SARS-CoV-2 identified through contact tracing of the Canton of Zurich, Switzerland, between August 2020 and January 2021. Participants completed two questionnaires and received up to two SARS-CoV-2 polymerase chain reaction tests, during and at the end of quarantine. Among 395 participants, quarantine duration ranged from 2 to 20days. By day 11 since the last contact, 11.1% [95% CI 8.4%-14.7%] were infected with SARS-CoV-2. The proportion of participants with symptoms of depression doubled from 9.3% before quarantine to 18.9% during quarantine, and 12.1% reported quarantine was very or extremely difficult. Although quarantine was only moderately burdensome for most participants, some experienced significant difficulties and burden. Policymakers need to balance infection control with potential harms placed on individuals.

Validation of Saliva as the Clinical Specimen Type for a University-Wide COVID-19 Surveillance Program.

At the beginning of the COVID-19 pandemic, the Georgia Institute of Technology made the decision to keep the university doors open for on-campus attendance. To manage COVID-19 infection rates, internal resources were applied to develop and implement a mass asymptomatic surveillance program. The objective was to identify infections early for proper follow-on verification testing, contact tracing, and quarantine/isolation as needed. Program success depended on frequent and voluntary sample collection from over 40,000 students, faculty, and staff personnel. At that time, the nasopharyngeal (NP) swab, not saliva, was the main accepted sample type for COVID-19 testing. However, due to collection discomfort and the inability to be self-collected, the NP swab was not feasible for voluntary and frequent self-collection. Therefore, saliva was selected as the clinical sample type and validated. A saliva collection kit and a sample processing and analysis workflow were developed. The results of a clinical sample-type comparison study between co-collected and matched NP swabs and saliva samples showed 96.7% positive agreement and 100% negative agreement. During the Fall 2020 and Spring 2021 semesters, 319,988 samples were collected and tested. The program resulted in maintaining a low overall mean positivity rate of 0.78% and 0.54% for the Fall 2020 and Spring 2021 semesters, respectively. For this high-throughput asymptomatic COVID-19 screening application, saliva was an exceptionally good sample type.

Tracing wide-spread infectious contacts using GeoSpark in preventive medicine

A threat to governments and the medical community globally are infectious illness outbreaks such as COVID-19, Spanish flu, and Ebola, which kill millions of people. Furthermore, because people are afraid to go to their employment, infectious diseases hinder economic progress. Therefore, it is imperative to implement interventions to lessen the spread of infectious diseases. From this angle, the practice of tracking contacts might be viewed as a mitigation strategy to stop the spread of contagious diseases. As this is going on, users’ trace data sets are growing exponentially larger over time, making it difficult to conduct contact tracing queries over them. In this paper, a novel Spark contact-tracing query processing method is proposed. This method determines if users are suspected cases by analyzing their paths based on two variables: nearby social distance and exposure time. Additionally, the developed method makes full use of the Spark framework to address scalability issues and effectively respond to contact tracing inquiries over a wide range of trajectories.

Impact of a University-Led COVID-19 Case Investigation and Contact Tracing Program.

The coronavirus disease 2019 (COVID-19) pandemic devastated societies and economies worldwide. Given the major disruptions to higher education, reflection on university responses to the COVID-19 pandemic may provide insights for future outbreaks. Here, we describe the epidemiology of COVID-19 on the Emory University campus during the 2020-2021 academic year and provide an evaluation of the performance of a university-led program with the purpose of describing the effectiveness of efforts to augment the public health authority's case investigation and contact tracing efforts during a public health emergency. Evaluation of a case investigation and contact tracing program regarding operations, timeliness, and performance. We analyzed quality metrics to determine the proportion of cases and contacts interviewed and the time to completion of each step from case diagnosis to testing of contacts. During the 2020-2021 academic year, 1267 COVID-19 cases among Emory students, faculty, and staff were confirmed by polymerase chain reaction, with 1132 reported close contacts. Among cases, the median test turnaround time was 1 day (interquartile range: 1, 2). Among both cases and close contacts, 98% were successfully interviewed. The team called a majority of cases on the same day as their test result was reported to the program (87%; n =1052). Almost all (98%; n =1247) cases completed isolation or were advised to isolate during the review period. Close to half (46%; n =513) of contacts interviewed began quarantine before their interview. Among close contacts interviewed, 13% (n=145) subsequently converted to an index case. The impact and performance of Emory's program may provide useful and actionable data for future university-led infectious disease outbreak response programs. The program structure, performance metrics, and information collected via interviews provide practical implications and an organized structure to guide other programs during future outbreaks.

The use of medical students to enhance inpatient contact tracing during the COVID-19 pandemic

The use of medical students to enhance inpatient contact tracing during the COVID-19 pandemic

Meeting Social Needs in a Crisis Context: Lessons Learned from Integrating the 'Take Care Initiative' into New York City's Testing and Contact Tracing Program.

The COVID-19 pandemic highlighted the importance of addressing social needs in a crisis context. Some US jurisdictions integrated a social service component into case investigation and contact tracing (CI/CT) programs, including the New York City (NYC) Test & Trace (T2) Program; the Take Care initiative referred NYC residents who tested positive or were exposed to COVID-19 to services to support isolation and quarantine and meet basic needs. More research is needed to determine effective implementation strategies for integrating social needs provision into CI/CT programs. To identify barriers and facilitators to the implementation of the Take Care initiative, we conducted key informant interviews with program staff, community-based organization partners, and cases and contacts as part of a larger evaluation of the T2 program. Interviews were recorded, transcribed, and analyzed using rapid qualitative methods. Key facilitators to implementation included utilizing a case management software system, employing strategies to encourage service uptake, leveraging cross-agency collaborations, and partnering with community-based organizations for resource navigation. Barriers identified included external management of the software system, challenges reaching and engaging the public, administrative complications due to shifting collaborations, and management of CBO partners' structure and hiring. Based on our findings, we provide recommendations to support effective planning and implementation of social needs service provision in a crisis context. Future research should focus on testing promising implementation strategies highlighted in this study and applying them to varied contexts and crisis situations.

Emulating target trials of postexposure vaccines using observational data.

Postexposure vaccination has the potential to prevent or modify the course of clinical disease among those exposed to a pathogen. However, due to logistical constraints, postexposure vaccine trials have been difficult to implement in practice. In place of trials, investigators have used observational data to estimate the effectiveness or optimal timing window for postexposure vaccines, but the relationship between these analyses and those that would be conducted in a trial is often unclear. Here, we define several possible target trials for postexposure vaccination and show how, under certain conditions, they can be emulated using observational data. We emphasize the importance of the incubation period and the timing of vaccination in trial design and emulation. As an example, we specify a protocol for postexposure vaccination against mpox and provide a step-by-step description of how to emulate it using data from a healthcare database or contact tracing program. We further illustrate some of the benefits of the target trial approach through simulation.

Personal characteristics and transmission dynamics associated with SARS-CoV-2 semi-quantitative PCR test results: an observational study from Belgium, 2021-2022.

Following harmonization efforts by the Belgian National Reference Center for SARS-CoV-2, semi-quantitative PCR test (SQ-PCR) results, used as a proxy for viral load, were routinely collected after performing RT-qPCR tests. We investigated both the personal characteristics associated with SQ-PCR results and the transmission dynamics involving these results. We used person-level laboratory test data and contact tracing data collected in Belgium from March 2021 to February 2022. Personal characteristics (age, sex, vaccination, and laboratory-confirmed prior infection) and disease stage by date of symptom onset were analyzed in relation to SQ-PCR results using logistic regression. Vaccine effectiveness (VE) against a high viral load (≥107 copies/mL) was estimated from the adjusted probabilities. Contact tracing involves the mandatory testing of high-risk exposure contacts (HREC) after contact with an index case. Odds ratios for test positivity and high viral load in HREC were calculated based on the SQ-PCR result of the index case using logistic regression models adjusted for age, sex, immunity status (vaccination, laboratory-confirmed prior infection), variant (Alpha, Delta, Omicron), calendar time, and contact tracing covariates. We included 909,157 SQ-PCR results of COVID-19 cases, 379,640 PCR results from index cases, and 72,052 SQ-PCR results of HREC. High viral load was observed more frequently among recent cases, symptomatic cases, cases over 25 years of age, and those not recently vaccinated (>90 days). The vaccine effectiveness (VE) of the primary schedule in the first 30 days after vaccination was estimated at 47.3% (95%CI 40.8-53.2) during the Delta variant period. A high viral load in index cases was associated with an increased test positivity in HREC (OR 2.7, 95%CI 2.62-2.79) and, among those testing positive, an increased likelihood of a high viral load (OR 2.84, 95%CI 2.53-3.19).

Vaccine-associated measles in an immunocompromised host: Hospital infection prevention and control and public health response

Introduction: Vaccine-associated measles is generally not considered to be transmissible, as opposed to wild-type measles, which is one of the most highly contagious diseases. Data on contact and exposure management of vaccine-associated measles is limited, with varied approaches to such cases described in the literature. Methods: We report the case of a 2-year-old immunosuppressed child who developed a febrile exanthem with mild conjunctivitis 18 days after receiving the measles-mumps-rubella-varicella vaccine. Results: Given the patient's recent measles-containing vaccination while on immunosuppressive medications, consistent clinical findings and the lack of epidemiological risk factors for wild-type infection, the decision was made to treat this as a presumptive case of vaccine-associated measles virus prior to return of confirmatory genotyping results. After consultation with public health experts, contact tracing was not considered necessary. No secondary measles cases were identified, despite a large exposure potential due to lack of consistent airborne precautions during hospital admission. Discussion: This case highlights the lack of transmissibility of vaccine-associated measles in immunocompromised hosts, adding to the scant body of literature on this topic, with the potential to inform hospital infection prevention and control as well as public health management in similar situations.

Characterization of azithromycin-resistant Shigella flexneri serotype 2a isolates using whole genome sequencing in Ontario from 2016 to 2018.

Azithromycin-resistant shigellosis is increasing globally. This retrospective analysis of Shigella flexneri serotype 2a isolates from 2016 to 2018 in Ontario found nearly half were azithromycin (47.7%, 72/151) and ciprofloxacin (50.7%, 77/152) resistant. Moreover, 34.7% (25/72) of azithromycin-resistant isolates were also ciprofloxacin-resistant. Four isolates were ceftriaxone-resistant, although all azithromycin-resistant isolates were ceftriaxone-susceptible. Overall, 83.6% (127/152) of all S. flexneri 2a isolates were recovered from males and 97.2% (70/72) of the azithromycin-resistant cases were males. Among the azithromycin-resistant cases, some (8/72) reported international travel. Phylogenetic analysis of azithromycin-resistant isolates revealed two large male-dominated clusters, and one cluster may have been due to importation of resistant strain. Comparison of plasmids isolated from the clusters in Ontario revealed the presence of incFII plasmid with high percentage of similarity to plasmids present in global outbreaks affecting mostly males including men who have sex with men (MSM). These two large azithromycin-resistant clusters are suggestive of an outbreak among MSM, though disease exposure or sexual orientation of patients was unknown. The presence of plasmid-borne azithromycin resistance in ciprofloxacin-resistant isolates is a public health concern. Antimicrobial surveillance is important for patient management, understanding the spread of novel resistance types in local communities which sometimes is introduced by travel. We found ongoing multidrug-resistant outbreaks spanning multiple years affecting males. Reduction of future outbreaks in high-risk communities like MSM requires consorted information flow between laboratory, public health, and physicians. We impart genomic and antimicrobial characteristics of multidrug S. flexneri 2a which may serve as reference by clinicians and public health.IMPORTANCEOral ciprofloxacin and azithromycin are generally considered as the first-line therapy of shigellosis. Here, we report the emergence and transmission of azithromycin and ciprofloxacin-resistant S. flexneri serotype 2a among male adults in Ontario during 2016-2018. The percentage of azithromycin and ciprofloxacin resistance among S. flexneri 2a is higher compared to previous reports from Canada and United States. Here, we show the genetic basis of the antimicrobial resistance among these unique groups of S. flexneri 2a isolates. We describe a domestically acquired azithromycin-resistant and ciprofloxacin-resistant S. flexneri 2a lineage in Ontario. Combining whole-genome sequencing (WGS) data with travel-associated data helped in understanding dissemination and transmission. We employed WGS, which not only helped us in understanding the genetic-relationship between isolates but also mine information regarding plasmids. In the future, linking WGS, travel-related data, and clinical data can provide enhanced contact tracing and improve public-health management.

Identifying Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data.

Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has not been investigated in the molecular epidemiology field. To understand how contact tracing influences a recovered phylogeny, we developed a new simulation tool called SEEPS (Sequence Evolution and Epidemiological Process Simulator) that allows for the simulation of contact tracing and the resulting transmission tree, pathogen phylogeny, and corresponding virus genetic sequences. Importantly, SEEPS takes within-host evolution into account when generating pathogen phylogenies and sequences from transmission histories. Using SEEPS, we demonstrate that contact tracing can significantly impact the structure of the resulting tree, as described by popular tree statistics. Contact tracing generates phylogenies that are less balanced than the underlying transmission process, less representative of the larger epidemiological process, and affects the internal/external branch length ratios that characterize specific epidemiological scenarios. We also examined real data from a 2007-2008 Swedish HIV-1 outbreak and the broader 1998-2010 European HIV-1 epidemic to highlight the differences in contact tracing and expected phylogenies. Aided by SEEPS, we show that the data collection of the Swedish outbreak was strongly influenced by contact tracing even after downsampling, while the broader European Union epidemic showed little evidence of universal contact tracing, agreeing with the known epidemiological information about sampling and spread. Overall, our results highlight the importance of including possible non-uniform sampling schemes when examining phylogenetic trees. For that, SEEPS serves as a useful tool to evaluate such impacts, thereby facilitating better phylogenetic inferences of the characteristics of a disease outbreak. SEEPS is available at github.com/MolEvolEpid/SEEPS.

Prediction of rail wear band evolution under excitation by periodic track irregularities and its influence on vehicle dynamic performance

Periodic track irregularities (PTIs) are an important and sensitive source of vehicle vibration and have attracted considerable attention from railway researchers. However, previous studies have mainly focused on the irregularities themselves, with limited investigation of how the rail wear band (RWB) generated by PTIs excitation affects vehicle responses. To assess this, a three-dimensional rail wear prediction model is developed in this study to simulate the evolution of the RWB under PTIs conditions and then the effect of RWB excitation on the vehicle dynamic performance is investigated. The results show that the spatial trace of the rail contact points generated by the PTIs also exhibits clear periodic characteristics. Accordingly, the distribution pattern of the RWB also reflects these periodic features. The excitation of the periodic rail wear band (PRWB) has a negative effect on the vehicle running stability, especially when the vehicle is traveling at speeds that induce coupling resonance, which exacerbates the consequences. As the wear level of the PRWB increases, there is also an escalation in the vibration of the carbody. Furthermore, the amplitude of the change in the wheelset balance position resulting from variations in rail profile is found to serve as an effective descriptor for characterizing the wear intensity of PRWB, and the vibration amplitude of the carbody exhibits a clear linear correlation with PRWB excitation. The research results are helpful for understanding the relationship between PRWB excitation and vehicle vibration behavior and serve as a theoretical basis for track maintenance and profile optimization.

Effectiveness of probabilistic contact tracing in epidemic containment: The role of superspreaders and transmission path reconstruction.

The recent COVID-19 pandemic underscores the significance of early stage nonpharmacological intervention strategies. The widespread use of masks and the systematic implementation of contact tracing strategies provide a potentially equally effective and socially less impactful alternative to more conventional approaches, such as large-scale mobility restrictions. However, manual contact tracing faces strong limitations in accessing the network of contacts, and the scalability of currently implemented protocols for smartphone-based digital contact tracing becomes impractical during the rapid expansion phases of the outbreaks, due to the surge in exposure notifications and associated tests. A substantial improvement in digital contact tracing can be obtained through the integration of probabilistic techniques for risk assessment that can more effectively guide the allocation of diagnostic tests. In this study, we first quantitatively analyze the diagnostic and social costs associated with these containment measures based on contact tracing, employing three state-of-the-art models of SARS-CoV-2 spreading. Our results suggest that probabilistic techniques allow for more effective mitigation at a lower cost. Secondly, our findings reveal a remarkable efficacy of probabilistic contact-tracing techniques in performing backward and multistep tracing and capturing superspreading events.