Tracing Program Research Articles

Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center study.

We determined the prevalence and epidemiological characteristics of COVID-19 in Jakarta and neighboring areas, Indonesia from March 2020 to February 2021, based on nasopharyngeal/oropharyngeal (NP/OP) swab specimens that were tested at the Eijkman Institute for Molecular Biology, Jakarta. NP/OP swab specimens were collected from COVID-19 suspects or individuals in contact tracing programs from primary healthcare centers (PHC) and hospitals. The specimens were screened for the SARS-CoV-2 by qRT-PCR. Demography data and clinical symptoms were collected using national standardized laboratory form. Of 64,364 specimens, 10,130 (15.7%) were confirmed positive for SARS-CoV-2, with the peak prevalence of infection in March 2020 (26.3%) follow by in January 2021 (23.9%) and February 2021 (21.8%). We found that the positivity rate of the specimens from Jakarta, West Java, and Banten was 16.3%, 13.3%, and 16.8%, respectively. Positivity rate was higher in specimens from hospitals (16.9%) than PHC (9.4%). Of the positive specimens, 29.6% were from individuals aged >60 years old, followed by individuals aged 41-60 years old (24.2%). Among symptomatic cases of SARS-CoV-2, the most common symptoms were cough, fever, and a combination of both cough & fever. In conclusion, this study illustrates the prevalence and epidemiological characteristics from one COVID-19 diagnostic center in Jakarta and neighbouring areas in Indonesia.

Learning from Shader Program Traces

AbstractDeep learning for image processing typically treats input imagery as pixels in some color space. This paper proposes instead to learn from program traces of procedural fragment shaders – programs that generate images. At each pixel, we collect the intermediate values computed at program execution, and these data form the input to the learned model. We investigate this learning task for a variety of applications: our model can learn to predict a low‐noise output image from shader programs that exhibit sampling noise; this model can also learn from a simplified shader program that approximates the reference solution with less computation, as well as learn the output of postprocessing filters like defocus blur and edge‐aware sharpening. Finally we show that the idea of learning from program traces can even be applied to non‐imagery simulations of flocks of boids. Our experiments on a variety of shaders show quantitatively and qualitatively that models learned from program traces outperform baseline models learned from RGB color augmented with hand‐picked shader‐specific featues like normals, depth, and diffuse and specular color. We also conduct a series of analyses that show certain features within the trace are more important, and even learning from a small subset of the trace outperforms the baselines.

Development of a high sensitivity RT-PCR assay for detection of SARS-CoV-2 in individual and pooled nasopharyngeal samples

The COVID-19 pandemic requires sensitive detection of the SARS-CoV-2 virus from samples to ensure accurate detection of infected patients, an essential component of effective national track and trace programs. Due to the scaling challenges of large sample numbers, sample pooling is an attractive solution to reduce both extraction and amplification reagent costs, if high sensitivity can be maintained. We demonstrate that the Erba Molecular ErbaMDx SARS-CoV-2 RT-PCR Kit (EM kit) delivers high sensitivity, achieving analytical detection of 5 copies/reaction SARS-CoV-2 genomic RNA, and 200 copies/mL SARS-CoV-2 inactivated virus spiked into nasopharyngeal swab (NP) samples and extracted through workflow. Furthermore, the EM Kit demonstrates high sensitivity in both pooled (1 in 5) and non-pooled NP samples when compared to an FDA Emergency Use Authorization approved assay, following published FDA guidelines. These findings demonstrate that the EM Kit is suitable for sample pooling, with minimal impact on assay performance. As the COVID-19 pandemic progresses, high sensitivity assays such as the EM Kit will have an important role in ensuring high throughput and sensitive testing using pooled samples can be maintained, delivering the most cost-effective sample extraction and amplification option for national test and trace programs.

Estimated COVID-19 Cases and Hospitalizations Averted by Case Investigation and Contact Tracing in the US

Evidence of the impact of COVID-19 case investigation and contact tracing (CICT) programs is lacking, but policy makers need this evidence to assess the value of such programs. To estimate COVID-19 cases and hospitalizations averted nationwide by US states' CICT programs. This decision analytical model study used combined data from US CICT programs (eg, proportion of cases interviewed, contacts notified or monitored, and days to case and contact notification) with incidence data to model outcomes of CICT over a 60-day period (November 25, 2020, to January 23, 2021). The study estimated a range of outcomes by varying assumed compliance with isolation and quarantine recommendations. Fifty-nine state and territorial health departments that received federal funding supporting COVID-19 pandemic response activities were eligible for inclusion. Data analysis was performed from July to September 2021. Public health case investigation and contact tracing. The primary outcomes were numbers of cases and hospitalizations averted and the percentage of cases averted among cases not prevented by vaccination and other nonpharmaceutical interventions. In total, 22 states and 1 territory reported all measures necessary for the analysis. These 23 jurisdictions covered 42.5% of the US population (approximately 140 million persons), spanned all 4 US Census regions, and reported data that reflected all 59 federally funded CICT programs. This study estimated that 1.11 million cases and 27 231 hospitalizations were averted by CICT programs under a scenario where 80% of interviewed cases and monitored contacts and 30% of notified contacts fully complied with isolation and quarantine guidance, eliminating their contributions to future transmission. As many as 1.36 million cases and 33 527 hospitalizations could have been prevented if all interviewed cases and monitored contacts had entered into and fully complied with isolation and quarantine guidelines upon being interviewed or notified. Across both scenarios and all jurisdictions, CICT averted an estimated median of 21.2% (range, 1.3%-65.8%) of the cases not prevented by vaccination and other nonpharmaceutical interventions. These findings suggest that CICT programs likely had a substantial role in curtailing the pandemic in most jurisdictions during the 2020 to 2021 winter peak. Differences in outcomes across jurisdictions indicate an opportunity to further improve CICT effectiveness. These estimates demonstrate the potential benefits from sustaining and improving these programs.

Contact tracing in epidemiology: Lessons learnt from COVID-19

Contact tracing is a powerful public health tool used in identifying people that might have been in contact with an infected person to assess the potential of being infected and transmitting the diseases. This review explores the history, implementation, and effects of contact tracing, as a significant public health strategy during the COVID-19 pandemic. The review started by giving a historical summary of contact tracing, then links it to early efforts at disease control for diseases such smallpox and TB. We further examine pre-COVID-19 contact tracing approaches, such as manual and early digital tools employed during past epidemics like Ebola and Zika. While investigating the development of digital innovations—such as Bluetooth-based applications and location data tracking—that were used to improve tracing efforts—the review emphasises the efficacy and problems of conventional manual contact tracing during COVID-19. Notably, we examine the hybrid models that combine manual and digital approaches, proving higher compliance and efficiency. Along with the difficulties countries with less efficient tracing systems—such as the United States and India—the review also includes worldwide case studies showing successful implementations in countries such Taiwan, South Korea, and New Zealand. Emphasising the need of public trust and the effect of the digital divide, it also covers public compliance and social elements affecting involvement in contact tracing programs. In order to strengthen public health preparedness for next pandemics, we offer potential options for contact tracing resilience, arguing for contact systems backed by technological developments and ethical protections. Informing best practices for next epidemiological tactics, this thorough analysis uncovers important insights and lessons learnt from the COVID-19 pandemic.

Knowledge, Practice, and Awareness about Preventive Measures of Chikungunya among Traders Community in Mitford Region of Dhaka City

Aim: Chikungunya virus (CHIKV) is an arbovirus transmitted by Aedes mosquitos that causes a regional epidemic and becomes a remarkable public health problem. Chikungunya disease outbreak was first identified in Bangladesh in 2008. Very limited information is available to assess knowledge, practice, and awareness of the community to prevent Chikungunya. As community engagement and motivational interventions are mainly focused to prevent mosquito bite and to control their breeding, the aim of this study was to assess knowledge, practice, and awareness (KPA) of the community for preventive measures about Chikungunya.
 Methods: This descriptive cross-sectional study was conducted in Mitford region of Dhaka city from January to May 2021 among 280 traders and data were collected using a self-administered structured questionnaire and observational checklist.
 Results: Most of the respondents had informed about Chikungunya from media (41.79%). About 50.71% respondents were informed about the transmitted vector of chikungunya and out of them, 47.18% also had knowledge that Aedes variant is the specific vector for this disease, but more than half (55.71%) did not know that it is a viral borne disease. Again, only 16.43% of the respondents knew about the actual biting time. Study also revealed that 38.93% respondents practiced bed net, 18.21% mosquito coils and 13.22% aerosol as effective preventive measures. Only 25% aware to keep drain, free from blockage, 20.72% aware to change water from house plant container and only 6.79% aware to notify city corporation authority to take necessary action to prevent spreading of disease though 50% of the respondent stated that they were aware about government existing activity of fogging the areas, destroying the bush (23.93%) and improving water drainage system (18.93%) that effectively destroy further breeding of vector and spreading of transmission. About 67.5% took paracetamol as the primary management and 11.79% aware to take bed rest but 11% did not aware about the management. 62% were conscious about the joint complication but 28.22% did not have any idea.
 Conclusion: This study found that community had lack of knowledge, practice, and awareness to take proper preventive measures that might be improved by formulating an extensive community-based guideline involving the concerned municipal authority and other stockholders by updating the gaps in knowledge, practice and to organize awareness tracing program among the community.

An overview of the establishment of a national contact tracing programme: a quality improvement approach in a time of pandemic

Background: With the onset of the coronavirus disease 2019 (COVID-19) pandemic, the Irish health system needed a contact tracing and management intervention at a national level to undertake high volume, low complexity contact tracing. This paper describes the establishment and first year of a national Contact Management Programme (CMP) in Ireland, its core components, outcomes on key measures (coverage, timeliness, and training) and learnings from the process. Methods: CMP is centred on four steps, 1) case: rapid notification to a person of a result and provision of advice, 2) contacts: rapid identification of contacts, 3) control: rapid public health management of contacts, which includes testing and 4) active follow-up of close contacts with additional testing and public health advice reminder SMS and calls. The outcome measures used in this study are: 1) The proportion of all Irish cases contact traced through the CMP (Coverage), 2) the time taken to complete the 3 types of CMP calls (timeliness), 3) number of contact tracers trained and their feedback (training). Results: 246,666 positive cases were recorded using the CMP between 17th March 2020 and 30th April 2021, with contact tracing successfully completed for 237,759 cases, representing 99% and 96%, respectively, of the 248,529 cases notified in Ireland up to the 30th of April 2021. The average time taken for contact tracing to be completed was 29.4 hours (95% CI 28.9, 29.9) and the median was 16.8 hours (approximate 95% CI 15.9, 17.7). Conclusion: Using the Quality Improvement (QI) approach, the Health Service Executive (HSE) successfully established and scaled up a Contact Management Programme that rapidly notified results to people and traced their close contacts. CMP contributed to the success of the Irish health service in managing the pandemic. CMP slowed COVID-19 transmission and lessened the impact on health services capacity.

Using a ray tracing program to calculate sunrise times over a digital terrain model based visible horizon using a simplified atmospheric model, part II

In a previous paper we compared observations to calculated values of the sunrise times for one place in Jerusalem. It was shown that the sunrise over the actual physical horizon could be modeled to an accuracy of about ±15 s for most of the year. Success of those calculations suggested that terrain modeling was the most important factor in obtaining this result. To investigate this point, we repeated our calculations using the ray tracing method and simplified atmosphere developed by Siebren Van der Werf, whose atmospheric model is easily applied to other places in the world. Our results show that the new calculation method maintained our requirement of ±15 s accuracy (required for publication of sunrise time tables, critical for daily Jewish observances worldwide). Standard formulas for atmospheric refraction produce approximately the same results even for near horizon zenith angles. For portions of the year where low altitude inversions are especially important, e.g., during those days associated with maximum radiative cooling, these additional atmospheric effects can be effectively modeled in a very simple way.

Implementation of a Case Investigation and Contact Tracing Program at an Academic Medical Center in New York City.

ProblemIn the spring of 2020, New York City was an epicenter of COVID-19 infections, hospitalizations, and mortality. One of the hardest hit areas in New York City was central Brooklyn, where State University of New York (SUNY) Downstate is located. As the severity of the initial wave of the COVID-19 pandemic waned in New York City, SUNY Downstate Health Sciences University planned to institute COVID-19 surveillance on campus to limit its spread among employees and students.ApproachIn collaboration with university leadership and students across schools, the SUNY Downstate Contact Tracing Corps was established in July 2020. Using guidance from the Centers for Disease Control and Prevention and the New York State Department of Health, protocols for case and contact investigations, including scripts, were developed. Students were recruited and trained in remote and confidential case and contact investigations.OutcomesFrom August 1, 2020, to March 23, 2021, there were 185 COVID-19 cases referred to the contact tracing program; of these, 180 were successfully investigated and isolated (97%). Case investigations identified 111 Downstate close contacts; 105 were investigated and quarantined (94.5%). There were 122 exposure-only investigations referred to the program, and 121 were successfully investigated and quarantined (99%).Next StepsThe SUNY Downstate Contact Tracing Corps transitioned to a core group of tracers in January 2021 and has been maintained at 4 to 6 tracers since that time. With the emergence of COVID-19 variants, the threat of new variants, and variable COVID-19 vaccination rates across Brooklyn, Downstate employees and students remain vulnerable to COVID-19 transmission. Given this, the SUNY Downstate Contact Tracing Corps will continue to conduct case and contact investigations.

Learning from the initial deployment of digital contact tracing apps

Learning from the initial deployment of digital contact tracing apps

Effects of the Laschamps Excursion on Geomagnetic Cutoff Rigidities

AbstractToday's geomagnetic field can prevent energetic particles, including solar energetic particles and galactic cosmic rays, from directly hitting the Earth's atmosphere. However, when the geomagnetic field strength is significantly decreased during geomagnetic field excursions or reversals, the geomagnetic field shielding effect becomes less prominent. Geomagnetic cutoff rigidity, as a quantitative estimation of the shielding effect, can be calculated using trajectory tracing or theoretical equations. We use a recent high‐resolution continuous geomagnetic field model (LSMOD.2) to study the geomagnetic cutoff rigidity during the Laschamps excursion. Global grids of the geomagnetic cutoff rigidities are presented, in particular for the excursion midpoint when the geomagnetic field is weak and not dipole‐dominated anymore at Earth's surface. We compare the cutoff rigidity calculation results between a trajectory tracing program and theoretical equations and we find that the influence of the non‐dipole component of the geomagnetic field cannot be ignored during the excursion. Our results indicate that the exposure of Earth's atmosphere to energetic particles of cosmic and solar origin is high and nearly independent of latitude in the middle of the Laschamps excursion. Our results will be useful for future studies associated with cosmic radiation dose rate and cosmogenic isotope production rate during the Laschamps excursion.

COVID-19 Case Investigation and Contact Tracing Programs and Practice: Snapshots From the Field.

Between Fall 2020 and Spring 2021, the Association of State and Territorial Health Officials conducted 2 rapid queries to collect information from the field regarding the status of COVID-19 case investigation and contact tracing (CI/CT) programs and practice. These short surveys were distributed to senior deputies in state and territorial health agencies, yielding a response rate of 45.8% (November 2020) and 40.7% (April 2021). Findings indicated that CI/CT staff roles and assigned functions varied across jurisdictions, as did staffing levels/capacity, approaches for linking individuals to social supports, and program changes that were planned or underway. Agency-reported staffing levels/capacity and programmatic challenges changed over time, highlighting the dynamic nature of CI/CT program practice and implementation. While findings from the surveys cannot be generalized to the national level, they provide critical insights from the field on CI/CT program implementation, challenges, and changes in response to the evolving COVID-19 epidemic in the United States.

Digital contact tracing in the pandemic cities: Problematizing the regime of traceability in South Korea

Since 2020, many countries worldwide have deployed digital contact tracing programs that rely on a range of digital sensors in the city to locate and map the routes of viral spread. Many critical commentaries have raised concerns about the privacy risks and trustworthiness of these programs. Extending these analyses, this paper opens up a different line of questioning that goes beyond privacy-centered single-axis critique of surveillance by considering digital contact tracing symptomatic of the broader changes in modes of urban governance that renders our cities traceable, knowable, and governable through data. Based on archival and real-time analysis of South Korean national and local COVID-19 dashboards, online forums, and interviews with South Korean public health practitioners, this paper offers a sociotechnical analysis of digital contact tracing that looks at the various intersections of state-political, bio-political, and techno-political power dynamics. In contrast to popular narratives that attributed the success of the Korean approach to digital contact tracing to its collectivist culture and smart city infrastructures, this paper suggests that the case can be better understood by looking at both the macro-level shift in the forms of governance that takes on a spatialized and networked character and the micro-level formation of moral responsibility that shape one's conduct as a health and safety-conscious citizens. As the latest realization of the expanding regime of traceability in digital/urban governance, the development of digital contract tracing is seen to parallel with concurrent changes occurring in multiple domains of life including knowledge production, cultural memory, and individual subjectivity.

Автоматизоване проектування друкованих плат у CАПР та їх подальше виготовлення за допомогою CNC-машин

The article presents methods and means of 3D design of printed circuit boards in CAx. Automated placement of elements on the board is implemented by means of API SolidWorks using Visual Studio C#. The API application works by an algorithm that allows you to create a 3D layout of printed circuit boards. Each component of the library contains a conditional graphic notation of the element. With the help of the implemented algorithm, a comprehensive approach is provided, which consists in the fact that already at this stage the preparation of the strategy for tracing the conductors of the future printed circuit board is carried out, the classes of circuits are determined and the necessary technological parameters are set, as well as the data necessary for the preparation of design documentation is generated. After the completion of the work on the input of the scheme, a check is made for the presence of errors and compliance with the specified parameters, and if the test is successful, a list of circuits is generated for transfer to the tracing program. From this moment, any possibility of errors in the subsequent stages of design is excluded. CAD DipTrace was used to trace printed circuit boards and generate g-code. Printed circuit board processing is carried out on a CNC machine - CNC3018 using the Candle program. The printed circuit board tracks are created by forming a groove between the track and the metallized coating of the textolite. With the help of the formed height map, the uniform removal of the metallization layer over the entire area of the textolite is ensured. In addition, holes are drilled for the output elements of the circuit, the printed circuit board is cut along the contour and covered with a layer of tin to prevent oxidation of its metallized coating. The considered CAD methods and tools made it possible to automate the design of the printed circuit board of the FM radio receiver control module. As a result of the performed work, means of automating the design of printed circuit boards were applied and a fully functional printed circuit board with a track width of 0.8 mm was obtained.

Design and optimization of transparent scattering solar concentrator based on SiO<sub>2</sub> aerogel

Scattering solar concentrators (SSCs), an important component of transparent/translucent photovoltaic devices, can concentrate large-area sunlight on small-area solar cells while allowing some sunlight to pass through the devices. However, owing to the lack of suitable scattering materials, there have been few reports on SSCs in recent years. In this study, we fabricated SiO<sub>2</sub> aerogel-based SSCs and tested their performances. The photoelectric performance was found to be moderate. Additionally, the results demonstrated excellent transmittance and color rendering index, which meet the lighting requirements of the windows. A Monte Carlo ray tracing program was developed to simulate an SSC and analyze the fate of all photons. We also analyzed the multiple scattering mechanism in SSCs that damages the photoelectric efficiency of a device via theoretical simulation. Finally, we proposed an anisotropic scattering device that can increase the primary scattering and suppress multiple scattering, resulting in excellent photoelectric efficiency.

Characterization of Unlinked Cases of COVID-19 and Implications for Contact Tracing Measures: Retrospective Analysis of Surveillance Data.

BackgroundContact tracing and intensive testing programs are essential for controlling the spread of COVID-19. However, conventional contact tracing is resource intensive and may not result in the tracing of all cases due to recall bias and cases not knowing the identity of some close contacts. Few studies have reported the epidemiological features of cases not identified by contact tracing (“unlinked cases”) or described their potential roles in seeding community outbreaks.ObjectiveFor this study, we characterized the role of unlinked cases in the epidemic by comparing their epidemiological profile with the linked cases; we also estimated their transmission potential across different settings.MethodsWe obtained rapid surveillance data from the government, which contained the line listing of COVID-19 confirmed cases during the first three waves in Hong Kong. We compared the demographics, history of chronic illnesses, epidemiological characteristics, clinical characteristics, and outcomes of linked and unlinked cases. Transmission potentials in different settings were assessed by fitting a negative binomial distribution to the observed offspring distribution.ResultsTime interval from illness onset to hospital admission was longer among unlinked cases than linked cases (median 5.00 days versus 3.78 days; P<.001), with a higher proportion of cases whose condition was critical or serious (13.0% versus 8.2%; P<.001). The proportion of unlinked cases was associated with an increase in the weekly number of local cases (P=.049). Cluster transmissions from the unlinked cases were most frequently identified in household settings, followed by eateries and workplaces, with the estimated probability of cluster transmissions being around 0.4 for households and 0.1-0.3 for the latter two settings.ConclusionsThe unlinked cases were positively associated with time to hospital admission, severity of infection, and epidemic size—implying a need to design and implement digital tracing methods to complement current conventional testing and tracing. To minimize the risk of cluster transmissions from unlinked cases, digital tracing approaches should be effectively applied in high-risk socioeconomic settings, and risk assessments should be conducted to review and adjust the policies.

Computational vector fiducial for deflectometry system alignment.

One of deflectometry's cardinal strengths is its ability to measure highly dynamically sloped optics without needing physical null references. Accurate surface measurements using deflectometry, however, require precise calibration processes. In this Letter, we introduce an alignment technique using a computational fiducial to align a deflectometry system without additional hardware equipment (i.e., algorithmic innovation). Using the ray tracing program, we build relationships between the plane of the screen and detector and algorithmically generate a fiducial pattern for the deflectometry configuration. Since the fiducial pattern is based on ideal system geometry, misalignment of the unit under test with its target position causes a discrepancy between the actual image on the camera detector and the ideal fiducial image. We leverage G and C vector polynomials to quantify misalignment and estimate the alignment status through a reverse optimization method. Simulation and experimental results demonstrate that the proposed algorithm can align the 195mm×80mm of a rectangular aperture freeform optic within 10 µm of peak-to-valley accuracy. The computational fiducial-based alignment algorithm is simple to apply and can be an essential procedure for conventional methods of deflectometry system alignment.

Cost-effectiveness of the COVID-19 test, trace and isolate program in Colombia

BackgroundDuring the COVID-19 pandemic, Test-Trace-Isolate (TTI) programs have been recommended as a risk mitigation strategy. However, many governments have hesitated to implement them due to their costs. This study aims to estimate the cost-effectiveness of implementing a national TTI program to reduce the number of severe and fatal cases of COVID-19 in Colombia.MethodsWe developed a Markov simulation model of COVID-19 infection combined with a Susceptible-Infected-Recovered structure. We estimated the incremental cost-effectiveness of a comprehensive TTI strategy compared to no intervention over a one-year horizon, from both the health system and the societal perspective. Hospitalization and mortality rates were retrieved from Colombian surveillance data. We included program costs of TTI intervention, health services utilization, PCR diagnosis test, productivity loss, and government social program costs. We used the number of deaths and quality-adjusted life years (QALYs) as health outcomes. Sensitivity analyses were performed.FindingsCompared with no intervention, the TTI strategy reduces COVID-19 mortality by 67%. In addition, the program saves an average of $1,045 and $850 per case when observed from the social and the health system perspective, respectively. These savings are equivalent to two times the current health expenditures in Colombia per year.InterpretationThe TTI program is a highly cost-effective public health intervention to reduce the burden of COVID-19 in Colombia. TTI programs depend on their successful and speedy implementation.FundingThis study was supported by the Colombian Ministry of Health through award number PUJ-04519-20 received by EPQ AVO and SDS declined to receive any funding support for this study. The contents are the responsibility of all the individual authors.

Strategies to increase downloads of COVID-19 exposure notification apps: A discrete choice experiment.

Exposure notification apps have been developed to assist in notifying individuals of recent exposures to SARS-CoV-2. However, in several countries, such apps have had limited uptake. We assessed whether strategies to increase downloads of exposure notification apps should emphasize improving the accuracy of the apps in recording contacts and exposures, strengthening privacy protections and/or offering financial incentives to potential users. In a discrete choice experiment with potential app users in the US, financial incentives were more than twice as important in decision-making about app downloads, than privacy protections, and app accuracy. The probability that a potential user would download an exposure notification app increased by 40% when offered a $100 reward to download (relative to a reference scenario in which the app is free). Financial incentives might help exposure notification apps reach uptake levels that improve the effectiveness of contact tracing programs and ultimately enhance efforts to control SARS-CoV-2. Rapid, pragmatic trials of financial incentives for app downloads in real-life settings are warranted.

Elevated Levels of Neutrophil Activated Proteins, Alpha-Defensins (DEFA1), Calprotectin (S100A8/A9) and Myeloperoxidase (MPO) Are Associated With Disease Severity in COVID-19 Patients.

Understanding of the basis for severity and fatal outcome of SARS-CoV-2 infection is of paramount importance for developing therapeutic options and identification of prognostic markers. So far, accumulation of neutrophils and increased levels of pro-inflammatory cytokines are associated with disease severity in COVID-19 patients. In this study, we aimed to compare circulatory levels of neutrophil secretory proteins, alpha-defensins (DEFA1), calprotectin (S100A8/A9), and myeloperoxidase (MPO) in COVID-19 patients with different clinical presentations. We studied 19 healthy subjects, 63 COVID-19 patients with mild (n=32) and severe (n=31) disease, 23 asymptomatic individuals identified through contact tracing programme and 23 recovering patients (1-4 months post-disease). At the time of disease presentation, serum levels of DEFA1 were significantly higher in patients with mild (mean230 ± 17, p<0.0001) and severe (mean452 ± 46, p<0.0001) disease respectively in comparison to healthy subjects (mean113 ± 11). S100A8/A9 proteins were significantly higher in COVID-19 patients (p<0.0001) irrespective of disease severity. The levels of DEFA1, S100A8/A9 and MPO reduced to normal in recovering patients and comparable to healthy subjects. Surprisingly, DEFA1 levels were higher in severe than mild patients in first week of onset of disease (p=0.004). Odds-ratio analysis showed that DEFA1 could act as potential biomarker in predicting disease severity (OR=11.34). In addition, levels of DEFA1 and S100A8/A9 were significantly higher in patients with fatal outcome (p=0.004 and p=0.03) respectively. The rise in DEFA1 levels was independent of secondary infections. In conclusion, our data suggest that induction of elevated levels of alpha-defensins and S100A8/A9 is associated with poor disease outcome in COVID-19 patients.