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Junna Oba,1 Masako Toriya,2 Yoshifumi Uwamino,3 Koichi Matsuo4 1Department of Extended Intelligence for Medicine, the Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan; 2Global Research Institute, Keio University, Tokyo, Japan; 3Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan; 4Collaborative Research Resources, Keio University School of Medicine, Tokyo, JapanCorrespondence: Masako Toriya, Global Research Institute, Keio University, 2-15-45 Mita, Minato-ku, Tokyo, 108-8345, Japan, Tel +81-3-5427-1379, Fax +81-3-5427-1703, Email masako.toriya@keio.jpBackground: During the COVID-19 pandemic, there was an increasing need to expand diagnostic testing in hospitals. At Keio University Hospital (KUH), clinical staff were concerned that the demand for PCR testing might exceed the capacity of the Clinical Laboratory. In response, basic researchers at Keio University School of Medicine (KUSM) set out to build a new, collaborative, PCR testing system. To be authorized to perform such diagnostic PCR testing, KUSM registered its core laboratory as an external clinical laboratory (ECL).Methods: In the pandemic, there was a pressure to build the PCR system quickly. Speed required discussions that developed a shared understanding of the unprecedented, new KUH/KUSM PCR system. To design, construct, and archive the new PCR testing system, we used a systems engineering (SE) approach. This included diagram visualization of functional flows and application of the Unified Architecture Framework (UAF), both of which are often used in system building. We considered daily demand for PCR testing at KUH and KUSM, and daily COVID-19 infections in Japan.Results: We operated the collaborative PCR testing system from August 2020 to June 2022. Given public health insurance reimbursement policies, KUH focused on individuals with suspicious symptoms, while the ECL at KUSM screened samples from asymptomatic individuals. KUSM performed about half as many tests as KUH. Interviewing KUH staff revealed that diagrams helped promote a better understanding of the KUH/KUSM PCR testing system.Conclusion: When designing temporary systems that may be repurposed in the future, we suggest using an SE approach with diagrams and UAF perspectives. This approach will enable stakeholders to understand what is being proposed to be built, and facilitate achieving an informed consensus on the proposed system. We suggest that SE approaches should be widely used in projects that involve building and operating complex, collaborative systems, and documenting the process. Keywords: COVID-19, PCR test, clinical laboratory, systems engineering, diagram, temporary system

Abstract Background In 2022/2023, Influenza A and Respiratory Syncytial Virus (RSV) reappeared in hospitalized patients, which was in parallel to ongoing SARS-CoV-2 infections. The aim of our study was to compare the characteristics and outcomes of these infections during the same time. Methods We included patients of all ages with a positive polymerase chain reaction (PCR) test for Influenza A/B, RSV, or SARS-CoV-2 virus hospitalized in the neurological, internal or paediatric units of the RoMed Hospital Rosenheim, Germany, between October 1st 2022 and February 28th 2023. Results A total of 906 patients were included (45.6% female; median age 68.0 years; 21.9% Influenza A, 48.2% SARS-CoV-2, 28.3% RSV). Influenza B (0.2%) and co-infections (1.5%) played a minor role. In patients aged ≥ 18 years (n = 637, 71%), Influenza A, SARS-CoV-2 and RSV groups differed in age (median 72, 79, 76 years, respectively; p

Introduction. Electronic devices capable of collecting individual telemetry data have opened up prospects for preclinical detection of COVID-19 signs. Known solutions involve the analysis of information that is difficult to obtain at the moment. We are talking, specifically, about the blood condition or a PCR test. This significantly limits the possibility of integrating algorithms with wrist gadgets. At the same time, the cardiovascular system as an object of observation is quite informative, the data collection is well developed. The article describes the problem of detecting covid anomalies in rhythm strips. The work aims at creating a mathematical model based on machine learning algorithms to automate the process of detecting covid abnormalities in the heart rhythm. The possibility of integrating the results obtained with fitness bracelets and smart watches is shown.Materials and Methods. The work involved an open technology stack: Python, Scikit-learn, Lightgbm. When assessing the quality of models for binary classification, metric F1 was used. 229 cardiac rhythm strips (сardiointervalographies) of patients with COVID-19 were studied. The presence or absence of signs of an anomaly was determined taking into account the time of the rhythm strip and the intervals between heartbeats. Deviations that could indicate infection were shown graphically. Based on the exploratory analysis results, a list of signs indicating an anomaly was made.Results. As a result of the work done, a mathematical model was obtained that detected heart rate abnormalities specific to COVID-19 with an accuracy of 83 %. The basic features determining the predictive ability of the model were identified and ranked. They included the current value of the interval between heartbeats, the derivatives at the subsequent and previous points of measuring the duration of the heartbeat, the first derivative at the current point, and the deviation of the current value of the duration of the RR-interval from the median. The first indicator in this list was recognized as the most significant, the last — the least. For machine learning purposes, the potential of five algorithms was evaluated: IsolationForest, LGBMClassifier, RandomForestClassifier, ExtraTreesClassifier, SGDOneClassSVM. The normal and abnormal results of observations in isolation trees were visualized. A parameter was set that corresponded to the probability of regular observation outside the norm, and its value was selected — 0.11. Taking into account this indicator, a graph was constructed for the SGDOneClassSVM model. Based on the data set, using the cross-validation technique, the quality metric was calculated. The case in hand was a rhythm strip with a time series of observations taken in one continuous time interval from one person. A step-by-step process of obtaining averaged metric values for each model was described. In comparison, the highest indicator was recorded for the LGBMClassifier model, the lowest — for SGDOneClassSVM and IsolationForest.Discussion and Conclusions. The resulting mathematical model takes up little space in the memory of a mobile device, i.e., it does not impose significant requirements on computing resources. The solution has an acceptable detection quality for preclinical screening of COVID-19-related cardiovascular disorders. The algorithm detects anomalies in 83 % of cases. Four minutes is enough to record a rhythm strip. The proposed scenario for using an integrated solution is concise and easy to implement. Widespread use of the development can contribute to the detection of COVID-19 at an early stage.

Wafa Elhag,1,2 Bahaeldin K Elamin,1,3 Ebtehal Idris,4 Azza Elsheikh,1 Khaled Ghaleb,4 Ibtihal Fallatah,5 Doaa Hassan,5 Mahmoud Elkhalifa,5 Ehssan Moglad,6 Ali Eleragi1 1Department of Basic Medical Sciences (Microbiology Unit), College of Medicine, University of Bisha, Bisha, Saudi Arabia; 2Microbiology Department, Faculty of Medical Laboratory Sciences, Al Neelain University, Khartoum, Sudan; 3Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan; 4Medical Laboratories Department, College of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia; 5Laboratory and ICU (Medical Department) King Abdullah Hospital-Bisha, Bisha, Saudi Arabia; 6Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi ArabiaCorrespondence: Wafa Elhag, Department of Basic Medical Sciences (Microbiology Unit), College of Medicine, University of Bisha, P.O.Box 1290, Bisha, 61922, Saudi Arabia, Email welhag@ub.edu.saBackground: Understanding COVID-19’s onset and clinical effects requires knowing host immune responses.Objective: To investigate the presence of IgM, IgG, and cytokine levels (IL-2 and IL-6) in individuals with COVID-19 who have had their diagnosis confirmed by PCR.Methods: This cross-sectional research included 70 adult ICU patients from King Abdullah Hospital in Bisha, Saudi Arabia. Subjects gave two blood samples. After hospital release, only 21 patients provided the second sample. Each patient provided a sample upon admission. Quantitative ELISAs evaluated IL-2, IL-6, and SARS-CoV-2-specific IgM and IgG antibodies.Results: All patients were critically ill and unvaccinated against COVID-19. 46 (65.7%) of the patients were male, and their age range was 33– 98 years (with a mean age of 66.5); 24.3%) were 51– 61 years old. IgG was positive in all patients, although IgM predominated in 57/70 (81.4%) (6– 1200 IU/mL). Total data analysis yielded these results. IL-6 was calculated at 10– 1900 ng/mL, whereas IL-2 was 4– 280. Discharged hospital patients had a statistically significant increase in IgM and IgG (P = 0.01, 0.004) but a statistically insignificant decline in IL-6 and IL-2 (P = 0.761, 0.071). Low IgM levels increased hospital stays. The study found lengthier hospital stays with higher IgG levels.Conclusion: The identification of IgM and IgG antibodies, greater IL-6 levels, and lower IL-2 levels can help diagnose and monitor COVID-19 infection.Keywords: COVID-19 patients, antibodies, cytokines levels, PCR test, ELISA, Saudi Arabia

Introduction: To date various oral manifestations in patients with coronavirus disease 2019 (COVID-19) have been reported. Objectives: In the present study, we investigated the relationship between Polymerase Chain Reaction (PCR) positivity and oral signs in patients with suspected COVID-19. Methods: A total of 383 patients who presented to the emergency department for the first time with any symptoms associated with COVID-19 were included in the study. Oral examinations were performed and the findings, PCR status, and thorax computerized tomography (CT) reports were recorded. Results: Oral mucosa was involved in 246 (64.2%) patients. 175 (78,4%) of patients with COVID-19 confirmed the diagnosis with PCR test or CT results had oral manifestation. Dry mouth, microvesicles on the tonsils or pharynx, and petechiae in the oropharynx were significantly higher in patients with positive PCR tests (P = 0.001, P < 0.001, P < 0.001, respectively). The ratio of intact oral mucosa was statistically significantly higher in patients with negative PCR tests compared to those with positive PCR tests (P < 0.001). Microvesicles on the tonsils or pharynx were most associated with PCR positivity in patients without lung involvement (P < 0.001). Dry mouth, erythema of the tonsils and pharynx, petechiae in the oropharynx, and primary/secondary herpes infection are more related to PCR positivity in patients without lung involvement (P < 0.05). Lung involvement in patients with PCR positivity is related to only cheilitis (P = 0.034). Conclusions: Our study revealed that especially microvesicles, petechiae, erythema on the tonsils or pharynx, and some other oral lesions such as dry mouth, oral aphthae, and primary/secondary herpes infection are associated with PCR positivity.

Multiple outbreaks of fatal infectious diseases throughout history have intensified the need for early diagnostic methods to efficiently control their spread. Polymerase chain reaction (PCR)-based diagnosis is a sensitive, accurate, and effective method for detecting infections. However, conventional PCR-based diagnosis is slow and consumes large amounts of energy, primarily because of bulky, power-consuming thermal cyclers. Herein, we review recently published PCR-based diagnostic methods, in which plasmonic light-to-heat conversion-based thermal cyclers replace conventional ones. First, we explain the structures of recently developed rapid plasmonic-based thermal cyclers and review the various materials used. Next, we review the fabrication methods used in recent developments in rapid plasmonic thermal cyclers. Then, we discuss sustainable methods that have been and can be implemented to develop a rapid plasmonic thermal cycler. With this review, the requirements for developing a plasmonic-based sustainable PCR with high speed, accuracy, and sensitivity can be understood to contain future pandemics.

Abstract Background Since social distancing during the COVID-19-pandemic had a profound impact on professional life, this study investigated the effect of PCR testing on on-site work. Methods PCR screening, antibody testing, and questionnaires offered to 4,890 working adults in Lower Saxony were accompanied by data collection on demographics, family status, comorbidities, social situation, health-related behavior, and the number of work-related contacts. Relative risks (RR) with 95 % confidence intervals were estimated for the associations between regular PCR testing and other work and health-related variables, respectively, and working on-site. Analyses were stratified by the suitability of work tasks for mobile office. Results Between April 2020 and February 2021, 1,643 employees underwent PCR testing. Whether mobile working was possible strongly influenced the work behavior. Persons whose work was suitable for mobile office (mobile workers) had a lower probability of working on-site than persons whose work was not suitable for mobile office (RR = 0.09 (95 % CI: 0.07 – 0.12)). In mobile workers, regular PCR-testing was slightly associated with working on-site (RR = 1.19 (0.66; 2.14)). In those whose working place was unsuitable for mobile office, the corresponding RR was 0.94 (0.80; 1.09). Compared to persons without chronic diseases, chronically ill persons worked less often on-site if their workplace was suitable for mobile office (RR = 0.73 (0.40; 1.33)), but even more often if their workplace was not suitable for mobile office (RR = 1.17 (1.04; 1.33)). Conclusion If work was suitable for mobile office, regular PCR-testing did not have a strong effect on presence at the work site. Trial registration An ethics vote of the responsible medical association (Lower Saxony, Germany) retrospectively approved the evaluation of the collected subject data in a pseudonymized form in the context of medical studies (No. Bo/30/2020; Bo/31/2020; Bo/32/2020).

Introduction: The lack of information about the impact of Covid-19 on pregnancy and the increased side-effects of the disease for pregnant mothers and fetuses showed the importance of investigating its impact on pregnancy and neonate. The present study was performed with aim to investigate the impact of positive test result of PCR on the weight and Apgar scores of infants. Methods: In this analytical study (retrospective cohort), sampling was conducted by examining the files of 98 pregnant women who gave birth between April 2020 and September 2021 using the apple system which were covered by health care centers located in Isfahan province. The information obtained from the comparison of two groups of mothers based on the results of the PCR test was analyzed by SPSS software (version 18) and Independent t-test. P

Abstract Background RSV-incidence estimates obtained from routinely-collected healthcare data (e.g., MarketScan) are commonly adjusted for under-reporting using test positivity reported in national Surveillance Systems (NREVSS). However, NREVSS lacks detail on patient-level characteristics and the validity of applying a single positivity estimate across diverse patient groups is uncertain. We aimed to describe testing practices and test positivity across subgroups of private health insurance enrollees in the US and illustrate the possible magnitude of misclassification when using NREVSS to correct for RSV under ascertainment. Methods Using billing records, we determined distributions of RSV-test claims and test positivity among a national sample of private insurance enrollees. Tests were considered positive if they coincided with an RSV-diagnosis. We illustrated the influence of positivity variation across sub-populations when accounting for untested acute respiratory infections. Results Most tests were for children (age 0–4: 65.8%) and outpatient encounters (78.3%). Test positivity varied across age (0–4: 19.8%, 5–17: 1.8%, adults: 0.7%), regions (7.6–16.1%), settings (inpatient 4.7%, outpatient 14.2%), and test indication (5.0–35.9%). When compared to age, setting or indication-specific positivity, bias due to using NREVSS positivity to correct for untested ARIs ranged from − 76% to 3556%. Conclusions RSV-test positivity depends on the characteristics of patients for whom those tests were ordered. NREVSS-based correction for RSV-under-ascertainment underestimates the true incidence among children and overestimate rates among adults. Demographic-specific detail on testing practice and positivity can improve the accuracy of RSV-incidence estimates.

Abstract Background COVID-19 has caused over 305 million infections and nearly 5.5 million deaths globally. With complete eradication unlikely, organizations will need to evaluate their risk and the benefits of mitigation strategies, including the effects of regular asymptomatic testing. We developed a web application and R package that provides estimates and visualizations to aid the assessment of organizational infection risk and testing benefits to facilitate decision-making, which combines internal and community information with malleable assumptions. Results Our web application, covidscreen, presents estimated values of risk metrics in an intuitive graphical format. It shows the current expected number of active, primarily community-acquired infections among employees in an organization. It calculates and explains the absolute and relative risk reduction of an intervention, relative to the baseline scenario, and shows the value of testing vaccinated and unvaccinated employees. In addition, the web interface allows users to profile risk over a chosen range of input values. The performance and output are illustrated using simulations and a real-world example from the employee testing program of a pediatric oncology specialty hospital. Conclusions As the COVID-19 pandemic continues to evolve, covidscreen can assist organizations in making informed decisions about whether to incorporate covid test based screening as part of their on-campus risk-mitigation strategy. The web application, R package, and source code are freely available online (see “Availability of data and materials”).

Abstract Background Point-of-care (POC) polymerase chain reaction (PCR) tests have the ability to improve testing efficiency in the Coronavirus disease 2019 (COVID-19) pandemic. However, real-world data on POC tests is scarce. Objective To evaluate the efficiency of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) POC test in a clinical setting and examine the prognostic value of cycle threshold (CT) on admission on the length of hospital stay (LOS) in COVID-19 patients. Methods Patients hospitalised between January and May 2021 were included in this prospective cohort study. Patients’ nasopharyngeal swabs were tested for SARS-CoV-2 with Allplex™2019-nCoV (Seegene Inc.) real-time (RT) PCR assay as gold standard as well as a novel POC test (Bosch Vivalytic SARS-CoV-2 [Bosch]) and the SARS-CoV-2 Rapid Antigen Test (Roche) accordingly. Clinical sensitivity and specificity as well as inter- and intra-assay variability were analyzed. Results 120 patients met the inclusion criteria with 46 (38%) having a definite COVID-19 diagnosis by RT-PCR. Bosch Vivalytic SARS-CoV-2 POC had a sensitivity of 88% and specificity of 96%. The inter- and intra- assay variability was below 15%. The CT value at baseline was lower in patients with LOS ≥ 10 days when compared to patients with LOS

ABSTRACT: Aims: The objective of the present study was to investigate the presence of SARS-CoV-2 in aerosol and COVID-19 contamination distance asssociated with ultrasonic scaling and tooth preparation. Methods: Twenty-four patients with COVID-19 were included in this study. Removal of supragingival plaque with ultrasonic instruments for 10 minutes and high-speed air-turbine using for the simulation of cutting the maxillary right canine tooth with a round diamond bur for 5 minutes were performed. Patients were randomly assigned to 2 groups: In group A, medium-volume suction was used during treatment. In group B, high-volume suction with an aerosol cannula was added to medium-volume suction. Prior to treatment, 5 glass petri dishes containing viral transport medium were placed in the operating room. After treatment, petri dishes were immediately delivered to a microbiology laboratory for real-time polymerase chain reaction (RT-PCR) analysis. Results: RT-PCR test results were negative for all specimens in group B. However, 5 positive test results for COVID-19 were detected in group A specimens. Conclusions: Suction with an aerosol cannula is very important to prevent COVID-19 viral contamination via aerosol. In addition, a high-volume suction capacity (air volume) of 150 mm Hg or 325 L/min is sufficient for elimination of viral contamination. Thus, high-volume suction should be used during dental treatments in COVID-19 patients.

Objective. Examine clinical manifestations, PCR test results, and visit outcomes in patients in COVID-outpatient clinics. Method. The survey was performed using the questionnaire, in February 2021. in patients in four COVID-outpatient clinics in Belgrade and one in Subotica. We got the data about their jobs, gender, age, present symptoms and comorbidities, PCR-testing, and visit outcomes. The data were processed using the software statistical package SPSS 17. Statistical significance was defined for level p

Polymerase chain reaction (PCR) for the detection of nucleic acids is the gold standard test for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is the probability of false-negative results with this test, which poses a threat to public health. Here, we highlight some important factors that should be considered for reducing the false-negative results of the SARS-CoV-2 PCR test. Copyright © 2022 Sabzevari and Nikbakht. Published by Global Health and Education Projects, Inc. This is an open-access article distributed under the terms of the Creative Commons Attribution License CC BY 4.0.

Abstract Background During the spike of COVID-19 pandemic in Kazakhstan (June-2020), multiple SARS-CoV-2 PCR-test negative pneumonia cases with higher mortality were reported by media. We aimed to study the epidemiologic characteristics of hospitalized PCR-test positive and negative patients with analysis of in-hospital and post-hospital mortality. We also compare the respiratory disease characteristics between 2019 and 2020. Methods The study population consist of 17,691 (March–July-2020) and 4600 (March–July-2019) hospitalized patients with respiratory diseases (including COVID-19). The incidence rate, case-fatality rate and survival analysis for overall mortality (in-hospital and post-hospital) were assessed. Results The incidence and mortality rates for respiratory diseases were 4-fold and 11-fold higher in 2020 compared to 2019 (877.5 vs 228.2 and 11.2 vs 1.2 per 100,000 respectively). The PCR-positive cases (compared to PCR-negative) had 2-fold higher risk of overall mortality. We observed 24% higher risk of death in males compared to females and in older patients compared to younger ones. Patients residing in rural areas had 66% higher risk of death compared to city residents and being treated in a provisional hospital was associated with 1.9-fold increased mortality compared to those who were treated in infectious disease hospitals. Conclusion This is the first study from the Central Asia and Eurasia regions, evaluating the mortality of SARS-CoV-2 PCR-positive and PCR-negative respiratory system diseases during the peak of COVID-19 pandemic. We describe a higher mortality rate for PCR-test positive cases compared to PCR-test negative cases, for males compared to females, for elder patients compared to younger ones and for patients living in rural areas compared to city residents.

Abstract Our work highlights patients at risk of prolonged viral shedding in COVID‐19 and its implications for isolation strategies and explores possible solution by PCR‐CT value testing (cycle threshold value). We also review the impact of HIV on COVID‐19.

This work has aimed to create a PCR test to identify avian and mammalian DNA in meat products. The test is based on phylogenetic analysis of 18S ribosomal RNA (rRNA) of four major groups of Tetrapod: Amphibia, Reptilia, Mammalia, and Aves. 18S rDNA complete coding sequences from GenBank have been used for phylogenetic analysis by the Maximum Likelihood method. The alignment of these 18S rDNA sequences has been used for PCR primers modeling. We have received the following PCR fragment for these primers: for birds – 97 base pairs (bp), and for mammals − 134 bp. The difference between them in 37 bp is sufficient for separating these fragments in standard agarose gel. We have tested this PCR to identify avian or mammalian DNA in sausage products and confirmed the suitability of this test for avian (chicken) and mammalian (sheep, cows) meat identification and meat identification in sausage products.

The rapid spread of highly transmissible respiratory infections in carceral settings occurs due to their conglomerate nature. The COVID-19 pandemic has resulted in large outbreaks in jails and prisons in many settings. Herein, we describe an outbreak of SARS-CoV2 infection in a prison in Alicante, Spain. Prior to January 2021, testing for coronavirus infection was not widely available in jails and prisons nationwide. Offering of testing services in Spanish carceral facilities, coincided with the deployment of COVID-19 vaccination in the larger community. However, COVID-19 vaccine role out of incarcerated individuals occurred later during the deployment plan. With the identification of the initial cases of this outbreak, two units of the facility were assigned for population management: one for inmates with confirmed infection by positive PCR detection of SARS-COV-2 infection in nasopharyngeal swabs. Inmates with confirmed exposure and thus considered close contacts were place in a second isolation unit. Functional quarantine was employed in some instances. A reactive testing strategy was instituted at baseline, and at 7 and 14 days of nasopharyngeal specimens by PCR. A total of 1,097 nasopharyngeal specimens were obtained for PCR testing during the outbreak, which lasted a total of 80 days between the index case the end of medical isolation of the last case. A total of 103 COVID-19 cases were identified during the outbreak. Of these, three inmates developed severe manifestations requiring hospitalization, and one died. Were identified, among which there were three hospitalized and one deceased. Among cases and confirmed contacts, we conducted close clinical monitoring, symptom screening, and daily temperature checks. The implementation of these interventions along with early medical isolation of cases, quarantining of contacts, and interval testing to detect presymptomatic or asymptomatic cases were instrumental in containing this outbreak.

The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place within the context of the world-wide SARS-CoV-2 crisis. Here, for the first time in history, laboratory test results have a dramatic impact on political decisions. Therefore, transparent, comprehensible, and reliable data is mandatory. It is in the nature of wet lab tests that their quality and outcome are influenced by multiple factors reducing their performance by handling procedures, underlying test protocols, and analytical reagents. These limitations in sensitivity and specificity have to be taken into account when calculating the real test results. As a resolution method, we have developed a Bayesian calculator, the Bayes Lines Tool (BLT), for analyzing disease prevalence, test sensitivity, test specificity, and, therefore, true positive, false positive, true negative, and false negative numbers from official test outcome reports. The calculator performs a simple SQL (Structured Query Language) query and can easily be implemented on any system supporting SQL. We provide an example of influenza test results from California, USA, as well as two examples of SARS-CoV-2 test results from official government reports from The Netherlands and Germany-Bavaria, to illustrate the possible parameter space of prevalence, sensitivity, and specificity consistent with the observed data. Finally, we discuss this tool’s multiple applications, including its putative importance for informing policy decisions.

Background COVID-19 has spread worldwide since its emergence in 2019. In contrast to many other countries with epidemics, Japan differed in that it avoided lockdowns and instead asked people for self-control. A travel campaign was conducted with a sizable budget, but the number of PCR tests was severely limited. These choices may have influenced the course of the epidemic. Methods The increase or decrease in the classes of SARS-CoV-2 variants was estimated by analyzing the published sequences with an objective multivariate analysis. This approach observes the samples in multiple directions, digesting complex differences into simpler forms. The results were compared over time with the number of confirmed cases, PCR tests, and overseas visitors. The kinetics of infection were analyzed using the logarithmic growth rate. Results The declared states of emergency failed to alter the movement of the growth rate. Three epidemic peaks were caused by domestically mutated variants. In other countries, there are few cases in which multiple variants have peaked. However, due to the relaxation of immigration restrictions, several infective variants have been imported from abroad and are currently competing for expansion, creating the fourth peak. By April 2021, these foreign variants exceeded 80%. The chaotic situation in Japan will continue for some time, in part because no effort has been made to identify asymptomatic carriers, and details of the vaccination program are undecided.

Background: COVID-19 infection is caused by a novel coronavirus. One of the most used strategies that can be used to control the spread of COVID-19 is the 3T (test, trace, and treatment) strategy. This study aimed to evaluate the 3T strategy to control COVID-19 infection in a COVID-19 Referral Hospital in Depok, West Java, Indonesia. Methods: this is a cross-sectional study conducted at the University of Indonesia Hospital. The study was conducted in June 2020 with 742 participants (staff members) using secondary data from polymerase chain reaction (PCR) test results. We presented data in the descriptive form and performed bivariate analysis using the chi-square/Fischer test for categorical data. Results: the PCR test results were positive in 83 (11.1%) participants, with a case-per-tracing ratio of 1:24 and 1:2 in the first and third phases of tracing, respectively. The COVID-19 case graph for the participants decreased along with the implementation of the 3T strategy. The positivity rate in the first phase of tracing was 20% and decreased to 5% in the third phase of tracing. Staff with confirmed positive test results were advised to isolate themselves (hospital or self-isolation). Hospital isolation was found to be associated with the duration of PCR test conversion (p

Molecular analysis revealed polymorphism for the MD-Exp7 gene, controlling expansin biosynthesis, in wild Malus species. Eight allelic forms of the gene were identified, and four of them were unique. The regularities in the allele distribution in 37 genotypes were found to be in accordance with their systematic positions. The trait was found to be broadly diverse both among the sections of the genus and within a particular section. Variants of the gene were identified in representatives of one species.