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ATLM (Apparent Time Lag Model) was extended to simulate the spread of infection in a mixed state of the variant virus and original wild type. It is applied to the 4th wave of infection spread in Tokyo, and (1) the 4th wave bottoms out near the end of the state of emergency, and the number of infected people increases again. (2) The rate of increase will be mainly by d strain (L452R) virus, while the increase by a strain (N501Y) virus will be suppressed. (3) It is anticipated that the infection will spread during the Olympic Games. (4) When variant viruses compete, the infection of highly infectious virus rises sharply while the infection by weakly infectious ones has converged. (5) It is effective as an infection control measure to find an infected person early and shorten the period from infection to quarantine by PCR test or antigen test as a measure other than the vaccine.

Background: Larger studies are needed to evaluate whether COVID-19 increases the risk of DKA presentation. Methods: We examined individual and joint associations of COVID-19 and preexisting diabetes (DM) with DKA presentation in a retrospective cohort of patients who presented to Montefiore Medical Center in the Bronx, NY from March to June 2020. We defined DKA as acidosis (pH 250 mg/dl. We defined COVID-19 status by PCR test result and preexisting DM by HbA1c ≥6.5%, ICD-10 code, or outpatient DM medications. Given likely bias in hospital presentation during the pandemic, a historical control from March to June 2019 was included in the COVID negative group. Data were analyzed using multivariate regression. Results: We included 46,479 patients: mean age 43 yrs, 56% male, 57% with DM of which 94% type 2 DM. COVID-19 alone was not associated with higher odds of DKA presentation, though as expected preexisting DM was. Adjusted regression analyses for interaction showed 64% higher odds of DKA for patients with both COVID-19 and preexisting DM than the additive effect of each condition alone (Table 1). Conclusions: COVID-19 has a multiplicative effect on the risk of hospital presentation of DKA in people with preexisting DM. Mechanistic studies examining DKA in COVID-19 in people with preexisting DM may help identify preventive targets. Disclosure J. Mathew: None. C. Schechter: None. W. Southern: None. J. P. Crandall: None. Y. Tomer: None. S. Agarwal: None.

To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 μl saliva in vials containing Darnell Rockefeller University Laboratory (DRUL) buffer and extracted RNA was assayed by RT-PCR (the DRUL saliva assay). The limit of detection was confirmed to be 1 viral copy/μl in 20 of 20 replicate extractions. Viral RNA was stable in DRUL buffer at room temperature up to seven days after sample collection, and safety studies demonstrated that DRUL buffer immediately inactivated virus at concentrations up to 2.75x106 PFU/ml. Results from SARS-CoV-2 positive nasopharyngeal (NP) swab samples collected in viral transport media and assayed with a standard FDA Emergency Use Authorization (EUA) test were highly correlated with samples placed in DRUL buffer. Direct comparison of results from 162 individuals tested by FDA EUA oropharyngeal (OP) or NP swabs with co-collected saliva samples identified four otherwise unidentified positive cases in DRUL buffer. Over six months, we collected 3,724 samples from individuals ranging from 3 months to 92 years of age. This included collecting weekly samples over 10 weeks from teachers, children, and parents from a pre-school program, which allowed its safe reopening while at-risk pods were quarantined. In sum, we validated a simple, sensitive, stable, and safe PCR-based test using a self-collected saliva sample as a valuable tool for clinical diagnosis and screening at workplaces and schools.

Introduction COVID-19 virus continues to spread and die worldwide. Some studies examining hydroxychloroquine as a prophylactic agent reported that its efficiency and reliability have not been proven so that it must not be used for prophylaxis other than clinical researches. However we think that the results of this study we conducted in a local area will contribute to the literature data. Methods The study was designed as adult patients who were in follow-up taking HC due to their chronic diseases were included. 384 patients who were taking hydroxychloroquine regularly and 299 patients who were not taking hydroxychloroquine were included. The primary outcome of this study is to detect a positive PCR result in patients who received a PCR test and to determine the incidence rate and its course of the disease among those who were taking HC and those who were not taking hydroxychloroquine. Results The majority of the patients (median age: 51.8- range 17-89) were women and housewives. In the patient group using hydroxychloroquine, 22 patients were tested for PCR and only 2 positive patients were found. Covid-19 was detected in 24 (8.02%) of 65 (21.73%) patients who underwent PCR test at Control group (n = 299). PCR positivity was statistically lower in the HK group (n = 2, 0.52%, n = 24, 8.02%, respectively, p = 0.0001). Conclusions Our study supported the fact that there is a lower PCR positivity and symptoms are milder among patients who are using HC regularly, as compared to those who are not using hydroxychloroquine.

Purpose - to study particular properties of the course of the infection among hospitalizedchildren depending on the nature of their treatment provided in pre-hospitalizationperiod in order to improve the results of treatment of children with COVID-19.Material and methods. In a random sample 263 children with COVID-19, admittedto the Department of infectious diseases of the Regional Children's Clinical Hospitalof Chernivtsi, have been examined. The first clinical group includes 68 patients thatreceived antiviral treatment as a part of symptomatic therapy (average age 6,5 ± 0,74years, male ratio 54,4%), and the comparison group - 195 children that did not receiveantiviral activity treatment (average age 6,4 ± 0,41 years, male ratio 50,8%).Results. Most patients with COVID-19 presented signs of moderate to severe medicalstate when admitted to hospital. Patients that did not receive any antiviral therapy in thepre-hospitalization period showed delayed body temperature normalization response (onaverage on the 5th day of the treatment) and, starting from the day 10 of hospitalization,experienced elevated body temperature again caused by infectious and inflammatoryprocess as a result of COVID-19 complications. Changes concerning hemostasisinclude an increase of absolute count of platelets in the blood, reduction in plasmarecalcification time and increase of plasma D-dimer levels (p

We aimed to estimate the risk of COVID-19 outbreaks associated with air travel to a COVID-19-free country [New Zealand (NZ)]. A stochastic version of the SEIR model CovidSIM v1.1, designed specifically for COVID-19 was utilised. We first considered historical data for Australia before it eliminated COVID-19 (equivalent to an outbreak generating 74 new cases/day) and one flight per day to NZ with no interventions in place. This gave a median time to an outbreak of 0.2 years (95% range of simulation results: 3 days to 1.1 years) or a mean of 110 flights per outbreak. However, the combined use of a pre-flight PCR test of saliva, three subsequent PCR tests (on days 1, 3 and 12 in NZ), and various other interventions (mask use and contact tracing) reduced this risk to one outbreak after a median of 1.5 years (20 days to 8.1 years). A pre-flight test plus 14 days quarantine was an even more effective strategy (4.9 years; 2,594 flights). For a much lower prevalence (representing only two new community cases per week in the whole of Australia), the annual risk of an outbreak with no interventions was 1.2% and had a median time to an outbreak of 56 years. In contrast the risks associated with travellers from Japan and the United States was very much higher and would need quarantine or other restrictions. Collectively, these results suggest that multi-layered interventions can markedly reduce the risk of importing the pandemic virus via air travel into a COVID-19-free nation. For some low-risk source countries, there is the potential to replace 14-day quarantine with alternative interventions. However, all approaches require public and policy deliberation about acceptable risks, and continuous careful management and evaluation.

The Coronavirus known as COVID-19 is one of the biggest pandemic in the human history. About 3.12 million deaths and more than 150 million cases have been diagnosed to date. The economic cost of the virus is also huge, due to lockdown in many parts of the world. The traditional method to detect COVID-19 is a PCR test, but it takes about 4–5 hours to get the results. Secondly, in some cases, the false-negative ratio is high in PCR kits. As an alternative method, radiology images, like CT-scan and chest X-rays, can be used for COVID-19 diagnosis. Deep learning has shown remarkable results in medical image analysis, such as tumor segmentation. This paper evaluates four famous CNN models, VGG-16, AlexNet, ResNet18, and Inception V3, on the dataset complied with the chest X-ray images for COVID-19 patient. The models are trained on two public datasets. The simulation results show the effectiveness of deep learning models for COVID-19 detection.

OBJECTIVES: This study aims to determine the prognostic significance of the lymphocyte/mean platelet volume ratio (LMR) in terms of the clinical course of the disease in patients with COVID-19. METHODS: Patients over 18 who were evaluated for COVID-19 during the period from April 1, to April 30, 2020 were retrospectively scanned. Patients with at least 1 positive PCR test result were as assigned to Group 1 while patients with negative test results were assigned to Group 2. The LMR ratio was calculated by dividing the lymphocyte value by that of MPV. The relationship between LMR, severity of patients' CT findings and 28-day mortality was evaluated. RESULTS: A total of 938 patients were included in the study. It was observed that the lymphocyte and LMR levels were significantly different in those who died within 28 days (p < 0.001, p ≤ 0.001). In the ROC analysis for the LMR level, the area under the curve (AUC) was found to be 0.737 (95% CI 0.639‒0.834). When the cut­off value of LMR was 0.045, the sensitivity was found to be 99.0 % and specificity was 15.2 %. CONCLUSION: LMR can be a guide in multiple cases of care provided to critical patients, as is the case in the COVID-19 pandemic and can be used in recognizing critical patients (Tab. 5, Fig. 1, Ref. 21).

Chlamydiosis is a public health important zoonosis, and its transmission to humans occurs mainly through contact with pet birds. These animals rank the second position in most popular pets in Brazil, where the occurrence of chlamydiosis is underestimated, although studies indicate that the disease is endemic in the country. Therefore, the present work aimed to investigate the occurrence of Chlamydia psittaci in 68 cockatiel chicks (Nymphicus hollandicus) of the city of Uberlandia, Minas Gerais, Brazil. Samples of choana, cloaca, and fresh fecal samples were collected for the detection of the bacteria by PCR test. The occurrence found was null. This work concluded that it is important to raise the awareness of owners and breeders about measures to prevent and control this disease, and that orienting them about the risks of overusing antibiotics is a public health issue., A clamidiose é uma zoonose de importância na saúde pública e sua transmissão para humanos ocorre, principalmente, por meio do contato com aves de estimação. Esses animais ocupam o segundo lugar no ranking de animais de estimação no Brasil, onde a ocorrência da clamidiose é subestimada, apesar de estudos indicarem que a doença é endêmica no país. Diante disso, o presente trabalho teve como objetivo investigar a ocorrência de Chlamydia psittaci em 68 aves de estimação da espécie calopsita (Nymphicus hollandicus) da cidade de Uberlândia-MG. Foram coletadas amostras de coana, cloaca e amostras fecais frescas para a detecção da bactéria por meio do teste da PCR. A ocorrência encontrada foi nula. Este trabalho concluiu que a conscientização dos tutores e criadores quanto à adoção de medidas para a prevenção e controle dessa doença é importante, e que a orientação destes quanto aos riscos do uso indiscriminado de antimicrobianos é uma questão de saúde pública. &nbsp

Objective The goal of this study was to investigate whether blood group type caused susceptibility to COVID-19 infection. Methods Two hundred and eleven consecutive patients admitted with various symptoms associated with COVID-19 were included. We compared the AB0 and Rh subgroup distributions between patients with a positive polymerase chain reaction (PCR) test result and the patients without. We compared the AB0 and Rh subgroup distributions between patients with lung involvement and patients without. Additionally, comparisons were performed between the patients both with positive PCR result and lung involvement, and the patients with a negative PCR result. Results No significant difference of ABO and Rh subgroup distributions was evident between patients with and without a positive PCR test result (p=0.632 and p=0.962). No significant difference of ABO and Rh subgroup distributions was evident between the patients with and without lung involvement (p=0.097 and p=0.797). No significant difference of ABO and Rh subgroup distributions was evident among patients both with PCR positivity and lung involvement, patients with only PCR positivity, and the patients with negative PCR test results (p=0.3 and p=0.993). Conclusion All blood group types seem to have an equal risk of COVID-19 infection. Everyone should follow the precautions to avoid the COVID-19 infection.

The gold standard for the diagnosis of coronavirus disease 2019 (COVID-19) is a nucleic acid detection test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which may occasionally reveal false-positive or false-negative results. Herein, we describe a case of a patient infected with human coronavirus NL63 (HCoV-NL63) who was falsely diagnosed with COVID-19 using the Ampdirect™ 2019-nCoV detection kit (Shimadzu Corporation, Japan) and SARS-CoV-2 Detection Kit (TOYOBO co., ltd.), and was admitted to a COVID-19 hospital ward. We suspected a cross-reaction between HCoV-NL63 and SARS-CoV-2; however, the reported genome sequences of HCoV-NL63 and N1/N2 primers for SARS-CoV-2 do not correspond. Thus, the PCR result was supposed to be a false positive possibly due to contamination or human error. Although the issue of a false-negative result has been the focus of much attention to prevent the spread of the disease, a false positive is fraught with problems as well. Physicians should recognize that unnecessary isolation violates human rights and a careful diagnosis is indispensable when the results of laboratory testing for COVID-19 are unclear. Generally, in cases such as a duplicate PCR test was partially positive, either N1 or N2 alone was positive, PCR testing for two or more target regions resulted in a positive only for single region, a high cycle threshold >35 was obtained, a false positive should be suspected. Especially, when these conditions coincide, we should recognize the high likelihood of a false positive.

Author(s): Bonadio, William; Jackson, Kaedrea; Gottlieb, Lindsey; Legome, Eric | Abstract: Introduction: We assessed the utility of an emergency department (ED) protocol using clinical parameters to rapidly distinguish likelihood of novel coronavirus 2019 (COVID-19) infection; the applicability aimed to stratify infectious-risk pre-polymerase chain reaction (PCR) test results and accurately guide early patient cohorting decisions.Methods: We performed this prospective study over a two-month period during the initial surge of the 2020 COVID-19 pandemic in a busy urban ED of patients presenting with respiratory symptoms who were admitted for in-patient care. Per protocol, each patient received assessment consisting of five clinical parameters: presence of fever; hypoxia; cough; shortness of breath/dyspnea; and performance of a chest radiograph to assess for bilateral pulmonary infiltrates. All patients received nasopharyngeal COVID-19 PCR testing.Results: Of 283 patients studied, 221 (78%) were PCR+ and 62 (22%) PCR-. Chest radiograph revealed bilateral pulmonary infiltrates in 85%, which was significantly more common in PCR+ (94%) vs PCR- (52%) patients (P l 0.0001). The rate of manifesting all five positive clinical parameters was significantly greater in PCR+ (63%) vs PCR- (6.5%) patients (P l 0.0001). For PCR+ outcome, the presence of all five positive clinical parameters had a specificity of 94%, positive predictive value of 98%, and positive likelihood ratio of 10.Conclusions: Using an ED protocol to rapidly assess five clinical parameters accurately distinguishes likelihood of COVID-19 infection prior to PCR test results, and can be used to augment early patient cohorting decisions.

Background: During the COVID-19 pandemic, many patients admitted to hospital for treatment have recovered and been discharged; however, in some instances, these same patients are re-admitted due to a second fever or a positive COVID-19 PCR test result. To ascertain whether it is necessary to treat these patients in hospitals, especially in asymptomatic cases, we summarize and analyze the clinical and treatment characteristics of patients re-admitted to hospital with a second COVID-19 infection.Methods: Of the 141 COVID-19 cases admitted to the Wenzhou Central Hospital between January 17, 2020, to March 5, 2020, which were followed until March 30, 2020, 12 patients were re-admitted with a second COVID-19 infection. Data was collected and analyzed from their clinical records, lab indexes, commuted tomography (CT), and treatment strategies.Results: Most of the 141 patients had positive outcomes from treatment, with only 12 (8.5%) being re-admitted. In this sub-group: one (8.3%) had a fever, a high white blood cell count (WBC), and progressive CT changes; and one (8.3%) had increased transaminase. The PCR tests of these two patients returned negative results. Another 10 patients were admitted due to a positive PCR test result, seven of which were clinically asymptomatic. Compared to the CT imaging following their initial discharge, the CT imaging of all patients was significantly improved, and none required additional oxygen or mechanical ventilation during their second course of treatment.Conclusions: The prognoses of the re-admitted patients were good with no serious cases. We conclude that home treatment with concentrated medical observation is a safe and feasible course of treatment if the patient returns a positive PCR test result but does not display serious clinical symptoms. During medical observation, patients with underlying conditions should remain a primary focus, but most do not need to be re-admitted to the hospital.

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.

From the point of view of the pandemic officer of a 300-bed specialty care hospital, the first year of the SARS-CoV‑2 (Severe Acute Respiratory Syndrome Coronavirus Type 2) pandemic with all the challenges for daily clinical routine was reviewed on the basis of the data collected with the aim of making future pandemic management easier to plan.The Caritas Hospital St. Josef in Regensburg employs around 1330 employees and treats almost 20,000 inpatients annually. All records of the pandemic officer between 1 March 2020 and 28 February 2021 were included in the present descriptive study.In all, 280 SARS-CoV-2-positive patients (mean age 68 ± 19 years) were treated during the observation period; 81% (n = 227) of these were treated as inpatients between November 2020 and February 2021. In addition to the analysis of these patients, an analysis of the test concept was carried out, both for the patients (53% of the tests in the so-called 2nd wave) and for the employees; 1633 PCR tests were carried out, with 5.6% of all employees being infected with SARS-CoV‑2 in the course of the pandemic. In addition, other measures such as reducing the surgical program and other general measures were evaluated.Many established processes had to be changed in the hospital during the pandemic. Both staff shortages due to SARS-CoV-2-positive employees and the quarantine measures of contact persons led to further tension in the already tight staffing levels, especially in the nursing care sector, and made patient care more difficult. The test concept in the hospital was very complex and asymptomatic tests in particular showed a low hit rate, while being associated with high personnel costs.HINTERGRUND: Aus dem Blickwinkel der Pandemiebeauftragten eines Schwerpunktkrankenhauses mit 300 Betten wurde das erste Jahr der SARS-CoV‑2(„Severe Acute Respiratory Syndrome Coronavirus Type 2“)-Pandemie mit allen Herausforderungen für den klinischen Alltag anhand der erhobenen Datenlage mit dem Ziel aufgearbeitet, das zukünftige Pandemiemanagement besser planbar zu machen.Das Caritas-Krankenhaus St. Josef in Regensburg beschäftigt rund 1330 Mitarbeitende (MA) und versorgt jährlich fast 20.000 stationäre Patienten. Sämtliche Aufzeichnungen des Pandemiebeauftragten zwischen dem 01.03.2020 und 28.02.2021 wurden in die vorliegende deskriptive Studie eingeschlossen.Im Beobachtungszeitraum wurden 280 SARS-CoV-2-positiv getestete Patienten (durchschnittliches Alter 68 ± 19 Jahre) behandelt. Zwischen 11/2020 und 02/2021 wurden 81 % (n = 227) dieser Patienten im Haus behandelt. Neben der Analyse dieser Patienten erfolgte eine Analyse des Testkonzepts sowohl der Patienten (53 % der Tests i. R. der sog. 2. Welle) als auch der MA; hier erfolgten 1633 PCR-Tests, wobei sich 5,6 % aller MA im Verlauf der Pandemie mit SARS-CoV‑2 infizierten. Zudem wurden auch weitere Maßnahmen wie die Reduktion des OP-Programms und andere Allgemeinmaßnahmen im Haus evaluiert.Viele etablierte Prozesse mussten im Krankenhaus während der Pandemie verändert werden. Sowohl der Ausfall der positiv getesteten MA wie auch die Quarantänezeiten von Kontaktpersonen führten zu einer weiteren Anspannung der insbesondere im Pflegesektor ohnehin engen Personaldecke und erschwerte die Patientenversorgung. Das Testkonzept im Krankenhaus war sehr komplex und gerade asymptomatische Tests wiesen eine geringe Trefferquote bei gleichzeitig hohem Personalaufwand auf.

A door-to-door survey was organised in Cuenca, Ecuador, to determine the prevalence of COVID-19 infection and adherence of the population to COVID-19 preventive measures. A total of 2457 persons participated in the study, 584 (23.7%) reported having experienced at least one flu-like symptom since the onset of the pandemic. The maximum SARS-CoV-2 seroprevalence in Cuenca was 13.2% (CI: 12–14.6%) (IgM or IgG positive). Considering PCR confirmed infections, the prevalence was 11% (CI: 10–12.4%). There was no significant difference in seroprevalence between rural and urban areas. Participants aged 35–49 years old, living with a COVID-19 positive person, at least six people in a household, physical contact with someone outside the household, a contact with a person outside the home with flu-like symptoms, using public transport, and not having enough resources for living, significantly increased the odds for SARS-CoV-2 seropositivity. Overall, there was good adherence to COVID-19 preventive measures. Having known someone who tested positive for COVID-19, having a primary or secondary level of education, and having enough resources for living, significantly increased the odds for higher adherence. In conclusion, despite good overall adherence of the population of Cuenca with COVID-19 preventive measures, our study suggests high ongoing COVID-19 transmission in Cuenca, particularly in certain parishes. Prevention should not only focus on behavioural change, but on intensified testing strategies in demographical risk groups.

BackgroundRoutine asymptomatic testing using RT-PCR of people who interact with vulnerable populations, such as medical staff in hospitals or care workers in care homes, has been employed to help prevent outbreaks among vulnerable populations. Although the peak sensitivity of RT-PCR can be high, the probability of detecting an infection will vary throughout the course of an infection. The effectiveness of routine asymptomatic testing will therefore depend on testing frequency and how PCR detection varies over time.MethodsWe fitted a Bayesian statistical model to a dataset of twice weekly PCR tests of UK healthcare workers performed by self-administered nasopharyngeal swab, regardless of symptoms. We jointly estimated times of infection and the probability of a positive PCR test over time following infection, we then compared asymptomatic testing strategies by calculating the probability that a symptomatic infection is detected before symptom onset and the probability that an asymptomatic infection is detected within 7 days of infection.FindingsWe estimated that the probability that the PCR test detected infection peaked at 77% (54 - 88%) 4 days after infection, decreasing to 50% (38 - 65%) by 10 days after infection. Our results suggest a substantially higher probability of detecting infections 1–3 days after infection than previously published estimates. We estimated that testing every other day would detect 57% (33-76%) of symptomatic cases prior to onset and 94% (75-99%) of asymptomatic cases within 7 days if test results were returned within a day.InterpretationOur results suggest that routine asymptomatic testing can enable detection of a high proportion of infected individuals early in their infection, provided that the testing is frequent and the time from testing to notification of results is sufficiently fast.FundingWellcome Trust, National Institute for Health Research (NIHR) Health Protection Research Unit, Medical Research Council (UKRI)

Viral tests including polymerase chain reaction (PCR) tests are recommended to diagnose COVID-19 infection during the acute phase of infection. A test should have high sensitivity; however, the sensitivity of the PCR test is highly influenced by viral load, which changes over time. Because it is difficult to collect data before the onset of symptoms, the current literature on the sensitivity of the PCR test before symptom onset is limited. In this study, we used a viral dynamics model to track the probability of failing to detect a case of PCR testing over time, including the presymptomatic period. The model was parametrized by using longitudinal viral load data collected from 30 hospitalized patients. The probability of failing to detect a case decreased toward symptom onset, and the lowest probability was observed 2 days after symptom onset and increased afterwards. The probability on the day of symptom onset was 1.0% (95% CI: 0.5 to 1.9) and that 2 days before symptom onset was 60.2% (95% CI: 57.1 to 63.2). Our study suggests that the diagnosis of COVID-19 by PCR testing should be done carefully, especially when the test is performed before or way after symptom onset. Further study is needed of patient groups with potentially different viral dynamics, such as asymptomatic cases.

Rapid point-of-care (POC) quantification of low virus RNA load would significantly reduce the turn-around time for the PCR test and help contain a fast-spreading epidemic. Herein, we report a droplet digital PCR (ddPCR) platform that can achieve this sensitivity and rapidity without bulky lab-bound equipment. The key technology is a flattened pipette tip with an elliptical cross-section, which extends a high aspect-ratio microfluidic chip design to pipette scale, for rapid (

To assess the effectiveness of the containment strategies proposed in Japan, an SEIAQR (susceptible-exposed-infected-asymptomatic-quarantined-recovered) model was established to simulate the transmission of COVID-19. We divided the spread of COVID-19 in Japan into different stages based on policies. The effective reproduction number Re and the transmission parameters were determined to evaluate the measures conducted by the Japanese Government during these periods. On 7 April 2020, the Japanese authority declared a state of emergency to control the rapid development of the pandemic. Based on the simulation results, the spread of COVID-19 in Japan can be inhibited by containment actions during the state of emergency. The effective reproduction number Re reduced from 1.99 (before the state of emergency) to 0.92 (after the state of emergency). The transmission parameters were fitted and characterized with quantifiable variables including the ratio of untracked cases, the PCR test index and the proportion of COCOA app users (official contact confirming application). The impact of these variables on the control of COVID-19 was investigated in the modelling analysis. On 8 January 2021, the Japanese Government declared another state of emergency. The simulated results demonstrated that the spread could be controlled in May by keeping the same strategies. A higher intensity of PCR testing was suggested, and a larger proportion of COCOA app users should reduce the final number of infections and the time needed to control the spread of COVID-19.

Background In a response to the pandemic, urgent care centers (UCCs) have gained a critical role as a common location for COVID-19 testing. We sought to characterize the changes in testing accessibility at UCCs between March and August 2020 on the basis of testing availability (including rapid antigen testing), wait time for test results, cost of visits, and cost of tests. Methods Data were collected using a secret shopper methodology. Researchers contacted 250 UCCs in 10 states. Investigators used a standardized script to survey centers on their COVID-19 testing availability and policies. UCCs were initially contacted in March and re-called in August. T-tests and chi-square tests were conducted to identify differences between March and August data and differences by center classification. Results Our results indicate that both polymerase chain reaction (PCR) tests to detect COVID-19 genetic material and rapid antigen COVID-19 tests have increased in availability. However, wait times for PCR test results have significantly increased to an average of 5.79 days. Additionally, a high proportion of UCCs continue to charge for tests and visits and no significant decrease was found in the proportion of UCCs that charge for COVID-19 testing from March to August. Further, no state reported a majority of UCCs with rapid testing available, indicating an overall lack of rapid testing. Conclusions From March to August, COVID-19 testing availability gradually improved. However, many barriers lie in access to COVID-19 testing, including testing costs, visit costs, and overall lack of availability of rapid testing in the majority of UCCs. Despite the passage of the CARES Act, these results suggest that there is room for additional policy to improve accessibility to testing, specifically rapid testing.

The present work aims to identify the predictors of COVID-19 in-hospital mortality testing a set of Machine Learning Techniques (MLTs), comparing their ability to predict the outcome of interest. The model with the best performance will be used to identify in-hospital mortality predictors and to build an in-hospital mortality prediction tool. The study involved patients with COVID-19, proved by PCR test, admitted to the “Ospedali Riuniti Padova Sud” COVID-19 referral center in the Veneto region, Italy. The algorithms considered were the Recursive Partition Tree (RPART), the Support Vector Machine (SVM), the Gradient Boosting Machine (GBM), and Random Forest. The resampled performances were reported for each MLT, considering the sensitivity, specificity, and the Receiving Operative Characteristic (ROC) curve measures. The study enrolled 341 patients. The median age was 74 years, and the male gender was the most prevalent. The Random Forest algorithm outperformed the other MLTs in predicting in-hospital mortality, with a ROC of 0.84 (95% C.I. 0.78–0.9). Age, together with vital signs (oxygen saturation and the quick SOFA) and lab parameters (creatinine, AST, lymphocytes, platelets, and hemoglobin), were found to be the strongest predictors of in-hospital mortality. The present work provides insights for the prediction of in-hospital mortality of COVID-19 patients using a machine-learning algorithm.

SARS-CoV-2 pandemic is the greatest public health concern of the year 2020. There are several worldwide reports of patients who have managed to recover from SARS-CoV-2 infection with negative PCR test results, that for unknown reasons convert back to positive PCR. We report a case of a patient in our hospital who developed positive PCR test results for SARS-CoV-2, after 4 consecutive results that were negative, along with a full-blown clinical syndrome of SARS-CoV-2 infection.

PCR was applied for the discovery of adulteration of crude and processed beef meat with horse and donkey tissue. This was performed by blending (w/w) horse or donkey meat to beef meat in an extent up to 1:10000 (0.01%). The sensitivity was resolved as high as 0.01%. All used primers showed specificity in the PCR reactions utilizing layout DNAs from three animal species. PCR application on 96 beef meat and meat product samples gathered randomly from street vendors and prominent retail markets (24 of burger, 16 of minced meat, 24 of kofta, 16 of sausage, 7 of raw meat and 9 of launcheon) uncovered 6 positive for donkey tissue (3 from sausage, 2 from minced meat and 1 from kofta) and 2 positive for horse tissue (from sausage). This basic PCR strategy effectively distinguished adulteration of raw and processed beef meat samples with horse and donkey tissue. This work also highlights on the severity of the meat adulteration problem in Egypt.

Latar belakang : Kecamatan Seram Barat merupakan salah satu wilayah di bagian timur Indonesiayang endemis malariadan dikategorikan tinggi dengan indikator API diatas angka nasional. Angka kesakitan malaria per 1000 penduduk pada tiga tahun terakhir fluktuatif dimana API tahun 2014 (22,8‰), 2015(6,147‰) dan 2016 (9,03‰) dengan441kasus klinis,248kasus positif, ditemukan 23 spesies namun belumterkonfirmasi sebagai vektor malaria. Tujuan : Menganalisis secara spasial karakteritik linkungan dan dinamika kepadatan Anophele s sp. pengharunya terhadap kejadian malaria di Kecamatan Seram Barat. Metode : Jenis Penelitian ini adalah observasional analitik, desainnya cross sectional yang pelaksananya di Kecamatan Seram Barat terhadap 100 orang yang dipilih secara purposive sampling. Pengumpulan data melalui wawancara, observasi dan Penangkapan nyamuk dengan metode upan orang didalam dan di halaman rumah. Analisis data menggunakan uji chi-square . Hasil : Hasil penelitian ditemukan 41 reponden positif malaria, 5 spesies Anopheles sp. yakni An.vagus, An.teselaltus, An.kochi, An.barbirotris, An.farauti dan tidak terkonfirmasi sebagai vektor malaria, variabel yang mempengaruhi kejadian malaria adalah Suhu udara (p= 0,022, PR = 2,082), Kelembaban (p= 0,003, PR = 3,421),Kepadatan Anopheles sp. (p=0,001, PR = 2,853), Jarak Breeding places (0,000, RP= 10,054). Kesimpulanadalahtedapat 41 kasus, 5 spesies Anophele s sp. Suhu udara, kelembaban, kepadatan Anophele s sp, jarak breeding places mempengaruhi kejadian malaria, tidak ditemukan Anopheles sp sebagai vektor malaria di Seram Barat berdasakan hasil uji PCR ABSTRACT Title: Spatial Analysis of Environmental characteristics and Dynamics of Density Anopheles sp. As The Effect on Malaria Case in West Seram District, Western Area of Seram Regency, Maluku . Background : West Seram District is one of the regions in eastern Indonesia that became malaria endemic area and categorized as high with the API indicator above the national figure. The number of malaria morbidity, per 1000 of population, had been fluctuating in last three years which shown by API in 2014 (22.8 ‰), 2015 (6,147 ‰) and 2016 (9.03 ‰) with 441 clinical cases, 248 positive cases, 23 species have been found but it has not been confirmed yet as a malaria vector . T he purpose of the study is to analyze spatially the characteristics of the environment and the dynamics of the density from Anopheles sp. as the effect on the case of malaria in West Seram District. Methods: the type of this research is boservational analytic with cross sectional design. The research was held in West Seram District toward 100 people that were selected by purposive sampling.The collecting data had been done through interview, observation, and catching the mosquitoes using bait people method inside and outside the house yard. The analysis were using chi-square test. Result : The results of the study found 41 respondents positive for malaria, 5 species of Anopheles sp. namely An.vagus, An.teselaltus, An. kochi, An. barbirotris, and An. farauti. The variables affecting the case of malaria were air temperature (p = 0.022, PR = 2.082), humidity (p = 0.003, PR = 3.421), density of Anopheles sp. (p = 0.001, PR = 2,853), breeding places distances (0,000, RP = 10,054). The result of PCR test shows that there are no species containing Plamodium were found. Conclusion; The result detected 41 cases, identified 5 species of Anopheles sp. air temperature, humidity, density of Anopheles sp, distance of breeding places affecting the case of malaria. There are no Anopheles sp were found as a malaria vector in Seram Barat based on PCR test result.

The aim of our work was to develop PCR test systems for the identification and differentiation of the Piscichlamydia salmonis and Clavochlamydia salmonicola, species, that are known epitheliocystis infection agents of gill and fish skin diseases, characterized by the presence of specific ‘inclusions’ in the epithelial cells of the gills. To date, the diseases of fish associated with chlamydial infections have been detected in more than 90 species of freshwater and marine fish worldwide. For now, there is no available information on the prevalence of Piscichlamydia salmonis and Clavochlamydia salmonicola, which can cause epitheliocystis of commercially important aquaculture species in Ukraine. Identification of these pathogens is possible only using molecular genetic methods. As a result of our research, we got PCR tests for the identification and species differentiation of Piscichlamydia salmonis and Clavochlamydia salmonicola. The use of diagnostics for the identification of Piscichlamydia salmonis and Clavochlamydia salmonicola makes chlamydial infections monitoring among various fish species possible and it will increase the economic efficiency of fish farms.

Introduction Bovine tuberculosis is a chronic contagious disease caused by Mycobacterium bovis or Mycobacterium caprae. Before widespread action conducted in Poland between 1959-1975 to combat bovine tuberculosis (BTB), about 40% of all tuberculosis cases in pigs was caused by the bovine bacillus. At the present time, correctly carried out, long-term control of cattle has resulted in cases of bovine tuberculosis in pigs and humans being extremely rare and sporadic. In pigs, tuberculosis is most often caught in a slaughterhouse during slaughter. Material and methods Samples came from pigs kept on the farm. Traditional bacteriological methods on solid media (Stonebrink, LJ with pyruvate) supported by the semi-automatic, liquid indicative culture method (MGIT) and PCR test were applied in targeted studies. The GenoType Mycobacterium MTBC and CM tests (Hain Lifescience, Germany) were used to additionally confirm that isolated strains classification was used. Results Strains of mycobacteria were isolated from all examined pigs. Mycobacterium bovis was determined by real time PCR and Hain Genotype methods. Conclusions In order to effectively fight against BTB, all animals on farms should be tested, regardless of species, while the milk of suspected cows should be utilized without being used for feed. It is important to adapt the current legal regulations to the current epidemiological situation.

Leaf spot of Brassica is an important bacterial seed borne disease caused by X. campestris pv. raphani (Xcr), one of the three pathovars of Xanthomonas campestris species which makes significant economic loss throughout the world. A rapid and reliable detection method will be helpful for early diagnosis of the disease. To do that, we designed Xcr specific sequence-characterized amplified region (SCAR) markers from the Xcr specific genomic fragments, identified by aligning the whole genome sequences of several closely related bacterial pathovars and other bacterial species. Our primer set Xcr_59 produced Xcr specific amplicon of 679 bp in PCR assays. This primer pair was also capable of detecting Xcr strains directly from the artificially infected leaf samples prepared by suspending the diseased leaf area in sterile water without extracting bacterial DNA. This rapid, sensitive and reliable detection technique will be useful for adopting any firsthand plant protection measures against the disease.

The purpose of the present study was to create a real-time PCR test system allowing simultaneous detection of nontuberculous mycobacteria (NTM) and Mycobacterium tuberculosis complex (MTBC) both in culture and sputum. NTM cultures (18 strains, 18 species), MTBC cultures (16 strains, 2 species) and non-mycobacterial microorganisms from the collection of the Central Research TB Institute (CTRI) were used for the preliminary evaluation of the test system. 301 NTM cultures from patients with mycobacteriosis were used to assess the sensitivity of the developed test system. Clinical respiratory samples (sputum) from 104 patients with mycobacteriosis, 3627 patients with tuberculosis and 118 patients with other lung diseases were used for diagnostic sensitivity and specificity testing. The specificity and sensitivity of the assay for MTBC was found to be 100% both in culture and sputum samples; for NTM, the specificity was 100% in culture and sputum, the sensitivity reached 100% in culture and 73.1% in sputum samples. Positive predictive value (PPV) and negative predictive value (NPV) of the assay for culture were both 100%, for clinical material 100% and 80.8%, respectively. The limit of detection at the probability of detection 95% (LoD95%) was estimated to be 16 cfu/ml for M. tuberculosis H37RV and 1200 cfu/ml for M. avium.

BackgroundTesting asymptomatic contacts of confirmed COVID-19 cases for the presence of SARS-CoV-2 could reduce onward transmission by improving case ascertainment and lessen the impact of self-isolation on un-infected individuals. This study investigated the feasibility and acceptability of implementing a ‘test to enable approach’ as part of England’s tracing strategy.MethodsContacts of confirmed COVID-19 cases were offered serial testing as an alternative to self-isolation using daily self-performed lateral flow device (LFD) tests for the first 7 days post exposure. Asymptomatic participants with a negative LFD result were given 24 hours of freedom from self-isolation between each test. A self-collected confirmatory PCR test was performed on testing positive or at the end of the LFD testing period.ResultsOf 1,760 contacts, 882 consented to daily testing, with 812 within 48 hours of exposure sent testing packs. Of those who declined to participate, 39.1% stated they had already accessed PCR testing. Of the 812 who were sent packs, 570 (70.2%) reported one or more LFD results; 102 (17.9%) tested positive. Concordance between reported LFD result and a supplied LFD image was 97.1%. 82.8% of PCR positive samples and 99.6% of PCR negative samples were correctly detected by LFD. The proportion of secondary cases from contacts of those who participated in the study and tested positive (6.3%; 95% CI: 3.4-11.1%) were comparable to a comparator group who self-isolated (7.6%; 95% CI: 7.3-7.8%).ConclusionThis study shows a high acceptability, compliance and positivity rates when using self-administered LFDs among contacts of confirmed COVID-19 cases. Offering routine testing as a structured part of the contact tracing process is likely to be an effective method of case ascertainment.

Background:Although the sensitivity of third generation anti-HCV CIA tests is high, false positivity rates, especially in populations with low HCV infection endemicity, are still high. Objectives:We aimed to determine the S/Co cut-off value of anti-HCV in the diagnosis of real positive patients based on the CIA test kit absorbance routinely used in our laboratory and to reveal the potential cost effectiveness of confirmatory tests for false positive samples. Methods:All anti-HCV CIA test results which were performed in the microbiology laboratory of our hospital between 2016-2019 were retrospectively screened and S/Co values of the patients were recorded. Among these, the results that were confirmed with HCV-RNA real-time PCR test were included. Patients who were previously diagnosed and treated were excluded. Results:A total of 257 patients, who were tested for HCV-RNA after reactive anti-HCV test results, were included in the study. Of the cases, 84(32.68%) had positive HCV-RNA. According to the ROC analysis, the optimal S/Co value was 8.58 with the sensitivity and specificity values 95.24% and 85.55%, respectively. According to this 8.58S/Co value, anti-HCV test was reactive in 105 cases and 80(76.2%) of these cases had active HCV infection. In order to prevent the false-negativity, the additional cost of using 1.0S/Co value to our institution was 4114.64USD, meaning that we spent 1028.66USD to diagnose per true-case of active HCV infection when using 1.0S/Co value. In our institution, approximately 6.25 working hours are spent to finalize the HCV-RNA PCR test. The hours spent for S/Co of 1.0 and 8.58 were 1606.25 and 658.25, respectively. Conclusions:False positive anti-HCV results are an economic burden on health economics of countries. At least, different S/Co values might be used in accordance with the purpose of the screening (like blood donors or pre-operative screening) and prevalence of HCV infection in different laboratories and different populations.

Objective: Aims to describe the initial symptoms most related to the prognosis of Covid-19. Design: This is a retrospective cross sectional, quantitative, data analyzed study. Site: This study was made in the family medicine centers (n = 82) of Çorlu district of Tekirdağ province, in Turkey. Participants: The study included patients (n = 1.506) who had a positive PCR test for Covid-19 from March to September 2020. And we asked them their initial symptoms which bring them to the family medicine centers before the test. Main measurements: The participants’ age, gender, presence of chronic disease, and initial symptoms which they come to a healthcare facility were evaluated. These variables were analyzed in terms of length of hospital stay, intensive care unit admission and mortality rates. Results: The most common initial symptom in Covid-19 patients was cough. The presence of a chronic disease, the shortness of breath, malaise, the loss of smell and taste, and vomiting were found to be associated with an increased mortality rate. Advanced age, the presence of cough, malaise, the loss of smell and taste, and vomiting as the initial symptoms were found to have increased the likelihood of being admitted to the intensive care unit. Conclusions: The authors advise placing more attention on the initial symptoms of cough, malaise, the loss of smell and taste and vomiting in Covid-19 patients. Because these symptoms are related with severe prognosis indicators. Resumen: Objetivo: Describir los síntomas iniciales más relacionados con el pronóstico de COVID-19. Diseño: Este es un estudio retrospectivo de análisis de datos transversales, cuantificativos. Emplazamiento: Este estudio se realizó en los centros de medicina familiar (n = 82) del distrito de Çorlu de la proviencia de Tekirdağ, en Turquía. Participantes: El estudio incluyó pacientes (n = 1.506) que tuvieron una prueba de PCR positiva para COVID-19 de marzo a septiembre de 2020. Se les preguntaron sus síntomas iniciales que los llevan a los centros de medicina familiar antes de la prueba. Mediciones principales: Se evaluaron la edad, el sexo, la presencia de enfermedad crónica y los síntomas iniciales de los participantes que llegaron a un centro de atención médica. Estas variables se analizaron en términos de duración de la estancia hospitalaria, ingreso a la unidad de cuidados intensivos y tasas de mortalidad. Resultados: El síntoma inicial de presentación más común en los pacientes con COVID-19 fue la tos. La presencia de una enfermedad crónica, la falta de aliento, el malestar, la pérdida de olor y sabor y los vómitos se asociaron a una mayor tasa de mortalidad. La edad avanzada, la presencia de tos, malestar, la pérdida de olor y sabor, y vómitos fueron los síntomas iniciales que se encontraron para incrementar la probabilidad de ser admitido en la unidad de cuidados intensivos. Conclusiones: Los autores aconsejan prestar más atención a los síntomas iniciales de tos, malestar, pérdida de olor y sabor y vómitos en pacientes con COVID-19, porque estos síntomas están relacionados con indicadores de pronóstico severo.

With more than 100 million confirmed COVID-19 cases as of March 2021, reinfection is still considered to be rare. In light of increasing reports of reinfected COVID-19 patients, the need to better understand the real risk for reinfection is critical, with potential effects on public health policies aimed at containing the spread of SARS-CoV-2. In this descriptive preliminary report, we conducted a large-scale assessment on the country level of the possible occurrence of COVID-19 reinfection within the members of a large healthcare provider in Israel. Out of 149,735 individuals with a documented positive PCR test between March 2020 and January 2021, 154 had two positive PCR tests at least 100 days apart, reflecting a reinfection proportion of 1 per 1000. Given our strict inclusion criteria, we believe these numbers represent true reinfection incidence in MHS and should be clinically regarded as such.

Background Previous studies showed that recovered coronavirus disease 2019 (COVID-19) patients can have a subsequent positive polymerase chain reaction (PCR) test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after they are discharged from the hospital. Understanding the epidemiological characteristics of recovered COVID-19 patients who have a re-positive test is vital for preventing a second wave of COVID-19. Methods This retrospective study analyzed the epidemiological and clinical features of 20,280 COVID-19 patients from multiple centers in Wuhan who had a positive PCR test between December 31, 2019, and August 4, 2020. The RT-PCR test results for 4079 individuals who had close contact with the re-positive cases were also obtained. Results In total, 2466 (12.16%) of the 20,280 patients had a re-positive SARS-CoV-2 PCR test after they were discharged from the hospital, and 4079 individuals had close contact with members of this patient group. All of these 4079 individuals had a negative SARS-CoV-2 PCR test. Conclusions This retrospective study in Wuhan analyzed the basic characteristics of recovered COVID-19 patients with re-positive PCR test and found that these cases may not be infectious.

Highlights • In the literature, the additional contribution of a second PCR test to the diagnosis is unknown. • Performing a second nasopharyngeal test causes the excessive use of tests and personal protective equipment, the loss of labor and time, and can be costly. • A second PCR test was performed in 91.6% the patients whose first tests were negative. Of them, only 6.6% were detected positive. • The strategy of using the second nasopharyngeal PCR test to confirm or exclude the diagnosis should be reconsidered, because its additional contribution to the first test is very low., Objective The World Health Organization (WHO) recommends performing a second test in patients with a high suspicion of novel coronavirus disease (COVID-19) whose first PCR test is negative. However, the additional contribution of the second PCR test to the diagnosis is unknown. Patients and methods In this study, we aimed to investigate the contribution of second SARS-CoV-2 PCR to diagnosis in patients with a suspicion of COVID-19 whose initial test was negative. Results A total of 1449 patients were hospitalized in infectious disease clinics with the suspicion of COVID-19 infection during the study period. We performed the second PCR test (697 nasopharyngeal sample, 5 tracheal aspirate) in 702/766 (91.6%) patients whose first tests were negative and only 6.6% (46) of them were positive. Conclusions The strategy of using the second nasopharyngeal PCR test to confirm or exclude the diagnosis seems to cause the loss of labor and time, and is costly, because its additional contribution to the first test is very low.

The aim of the study was to compare the performance of various computed tomography (CT) reporting tools, including zonal CT visual score (ZCVS), the number of involved lobes, and Radiological Society of North America (RSNA) categorization in predicting adverse outcomes among patients hospitalized due to the lower respiratory symptoms during the coronavirus disease 2019 (COVID-19) pandemic. A total of 405 patients admitted with severe respiratory symptoms who underwent a chest CT were enrolled. The primary adverse outcome was intensive care unit (ICU) admission of patients. Predictive performances of reporting tools were compared using the area under the receiver operating characteristic curves (AUC ROC). Among the 405 patients, 39 (9.63%) required ICU support during their hospital stay. At least two or more observers reported a typical and indeterminate COVID-19 pneumonia CT pattern according to RSNA categorization in 70% (285/405) of patients. Among these, 63% (179/285) had a positive polymerase chain reaction (PCR test for the SARS-CoV-2 virus. The median number of lobes involved according to CT was higher in patients who required ICU support (median interquartile range [IQR], 5[3; 5] vs. 3[0; 5]). The median ZCVS score was higher among the patients that subsequently required ICU support (median [IQR], 4[0; 12] vs. 13[5.75; 24]). The bootstrap comparisons of AUC ROC showed significant differences between reporting tools, and the ZCVS was found to be superior (AUC ROC, 71-75%). The ZCVS score at the first admission showed a linear and significant association with adverse outcomes among patients with the lower respiratory tract symptoms during the COVID-19 pandemic.

Identifying patients at increased risk for severe COVID-19 is of high priority during the pandemic as it could affect clinical management and shape public health guidelines. In this study we assessed whether a second PCR test conducted 2-7 days after a SARS-CoV-2 positive test could identify patients at risk for severe illness. Analysis of a nationwide electronic health records data of 1,683 SARS-CoV-2 positive individuals indicated that a second negative PCR test result was associated with lower risk for severe illness compared to a positive result. This association was seen across different age groups and clinical settings. More importantly, it was not limited to recovering patients but also observed in patients who still had evidence of COVID-19 as determined by a subsequent positive PCR test. Our study suggests that an early second PCR test may be used as an additional risk-assessment tool to improve disease management and patient care.

BACKGROUND: After the first COVID-19 case, reported neurological complications are increasing day by day. METHOD: In this paper, we present a benign-course Guillain-Barre syndrome (GBS) emerging 2 weeks after COVID-19 infection in a 35-years-old male. RESULTS: Cough and fever were started 18 days ago and his PCR test was resulted positive for COVID-19 infection. After treatment and quarantine were completed, he developed sudden leg weakness following autonomic features. Cerebrospinal fluid was suggestive for GBS despite the electrodiagnostic test was not helpful because it was done in the first days. He recovered without needing any immunotherapy. CONCLUSION: Our case suggested that COVID-19 can cause atypical benign GBS forms in addition to well-known variants. Comprehensive studies are needed to describe the unknowns and determine the exact prevalence of GBS after COVID-19 infection, including mild cases that did not require hospital admission.

Seroprevalence survey, for antibodies to SARS-CoV-2, of healthcare workers (HCW) working in three Government run hospitals in Mumbai was carried out in June 2020. Among the 801 HCWs tested, seroprevalence was 11.1%. Males (13.5% vs. 8.9% in females) and ancillary workers (18.5% vs 6.9% in doctors and nurses) were more likely to be seropositive. Sixty-two (7.74%) had been previously diagnosed with RT PCR test for SARS-CoV-2. Of these, 44 (71%) were seronegative. Upto 28 days after a positive PCR test, 90% of subjects were found to be seropositive. This reduced to less than half (38.5%) between 29 and 42 days. None of 28 infected HCWs who had the RT-PCR more than 50 days ago tested positive for antibodies. It seems likely that cellular immunity plays a larger role in defence against the illness.

CASE REPORT OF COVID 19—Recurrence We describe as case series of 7 patients who presented with a recurrence of COVID 19 by PCR test an average of 94.9 days after their initial symptomatic presentation of illness. Patients had tested negative by PCR or had evidence of antibodies in between the 2 episodes. The majority of patients were asymptomatic on the second presentation and were found incidentally on prescreen for procedures, surgery. The subsequent positive COVID-19 PCR tests resulted in cancellations of clinic, procedures, surgery, and impacted patients’ home and employment status. Further studies are needed to understand the mechanisms and ultimate outcomes of these recurrences.

Various tests are used to detect the severe acute respiratory syndrome-coronirus-2 (SARS-CoV-2) virus causing Coronavirus disease-19 (COVID-19) disease Today, the realtime (RT) -PCR test combined with the reverse-transcription reaction is the gold standard method used to diagnose SARS-CoV-2 This method is referred to as quantitative realtime PCR (RT-qPCR) because it determines not only the presence of SARS-CoV-2 but also the amount of virus in the specimen Due to the use of virus-specific primers, the specificity of the tests is considered to be 100% For this test, swab samples taken from the upper respiratory tract such as nasopharyngeal and throat, samples from the lower respiratory tract areas such as sputum and bronchoalveolar lavage fluid, rectal swab, feces, serum and urine samples are preferred Correct use of personal protective equipment (PPE) by healthcare professionals during sampling and testing is important Rapid antigen tests used in addition to RT-qPCR test for the diagnosis of SARS-CoV-2 are advantageous due to the theoretical rapid result time and low cost, but the sensitivity of this method is known to be very low Virus detection in cell cultures can be used to detect SARS-CoV-2, but it is not for routine diagnostic because the results take a long time, require labor, and expertise Serological tests are frequently used in the diagnosis and follow-up of this disease These are mainly ELISA, CLIA, immunofluorescence test (IFA), western blot (WB), protein microarray (microarray) and neutralization ELISA based immunoglobulin (Ig)M and IgG antibody tests have more than 95% specificity in the diagnosis of COVID-19 (English) [ABSTRACT FROM AUTHOR] Koronavirus hastaligi-19 (COVID-19) hastaligina neden olan siddetli akut solunum yolu enfeksiyonu CoV-2 (SARS-CoV-2) virusunu tespit etmek amaciyla cesitli testler kullanilmaktadir Gunumuzde revers-transkripsiyon tepkimesiyle birlestirilmis Realtime (RT)- polimeraz zincir reaksiyonu (PZR) testi SARS-CoV-2'yi teshis etmek icin kullanilan altin standart yontemdir Bu yontem, ornekte sadece SARS-CoV-2'nin varligini degil ayni zamanda virus miktarinida belirledigi icin kantitatif PZR (RT-qPZR) olarak anilmaktadir Viruse ozgul primerlerin kullanilmasi sebebiyle testlerin ozgullugu %100 olarak kabul edilmektedir Bu test icin nazofarengeal ve bogaz gibi ust solunum yollarindan alinan suruntu ornekleri, balgam ve bronkoalveoler lavaj sivisi gibi alt solunum yollarina ait alanlardan alinan ornekler, rektal suruntu, diski, serum ve idrar ornekleri tercih edilmektedir Ornek alma ve test calisilmasi sirasinda kisisel koruyucu ekipmanlarin saglik calisanlari tarafindan dogru kullanimi onemlidir SARS-CoV-2 tanisi icin RT-qPZR testine ilave olarak kullanilan hizli antijen testleri teorik olarak hizli sonuclanma zamani ve dusuk maliyetli olmasindan dolayi avantaj saglar ancak bu yontemin duyarliliginin oldukca dusuk oldugu bilinmektedir Hucre kulturu SARS-CoV-2 tespit etmek amaciyla kullanilabilir ancak sonuclarin uzun zaman almasi, emek gerektirmesi ve uzmanlik isteyen bir yontem olmasi nedeniyle tani amacli ve rutin olarak gerceklestirilmez Serolojk testler bu hastaligin tanisinda ve takibinde siklikla kullanilmaktadir Bunlar esas olarak ELISA, kemiluminesans testi (CLIA), immunofloresan testi (IFA), western blot (WB), protein microarray (mikrodizi) ve notralizasyondur ELISA bazli immunoglobulin (Ig)M ve IgG antikor testlerinin, COVID-19 tanisinda %95'ten fazla ozgulluge sahip oldugu belirtilmektedir SARS-CoV-2 ile enfekte olan hastalarda en erken 7-11 gun sonra antikor cevabi gelistigi icin hastaligin akut tanisinda yararli degildir Virus notralizasyon testleri antikorlarin islevselligini ortaya koymasi nedeniyle diger serolojik testlere gore daha anlamli sonuclar ortaya koymaktadir (Turkish) [ABSTRACT FROM AUTHOR] Copyright of Bezmialem Science is the property of Galenos Yayinevi Tic LTD STI and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission However, users may print, download, or email articles for individual use This abstract may be abridged No warranty is given about the accuracy of the copy Users should refer to the original published version of the material for the full abstract (Copyright applies to all Abstracts )

The aim was to determine hematological and biochemical changes in children who are carriers of SARS-CoV-2. Unlike H1N1 influenza-like illness the predictive factors of SARS-CoV-2 in asymptomatic children (carriers of SARS-CoV-2) are distinctive ratio between lymphocytes and monocytes more than 2, with occasional eosinophila, and a dicrease in erythrocyte indices (MCH and MCV), and a rapid and strong increase in serum LDH value. The predictive factors are, presumably, useful for fast and cheap triage of children “from contact” until a PCR test result for SARS-CoV-2 arrives.

Aims Delay and false positivity in PCR test results have necessitated accurate chest CT reporting for management of patients with COVID-19 suspected symptoms. Pandemic related workload and level of experience on covid-dedicated chest CT scans might have effected diagnostic performance of on-call radiologists. The aim of this study is to reveal the interpretation errors in chest-CT reports of COVID-19 suspected patients admitted to the ER. Methods COVID-19 dedicated chest-CT scans which were performed between March and June 2020 were re-evaluated and compared with the former reports of these scans and PCR test results. CT scan results were classified into four groups. Parenchymal involvement ratios, radiology departments’ workload, COVID-19 related educational activities have examined. Results Out of 5721 Chest-CT scans, 783 CTs belonging to 664 patients (340 female, 324 male) were included to this study. RT-PCR test was positive in 398; negative in 385 cases. PCR positivity was found to be highest in “normal” and “typical for covid” groups whereas lowest in “atypical for covid” and “not covid” groups. 5-25% parenchymal involvement ratio was found in 84.2% of the cases. Regarding number of chest CT scans performed, radiologists’ workload have found to be increased six-folds compared to the same months of the former year. With the re-evaluation, a total of 145 IEs (18.5%) have been found. IEs were mostly precipitated in the first two months (88.3%) and mostly in “not covid” class (60%) regardless of PCR positivity. COVID-19 and radiology entitled educational activities along with the ER admission rates within the first two months of pandemic have seem to be related with the decline of IEs within time. Conclusion COVID-19 pandemic made a great impact on radiology departments with an inevitable burden of daily chest-CT reporting. This workload and concomitant factors have possible effects on diagnostic challenges in COVID-19 pneumonia.

Objective: Increases in the incidence of mental illness is a concern during the COVID-19 pandemic. The fear of becoming ill may compound the stress of loneliness in isolation. Using a unique COVID-19 symptom reporting dataset, we examine whether quarantine status, test status, and reported symptoms are predictive of clinical depression, as measured by Patient Health Questionnaire-2 scores.Results: We find that those who test positive for COVID-19 are at six-fold risk of clinical depression, and may require clinical intervention.

Several mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging. Mismatch(es) in primer/probe binding regions would decrease the detection sensitivity of the PCR test, thereby affecting the results of clinical testing. In this study, we conducted an in silico survey on SARS-CoV-2 sequence variability within the binding regions of primer/probe published by the Japan National Institute of Infectious Diseases (NIID) and Centers for Disease Control and Prevention (CDC). In silico analysis revealed the presence of mutations in the primer/probe binding regions. We performed RT-PCR assays using synthetic RNAs containing the mutations and showed that some mutations significantly decreased the detection sensitivity of the RT-PCR assays.Our results highlight the importance of genomic monitoring of SARS-CoV-2 and evaluating the effects of mismatches on PCR testing sensitivity.

In diphtheria laboratory examinations, the PCR test can be applied to isolates and clinical specimens. This study aimed to develop a PCR assay to identify the species and toxigenicity of diphtheria-causing bacteria, including the prediction of some NTTB types. Seven reference isolates, four synthetic DNA samples, 36 stored isolates, and 487 clinical samples used for PCR optimization. The PCR results was confirmed by DNA sequence analysis. The results of the PCR examination of the 7 reference isolates and 36 stored isolates were similar to the results obtained using conventional methods as gold standard, both for diphtheria-causing and non-diphtheria-causing bacteria. The validation of the PCR results using DNA sequence analysis showed that there was no mispriming or misamplification. The multiplex PCR assay developed in this study could correctly identify the species and toxigenicity of diphtheria-causing bacteria, including the prediction of some NTTB types not yet covered by established PCR methods.

In this work, we put forward a novel test strategy, that allows to significantly increase the test capacity for SARS-CoV-2. The test strategy is based on an a priory risk assessment scheme, that allows to dynamically find and adapt an optimal clustering size of test pools. We, furthermore, suggest a method to overcome the efficiency loss of test clustering by avoiding concentration losses in the test samples. We validated our method with several thousand probe pools performing RT-PCR tests, and found it highly effective.

Objectives: To evaluate the diagnostic value of the rtRT-PCR test and CT in patients presenting with typical clinical symptoms of COVID-19. Methods: The study with the participation of four center in Turkey was performed retrospectively from 20 March-15 April 2020 in 203 patients confirmed for COVID-19. The initial rtRT-PCR test was positive in 142 (70.0%) of the patients (Group-I) and negative in 61 patients (Group-II). Results: The mean age of the patients in Group-I was 49.7±18.0 years and the time between the onset of symptoms and admission to the hospital was 3.6±2.0 days; whereas the same values for the patients in Group-II were 58.1±19.9 and 5.3±4.2, respectively (p=0.004; p=0.026). Initial rtRT-PCR was found positive with 83.5% sensitivity and 74.1% PPV in patients with symptom duration of less than five days. It was found that rtRT-PCR positivity correlated negatively with the presence of CT findings, age, comorbidity, shortness of breath, and symptom duration, while rtRT-PCR positivity correlated positively with headache. Presence of CT findings was positively correlated with age, comorbidity, shortness of breath, fever, and the symptom duration. Conclusions: It should be noted that a negative result in the rtRT-PCR test does not rule out the possibility of COVID-19 diagnosis in patients whose symptom duration is longer than five days, who are elderly with comorbidities and in particular who present with fever and shortness of breath. In these patients, typical CT findings are diagnostic for COVID-19. A normal chest CT is no reason to loosen up measures of isolation in patients with newly beginning symptoms until the results are obtained from the PCR test. doi: https://doi.org/10.12669/pjms.37.1.2956 How to cite this:Kostakoglu U, Kant A, Atalar S, Ertunc B, Erensoy S, Dalmanoglu E, et al. Diagnostic value of Chest CT and Initial Real-Time RT-PCR in COVID-19 Infection. Pak J Med Sci. 2021;37(1):-234-238. doi: https://doi.org/10.12669/pjms.37.1.2956 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Background: Due to the increasing prevalence of covid-19, the World Health Organization declared on 30 January 2020, the spread of the new coronavirus as a 6th public health emergency of international concern. Objectives: To assess the extent of the disease in the pediatric population in our region, we conducted a clinical pediatric screening for Covid-19 and evaluated factors that affected its manifestation in children. Methods: In this study, 474761 children under 19 years of age were screened in two phases. In the first phase, 680 cases were considered as suspect and referred to the health centers, where the second phase of screening took place. Finally, 230 probable cases were referred to specialized centers for further investigation. Results: Almost all of the cases had pneumonia and symptoms of shortness of breath, cough, and fever over 38°C (56.7%). Other clinical symptoms included hypotension (17.4%), Hemoptysis (16.1), sore throat (11.6%) and difficult breathing (6.7%). 26% of patients had a history of chronic disease (mainly pulmonary and cardiac). There was a statistically significant relationship between the probable causes and the symptoms of the disease (P < 0.05), between age and probable cases (P < 0.05), and between death and underlying disease (P < 0.05). However, of all the cases, only 15 (6.5%) had a positive PCR test, 39 patients were hospitalized (17%), 173 cases (75%) received outpatient treatment and 18 cases (7.8%) died. Conclusions: Children with shortness of breath, cough, pneumonia, fever over 38 and underlying disease are suspicious for Covid-19 and should be hospitalized to be evaluated with laboratory tests.