Reverse Transcriptase-polymerase Chain Reaction Results Research Articles

Clinical evaluation of single-swab sampling for rapid COVID-19 detection in outbreak settings in Dutch nursing homes

To assess whether one swab can be used to perform both the antigen-detection rapid diagnostic test (Ag-RDT) and reverse transcriptase polymerase chain reaction (RT-PCR) for COVID-19 detection during an outbreak in the nursing home (NH) setting. The single-swab method (SSM), where the Ag-RDT is performed with the transport medium used for RT-PCR, was evaluated in three Dutch NHs and compared to the laboratory setting. We collected Ag-RDT and RT-PCR results, NH resident characteristics and symptomatology. In addition, two focus groups were held with the involved care professionals to gain insight into the feasibility of the SMM in the NH setting. In the NH setting, the SSM had a sensitivity of 51% and a specificity of 89% compared to RT-PCR. These were lower than in the laboratory setting (69% and 100% respectively). Yet, when stratified for cycle threshold values, the sensitivity became comparable between the settings. Symptoms occurred more frequent in the Ag-RDT+ group than Ag-RDT- group. Resident characteristics did not differ between these groups. Based on the focus groups, the SSM was feasible to perform if certain requirements, such as availability of staff, equipment and proper training, were met. However, the rapid availability of the test results were perceived as a dilemma. The advantages and disadvantages need to be considered before implementation of the SSM can be recommended in the NH setting. For the vulnerable NH residents, it is important to find the right balance between effective testing policy and the burden this imposes.

Multireader evaluation of radiologist performance for COVID-19 detection on emergency department chest radiographs

BackgroundChest radiographs (CXR) are frequently used as a screening tool for patients with suspected COVID-19 infection pending reverse transcriptase polymerase chain reaction (RT-PCR) results, despite recommendations against this. We evaluated radiologist performance for COVID-19 diagnosis on CXR at the time of patient presentation in the Emergency Department (ED). Materials and methodsWe extracted RT-PCR results, clinical history, and CXRs of all patients from a single institution between March and June 2020. 984 RT-PCR positive and 1043 RT-PCR negative radiographs were reviewed by 10 emergency radiologists from 4 academic centers. 100 cases were read by all radiologists and 1927 cases by 2 radiologists. Each radiologist chose the single best label per case: Normal, COVID-19, Other – Infectious, Other – Noninfectious, Non-diagnostic, and Endotracheal Tube. Cases labeled with endotracheal tube (246) or non-diagnostic (54) were excluded. Remaining cases were analyzed for label distribution, clinical history, and inter-reader agreement. Results1727 radiographs (732 RT-PCR positive, 995 RT-PCR negative) were included from 1594 patients (51.2% male, 48.8% female, age 59 ± 19 years). For 89 cases read by all readers, there was poor agreement for RT-PCR positive (Fleiss Score 0.36) and negative (Fleiss Score 0.46) exams. Agreement between two readers on 1638 cases was 54.2% (373/688) for RT-PCR positive cases and 71.4% (679/950) for negative cases. Agreement was highest for RT-PCR negative cases labeled as Normal (50.4%, n = 479). Reader performance did not improve with clinical history or time between CXR and RT-PCR result. ConclusionAt the time of presentation to the emergency department, emergency radiologist performance is non-specific for diagnosing COVID-19.

Predictive usefulness of RT-PCR testing in different patterns of Covid-19 symptomatology: analysis of a French cohort of 12,810 outpatients

Reverse transcriptase polymerase chain reaction (RT-PCR) is a key tool to diagnose Covid-19. Yet it may not be the most efficient test in all patients. In this paper, we develop a clinical strategy for prescribing RT-PCR to patients based on data from COVIDOM, a French cohort of 54,000 patients with clinically suspected Covid-19, including 12,810 patients tested by RT-PCR. We use a machine-learning algorithm (decision tree) in order to predict RT-PCR results based on the clinical presentation. We show that symptoms alone are sufficient to predict RT-PCR outcome with a mean average precision of 86%. We identify combinations of symptoms that are predictive of RT-PCR positivity (90% for anosmia/ageusia) or negativity (only 30% of RT-PCR+ for a subgroup with cardiopulmonary symptoms): in both cases, RT-PCR provides little added diagnostic value. We propose a prescribing strategy based on clinical presentation that can improve the global efficiency of RT-PCR testing.

The Investigation of Canine Distemper Virus in Different Diagnosis Materials of Dogs using Molecular and Pathological Methods, Northeastern Turkey

Background: Canine distemper virus (CDV) is highly contagious disease that affects dogs despite several control measures. This study was aimed at investigating the presence of CDV nucleic acid in different clinical and tissue materials, from naturally infected dogs, by reverse transcriptase-polymerase chain reaction (RT-PCR) and to molecularly characterize distemper strains according to the partial Nucleoprotein (NP) gene sequence. Furthermore, tissue samples under went histopathological examination for distemper infection. Methods: A total of 202 different diagnosis materials were collected from dogs (n=60) in the Kars region in northeastern Turkey. The samples were tested for CDV using RT-PCR with primers designed for the CDV NP gene. Samples determined as positive for CDV (n=7) were sequenced. Tissue samples underwent histopathological examination. Result: Most of the cases were in animals aged 0-6 months. The most common clinical finding was severe respiratory system infection. This finding was accompanied by gastrointestinal and nervous system infections. CDV nucleic acid was detected in 112 of 202 materials by RT-PCR. According to RT-PCR results, positivity rates of 88.2% (30/34), 72.2% (13/18), 60% (3/5), 55.5% (10/18), 55.5% (10/18), 51.6% (16/31), 45.5% (5/11), 37.8% (14/37) and 36.7% (11/30) were detected in nasal swab, lung, footpad, kidney, spleen, rectal swab, cerebrospinal fluids (CSF), leuokocyte and cerebellum samples, respectively. Viral nucleic acids were detected at higher rates in nasal swabs. The phylogenetic assessment of the amplicon sequences revealed a 97.7%-100% similarity among the Turkish CDV strains, which are independent from vaccine strains, were found to be more closely related to the European lineage. Intranuclear and intracytoplasmic inclusion bodies were detected by histopathology. This is the first study to investigate CDV in naturally infected dogs from northeastern Turkey and to provide novel and updated epidemiological information.

HRCT Thorax as a tool for preoperative assessment of RT-PCR Covid-19 negative patients with malignancies

Background: According to WHO, Cancer is the second leading cause of death globally, accounting for an estimated 9.6 million deaths, or one in six deaths, in 2018. Due to recent pandemic of COVID 19 there were limitations of health services in the country. For those patients in whom Surgery is the mainstay of treatment, the delay in the treatment was due to cancellations of elective surgeries as per government regulations and lack of transportation for patients due lockdown and curfew imposed to curtail the pandemic. In the latter half of the initial relaxation of the lockdown, a institutional protocol was framed for all those requiring surgical treatment. All patients were asked to get a RT-PCR (Reverse Transcriptase-Polymerase Chain Reaction) test done from GIIMS hospital, Kalaburagi. RT-PCR negative patients were admitted for surgery and subjected to HRCT Thorax (High-resolution Computer Tomography). This was done to avoid risk to health care workers, patients, and attenders and also screen asymptomatic carriers and false negative RTPCR statusMaterials and methods: This is a Retrospective data based study conducted in department of radiology, Kidwai VTSM Peripheral Cancer Centre, Kalaburagi. HRCT Reports of 100 patients were analyzed by experienced radiologist of the institution.Results: The number of patients under the CO-RADS 1 category was 63 and CO-RADS 2 category was 37, according to CO-RADS classification. The results of RT-PCR and HRCT were compared and there was a 100% positive correlation between RT-PCR and HRCT Thorax.Conclusion: Above study supported the use of HRCT Thorax as a diagnostic tool in preoperative screening of cancer patients for COVID 19, particularly in RT-PCR negative cases.

Comparison of COVID-19 Antigen Test and HRCT Chest with RT- PCR Test for Diagnosis of COVID-19

Introduction: We aim to compare Rapid Antigen Test and HRCT chest with Reverse Transcriptase-Polymerase chain reaction (RT-PCR) for diagnosis of COVID-19. Methods: This was a cross-sectional analytical study that included patients tested with RT-PCR and at least one of Rapid Antigen test or HRCT chest, conducted at College of Medical Sciences, Bharatpur, from June 2020 to Feb 2021 after obtaining the ethical clearance. Data analysis was done using statistical packages for social sciences version 16. Results: 315 of 755(41.7%) patients had positive RT-PCR and 18.4% of 733 patients had positive antigen test. Of 600 patients, 106(14.0%) were found to have CO-RADS 1,152(20.1%) had CO-RADS 2, 77(10.2%) had CO-RADS 3, 18(2.4%) had CO-RADS 4 and 247(32.7%) had CO-RADS 5 score on HRCT. Rapid Antigen Test was found to have 43.6% sensitivity, 98.6% specificity, 95.6% Positive predictive value (PPV) and 72.1% negative predictive value (NPV).CO-RADS scoring system was able to distinguish between RT-PCR positive and RT-PCR negative results with an average Area under curve 0.787. CO-RADS 5 had a sensitivity of 71.6%, specificity of 85.1%, PPV of 80.6% and NPV of 77.6% for a positive RT-PCR result. A combination of CO-RADS 1 in HRCT chest and Negative Antigen test can predict PCR negative result with 23.6% sensitivity, 97.3% specificity, 90.5% PPV and 54.0% NPV. Conclusions: Rapid Antigen Test is a better tool for confirmation rather than screening of COVID-19. HRCT chest with higher CO-RADS can be useful to diagnose COVID-19 in suspected patients, even if RT-PCR is negative.

Serial quantitative chest computed tomography imaging as prognosticators of coronavirus disease 2019 pneumonia

In 2019, a large outbreak of a novel coronavirus disease (COVID-19) occurred in China. The purpose of this study is to quantitatively analyze the evolution of chest computed tomography (CT) imaging features in COVID-19. Nine patients with positive real-time reverse-transcriptase polymerase chain reaction results were included in this study. Totally 19 CT scans were analyzed. Lesion density, lesion volume, and lesion load were higher in the severe group than in the mild group. A significantly positive correlation was noted between major laboratory prognosticators with lesion volume and load. Lesion load at the first week of disease was significantly higher in severe group (p = 0.03). Our study revealed that several CT features were significantly different between severely and mildly infected forms of COVID-19 pneumonia. The CT lesion load value at the first week of infection may be applied as an outcome predictor of the disease.

Factors associated with length of stay and treatment outcome of Ebola patients treated at an Ebola treatment center in Sierra Leone during the peak period of the West African Ebola outbreak 2013\u20132016

BackgroundThe World Health Organization (WHO) declared the West Africa Ebola epidemic as a Public Health Emergency of International Concern in August 2014. During the outbreak period, there were calls for the affected countries to construct Ebola treatment centres and reliable diagnostic laboratories closer to areas of transmission in order to improve the quality care of Ebola Virus Disease (EVD) patients. Delay in seeking treatment has been reported to have led to poor treatment outcome of EVD patients. Sierra Leone recorded more than 8000 probable and confirmed cases and more than 4000 EVD -related deaths nation-wide.MethodsIn this retrospective study, we investigated the effects of treatment delay, length of symptomatic period, EVD patients’ sex, age, occupation, region of residence, and clinical characteristics on the treatment outcome of 205 laboratory-confirmed EVD patients who were admitted at the Kenema Government Hospital Ebola Treatment Center (KGHETC) from 13/09/2014–26/11/2014; i.e. during the peak of 2013–2016 EVD outbreak in Sierra Leone. Specifically also, we determined the factors that were associated with the length of stay for EVD treatment for patients who were discharged alive.ResultsMajority (66.3%, n = 205/309) of the 309 suspected EVD patients with medical records at the KGHETC triage during the period under review were tested positive for EVD using reverse-transcriptase-polymerase chain reaction (RT-PCR) and had a definitive treatment outcome. Few (33.7%, n = 104/309) suspected EVD patients were not included in our analysis and were classified thus: 29.1% (n = 90/309) suspect EVD cases with negative RT-PCR results, 4.5% (n = 14/309) suspect cases with non-available RT-PCR result.Of the 205 patients, 99 (48.3%) had a fatal outcome. For EVD patients that survived, we recorded a significant association (− 0.06, 95% Confidence Interval (CI) = − 0.14 – - 0.02, p = 0.004) between the Length of Stay (LOS) and for each kilometer travelled to seek treatment at the KGHETC. However, the association between EVD patients that were low skilled workers (− 5.91, 95% CI = − 24.60 – 12.79, p = 0.73), EVD patients who were children and pupils in junior school (− 0.86, 95% CI = − 12.86 – 11.14, p = 0.73), health seeking delay for EVD patients who resided in Kenema District where the KGHETC was located (− 0.49, 95% CI = − 0.12 – 1.09, p = 0.24), sex (− 1.77, 95% CI = − 8.75 – 5.21, p = 0.50), age (0.21, 95% CI = − 0.36 – 0.77, p = 0.57), referral status (1.21, 95% CI = − 17.67 – 20.09, p = 0.89) and the LOS in surviving patients were not statistically significant.ConclusionThe high LOS for either treatment outcome for EVD patients that resided in the district in which the EVD treatment facility was located compared to those patients from other districts implies that health authorities should consider intensive health education with high priority given to seeking early EVD treatment, and the construction of strategic ETCs as important components in their response strategy.

Diagnostic accuracy of screening tests for patients suspected of COVID-19, a retrospective cohort study

Background The diagnostic gold standard for Coronavirus-2019 disease (CoViD-19) is reverse transcriptase-polymerase chain reaction (RT-PCR). However, its sensitivity might be suboptimal. The current study aims to investigate predictive factors for false-negative nasopharyngeal RT-PCR in CoViD-19 patients. Additionally, the specificity and sensitivity of RT-PCR on the nasopharyngeal swab, serology and chest computerized-tomography (CCT) as a screening tool for the diagnosis of CoViD-19 were investigated. Methods Medical records of patients admitted at the university hospital UZ Brussel during the CoViD-19 epidemic were reviewed. A group of CoViD-19 patients with false-negative RT-PCR was identified through scrupulous examination of medical records. Serological testing was performed through chemiluminescent microparticle assay. Results Eighteen CoViD-19 patients with ‘false negative’ RT-PCR were identified and compared to 51 ‘true positives’. Logistic regression for prediction of ‘false negative’ RT-PCR found significantly higher serology results at hospitalization and more intensive care unit admission in the group with false-negative testing. In a cohort of 228 patients, the sensitivity of RT-PCR for the diagnosis of CoViD-19 was 85%. The sensitivity of serology was 86% and its specificity 92%. Chest computerized-tomography (CCT) showed a sensitivity of 93%, its specificity was 62%. By combining RT-PCR and serology results any ‘false negative’ could be excluded. Conclusions In this cohort, the sensitivity and specificity of RT-PCR and serology for the diagnosis of CoViD-19 were high and comparable. CCT had the highest sensitivity and confirmed its efficacy as a screening tool. CoViD-19 patients, who have a more severe presentation, might have negative RT-PCR and positive serology results.

Concordance of Preprocedure Testing With Time-of-Surgery Testing for SARS-CoV-2 in Children.

* Abbreviations: CHOP — : Children’s Hospital of Philadelphia COVID-19 — : coronavirus disease 2019 RT-PCR — : reverse transcriptase polymerase chain reaction SARS-CoV-2 — : severe acute respiratory syndrome coronavirus 2 Surgery in patients with coronavirus disease 2019 (COVID-19) is associated with increased mortality and complications.1 Procedures may generate aerosols or require endotracheal intubation, increasing risk of occupational exposure of health care workers. As medical centers navigate aerosol-generating procedures, preprocedure testing is important for patient and provider safety. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immediately before the procedure would yield the most accurate results. However, scheduling logistics and inadequate turnaround times often necessitate preprocedure testing several days in advance. Thus, patients may have negative preprocedure testing results, yet have active viral replication at the time of surgery. Although patients are instructed to monitor for symptoms after testing, symptom reporting is likely to be insensitive in children because most have mild or no … Address correspondence to Audrey R. Odom John, MD, PhD, 907C ARC/Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA 19104-4318. E-mail: johna3{at}email.chop.edu

A multidisciplinary evaluation of suspected, non-confirmed cases of COVID-19 including chest CT, as compared to World Health Organization recommendations

AIMTo report an audit of the evaluation of suspected, unconfirmed cases of COVID-19 including chest computed tomography (CT), as compared to World Health Organization recommendations.METHODSA clinical audit was undertaken examining the evaluation of patients with suspected COVID-19 with negative SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) results, with comparison to WHO recommendations. A retrospective chart review was undertaken for 90 patients examining investigations, in particular CT, used to clarify the diagnosis.RESULTSNinety patients underwent additional investigation. Seventy-five per cent adherence to WHO recommendations was observed. Fifty-two men (57.78%) and 38 (42.22%) women were investigated, with a median age of 69 years (range 20–96 years). Seventy-nine chest CT examinations demonstrated positive, indeterminate, and negative rates for COVID-19 of 3.79%, 24.1%, and 72.15% respectively. Three patients had discordant swab results with initially negative and subsequently positive results for SARS-CoV-2, resulting in false-negative rates of 5.1% for those retested. Combining discordant RT-PCR swab results, positive radiology, and patients treated as COVID-19-positive due to indeterminate radiology and highly consistent symptoms, resulted in a false-negative rate for initial SARS-CoV-2 RT-PCR swabs of 16.67%.CONCLUSIONSeventy-five per cent compliance with relevant WHO guidance and a false-negative rate for initial swabs of 16.67% was demonstrated. Further evidence is needed to fully determine the utility of chest CT in the diagnosis of COVID-19 in the context of initial false-negative RT-PCR results.

Recurrent and More Severe COVID-19 Infection: Two Elderly Case Reports.

Although the sensitivity of reverse transcriptase-polymerase chain reaction (RT-PCR) is low in the diagnosis of coronavirus disease 2019 (COVID-19), it is the gold standard. Clinical improvement is prioritized in the follow-up of patients with COVID-19 who are followed as possible or definitive cases. Although the priority in the discharge decision is the resolution of complaints, it is also important to see radiological improvement and RT-PCR negativity. A total of 2 of our patients who were hospitalized and treated in our clinic with a diagnosis of COVID-19 were discharged after their complaints were resolved and their treatment was completed. The patients had 2 negative RT-PCR results at discharge. Both of them presented to the hospital with symptoms such as fever, cough, and shortness of breath after the discharge, and both showed positive RT-PCR results. Considering recurrent COVID-19 infection, we aimed to present treatment and the 2 cases we followed.

Detection of SARS-CoV-2 in Simultaneously Collected Tear and Throat Swab Samples from the Patients with 2019- new SARS-CoV-2 Infection Disease: A Single Center Cross-sectional Study

ABSTRACT Objecive : This study aimed to evaluate whether Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can be detected in the tears in the eyes of Coronavirus Disease 2019 (COVID-2019) infected patients and compare the detection consistency of two simultaneously collected samples, from the tears and throat swabs. Methods : A total of 35 COVID-2019 patients were included in this cross-sectional case series study. Throat samples from all enrolled patients were collected with sampling swab, and simultaneously, tear samples were collected with sampling swab from 9 patients (No.1–9) and with Schirmer’s strip from the remaining patients (No.10–35) (bilateral eyes for all patients). Sample collecting and testing were performed in three separate time points: first from patients No.1–9, second from patients No.10–29, and third from patients No. 30–35. Reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay was performed. Results : Among enrolled patients, 29 (No.1–29) had mild or moderate clinical symptoms and 6 (No.30–35) had severe symptoms. The mean time interval from the sample collection day to diagnosis confirmation day was 9.71 ± 6.50 days (ranged from 3 to 29 days). None of the patients had conjunctivitis. Nineteen out of 35 (54.3%) throat samples presented positive Rt-PCR results. Three (no.13,21,31) out of 35 (8.6%) tear samples presented positive RT-PCR results. Two (no.21, 31) of these three patients were throat swab positive and one (No. 13) was negative. The consistency analysis indicated that tears and throat samples showed poor consistency (Kappa = −0.009, P = .9).The cycle threshold value (Ct-value) of tear samples collected by sampling swab was significantly higher than that by Schirmer’s strip (t = 2.288, P = .03). Conclusion : In spite of the low SARS-CoV-2 positive detection rate of tear samples from COVID-2019 patients, we cannot fully rule out the transmission by ocular surface. Whether tear testing can be used as an aid in judging of SARS-CoV-2 infection need further investigation.

Evaluation of the RSNA and CORADS classifications for COVID-19 on chest computed tomography in the Brazilian population

OBJECTIVE:To determine the correlation between the two tomographic classifications for coronavirus disease (COVID-19), COVID-19 Reporting and Data System (CORADS) and Radiological Society of North America Expert Consensus Statement on Reporting Chest Computed Tomography (CT) Findings Related to COVID-19 (RSNA), in the Brazilian population and to assess the agreement between reviewers with different experience levels.METHODS:Chest CT images of patients with reverse transcriptase-polymerase chain reaction (RT-PCR)-positive COVID-19 were categorized according to the CORADS and RSNA classifications by radiologists with different levels of experience and who were initially unaware of the RT-PCR results. The inter- and intra-observer concordances for each of the classifications were calculated, as were the concordances between classifications.RESULTS:A total of 100 patients were included in this study. The RSNA classification showed an almost perfect inter-observer agreement between reviewers with similar experience levels, with a kappa coefficient of 0.892 (95% confidence interval [CI], 0.788-0.995). CORADS showed substantial agreement among reviewers with similar experience levels, with a kappa coefficient of 0.642 (95% CI, 0.491-0.793). There was inter-observer variation when comparing less experienced reviewers with more experienced reviewers, with the highest kappa coefficient of 0.396 (95% CI, 0.255-0.588). There was a significant correlation between both classifications, with a Kendall coefficient of 0.899 (p<0.001) and substantial intra-observer agreement for both classifications.CONCLUSION:The RSNA and CORADS classifications showed excellent inter-observer agreement for reviewers with the same level of experience, although the agreement between less experience reviewers and the reviewer with the most experience was only reasonable. Combined analysis of both classifications with the first RT-PCR results did not reveal any false-negative results for detecting COVID-19 in patients.

Evaluation of the RSNA and CORADS classifications for COVID-19 on chest computed tomography in the Brazilian population

OBJECTIVE:To determine the correlation between the two tomographic classifications for coronavirus disease (COVID-19), COVID-19 Reporting and Data System (CORADS) and Radiological Society of North America Expert Consensus Statement on Reporting Chest Computed Tomography (CT) Findings Related to COVID-19 (RSNA), in the Brazilian population and to assess the agreement between reviewers with different experience levels.METHODS:Chest CT images of patients with reverse transcriptase-polymerase chain reaction (RT-PCR)-positive COVID-19 were categorized according to the CORADS and RSNA classifications by radiologists with different levels of experience and who were initially unaware of the RT-PCR results. The inter- and intra-observer concordances for each of the classifications were calculated, as were the concordances between classifications.RESULTS:A total of 100 patients were included in this study. The RSNA classification showed an almost perfect inter-observer agreement between reviewers with similar experience levels, with a kappa coefficient of 0.892 (95% confidence interval [CI], 0.788-0.995). CORADS showed substantial agreement among reviewers with similar experience levels, with a kappa coefficient of 0.642 (95% CI, 0.491-0.793). There was inter-observer variation when comparing less experienced reviewers with more experienced reviewers, with the highest kappa coefficient of 0.396 (95% CI, 0.255-0.588). There was a significant correlation between both classifications, with a Kendall coefficient of 0.899 (p<0.001) and substantial intra-observer agreement for both classifications.CONCLUSION:The RSNA and CORADS classifications showed excellent inter-observer agreement for reviewers with the same level of experience, although the agreement between less experience reviewers and the reviewer with the most experience was only reasonable. Combined analysis of both classifications with the first RT-PCR results did not reveal any false-negative results for detecting COVID-19 in patients.

Field Validation of a Rapid Recombinase Aided Amplification Assay for SARS-CoV-2 RNA at Customs — Zhejiang Province, China, January 2021

IntroductionThe best approach to preventing the importation of coronavirus disease 2019 (COVID-19) is enhancing the detection capacity at customs. The rapid detection is of utmost importance and therefore highly demanded.MethodsWe conducted a field validation study of a duplex real-time reverse transcription recombinase-aided amplification (RT-RAA) assay in Zhoushan and Hangzhou customs, in Zhejiang Province, China. The reverse transcriptase polymerase chain reaction (RT-PCR) assay kit routinely used at customs was used in parallel, and the duration the two methods took to complete a specific number of samples was compared.ResultsAmong 506 samples collected, RT-RAA results were consistent with the RT-PCR results. The sensitivity and specificity were 100%, the total coincidence rate was 100%, and the Kappa value was 1 (P<0.05) for both methods. The RT-RAA kit took a significantly shorter time in testing the 20–200 samples than the RT-PCR kit. DiscussionThe RT-RAA detection method is more efficient and suitable for use at customs than RT-PCR assay to realize rapid customs clearance of 200 or fewer samples.

Utility of Nucleic Acid Extraction Free COVID-19 Real Time PCR Protocol in Resource Limited Setting: A Pilot Study

Introduction: Coronavirus Disease (COVID-19), a respiratory infection, caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, Hubei province, China in December 2019. Alarming increase in the number of cases has put tremendous pressure on existing health resources. Real Time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR), a molecular diagnostic method, is considered gold standard for diagnosis of SARS-CoV-2 infection. It involves RNA extraction as the preliminary step. Innovations to cut down cost and time involved in SARS-CoV-2 testing are need of hour. Aim: The aim of this study was to assess the feasibility of Nucleic Acid Extraction Free (NEF) protocol for COVID-19 diagnosis in resource limited settings. Materials and Methods: In this pilot study a panel of 148 Nasopharyngeal (NP) samples was subjected to the novel NEF RT-PCR protocol and results were compared to gold standard RT-PCR on RNA extracted from NP specimen. The cycle threshold value for each target was tabulated in MS Excel Spreadsheet and data analysis was performed using Statistical Package for Social Sciences (SPSS) software version 15.0. Results: Out of 148 collected samples, 120 showed amplification of E and RdRp targets by RNA extraction-based RT-PCR. Overall sensitivity and specificity observed for NEF protocol was 43.94% and 96.42%, respectively. Conclusion: Further refinement in the protocol would be required to improve the sensitivity of NEF protocol and widespread use in laboratories.

Role of HRCT Thorax in pre-operative assessment of RT-PCR COVID-19 negative oral cancer patients

Background: Oral cancer accounts for 30% of all types of cancer in India. Surgery is the mainstay of treatment but due to the recent outbreak of COVID-19, there is a partial or complete disruption of health services in the country. The initial delay in the treatment was due to cancellations of planned surgeries as per government regulations and reduction in public transportation. In the latter half of the initial relaxation of the lockdown, we formulated our institutional protocol for the surgical treatment of oral cancer patients. On admission, all patients were kept in isolated wards followed by RT-PCR (Reverse Transcriptase-Polymerase Chain Reaction) testing on the same day. RT-PCR negative patients are subjected to HRCT Thorax (High-resolution Computer Tomography). This ensured the safety of health care workers, patients, and patient attendees. Keeping this in mind, we did an observational study on the role of HRCT in the pre-operative screening of asymptomatic oral cancer patients. Materials and methods: Retrospective analysis of prospectively collected data of 150 patients was done. HRCT reporting was done by two experienced senior radiologists of the Department of Radiology at our hospital. Results: The number of patients under the CO-RADS 1 category was 121 and CO-RADS 2 category was 29, according to CO-RADS classification. The results of RT-PCR and HRCT were compared and there was a 100% positive correlation between RT-PCR and HRCT Thorax. Conclusion: Our study supported the use of HRCT Thorax as a diagnostic tool in pre-operative screening of oral cancer patients for COVID 19, particularly in RT-PCR negative cases.

Imaging in coronavirus disease 2019 (COVID-19) pneumonia

In December 2019, an outbreak of coronavirus disease 2019 (COVID-19) (formerly known as 2019-nCoV) pneumonia began in Wuhan (Hubei Province, China). The COVID-19 spread rapidly across China and many other countries and assumed a pandemic proportion. As of January 30, 2020, the World Health Organization (WHO) has designated this outbreak as a global health emergency. Respiratory droplets and direct contact are likely to be the most important routes of transmission. Therefore, early diagnosis and isolation becomes essential against novel coronavirus. Reverse transcriptase polymerase chain reaction (RT-PCR) is the reference standard to confirm the diagnosis of COVID-19 infection. However, more and more false negative RT-PCR results have been reported recently making the diagnosis rather challenging. Currently, HRCT is one of the best tools for screening, primary diagnosis, estimation of disease severity, and prediction of the prognosis. HRCT manifestations of COVID-19 pneumonia have not been well known. Recent studies showed that typical HRCT findings included bilateral pulmonary parenchymal ground glass and consolidative opacities, with a peripheral lung distribution However, the HRCT features of COVID-19 are very diverse, and it is difficult to differentiate it from other kinds of viral pneumonia. This article describes the salient features of COVID-19 pneumonia in lung and the temporal progression of the changes and also the common and important imaging differential diagnoses to be considered. Keywords: COVID-19; pneumonia; SARS-CoV-2; coronavirus disease; pandemic

Experience of an Orthopaedic Surgery Department Early During the COVID-19 Outbreak in Japan Including Real-Time Polymerase Chain Reaction Assay Results for SARS-CoV-2.

IntroductionThe coronavirus disease 2019 (COVID-19) epidemic beginning December 2019 in China has now become a worldwide pandemic. With the need to develop an approach to manage orthopaedic surgeries, we aimed to evaluate the most current data on all the surgical cases in our department including the results of the reverse-transcriptase polymerase chain reaction (RT-PCR) assay for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).MethodsThe monthly number of surgical cases from 2016 were reviewed, and compared the numbers of surgical cases both in elective and emergency surgery during the pandemic with the pre-pandemic period. The results of RT-PCR for SARS-CoV-2 in 94 orthopaedic surgery cases from May 13 to June 30, 2020, and clinical signs/symptoms, and laboratory data of 48 consecutive cases within a month from May 13 were also evaluated.ResultsThe mean monthly number of surgeries from January to May 2020 was significantly lower than the mean number in 2019 (73.8 vs 121.9, respectively, p=0.01). The proportion of emergency surgeries in all surgeries performed in May 2020 was 35.5%, which is significantly more than the mean rate of 20.4% in 2019 (p=0.04). Hip arthroplasties and spine surgeries showed the greatest reduction, at greater than 80% and 65%, respectively. Although none of the 94 patients were positive for SARS-CoV-2, 66.7% showed signs/symptoms typical of COVID-19. The most frequent signs/symptoms were production of nasal mucus (25.5%), followed by dry cough (19.1%); and fatigue, headache, and dizziness (17.0% each). The incidence of abnormal values, which are commonly noted in COVID-19 patients, were eosinopaenia 37.5%; lymphopaenia 18.8%; thrombocytopaenia 8.3%; and elevated prothrombin time 10.4%.ConclusionsOur results show that our RT-PCR negative patients showed signs/symptoms and abnormal laboratory values typical of COVID-19, indicating surgeons should be aware of these abnormalities in patients and the need to rule out COVID-19 before proceeding with surgery.