The value of anal swab RT-PCR for COVID-19 diagnosis in adult Indonesian patients

ObjectiveThis study will test the performance of the anal swab PCR test when compared with the nasopharyngeal swab PCR test as a diagnostic tool for COVID-19.DesignAn observational descriptive study which included hospitalised suspected, or probable cases of hopitalised COVID-19 patients, conducted in Dr. Cipto Mangunkusumo National Hospital, Ciputra Hospital, Mitra Keluarga Depok Hospital and Mitra Keluarga Kelapa Gading Hospital, Indonesia. Epidemiological, clinical, laboratory and radiology data were obtained. Nasopharyngeal and anal swabs specimens were collected for SARS-CoV-2 RNA detection.ResultsWe analysed 136 subjects as part of this study. The clinical spectrum of COVID-19 manifesation in this study was typical of hospitalised patients, with 25% classified as mild cases, 14.7% in severe condition and 12.5% of subjects classified as having acute respiratory distress syndrome. When compared with nasopharyngeal swab as the standard specimen for reverse transcription polymerase chain reaction (RT-PCR) detection of SARS-CoV-2 antigen, the sensitivity and specificity of the anal swab was 36.7% and 93.8%, respectively. The positive and negative predictive value were 97.8% and 16.5 %, respectively. The performance of the anal swab remained similar when only the subgroup of patients with gastrointestinal symptoms (n=92, 67.6%) was analysed (sensitivity 40% and specificity 91.7%). Out of all the subjects included in analysis, 67.6% had gastrointestinal symptoms. Similarly, 73.3% of patients in the anal swab-positive group had gastrointestinal symptoms. The two most common gastrointestinal symptoms in the subjects’ population were nausea and anorexia.ConclusionAnal swab specimen has low sensitivity (36.7%) but high specificity (93.8%) for detecting SARS-CoV-2 antigen by RT-PCR. Only one additional positive result was found by anal swab among the nasopharyngeal swab-negative group. Anal swab may not be needed as an additional test at the beginning of a patient’s diagnostic investigation and nasopharyngeal swab RT-PCR remains as the standard diagnostic test for COVID-19.

Download Full-text

Pulmonary abscess as a complication of COVID-19 associated pneumonia: a clinical case

Tuberculosis and lung diseases ◽

10.21292/2075-1230-2021-99-12-7-12 ◽

2022 ◽

Vol 99 (12) ◽

pp. 7-12

Author(s):

T. I. Kalenchits ◽

S. L. Kabak ◽

S. V. Primak ◽

N. M. Shirinaliev

Keyword(s):

Clinical Laboratory ◽

Lower Lobe ◽

Pleural Empyema ◽

Lung Abscess ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Pulmonary Abscess ◽

Causative Factors ◽

The Right ◽

Test Result

The article describes a case of polysegmental destructive viral-bacterial pneumonia complicated with acute pulmonary abscess, pleural empyema, and pneumopleurofibrosis in a 50-year-old female patient infected with the SARS-CoV-2 virus. The first clinical, laboratory and radiological signs of purulent-necrotic inflammation appeared only 20 days after receiving a positive RT-PCR test result with a nasopharyngeal swab. A month later, an emerging abscess in the lower lobe of the right lung was diagnosed. Subsequently, it spontaneously drained into the pleural cavity.Coagulopathy with the formation of microthrombi in small pulmonary vessels is one of the causative factors of lung abscess in patients infected with the SARS-CoV-2 virus.

Download Full-text

Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections

10.1101/2020.11.24.20229948 ◽

2020 ◽

Cited By ~ 2

Author(s):

Joel Hellewell ◽

Timothy W. Russell ◽

Rupert Beale ◽

Gavin Kelly ◽

Catherine Houlihan ◽

...

Keyword(s):

Vulnerable Populations ◽

Research Unit ◽

Asymptomatic Infection ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Symptomatic Infection ◽

Testing Frequency ◽

Peak Sensitivity ◽

Pcr Test ◽

Over Time

AbstractBackgroundRoutine 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)

Download Full-text

Early chest computed tomography to diagnose COVID-19 from suspected patients: A multicenter retrospective study

10.1101/2020.03.24.20042432 ◽

2020 ◽

Cited By ~ 3

Author(s):

Congliang Miao ◽

Mengdi Jin ◽

Li Miao ◽

Xinying Yang ◽

Peng Huang ◽

...

Keyword(s):

Ground Glass Opacity ◽

High Specificity ◽

Diagnostic Value ◽

Chest Ct ◽

Imaging Features ◽

Rt Pcr ◽

Polymerase Chain ◽

Low Sensitivity ◽

Chest Ct Scan ◽

Ct Features

AbstractObjectiveThe purpose of this study is to distinguish the imaging features of COVID-19 with other chest infectious diseases and evaluate diagnostic value of chest CT for suspected patients.MethodsAdult suspected patients aged>18 years within 14 days who underwent chest CT scan and reverse-transcription polymerase-chain-reaction (RT-PCR) tests were enrolled. The enrolled patients were confirmed and grouped according to results of RT-PCR tests. The data of basic demographics, single chest CT features, and combined chest CT features were analyzed for confirmed and non-confirmed groups.ResultsA total of 130 patients were enrolled with 54 cases positive and 76 cases negative. The typical CT imaging features of positive group were ground glass opacity (GGO), crazy-paving pattern and air bronchogram. The lesions were mostly distributed bilaterally, close to the lower lungs or the pleura. When features combined, GGO with bilateral pulmonary distribution and GGO with pleural distribution were more common, of which were 31 cases (57.4%) and 30 cases (55.6%) respectively. The combinations were almost presented statistically significant (P<0.05) except for the combination of GGO with consolidation. Most combinations presented relatively low sensitivity but extremely high specificity. The average specificity of these combinations is around 90%.ConclusionsThe combinations of GGO could be useful in the identification and differential diagnosis of COVID-19, which alerts clinicians to isolate patients for treatment promptly and repeat RT-PCR tests until incubation ends.

Download Full-text

Role of endoscopy in suspicion of atrophic gastritis with and without intestinal metaplasia in comparison to histopathology

Acta Gastro Enterologica Belgica ◽

10.51821/84.1.208 ◽

2021 ◽

Vol 84 (1) ◽

pp. 9-17

Author(s):

H Ibrahim ◽

A Shams El-Deen ◽

ZA Kasemy ◽

M Saad ◽

AA Sakr

Keyword(s):

Atrophic Gastritis ◽

Intestinal Metaplasia ◽

Sensitivity And Specificity ◽

Chronic Gastritis ◽

Gastrointestinal Symptoms ◽

High Sensitivity ◽

High Specificity ◽

Poor Correlation ◽

Gastric Lesions ◽

Low Sensitivity

Background and study aims : Atrophic gastritis (AG) and intestinal metaplasia (IM) are established premalignant gastric lesions. Many studies documented a poor correlation between esophagogastroduodenoscopy (EGD) and histopathological (HP) findings of precancerous gastric lesions. The aim was to bridge the gap between endoscopy and HP in detection of chronic gastritis, AG and IM. Patients and methods : a prospective single-center study involved 150 patients with endoscopic criteria of gastric lesions with upper gastrointestinal symptoms referred for upper GI endoscopy met the endoscopic criteria and classified according to HP of biopsies from targeted gastric lesions into chronic gastritis (GI), AG(GII) or IM(GIII). We correlated the endoscopic criteria of the 3 groups with the HP results. Results : (73males & 75 females) with ages ranged17-75 years and mean± SD was 41.96 ± 15.95. GI, GII &GIII were [42 patients (28%),82 patients (54.7%) and 26 patients (17.3%)], respectively. Diffuse gastric mottling was more common in GI (74.3%, P<0.001), visible submucosal vessels, gastric atrophy predominated in GII (75.6, 82.3 & 73.1% (P 0.005,0.4 & <0.01)), respectively. Whitish raised lesions were more specific in GIII (85.7%) (P<0.001). The sensitivity and specificity of endoscopic suspicion of chronic gastritis were (86&88% in GI), (87&85% in GII) and (54% &100% in GIII) (p-0.001). The logistic regression model for risk factors was χ2= 25.74 and 49.32, p < 0.001. Conclusion : Conventional endoscopy has high sensitivity and specificity for suspicion of chronic gastritis and AG, but low sensitivity and very high specificity for IM. Targeted biopsies may be valuable with image enhanced techniques.

Download Full-text

Evaluation Of Clinical, Laboratory And Radiological Findings In Pediatric Covid-19 Cases And Their Relation With RT-PCR Result

10.22541/au.161248601.18537576/v1 ◽

2021 ◽

Author(s):

Muhammet Asena ◽

ilyas yolbaş ◽

murat Kanğın

Keyword(s):

Computed Tomography ◽

Respiratory Distress ◽

Clinical Laboratory ◽

Age Groups ◽

Age Group ◽

Test Results ◽

Rt Pcr ◽

Radiological Findings ◽

Laboratory Findings ◽

Pcr Test

Background: The pandemic of the new coronavirus disease (COVID-19) continues to be a major health problem globally. In this study, clinical findings, radiological findings, laboratory findings and polymerase chain reaction (PCR) test results were evaluated according to age groups in pediatric patients with COVID-19. Methods: In this study, PCR (+) and PCR (-) 278 cases diagnosed with COVID-19 between March 15, 2020 and September 30, 2020 were assessed considering clinical symptoms, radiological and laboratory findings and RT-PCR test results. Results: 43.9% of the cases consisted of RT-PCR (+) and 56.1% of RT-PCR (-) cases. Fever was observed at the rate of 64.7%, cough 53.2%, respiratory distress 12.2%, myalgia 24.5%, diarrhea 12.9%, chest X-ray findings 48.2% and computed tomography findings 43.6%. Diarrhea and cough, alanine aminotransferase, aspartate aminotransferase, leukocyte and lymphocyte elevation were determined as significantly higher in younger age group cases, while high myalgia and neutrophilia was observed in older age group children (p <0.05). Fever, high CRP, leukocytosis frequency, high neutrophil, were significantly higher in PCR(-) cases and the frequency of respiratory distress, high lymphocyte and chest computed tomography findings in PCR(+) cases (p <0.05). Conclusion: COVID-19 infection may indicate different nonspecific clinical, laboratory and radiological findings in children according to both adults and pediatric age groups. In addition, the results of the PCR test may give erroneous results in cases due to conditions such as fever, respiratory distress, high CRP, leukocytosis, high neutrophil and CT finding. Keywords: pediatric, COVID-19, RT-PCR

Download Full-text

Avoiding COVID-19 Hospital Outbreaks: RT-PCR Swab and Clinical Assessment

10.22541/au.161360746.67677725/v1 ◽

2021 ◽

Author(s):

Luca Allievi ◽

Amedeo Bongarzoni ◽

Guido Tassinario ◽

Stefano Carugo

Keyword(s):

Clinical Assessment ◽

False Negative ◽

False Negative Rate ◽

High Specificity ◽

Diagnostic Process ◽

Rt Pcr ◽

Negative Results ◽

High False Negative Rate ◽

Degree Of Confidence ◽

Low Sensitivity

Nasopharyngeal RT-PCR swab test for COVID-19 diagnosis has a high specificity but also a low sensitivity. The high false-negative rate and the overconfidence in negative results sometimes lead to hospital outbreaks. Therefore, we recommend always integrating the clinical assessment in the diagnostic process, mostly after the test, to determine what degree of confidence can be attributed to a negative result.

Download Full-text

Acute Pancreatitis as a Possible Unusual Manifestation of COVID-19 in Children

Case Reports in Pediatrics ◽

10.1155/2021/6616211 ◽

2021 ◽

Vol 2021 ◽

pp. 1-4

Author(s):

Niloufar Bineshfar ◽

Alireza Mirahmadi ◽

Fereshteh Karbasian ◽

Elham Pourbakhtyaran ◽

Abdollah Karimi ◽

...

Keyword(s):

Acute Pancreatitis ◽

Pediatric Patients ◽

Gastrointestinal Symptoms ◽

Amylase Level ◽

Rt Pcr ◽

Chain Reaction ◽

Unusual Manifestation ◽

The World ◽

Polymerase Chain ◽

Pcr Test

Coronavirus disease-2019 (COVID-19) which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has spread throughout the world causing problems for millions of people. Symptoms of COVID-19 in pediatric patients include both respiratory and gastrointestinal symptoms. The most common symptoms are fever, cough, and fatigue. In this report, we describe a case of a previously well 14-year-old boy, who presented to our emergency department with a complaint of abdominal pain, nausea, and vomiting without fever or respiratory symptoms. He was diagnosed with acute pancreatitis based on an abnormal amylase level and abdomen computed tomography (CT) and later found to be infected by SARS-CoV-2, by a positive reverse transcriptase-polymerase chain reaction (RT-PCR) test.

Download Full-text

Evaluation of RNA extraction free method for detection of SARS-COV-2 in salivary samples for mass screening for COVID-19

10.1101/2021.03.15.21253570 ◽

2021 ◽

Author(s):

Sally A. Mahmoud ◽

Esra Ibrahim ◽

Subhashini Ganesan ◽

Bhagyashree Thakre ◽

Juliet G Teddy ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Gold Standard ◽

Rna Extraction ◽

High Sensitivity ◽

High Specificity ◽

Cost Effective ◽

Kappa Coefficient ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Good Percentage

AbstractIn this current COVID - 19 pandemic, there is a dire need for cost effective and less time-consuming alternatives for SARS-COV-2 testing. The RNA extraction free method for detecting SARS-COV-2 in saliva is a promising option, this study found that it has high sensitivity (85.34%), specificity (95.04%) and was comparable to the gold standard nasopharyngeal swab. The method showed good percentage of agreement (kappa coefficient) 0.797 between salivary and NPS samples. However, there are variations in the sensitivity and specificity based on the RT-PCR kit used. The Thermo Fischer-Applied biosystems showed high sensitivity, PPV and NPV but also showed higher percentage of invalid reports. Whereas the BGI kit showed high specificity, better agreement (kappa coefficient) between the results of saliva and NPS samples and higher correlation between the Ct values of saliva and NPS samples. Thus, the RNA extraction free method for salivary sample serves as an effective alternative for SARS-CoV 2-testing.

Download Full-text

Continued nucleic acid tests for SARS-CoV-2 following discharge of patients with COVID-19 in Lu’an, China

PeerJ ◽

10.7717/peerj.11617 ◽

2021 ◽

Vol 9 ◽

pp. e11617

Author(s):

Yong Lyu ◽

Danni Wang ◽

Xiude Li ◽

Tianqi Gong ◽

Pengpeng Xu ◽

...

Keyword(s):

Nucleic Acid ◽

Throat Swab ◽

Nucleic Acid Testing ◽

Rt Pcr ◽

Positive Group ◽

The Third ◽

Anal Swab ◽

Discharge Criteria ◽

Pcr Test

Background Studies have shown that discharged Coronavirus disease 2019 (COVID-19) patients have retested positive for SARS-CoV-2 during a follow-up RT-PCR test. We sought to assess the results of continued nucleic acid testing for SARS-CoV-2 patients in COVID-19 patients after they were discharged in Lu’an, China. Methods We conducted RT-PCR tests on sputum, throat swabs, fecal or anal swabs, and urine samples collected from 67 COVID-19 patients following discharge. Samples were collected on the 7th and 14th days following discharge. Patients testing positive on the 7th or 14th day were retested after 24 hours until they tested negative twice. Results Seventeen (17/67, 25.4%) discharged COVID-19 patients had a positive RT-PCR retest for SARS-CoV-2. Among them, 14 (82.4%) were sputum positive, five (29.4%) were throat swab positive, seven (41.2%) were fecal or anal swab positive, one (5.9%) was urine sample positive, five (29.4%) were both sputum and throat swab positive, four (23.5%) were both sputum and fecal test positive, and one (5.9%) was positive of all four specimens. The shortest period of time between discharge and the last positive test was 7 days, the longest was 48 days, and the median was 16 days. The proportion of positive fecal or anal swab tests increased from the third week. The median Cq cut-off values after onset were 26.7 after the first week, 37.7 the second to sixth week, and 40 after the sixth week. There were no significant differences between the RT-PCR retest positive group and the unrecovered positive group. Conclusions There was a high proportion of patients who retested positive for COVID-19. Discharge criteria have remained fairly consistent so we encourage regions affected by COVID-19 to appropriately amend their current criteria.

Download Full-text

Evaluation of Efficacy of Rapid Antigen Test against RT-PCR and its Correlation with Cycle Threshold (CT) values: an Institutional Experience

Indian Journal of Applied Microbiology ◽

10.46798/ijam.2021.v23i01.003 ◽

2021 ◽

Vol 23 (1) ◽

Author(s):

Uma Shankar Saha ◽

Minakshi Gupta ◽

Minakshi Mishra ◽

Rajan Chaudhry ◽

Sudhir Rai

Keyword(s):

Viral Load ◽

Standard Procedure ◽

Antigen Test ◽

Sample Collection ◽

Rt Pcr ◽

Transmission Chain ◽

Rapid Result ◽

Institutional Experience ◽

Low Sensitivity ◽

Pcr Test

Rapidly increasing COVID-19 or SARS-CoV-2 in whole world caused a tremendous pressure on existing diagnostic setup to give accurate diagnosis on time by gold standard RT-PCR technique forcing scientist to think beyond RT-PCR which ultimately ended with invent of Rapid antigen test which can give about 100% specific and rapid result but may miss many case due to low sensitivity. So we wanted to evaluate the Rapid antigen test against RT-PCR for its diagnostic accuracy. We followed standard procedure for sample collection, Rapid antigen test and RT-PCR test. In about one and half month span we collected 554 antigen negative samples in our hospital. About 13% sample (74/554) turned out as positive by RT-PCR test. About 40 % (30/74) positive samples had low Ct value (<25) indicating higher viral load present in those patients. Above findings indicate that only antigen test will miss a significant portion of positive cases with higher viral load which may complicate the pandemic by unknowingly spreading the virus within the society. So we should try to improve our infrastructure to carry out more RTPCR test so we can detect more cases to identify and isolate them from others to prevent or slowdown the transmission chain.

Download Full-text