scholarly journals A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality

2021 ◽  
Author(s):  
Pierre FILLATRE ◽  
Marie Jose DUFOUR ◽  
Sylvie BEHILLIL ◽  
Remi VATAN ◽  
Pascale REUSSE ◽  
...  
Keyword(s):  
Cox Model ◽  
Severe Disease ◽  
Nosocomial Outbreak ◽  
Inclusion Criteria ◽  
Rt Pcr ◽  
Logrank Test ◽  
Respiratory Sample ◽  
Radiological Data ◽  
New Variant ◽  
Chest Ct Scan

Background: In early January 2021, an outbreak of nosocomial cases of COVID 19 emerged in Western France, with RT PCR tests repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole genome sequencing (WGS) revealed a new variant, currently defining a novel SARS CoV 2 lineage: B.1.616. In March, WHO classified this variant as "under investigation" (VUI). We analyzed the characteristics and outcomes of COVID 19 cases related to this new variant. Methods: Clinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled patients with at least one of the following: i) positive SARS CoV 2 RT PCR on a respiratory sample; ii) seroconversion with anti SARS CoV 2 IgG/IgM; iii) suggestive symptoms and typical features of COVID 19 on chest CT scan. Cases were categorized as either: i) B.1.616; ii) variant of concern (VOC); iii) unknown. Findings: From January 1st to March 24th, 2021, 114 patients fulfilled the inclusion criteria: B.1.616 (n=34), VOC (n=32), and unknown (n=48). B.1.616 related cases were older than VOC related cases (81 years [73-88], vs 73 years [67-82], P<0.05) and their first RT PCR tests were less often positive (5/34, 15% vs 31/32, 97%, P<0.05). The B.1.616 variant was independently associated with severe disease (multivariable Cox model HR 4.2 [1.3 , 13.5], P=0.018), and increased lethality (logrank test P=0.01): 28day mortality 15/34 (44%) with B.1.616, vs. 5/32 (16%) for VOC, P=0.036. Interpretation: We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, poorly detected by RT PCR on nasopharyngeal samples, with high lethality.

scholarly journals Can chest CT improve sensitivity of COVID-19 diagnosis in comparison to PCR? A meta-analysis study

2020 ◽  
Vol 36 (1) ◽  
Author(s):  
Heba Mahmoud ◽  
Mohamed Shehata Taha ◽  
Anas Askoura ◽  
Mohammed Aleem ◽  
Azza Omran ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Meta Analysis ◽  
Chest Ct ◽  
Main Body ◽  
Inclusion Criteria ◽  
Rt Pcr ◽  
Laboratory Findings ◽  
Analysis Study ◽  
Patient Presentation ◽  
Chest Ct Scan

Abstract Background In December 2019, SARS-CoV-2 was identified as the causative agent of pneumonia cases in China. This virus is spread by coughing or sneezing and can infect other persons by on contacting mucous membranes. SARS-Cov-2 most frequent serious manifestation is pneumonia. Chest computed tomography in COVID-19 patients usually shows ground-glass opacities that may be accompanied by consolidation lesions. Early diagnosis of the disease and rapid isolation of the patient is of great importance. So far, confirmation of COVID-19 infection is made by RT-PCR of nasopharyngeal or respiratory specimens. Recent research reported that the sensitivity of computed tomography in diagnosing COVID-19 is 98% while RT-PCR sensitivity is 71%. Herein, we compare the sensitivity of both chest CT and RT-PCR in diagnosing COVID-19 at initial patient presentation through a meta-analysis study. Main body Using MEDLINE database a systematic literature search was conducted to identify relevant published studies within from November 2019 to April 2020. Only articles with full text were examined to determine eligibility and extract data by two reviewers. It was decided to include studies mentioning sensitivity of chest CT scan and sensitivity of RT-PCR and both done at the same time. Results Potentially relevant 15,300 studies were identified in our search in MEDLINE whose titles were quickly reviewed. Potentially eligible studies missing any of the forementioned inclusion criteria were excluded. This process left 7 eligible articles that fulfilled the inclusion criteria and were thus included in the meta-analysis and used for further analyses. Conclusion The meta-analysis study showed that chest CT may be beneficial in early detection of cases of COVID-19. Imaging, in adjunct to clinical and laboratory findings, should be used for monitoring of disease course, until further evidence is available.

scholarly journals Can initial chest CT scan predict status and clinical outcomes of COVID-19 infection? A retrospective cohort study

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Iman Abdollahi ◽  
Mehrdad Nabahati ◽  
Mostafa Javanian ◽  
Hoda Shirafkan ◽  
Rahele Mehraeen
Keyword(s):  
Cohort Study ◽  
Ct Scan ◽  
Disease Severity ◽  
Retrospective Cohort Study ◽  
Retrospective Cohort ◽  
Severe Disease ◽  
Chest Ct ◽  
Rt Pcr ◽  
Icu Admission ◽  
Chest Ct Scan

Abstract Background We aimed to investigate the association of initial chest CT scan findings with status and adverse outcomes of COVID-19 (including ICU admission, mortality, and disease severity). This retrospective cohort study was performed in three hospitals in Babol, northern Iran, between February and March 2020. Cases were confirmed by real-time polymerase chain reaction (RT-PCR). Clinical and paraclinical data of the patients were collected from their medical records. CT severity score (CSS) was calculated by a senior radiologist. Disease severity was determined based on the World Health Organization criteria. Results In total, 742 patients were included, of whom 451 (60.8%) were males and 291 (39.2%) were females. The mean age was 56.59 ± 14.88 years old. Also, 523 (70.5%) were RT-PCR-positive. Ground glass opacity was directly associated with RT-PCR positivity (odds ratio [OR] = 2.07). Also, RT-PCR-positive cases had significantly a higher CSS than RT-PCR-negative cases (p = 0.037). In patients confirmed with COVID-19, peribronchovascular distribution of lesions, number of zones involved, and CSS were associated with increased risk of ICU admission (OR = 2.93, OR = 2.10, and OR = 1.14, respectively), mortality (OR = 2.30, OR = 1.35, and OR=1.08, respectively), severe disease (OR = 2.06, OR = 1.68, and OR = 1.10, respectively), and critical disease (OR = 4.62, OR = 3.21, and OR = 1.23, respectively). Also, patients who had consolidation were at a higher risk of severe disease compared with those who did not (OR = 4.94). Conclusion Initial chest CT scan can predict COVID-19 positivity, ICU admission, mortality, and disease severity, specifically through CSS.

scholarly journals Chest CT imaging features of Covid-19 patients: Single center observational study

2021 ◽  
Vol 8 (10) ◽  
pp. 586-593
Author(s):  
İsmail Karluka ◽  
Fahrettin Güngördü ◽  
Ahmet Aslan ◽  
Ali Avcı ◽  
Orhun Öztürk
Keyword(s):  
Ct Scan ◽  
Reporting System ◽  
Chest Ct ◽  
Imaging Features ◽  
Imaging Findings ◽  
Inclusion Criteria ◽  
Rt Pcr ◽  
Chest Radiology ◽  
Chest Ct Scan ◽  
Single Center Observational Study

Objective: The aim of this study was to explore the chest Computer Tomography (CT) features of COVID-19 patients and compare the diagnostic performance of chest CT with that of RT-PCR at our center. Material and Methods: The study was conducted by retrospectively scanning the files of patients admitted to the Emergency Department of Karaman State Hospital under suspicion of COVID-19 between March 15 and May 18, 2020. The study included 218 patients (124 males, 94 females, 1-90 years of age, median 48.5) who met the inclusion criteria. Chest CT scan findings were recorded in detail by two radiologists with experience in chest radiology. Furthermore, the CT findings were categorized into four groups in the form of typical, indeterminate, atypical, and negative CT according to the structured reporting system. Results: The RT-PCR results were positive in 41% of 139 cases with positive CT results, while the RT-PCR results were positive in 15.2% of the cases with negative CT results. Regarding the analysis between CT and RT-PCR, the sensitivity was 82.61%, the specificity was 44.97%, the PPV was 41.01%, the NPV was 84.81%. The positivity rate was 82.9% in those with typical imaging findings, 51.5% in those assessed as indeterminate. Those with a typical appearance had a higher rate of positivity than others. Conclusion: The chest CT scan was found to have a high correlation with the RT-PCR in the patients with typical imaging findings in CT. The specificity was found to be low in the CT scan findings without subgroup analysis.

Cancer surgery during the COVID‐19 pandemic: The experience of a comprehensive cancer center performing preoperative screening by RT‐PCR and chest CT scan

2021 ◽  
Vol 123 (4) ◽  
pp. 815-822
Author(s):  
Joanne Guerlain ◽  
Fabienne Haroun ◽  
Alexandra Voicu ◽  
Charles Honoré ◽  
Franck Griscelli ◽  
...  
Keyword(s):  
Ct Scan ◽  
Chest Ct ◽  
Cancer Surgery ◽  
Comprehensive Cancer Center ◽  
Cancer Center ◽  
Preoperative Screening ◽  
Rt Pcr ◽  
Chest Ct Scan

A Case Series of SARS-CoV-2 RT-PCR-Positive Hospitalized Infants 60 Days of Age or Younger From 2 New York City Pediatric Emergency Departments

2021 ◽  
Vol 60 (4-5) ◽  
pp. 247-251
Author(s):  
Ameer Hassoun ◽  
Nessy Dahan ◽  
Christopher Kelly
Keyword(s):  
New York ◽  
Case Reports ◽  
Severe Disease ◽  
Case Series ◽  
Pediatric Emergency ◽  
Rt Pcr ◽  
Vulnerable Group ◽  
Mild Disease ◽  
Young Infants ◽  
Novel Coronavirus

The emergence of novel coronavirus disease-2019 poses an unprecedented challenge to pediatricians. While the majority of children experience mild disease, initial case reports on young infants are conflicting. We present a case series of 8 hospitalized infants 60 days of age or younger with coronavirus disease-2019. A quarter of these patients had coinfections (viral or bacterial). None of these infants had severe disease. Continued vigilance in testing this vulnerable group of infants is warranted.

scholarly journals A meta-analysis of accuracy and sensitivity of chest CT and RT-PCR in COVID-19 diagnosis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Fatemeh Khatami ◽  
Mohammad Saatchi ◽  
Seyed Saeed Tamehri Zadeh ◽  
Zahra Sadat Aghamir ◽  
Alireza Namazi Shabestari ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Ct Scan ◽  
Predictive Value ◽  
Meta Analysis ◽  
Chest Ct ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Chest Ct Scan

AbstractNowadays there is an ongoing acute respiratory outbreak caused by the novel highly contagious coronavirus (COVID-19). The diagnostic protocol is based on quantitative reverse-transcription polymerase chain reaction (RT-PCR) and chests CT scan, with uncertain accuracy. This meta-analysis study determines the diagnostic value of an initial chest CT scan in patients with COVID-19 infection in comparison with RT-PCR. Three main databases; PubMed (MEDLINE), Scopus, and EMBASE were systematically searched for all published literature from January 1st, 2019, to the 21st May 2020 with the keywords "COVID19 virus", "2019 novel coronavirus", "Wuhan coronavirus", "2019-nCoV", "X-Ray Computed Tomography", "Polymerase Chain Reaction", "Reverse Transcriptase PCR", and "PCR Reverse Transcriptase". All relevant case-series, cross-sectional, and cohort studies were selected. Data extraction and analysis were performed using STATA v.14.0SE (College Station, TX, USA) and RevMan 5. Among 1022 articles, 60 studies were eligible for totalizing 5744 patients. The overall sensitivity, specificity, positive predictive value, and negative predictive value of chest CT scan compared to RT-PCR were 87% (95% CI 85–90%), 46% (95% CI 29–63%), 69% (95% CI 56–72%), and 89% (95% CI 82–96%), respectively. It is important to rely on the repeated RT-PCR three times to give 99% accuracy, especially in negative samples. Regarding the overall diagnostic sensitivity of 87% for chest CT, the RT-PCR testing is essential and should be repeated to escape misdiagnosis.

scholarly journals Diagnostic performance of chest CT in differentiating COVID-19 from other causes of ground-glass opacities

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Ali H. Elmokadem ◽  
Dalia Bayoumi ◽  
Sherif A. Abo-Hedibah ◽  
Ahmed El-Morsy
Keyword(s):  
Diagnostic Performance ◽  
Pulmonary Nodules ◽  
Ground Glass Opacity ◽  
Chest Ct ◽  
Ground Glass ◽  
Rt Pcr ◽  
Laboratory Findings ◽  
Halo Sign ◽  
Traction Bronchiectasis ◽  
Chest Ct Scan

Abstract Background To evaluate the diagnostic performance of chest CT in differentiating coronavirus disease 2019 (COVID-19) and non-COVID-19 causes of ground-glass opacities (GGO). Results A total of 80 patients (49 males and 31 females, 46.48 ± 16.09 years) confirmed with COVID-19 by RT-PCR and who underwent chest CT scan within 2 weeks of symptoms, and 100 patients (55 males and 45 females, 48.94 ± 18.97 years) presented with GGO on chest CT were enrolled in the study. Three radiologists reviewed all CT chest exams after removal of all identifying data from the images. They expressed the result as positive or negative for COVID-19 and recorded the other pulmonary CT features with mention of laterality, lobar affection, and distribution pattern. The clinical data and laboratory findings were recorded. Chest CT offered diagnostic accuracy ranging from 59 to 77.2% in differentiating COVID-19- from non-COVID-19-associated GGO with sensitivity from 76.25 to 90% and specificity from 45 to 67%. The specificity was lower when differentiating COVID-19 from non-COVID-19 viral pneumonias (30.5–61.1%) and higher (53.1–70.3%) after exclusion of viral pneumonia from the non-COVID-19 group. Patients with COVID-19 were more likely to have lesions in lower lobes (p = 0.005), peripheral distribution (p < 0.001), isolated ground-glass opacity (p = 0.043), subpleural bands (p = 0.048), reverse halo sign (p = 0.005), and vascular thickening (p = 0.013) but less likely to have pulmonary nodules (p < 0.001), traction bronchiectasis (p = 0.005), pleural effusion (p < 0.001), and lymphadenopathy (p < 0.001). Conclusions Chest CT offered reasonable sensitivity when differentiating COVID-19- from non-COVID-19-associated GGO with low specificity when differentiating COVID-19 from other viral pneumonias and moderate specificity when differentiating COVID-19 from other causes of GGO.

scholarly journals Update on the Transmission of Zika Virus Through Breast Milk and Breastfeeding: A Systematic Review of the Evidence

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 123
Author(s):  
Elizabeth Centeno-Tablante ◽  
Melisa Medina-Rivera ◽  
Julia L. Finkelstein ◽  
Heather S. Herman ◽  
Pura Rayco-Solon ◽  
...  
Keyword(s):  
Breast Milk ◽  
Zika Virus ◽  
Mother To Child Transmission ◽  
Inclusion Criteria ◽  
Rt Pcr ◽  
Child Transmission ◽  
Zikv Infection ◽  
Milk Samples ◽  
Clinical Complications ◽  
Mother To Child

We systematically searched regional and international databases and screened 1658 non-duplicate records describing women with suspected or confirmed ZIKV infection, intending to breastfeed or give breast milk to an infant to examine the potential of mother-to-child transmission of Zika virus (ZIKV) through breast milk or breastfeeding-related practices. Fourteen studies met our inclusion criteria and inform this analysis. These studies reported on 97 mother–children pairs who provided breast milk for ZIKV assessment. Seventeen breast milk samples from different women were found positive for ZIKV via RT-PCR, and ZIKV replication was found in cell cultures from five out of seven breast milk samples from different women. Only three out of six infants who had ZIKV infection were breastfed, no evidence of clinical complications was found to be associated with ZIKV RNA in breast milk. This review updates our previous report by including 12 new articles, in which we found no evidence of ZIKV mother-to-child transmission through breast milk intake or breastfeeding. As the certainty of the present evidence is low, additional studies are still warranted to determine if ZIKV can be transmitted through breastfeeding.

scholarly journals The role of CT imaging for management of COVID-19 in epidemic area: early experience from a University Hospital

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Vikram rao Bollineni ◽  
Koenraad Hans Nieboer ◽  
Seema Döring ◽  
Nico Buls ◽  
Johan de Mey
Keyword(s):  
Ct Scan ◽  
Predictive Value ◽  
Ct Imaging ◽  
Chest Ct ◽  
University Hospital ◽  
Rt Pcr ◽  
Ct Findings ◽  
Epidemic Area ◽  
Chest Ct Scan ◽  
Pcr Test

Abstract Background To evaluate the clinical value of the chest CT scan compared to the reference standard real-time polymerase chain reaction (RT-PCR) in COVID-19 patients. Methods From March 29th to April 15th of 2020, a total of 240 patients with respiratory distress underwent both a low-dose chest CT scan and RT-PCR tests. The performance of chest CT in diagnosing COVID-19 was assessed with reference to the RT-PCR result. Two board-certified radiologists (mean 24 years of experience chest CT), blinded for the RT-PCR result, reviewed all scans and decided positive or negative chest CT findings by consensus. Results Out of 240 patients, 60% (144/240) had positive RT-PCR results and 89% (213/240) had a positive chest CT scans. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of chest CT in suggesting COVID-19 were 100% (95% CI: 97–100%, 144/240), 28% (95% CI: 19–38%, 27/240), 68% (95% CI: 65–70%) and 100%, respectively. The diagnostic accuracy of the chest CT suggesting COVID-19 was 71% (95% CI: 65–77%). Thirty-three patients with positive chest CT scan and negative RT-PCR test at baseline underwent repeat RT-PCR assay. In this subgroup, 21.2% (7/33) cases became RT-PCR positive. Conclusion Chest CT imaging has high sensitivity and high NPV for diagnosing COVID-19 and can be considered as an alternative primary screening tool for COVID-19 in epidemic areas. In addition, a negative RT-PCR test, but positive CT findings can still be suggestive of COVID-19 infection.

A Nosocomial Outbreak of Feline Calicivirus Associated Virulent Systemic Disease in France

2009 ◽  
Vol 11 (8) ◽  
pp. 633-644 ◽  
Author(s):  
Brice S. Reynolds ◽  
Hervé Poulet ◽  
Jean-Luc Pingret ◽  
Dominique Jas ◽  
Sylvie Brunet ◽  
...  
Keyword(s):  
Systemic Disease ◽  
Feline Calicivirus ◽  
Nosocomial Outbreak ◽  
Rt Pcr ◽  
Genetic Sequencing ◽  
Viral Excretion ◽  
Clinicopathological Findings ◽  
The Us ◽  
Sequencing Studies ◽  
Polymerase Chain

This report describes a nosocomial outbreak of feline calicivirus (FCV) associated virulent systemic disease (VSD) in a French veterinary teaching hospital in 2005. The outbreak started in March and resolved within 1 month. Signs, clinical course, clinicopathological findings and lesions were typical of FCV-induced VSD. FCV infection was confirmed by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). Among the eight infected cats, two had to be euthanased, three died, and three recovered after medical treatment. Virus could not be confined inside the animal hospital and on two occasions, students' own cats became infected. Subsequent genetic sequencing studies confirmed that the eight cats were infected with the same strain of virus, and that it was distinct from those involved in the US and UK outbreaks of VSD. Virulence and viral excretion patterns of the isolated strain were further characterised by experimental infection.

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