Evaluation of using distal part of endotracheal tube samples for SARS-COV-2 diagnosis by RT-PCR

Objective: The reverse transcription-polymerase chain reaction (RT-PCR) analyses method is the most important diagnostic method in the diagnosis of SARS-CoV-2 virus infection. In this research, we aimed to investigate the positivity of SARS-CoV-2 by RT-PCR from distal part of the endotracheal tube (DPET) samples, which have not been investigated in any study yet. Materials and Methods: A total of 48 patients with a diagnosis of COVID-19 hospitalized in the intensive care unit receiving mechanical ventilation and whose conditions resulted in death or extubation were included in the study. The distal 6 cm part of the orotracheal intubation tube was removed from the patient (including the cuff). DPET samples were mixed with viral transport medium and vortexed; then, it was centrifuged at 4500g for 4 minutes. RNA isolation was performed by taking 400 µl from the supernatant and then SARS-CoV-2 RT-PCR was studied. Results: In 15 patients (31.25 %) the swab samples were PCR positive, 42 patients (87.5 %) had positive computed tomography finding and 48 patients (100 %) had positive clinical findings. Among the patients whose oropharynx (OP)/nasopharynx (NP) combined swab sample was positive for RT-PCR, the rate of RT-PCR positivity detected in DPET samples was 26.7%. While OP/NP combined swab sample was negative, DPET RT-PCR positivity rate was found to be 9.09%. Conclusions: Patients with positive DPET RT-PCR are detected when the swab is negative. These findings suggest that DPET can be used as a good lower respiratory sample without the risk of particle spread and transmission to healthcare personnel.

A SARS-CoV-2 antigen rapid diagnostic test for resource limited settings

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19 disease. RT-qPCR has been the primary method of diagnosis; however, the required infrastructure is lacking in many developing countries and the virus has remained a global challenge. More inexpensive and immediate test methods are required to facilitate local, regional, and national management strategies to re-open world economies. Here we have developed a SARS-CoV-2 antigen test in an inexpensive lateral flow format to generate a chromatographic result identifying the presence of the SARS-CoV-2 antigen, and thus an active infection, within a patient anterior nares swab sample. Our 15-min test requires no equipment or laboratory infrastructure to administer with a limit of detection of 2.0 × 102 TCID50/mL and 87.5% sensitivity, 100% specificity when tested against 40 known positive and 40 known negative patient samples established by a validated RT-qPCR test.

Prospective Study of the Performance of Parent-Collected Nasal and Saliva Swab Samples, Compared with Nurse-Collected Swab Samples, for the Molecular Detection of Respiratory Microorganisms

RTIs are ubiquitous among children. Diagnosis involves a swab sample being taken by a health professional, which places a considerable burden on community health care systems, given the number of cases involved.

C-reactive protein levels associated with COVID-19 outcomes in the United States

Context COVID-19 caused a worldwide pandemic, and there are still many uncertainties about the disease. C-reactive protein (CRP) levels could be utilized as a prognosticator for disease severity in COVID-19 patients. Objectives This study aims to determine whether CRP levels are correlated with COVID-19 patient outcomes and length of stay (LoS). Methods A retrospective cohort study was conducted utilizing data obtained between March and May 2020. Data were collected by abstracting past medical records through electronic medical records at 10 hospitals within CommonSpirit Health. Patients were included if they had a positive COVID-19 test from a nasopharyngeal swab sample, and if they were admitted and then discharged alive or had in-hospital mortality and were ≥18 years. A total of 541 patients had CRP levels measured and were included in this report. Patient outcome and LoS were the endpoints measured. Results The 541 patients had their CRP levels measured, as well as the demographic and clinical data required for analysis. While controlling for body mass index (BMI), number of comorbidities, and age, the first CRP was significantly predictive of mortality (p<0.001). The odds ratio for first CRP indicates that for each one-unit increase in CRP, the odds of death increased by 0.007. For LoS, the first CRP was a significant predictor (p<0.001), along with age (p=0.002). The number of comorbidities also predicted LoS (p=0.007), but BMI did not. The coefficient for the first CRP indicates that, for each one-unit increase in CRP, LoS increased 0.003 days. Conclusions The results indicate that there is a positive correlation between the CRP levels of COVID-19 patients and their respective outcomes with regard to death and LoS.

Urgent Care Study of the LumiraDx SARS-CoV-2 Ag Test for Rapid Diagnosis of COVID-19

BackgroundTesting individuals suspected of SARS-CoV-2 infection is essential to reduce the spread of disease. The purpose of this study was to determine the false negativity rate of the LumiraDx SARS-CoV-2 Ag Test when utilized for testing individuals suspected of SARS-CoV-2 infection within 12 days of symptom onset. MethodsConcurrent swab samples were collected from patients suspected of SARS-CoV-2 infection by their healthcare provider within two different urgent care centers. One swab was tested using the LumiraDx SARS-CoV-2 Ag Test. Negative results in patients considered at moderate to high risk of SARS-CoV-2 infection were confirmed at a regional reference laboratory by PCR using the additional swab sample. ResultsFrom October 19, 2020 – January 3, 2021, a total of 2241 tests were performed using the LumiraDx SARS-CoV-2 Ag Test, with 549 (24.5%) testing positive and 1692 (75.5%) testing negative. A subset (800) of the samples rendering a negative LumiraDx SARS-CoV-2 Ag Test were also tested using a PCR-based test for SARS-CoV-2. Of this subset, 770 (96.3%) tested negative, and 30 (3.8%) tested positive. A cycle threshold (CT) was available for 17 of the 30 specimens that yielded discordant results, with an average CT value of 31.2, an SD of 3.0, and a range of 25.2–36.3. CT was >30.0 in 11/17 specimens (64.7%). ConclusionsThis study demonstrates that negative results obtained with the LumiraDx SARS-CoV-2 Ag Test had 96.3% agreement with PCR-based SARS-CoV-2 tests, with a low false negative rate of 3.8% when used in a community-based setting.

Case report: change of dominant strain during dual SARS-CoV-2 infection

Background The dual infection with SARS-CoV-2 is poorly described and is currently under discussion. We present a study of two strains of SARS-CoV-2 detected in the same patient during the same disease presentation. Case presentation A patient in their 90 s was hospitalised with fever. Oropharyngeal swab obtained on the next day (sample 1) tested positive for SARS-CoV-2. Five days later, the patient was transferred to the ICU (intensive care unit) of the hospital specialising in the treatment of COVID-19 patients, where the patient's condition progressively worsened and continuous oxygen insufflation was required. Repeated oropharyngeal swab (sample 2), which was taken eight days after the first one, also tested positive for SARS-CoV-2. After 5 days of ICU treatment, the patient died. The cause of death was a coronavirus infection, which progressed unfavourably due to premorbid status. We have performed sequencing of full SARS-CoV-2 genomes from oropharyngeal swabs obtained eight days apart. Genomic analysis revealed the presence of two genetically distant SARS-CoV-2 strains in both swabs. Detected strains belong to different phylogenetic clades (GH and GR) and differ in seven nucleotide positions. The relative abundance of strains was 70% (GH) and 30% (GR) in the first swab, and 3% (GH) and 97% (GR) in the second swab. Conclusions Our findings suggest that the patient was infected by two genetically distinct SARS-CoV-2 strains at the same time. One of the possible explanations is that the second infection was hospital-acquired. Change of the dominant strain ratio during disease manifestation could be explained by the advantage or higher virulence of the GR clade strain.

A study to evaluate etiology of denture stomatitis and to determine interrelationship with trauma and candida albicans count

Denture stomatitis (DS) is a disease characterized by inflammation and erythema of the oral mucosa areas covered by the denture. Multifactorial etiological factors contribute to denture stomatitis. The purpose of this study is to identify the etiology of denture stomatitis and to establish the role of trauma and fungal infection in denture stomatitis.Subjects wearing previously fabricated removable partial or complete denture who were diagnosed with denture stomatitis were included. It is a cross sectional questionnaire-based study, for mycological study swab sample was smeared, Sabouraud Dextrose Agar (SDA) was used as culture media. Germ tube test was used to identify Candida albicans. To test significance between different variablesKruskal-Wallis test was used. Out of 195 subjects’ slight stomatitis was present in 52.80% patients, followed by moderate stomatitis in 32.31% and no stomatitis in 2.56% subjects. Candida was present in 25.64% patients. Candida significantly more common in moderate stomatitis than others.This study has suggested that there is a significant relation in denture stomatitis and Candida albicans in north Indian population. No significant role of trauma was noticed. Strong correlation has been found in Denture hygiene, cleaning habits and Denture Stomatitis.

Clinical Evaluation of In-House-Produced 3D-Printed Nasopharyngeal Swabs for COVID-19 Testing

3D-printed alternatives to standard flocked swabs were rapidly developed to provide a response to the unprecedented and sudden need for an exponentially growing amount of diagnostic tools to fight the COVID-19 pandemic. In light of the anticipated shortage, a hospital-based 3D-printing platform was implemented in our institution for the production of swabs for nasopharyngeal and oropharyngeal sampling based on the freely available, open-source design provided to the community by University of South Florida’s Health Radiology and Northwell Health System teams as a replacement for locally used commercial swabs. Validation of our 3D-printed swabs was performed with a head-to-head diagnostic accuracy study of the 3D-printed “Northwell model” with the cobas PCR Media® swab sample kit. We observed an excellent concordance (total agreement 96.8%, Kappa 0.936) in results obtained with the 3D-printed and flocked swabs, indicating that the in-house 3D-printed swab could be used reliably in the context of a shortage of flocked swabs. To our knowledge, this is the first study to report on autonomous hospital-based production and clinical validation of 3D-printed swabs.

Urgent Care Study of the LumiraDx SARS-CoV-2 Ag Test for Rapid Diagnosis of COVID-19

BackgroundTesting individuals suspected of SARS-CoV-2 infection is essential to reduce the spread of disease. The purpose of this study was to determine the false negativity rate of the LumiraDx SARS-CoV-2 Ag Test when utilized for testing individuals suspected of SARS-CoV-2 infection within 12 days of symptom onset. MethodsConcurrent swab samples were collected from patients suspected of SARS-CoV-2 infection by their healthcare provider within two different urgent care centers. One swab was tested using the LumiraDx SARS-CoV-2 Ag Test. Negative results in patients considered at moderate to high risk of SARS-CoV-2 infection were confirmed at a regional reference laboratory by PCR using the additional swab sample. ResultsFrom October 19, 2020 – January 3, 2021, a total of 2241 tests were performed using the LumiraDx SARS-CoV-2 Ag Test, with 549 (24.5%) testing positive and 1692 (75.5%) testing negative. A subset (800) of the samples rendering a negative LumiraDx SARS-CoV-2 Ag Test were also tested using a PCR-based test for SARS-CoV-2. Of this subset, 770 (96.3%) tested negative, and 30 (3.8%) tested positive. A cycle threshold (CT) was available for 17 of the 30 specimens that yielded discordant results, with an average CT value of 31.2, an SD of 3.0, and a range of 25.2–36.3. CT was >30.0 in 11/17 specimens (64.7%). ConclusionsThis study demonstrates that negative results obtained with the LumiraDx SARS-CoV-2 Ag Test had 96.3% agreement with PCR-based SARS-CoV-2 tests, with a low false negative rate of 3.8% when used in a community-based setting.