Comparison between RT-qPCR for SARS-CoV-2 and expanded triage in sputum of symptomatic and asymptomatic COVID-19 subjects in Ecuador

BMC Infectious Diseases volume 21, Article number: 558 (2021) 

Abstract

Background

The quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) effectively detects the SARS-COV-2 virus. SARS-CoV-2 Nevertheless, some critical gaps remain in the identification and monitoring of asymptomatic people.

Methods

This retrospective study included 733 asymptomatic and symptomatic COVID-19 subjects, who were submitted to the RT-qPCR test. The objective was to assess the efficacy of an expanded triage of subjects undergoing the RT-qPCR test for SARS-COV-2 to identify the largest possible number of COVID-19 cases in a hospital setting in Ecuador. SARS-CoV-2 Firstly, the sensitivity and specificity as well as the predictive values of an expanded triage method were calculated. In addition, the Kappa coefficient was also determined to assess the concordance between laboratory test results and the expanded triage.

Results

Of a total of 733 sputum samples; 229 were RT-qPCR-positive (31.2%) and mortality rate reached 1.2%. Overall sensitivity and specificity were 86.0% (95% confidence interval: 81.0–90.0%) and 37.0% (95% confidence interval: 32.0–41.0%) respectively, with a diagnostic accuracy of 52.0% and a Kappa coefficient of 0.73. An association between the positivity of the test and its performance before 10 days was found.

Conclusions

The clinical sensitivity for COVID-19 detection was within acceptable standards, but the specificity still fell below the values of reference. The lack of symptoms did not always mean to have a negative SARS-COV-2 RT-qPCR test. The expanded triage identified a still unnoticed percentage of asymptomatic subjects showing positive results for the SARS-COV-2 RT-qPCR test. The study also revealed a significant relationship between the number of RT-qPCR-positive cases and the performance of the molecular diagnosis within the first 10 days of COVID-19 in the symptomatic group.

For More Information: https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-021-06272-8

Analysis of the Study of the Expression of Apoptosis Markers (CD95) and Intercellular Adhesion Markers (CD54) in Healthy Individuals and Patients Who Underwent COVID-19 When Using the Drug Mercureid

Authors: Sergey N Gusev1*, Velichko LN2, Bogdanova AV2, Khramenko NI2, Konovalova NV2 Published Date: 26-08-2021

Abstract

SARS-CoV-2, the pathogen, which is responsible for coronavirus disease 2019 (COVID-19), has caused unprecedented morbidity and mortality worldwide. Scientific and clinical evidence testifies about long-term COVID-19 effects that can affect many organ systems. Cellular damage, overproduction of proinflammatory cytokines and procoagulant abnormalities caused by SARS-CoV-2 infection may lead to these consequences. After suffering from COVID-19, a negative PCR test is only the beginning of a difficult path to full recovery. 61 % of patients will continue to have the signs of post-covid syndrome with the risk of developing serious COVID-19 health complications for a long time. Post-COVID syndrome is an underestimated large-scale problem that can lead to the collapse of the healthcare system in the nearest future.

The treatment and prevention of post-covid syndrome require integrated rather than organ or disease specific approaches and there is an urgent need to conduct a special research to establish the risk factors.

For this purpose, we studied the expression of markers of apoptosis (CD95) and intercellular adhesion (CD54) in healthy individuals and patients who underwent COVID-19, as well as the efficacy of the drug Mercureid for the treatment of post-covid syndrome.

The expression level of the apoptosis marker CD95 in patients who underwent COVID-19 is 1.7-2.5 times higher than the norm and the intercellular adhesion marker CD54 is 2.9-4.4 times higher. This fact indicates a persistent high level of dysfunctional immune response in the short term after recovery. The severity of the expression of the intercellular adhesion molecule (ICAM-1, CD54) shows the involvement of the endothelium of the vascular wall in the inflammatory process as one of the mechanisms of the pathogenesis of post-covid syndrome.

The use of Mercureid made it possible to reduce the overexpression of CD95 in 73.4 % of patients that led to the restoration of the number of CD4+/CD8+ T-cells, which are crucial in the restoration of functionally active antiviral and antitumor immunity of patients. Also, the use of Mercureid led to a normalization of ICAM-1 (CD54) levels in 75.8 % of patients.

The pharmacological properties of the new targeted immunotherapy drug Mercureid provide new therapeutic opportunities for the physician to influence a number of therapeutic targets, such as CD95, ICAM-1 (CD54), to reduce the risk of post-COVID complications.

For More Information: https://athenaeumpub.com/analysis-of-the-study-of-the-expression-of-apoptosis-markers-cd95-and-intercellular-adhesion-markers-cd54-in-healthy-individuals-and-patients-who-underwent-covid-19-when-using-the-drug-mercureid/

Pathological findings in organs and tissues of patients with COVID-19: A systematic review

Authors: Sasha Peiris 1 2Hector Mesa 3Agnes Aysola 4Juan Manivel 5Joao Toledo 1 2Marcio Borges-Sa 6Sylvain Aldighieri 1 2Ludovic Reveiz 2 7

Abstract

Background: Coronavirus disease (COVID-19) is the pandemic caused by SARS-CoV-2 that has caused more than 2.2 million deaths worldwide. We summarize the reported pathologic findings on biopsy and autopsy in patients with severe/fatal COVID-19 and documented the presence and/or effect of SARS-CoV-2 in all organs.

Methods and findings: A systematic search of the PubMed, Embase, MedRxiv, Lilacs and Epistemonikos databases from January to August 2020 for all case reports and case series that reported histopathologic findings of COVID-19 infection at autopsy or tissue biopsy was performed. 603 COVID-19 cases from 75 of 451 screened studies met inclusion criteria. The most common pathologic findings were lungs: diffuse alveolar damage (DAD) (92%) and superimposed acute bronchopneumonia (27%); liver: hepatitis (21%), heart: myocarditis (11.4%). Vasculitis was common only in skin biopsies (25%). Microthrombi were described in the placenta (57.9%), lung (38%), kidney (20%), Central Nervous System (CNS) (18%), and gastrointestinal (GI) tract (2%). Injury of endothelial cells was common in the lung (18%) and heart (4%). Hemodynamic changes such as necrosis due to hypoxia/hypoperfusion, edema and congestion were common in kidney (53%), liver (48%), CNS (31%) and GI tract (18%). SARS-CoV-2 viral particles were demonstrated within organ-specific cells in the trachea, lung, liver, large intestine, kidney, CNS either by electron microscopy, immunofluorescence, or immunohistochemistry. Additional tissues were positive by Polymerase Chain Reaction (PCR) tests only. The included studies were from numerous countries, some were not peer reviewed, and some studies were performed by subspecialists, resulting in variable and inconsistent reporting or over statement of the reported findings.

Conclusions: The main pathologic findings of severe/fatal COVID-19 infection are DAD, changes related to coagulopathy and/or hemodynamic compromise. In addition, according to the observed organ damage myocarditis may be associated with sequelae.

For More Information: https://pubmed.ncbi.nlm.nih.gov/33909679/

Overweight/obesity as the potentially most important lifestyle factor associated with signs of pneumonia in COVID-19

PLOS
  • Published: November 18, 2020

Abstract

Objective

The occurrence of pneumonia separates severe cases of COVID-19 from the majority of cases with mild disease. However, the factors determining whether or not pneumonia develops remain to be fully uncovered. We therefore explored the associations of several lifestyle factors with signs of pneumonia in COVID-19.

Methods

Between May and July 2020, we conducted an online survey of 201 adults in Germany who had recently gone through COVID-19, predominantly as outpatients. Of these, 165 had a PCR-based diagnosis and 36 had a retrospective diagnosis by antibody testing. The survey covered demographic information, eight lifestyle factors, comorbidities and medication use. We defined the main outcome as the presence vs. the absence of signs of pneumonia, represented by dyspnea, the requirement for oxygen therapy or intubation.

Results

Signs of pneumonia occurred in 39 of the 165 individuals with a PCR-based diagnosis of COVID-19 (23.6%). Among the lifestyle factors examined, only overweight/obesity was associated with signs of pneumonia (odds ratio 2.68 (1.29–5.59) p = 0.008). The observed association remained significant after multivariate adjustment, with BMI as a metric variable, and also after including the antibody-positive individuals into the analysis.

Conclusions

This exploratory study finds an association of overweight/obesity with signs of pneumonia in COVID-19. This finding suggests that a signal proportional to body fat mass, such as the hormone leptin, impairs the body’s ability to clear SARS-CoV-2 before pneumonia develops. This hypothesis concurs with previous work and should be investigated further to possibly reduce the proportion of severe cases of COVID-19.

For More Information: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0237799

Simple blood test can tell whether patients will suffer from ‘long COVID’

Authors: by Study Finds AUGUST 15, 2021

CAMBRIDGE, England — A simple blood test for long COVID is on the horizon. Biological “fingerprints” can identify individuals with the debilitating syndrome, according to new research. This opens the door to the first accurate diagnosis of the mysterious condition. Sufferers complain it is hard to convince doctors of their disease.

Long COVID is an umbrella term for symptoms of the virus lasting more than 12 weeks. They range from fatigue, headaches, and breathlessness to fever and tummy pain. At least one fourth of patients have developed some form of long COVID, per research out of the University of California, Davis.

“We need a reliable and objective way of saying whether someone has had COVID-19,” says study co-leader Dr. Mark Wills of the University of Cambridge. “Antibodies are one sign we look for. But not everyone makes a very strong response and this can wane over time and become undetectable.”

The new technique is based on chemicals called cytokines that control blood cells. When released, the tiny proteins trigger the immune system’s T-cells to fight foreign invaders.

“We’ve identified a cytokine that is also produced in response to infection by T-cells and is likely to be detectable for several months — and potentially years — following infection,” adds Wills. “We believe this will help us develop a much more reliable diagnostic for those individuals who did not get a diagnosis at the time of infection.”

The discovery could revolutionize treatment by complementing existing antibody tests and identifying vulnerable individuals. It builds on a pilot study of 85 patients from the Long COVID Clinic at Addenbrooke’s Hospital in Cambridge. Blood samples were collected at the time of diagnosis and follow-up intervals over several months. Analyses identified a molecule known as a cytokine produced by T-cells in response to infection.

For More Information: https://www.studyfinds.org/long-covid-blood-test/

COVID-19-Associated Bronchiectasis and Its Impact on Prognosis

Authors: Aasir M. SulimanBassel W. BitarAmer A. FarooqiAnam M. ElarabiMohamed R. AboukamarAhmed S. Abdulhadi

Abstract

Coronavirus disease 2019 (COVID-19), which initially emerged in Wuhan, China, has rapidly swept around the world, causing grave morbidity and mortality. It manifests with several symptoms, on a spectrum from asymptomatic to severe illness and death. Many typical imaging features of this disease are described, such as bilateral multi-lobar ground-glass opacities (GGO) or consolidations with a predominantly peripheral distribution. COVID-19-associated bronchiectasis is an atypical finding, and it is not a commonly described sequel of the disease. Here, we present a previously healthy middle-aged man who developed progressive bronchiectasis evident on serial chest CT scans with superimposed bacterial infection following COVID-19 pneumonia. The patient’s complicated hospital course of superimposed bacterial infection in the setting of presumed bronchiectasis secondary to COVID-19 is alleged to have contributed to his prolonged hospital stay, with difficulty in weaning off mechanical ventilation. Clinicians should have high suspicion and awareness of such a debilitating complication, as further follow-up and management might be warranted.

Introduction

Beginning in December 2019, a series of pneumonia cases were reported in Wuhan City, Hubei Province, China. Further investigations revealed that it was a new type of viral pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), which was termed coronavirus disease 2019 (COVID-19). Symptoms are variable, nonspecific, and include dry cough, fever, fatigue, myalgia, dyspnea, anosmia, and ageusia [1]. The real-time reverse transcription-polymerase chain reaction (rRT-PCR) test is the current gold standard for confirming infection and is performed using nasal or pharyngeal swab specimens.

Computerized tomography of the thorax (CT thorax), as a routine imaging tool for pneumonia diagnosis, is of great importance in the early detection and treatment of patients affected by COVID-19. Chest CT may detect the early parenchymal abnormalities in the absence of positive rRT-PCR at initial presentation [2]. Since chest CT was introduced as a diagnostic tool for COVID-19 pneumonia, many typical features of this disease were described such as bilateral multi-lobar ground-glass opacification (GGO) with a prevalent peripheral or posterior distribution, mainly in the lower lobes; sometimes, consolidative opacities superimposed on GGOs could be found [3]. To our knowledge, bronchiectasis is not a classical finding in COVID-19 pneumonia, with a paucity of reporting on its development and progression during the disease course.

For More Information: https://www.cureus.com/articles/59350-covid-19-associated-bronchiectasis-and-its-impact-on-prognosis

Antigen and Molecular Tests

Diagnostic tests are used to detect current, active infections of the SARS-CoV-2 virus. Diagnostic tests can be antigen based (“rapid antigen” tests), which look for protein markers on the outside of the virus, or they can be molecular based (including PCR, LAMP, CRISPR), which look for viral genomic material specific to SARS-CoV-2. Molecular based tests that amplify genetic material are also called nucleic acid amplification tests (NAAT). 

More about antigen and molecular tests:

For More Information: https://www.centerforhealthsecurity.org/covid-19TestingToolkit/testing-basics/types-of-COVID-19-tests/antigen-and-molecular-tests.html

Performance of an Antigen-Based Test for Asymptomatic and Symptomatic SARS-CoV-2 Testing at Two University Campuses

Authors: Ian W. Pray, PhD1,2,3,*; Laura Ford, PhD1,2,*; Devlin Cole, MD3,4; Christine Lee, PhD1,5; John Paul Bigouette, PhD1,2; Glen R. Abedi, MPH1; Dena Bushman, MSN, MPH1,2; Miranda J. Delahoy, PhD1,2; Dustin Currie, PhD1,2; Blake Cherney, MS1; Marie Kirby, PhD1; Geroncio Fajardo, MD1; Motria Caudill, PhD1,6; Kimberly Langolf, MS7; Juliana Kahrs, MS7; Patrick Kelly, MD4,8; Collin Pitts, MD4,8; Ailam Lim, PhD9; Nicole Aulik, PhD9; Azaibi Tamin, PhD1; Jennifer L. Harcourt, PhD1; Krista Queen, PhD1; Jing Zhang, PhD1; Brett Whitaker, PhD1; Hannah Browne1; Magdalena Medrzycki, PhD1; Patricia Shewmaker, PhD1; Jennifer Folster, PhD1; Bettina Bankamp, PhD1; Michael D. Bowen, PhD1; Natalie J. Thornburg, PhD1; Kimberly Goffard, MBA10; Brandi Limbago, PhD1; Allen Bateman, PhD7,11; Jacqueline E. Tate, PhD1; Douglas Gieryn10; Hannah L. Kirking, MD1; Ryan Westergaard, MD, PhD3,4; Marie Killerby, VetMB1; CDC COVID-19 Surge Laboratory Group (View author affiliations)

Summary

What is already known about this topic?

Antigen tests for SARS-CoV-2 are inexpensive and can return results within 15 minutes, but test performance data in asymptomatic and symptomatic persons are limited.

What is added by this report?

Compared with real-time reverse transcription–polymerase chain reaction (RT-PCR) testing, the Sofia antigen test had a sensitivity of 80.0% and specificity of 98.9% among symptomatic persons; accuracy was lower (sensitivity 41.2% and specificity 98.4%) when used for screening of asymptomatic persons.

What are the implications for public health practice?

To account for reduced antigen test accuracy, confirmatory testing with a nucleic acid amplification test (e.g., RT-PCR) should be considered after negative antigen test results in symptomatic persons and positive antigen test results in asymptomatic persons.

For More Information: https://www.cdc.gov/mmwr/volumes/69/wr/mm695152a3.htm

Hydroxychloroquine for the Prevention of Covid-19 — Searching for Evidence

Authors: Myron S. Cohen, M.D.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (Covid-19), has generated a worldwide pandemic. The interruption of its spread depends on a combination of pharmacologic and nonpharmacologic interventions. Initial SARS-CoV-2 prevention includes social distancing, the use of face masks, environmental hygiene, and hand washing.1 Although the most important pharmacologic interventions to prevent SARS-CoV-2 infection are likely to be vaccines, the repurposing of established drugs for short-term prophylaxis is another, more immediate option.

Some researchers have promoted chloroquine and hydroxychloroquine for the treatment and prevention of illness from a variety of microorganisms, including SARS-CoV.2 Hydroxychloroquine can inhibit replication of SARS-CoV-2 in vitro.3 Some observational studies have suggested benefits of hydroxychloroquine for the treatment of Covid-19, whereas other treatment reports have described mixed results.4

Boulware et al. now report in the Journal the results of a randomized trial testing hydroxychloroquine as postexposure prophylaxis for Covid-19.5 This is described by the investigators as a “pragmatic” trial in which participants were recruited through social media and almost all data were reported by the participants. Adults who described a high-risk or moderate-risk exposure to someone with Covid-19 in their household or an occupational setting were provided hydroxychloroquine or placebo (by mail) within 4 days after the reported exposure, and before symptoms would be expected to develop. The authors enrolled 821 participants; an illness that was considered to be consistent with Covid-19 developed in 107 participants (13.0%) but was confirmed by polymerase-chain-reaction assay in less than 3% of the participants. The incidence of a new illness compatible with Covid-19 did not differ significantly between participants receiving hydroxychloroquine (49 of 414 [11.8%]) and those receiving placebo (58 of 407 [14.3%]). Although participant-reported side effects were significantly more common in those receiving hydroxychloroquine (40.1%) than in those receiving placebo (16.8%), no serious adverse reactions were reported.

This trial has many limitations, acknowledged by the investigators. The trial methods did not allow consistent proof of exposure to SARS-CoV-2 or consistent laboratory confirmation that the symptom complex that was reported represented a SARS-CoV-2 infection. Indeed, the specificity of participant-reported Covid-19 symptoms is low,6 so it is hard to be certain how many participants in the trial actually had Covid-19. Adherence to the interventions could not be monitored, and participants reported less-than-perfect adherence, more notably in the group receiving hydroxychloroquine. In addition, those enrolled in the trial were younger (median age, 40 years) and had fewer coexisting conditions than persons in whom severe Covid-19 is most likely to develop,7 so enrollment of higher-risk participants might have yielded a different result.

For More Information: https://www.nejm.org/doi/full/10.1056/NEJMe2020388

Virology, transmission, and pathogenesis of SARS-CoV-2

Authors: Muge Cevik, clinical lecturer2,  Krutika Kuppalli, assistant professor3,  Jason Kindrachuk, assistant professor of virology4,  Malik Peiris, professor of virology5

What you need to know

  • SARS-CoV-2 is genetically similar to SARS-CoV-1, but characteristics of SARS-CoV-2—eg, structural differences in its surface proteins and viral load kinetics—may help explain its enhanced rate of transmission
  • In the respiratory tract, peak SARS-CoV-2 load is observed at the time of symptom onset or in the first week of illness, with subsequent decline thereafter, indicating the highest infectiousness potential just before or within the first five days of symptom onset
  • Reverse transcription polymerase chain reaction (RT-PCR) tests can detect viral SARS-CoV-2 RNA in the upper respiratory tract for a mean of 17 days; however, detection of viral RNA does not necessarily equate to infectiousness, and viral culture from PCR positive upper respiratory tract samples has been rarely positive beyond nine days of illness
  • Symptomatic and pre-symptomatic transmission (1-2 days before symptom onset), is likely to play a greater role in the spread of SARS-CoV-2 than asymptomatic transmission
  • A wide range of virus-neutralizing antibodies have been reported, and emerging evidence suggests that these may correlate with severity of illness but wane over time.

Since the emergence of SARS-CoV-2 in December 2019, there has been an unparalleled global effort to characterize the virus and the clinical course of disease. Coronavirus disease 2019 (covid-19), caused by SARS-CoV-2, follows a biphasic pattern of illness that likely results from the combination of an early viral response phase and an inflammatory second phase. Most clinical presentations are mild, and the typical pattern of covid-19 more resembles an influenza-like illness—which includes fever, cough, malaise, myalgia, headache, and taste and smell disturbance—rather than severe pneumonia (although emerging evidence about long term consequences is yet to be understood in detail).1 In this review, we provide a broad update on the emerging understanding of SARS-CoV-2 pathophysiology, including virology, transmission dynamics, and the immune response to the virus. Any of the mechanisms and assumptions discussed in the article and in our understanding of covid-19 may be revised as further evidence emerges.

For More Information: https://www.bmj.com/content/371/bmj.m3862