Persistence of SARS-COV-2 in body fluids: a bystander or whistle blower

The novel Coronavirus COVID-19 is wrecking a havoc across the globe and has been declared as a pandemic by WHO. Apart from transmission and shedding of the virus through respiratory secretions in the form of droplets (mainly), several studies have shown the presence of the virus in various samples such as stool, urine and occasionally in blood, semen, tears and breastmilk. Whereas government authority guidelines consider a person as cured from COVID-19 when along with clinical improvement no more virus can be detected primarily on respiratory samples along with clinical improvement; the persistence of the virus in these body fluids even after clinical recovery and negative RT-PCR test results on respiratory samples, has raised many questions about the elusive nature of this novel virus along with the possibility of other routes of transmission of this virus in the community. Although studies performed till now across the globe on persistence of SARSCOV-2 in various body fluids are sparse, in this review we would like to present and analyse the results of those studies performed globally on the aforesaid topic to get a better insight of this side of the COVID-19 story.

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Association of Underlying Diseases and Clinical Characteristics with Mortality in Patients with 2019 Novel Coronavirus in Iran

Archives of Clinical Infectious Diseases ◽

10.5812/archcid.104621 ◽

2020 ◽

Vol 15 (5) ◽

Author(s):

Mohammadhossein Zamanian ◽

Zohre Foroozanfar ◽

Zhila Izadi ◽

Samira Jafari ◽

Hossein Derakhshankhah ◽

...

Keyword(s):

Heart Disease ◽

Clinical Characteristics ◽

Underlying Disease ◽

Test Results ◽

Rt Pcr ◽

Factors Associated ◽

History Of ◽

Novel Coronavirus ◽

Underlying Diseases ◽

Pcr Test

Objectives: The first case of 2019 novel coronavirus disease (COVID-19) was reported in Iran in February 2020. Here, we report the epidemiological and clinical characteristics of patients with COVID-19 and factors associated with mortality in these patients. Methods: A retrospective cohort study was conducted from February 22, 2020, to March 24, 2020, in Golestan Hospital in Kermanshah, Iran. Demographic data including underlying diseases and clinical data including the presenting symptoms, chest computed tomography (CT) scan, reverse transcription polymerase chain reaction (RT-PCR) test results, and outcomes were extracted from electronic medical records. Simple and multiple logistic regression methods were used to explore the factors associated with mortality. Results: Of 245 patients admitted with COVID-19, 155 (63.30%) were male. The mean age of the subjects was 54.68 ± 19.21. Forty-five (18.48%) patients had underlying diseases. Common symptoms were dyspnea (n = 137; 55.9%), cough (n = 93; 38.0%), and fever (n = 78; 31.8%). All patients had pneumonia with abnormal findings on chest CT scan (100%), and RT-PCR test results were positive in 87 (35.50%) patients. Of the total admitted cases, 38 (15.5%) patients died during hospitalization. An old age (OR = 1.09; 95% CI: 1.02 to 1.06), history of heart disease (OR = 5.07; 95% CI: 1.46 to 17.58), hypertension (OR = 5.82; 95% CI: 1.13 to 30.04), smoking (OR = 11.44; 95% CI: 1.01 to 29.53), history of at least one underlying disease (OR = 3.31; 95%CI: 1.54 to 7.09), and symptoms of decreased consciousness at the time of admission (OR = 24.23; 95% CI: 2.62 to 223.39) were associated with mortality. Also, the symptoms of cough (OR = 0.383; 95% CI: 0.17 to 0.88) and fever (OR = 0.278; 95% CI: 0.10 to 0.74) had a negative association with mortality. Conclusions: In the current study, factors including old age, smoking, symptoms of decreased consciousness, and underlying diseases such as heart disease, hypertension, and history of at least one underlying disease were associated with mortality. Factors associated with mortality should be considered so that we can better manage patients with COVID-19.

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Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus

10.1101/2020.02.22.20025460 ◽

2020 ◽

Cited By ~ 18

Author(s):

Tieying Hou ◽

Weiqi Zeng ◽

Minling Yang ◽

Wenjing Chen ◽

Lili Ren ◽

...

Keyword(s):

Single Copy ◽

Health Concern ◽

The Novel ◽

Rt Pcr ◽

Clinical Sensitivity ◽

Reverse Transcription Pcr ◽

Technology Platforms ◽

Novel Virus ◽

Novel Coronavirus ◽

High Degree

BackgroundThe recent outbreak of infections by the 2019 novel coronavirus (2019-nCoV), the third zoonotic CoV has raised great public health concern. The demand for rapid and accurate diagnosis of this novel pathogen brought significant clinical and technological challenges. Currently, metagenomic next-generation sequencing (mNGS) and reverse-transcription PCR (RT-PCR) are the most widely used molecular diagnostics for 2019-nCoV.Methods2019-nCoV infections were confirmed in 52 specimens by mNGS. Genomic information was analyzed and used for the design and development of an isothermal, CRISPR-based diagnostic for the novel virus. The diagnostic performance of CRISPR-nCoV was assessed and also compared across three technology platforms (mNGS, RT-PCR and CRISPR)Results2019-nCoVs sequenced in our study were conserved with the Wuhan strain, and shared certain genetic similarity with SARS-CoV. A high degree of variation in the level of viral RNA was observed in clinical specimens. CRISPR-nCoV demonstrated a near single-copy sensitivity and great clinical sensitivity with a shorter turn-around time than RT-PCR.ConclusionCRISPR-nCoV presents as a promising diagnostic option for the emerging pathogen.

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Corticosteroid treatment has no effect on hospital mortality in COVID-19 patients

Scientific Reports ◽

10.1038/s41598-020-80654-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Filippo Albani ◽

Federica Fusina ◽

Enza Granato ◽

Cristina Capotosto ◽

Claudia Ceracchi ◽

...

Keyword(s):

Intensive Care ◽

Hospital Mortality ◽

Corticosteroid Therapy ◽

Corticosteroid Treatment ◽

Limited Resources ◽

The Novel ◽

Rt Pcr ◽

The Subject ◽

Novel Coronavirus ◽

Pcr Test

AbstractSince the start of the novel coronavirus 2019 (COVID-19) pandemic, corticosteroid use has been the subject of debate. The available evidence is uncertain, and knowledge on the subject is evolving. The aim of our cohort study was to evaluate the association between corticosteroid therapy and hospital mortality, in patients hospitalized with COVID-19 after balancing for possible confounders. One thousand four hundred forty four patients were admitted to our hospital with a positive RT-PCR test for SARS-CoV-2, 559 patients (39%) were exposed to corticosteroids during hospital stay, 844 (61%) were not exposed to corticosteroids. In the cohort of patients exposed to corticosteroids, 171 (30.6%) died. In the cohort of patients not exposed to corticosteroids, 183 (21.7%) died (unadjusted p < 0.001). Nonetheless, exposure to corticosteroids was not associated with in-hospital mortality after balancing with overlap weight propensity score (adjusted p = 0.25). Patients in the corticosteroids cohort had a reduced risk of ICU admission (adjusted p < 0.001). Treatment with corticosteroids did not affect hospital mortality in patients with COVID-19 after balancing for confounders. A possible advantage of corticosteroid therapy was to reduce Intensive Care Unit admission, which could be useful in reducing pressure on Intensive Care Units in times of limited resources, as during the COVID-19 pandemic.

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Prehospital identification of Covid-19: an observational study

Scandinavian Journal of Trauma Resuscitation and Emergency Medicine ◽

10.1186/s13049-020-00826-6 ◽

2021 ◽

Vol 29 (1) ◽

Author(s):

Douglas Spangler ◽

Hans Blomberg ◽

David Smekal

Keyword(s):

Predictive Value ◽

Prehospital Care ◽

The Novel ◽

Test Results ◽

Care Providers ◽

Care Systems ◽

Primary Hospital ◽

Novel Coronavirus ◽

Rule Out ◽

Descriptive Statistical Analysis

Abstract Background The novel coronavirus disease 2019 (Covid-19) pandemic has affected prehospital care systems across the world, but the prehospital presentation of affected patients and the extent to which prehospital care providers are able to identify them is not well characterized. In this study, we describe the presentation of Covid-19 patients in a Swedish prehospital care system, and asses the predictive value of Covid-19 suspicion as documented by dispatch and ambulance nurses. Methods Data for all patients with dispatch, ambulance, and hospital records between January 1–August 31, 2020 were extracted. A descriptive statistical analysis of patients with and without hospital-confirmed Covid-19 was performed. In a subset of records beginning from April 14, we assessed the sensitivity and specificity of documented Covid-19 suspicion in dispatch and ambulance patient care records. Results A total of 11,894 prehospital records were included, of which 481 had a primary hospital diagnosis code related to-, or positive test results for Covid-19. Covid-19-positive patients had considerably worse outcomes than patients with negative test results, with 30-day mortality rates of 24% vs 11%, but lower levels of prehospital acuity (e.g. emergent transport rates of 14% vs 22%). About half (46%) of Covid-19-positive patients presented to dispatchers with primary complaints typically associated with Covid-19. Six thousand seven hundred seventy-six records were included in the assessment of predictive value. Sensitivity was 76% (95% CI 71–80) and 82% (78–86) for dispatch and ambulance suspicion respectively, while specificities were 86% (85–87) and 78% (77–79). Conclusions While prehospital suspicion was strongly indicative of hospital-confirmed Covid-19, based on the sensitivity identified in this study, prehospital suspicion should not be relied upon as a single factor to rule out the need for isolation precautions. The data provided may be used to develop improved guidelines for identifying Covid-19 patients in the prehospital setting.

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Death and COVID-19 Anxiety in Home-Quarantined Individuals Aged 65 and Over During the Pandemic

OMEGA - Journal of Death and Dying ◽

10.1177/00302228211059894 ◽

2021 ◽

pp. 003022282110598

Author(s):

Hümeyra Aslaner ◽

Betül Özen ◽

Zeliha K. Erten ◽

Mebrure Beyza Gökçek

Keyword(s):

Polymerase Chain Reaction ◽

Death Anxiety ◽

Short Form ◽

Anxiety Score ◽

Test Results ◽

Rt Pcr ◽

Chain Reaction ◽

Polymerase Chain ◽

Test Result ◽

Pcr Test

Urgent measures were taken for those at the age of 65 and over who were at the risk group all over the world due to the COVID-19 pandemic. It is known that many individuals at the age of 65 and over have experienced anxiety due to the uncertainties. This study aimed to determine the anxiety and death anxiety in individuals aged 65 and over who were isolation at home due to being diagnosed with COVID-19 or being in contact during the pandemic process. The study is descriptive and cross-sectional. It was performed with 656 home-quarantined individuals aged between 65–80 years with positive or negative real-time polymerase chain reaction (RT-PCR) test result. A form including questions about the death anxiety and the Coronavirus Anxiety Scale Short Form prepared by the researchers were administered to the individuals by phone call. Of the participants, 49.5% were male. Median COVID-19 anxiety score was 4 (0–18). Anxiety scores of the male and female participants were similar. Participants with negative polymerase chain reaction (PCR) results and those with death anxiety had higher COVID anxiety scores. Death anxiety has increased by 1.661 times in male gender, 1.983 times in RT-PCR positivity and 0.146 times in the presence of symptoms. Individuals with positive COVID-19 test results or those aged 65 and over who had death anxiety and negative COVID-19 test result but who were in home-isolation due to being a contact had higher anxiety score. For this reason, those with death anxiety can be supported in line with their religious beliefs to reduce anxiety. Those with negative PCR test results in quarantine can be adequately informed about the COVID-19.

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Accuracy of Computed Tomography for Detection of COVID-19 among Suspected Patients

10.53350/pjmhs211592474 ◽

2021 ◽

Vol 15 (9) ◽

pp. 2474-2476

Author(s):

Maham Munir Awan ◽

Afshan Noreen ◽

Farah Kalsoom ◽

Muhammad Tahir ◽

Umaima Majeed ◽

...

Keyword(s):

Computed Tomography ◽

Predictive Value ◽

Gold Standard ◽

Radiology Department ◽

True Positive ◽

Test Results ◽

Rt Pcr ◽

Radiological Society ◽

Medical University ◽

Pcr Test

Objective: To determine the accuracy of CT chest in diagnosis of COVID-19 taking RT-PCR-testing as gold standard. Materials and Methods: A total of 150 patients of suspicion of COVID-19 who were referred for CT Chest in Radiology Department of Nishtar Medical University Multan from June-2020 to May-2021 were included. In all patients, two RT-PCR test results were obtained with 7 days of admission in hospital. Presence of any of these positive was labelled as COVID-19 infection. CT chest was performed in all patients within 2 days of admission in hospital using 128 slices CT scan machine. The diagnosis of COVID-19 infection was made according to the recommendations by Radiological Society of North America (RSNA) protocol. Results: Mean age was 51.3±14.7 years. 78 (52%) patients were male and 72 (48%) patients were female. RTPCR test was positive in 89 (59.3%) patients. While the CT chest findings were suggestive of COVID-19 infection in 130 (86.7%) patients. The sensitivity of CT chest was 95.5%, specificity 26.2%, PPV wad 65.4% and NPV was 80.0%. Conclusion: CT chest has a very good sensitivity for detection of COVID-19, it can be used as a rapid diagnostic tool especially in areas of pandemic. However, the specificity of CT chest is low, that can limit its use in low COVID-19 affected areas. Keywords: COVID-19, Computed tomography, False Positive, True Positive, Positive Predictive Value, Negative Predictive Value.

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DIAGNOSTIC ROLE OF CHEST CT USING CO-RADS CATEGORIZATION IN SARS-COV-2 INFECTION WITH EMPHASIS ON IMPACT OF CT IN PATIENTS WITH DELAYED OR NEGATIVE INITIAL RTPCR TEST

10.36106/ijar/9301921 ◽

2021 ◽

pp. 51-52

Author(s):

Tharani Putta ◽

Kaushik Deconda

Keyword(s):

Diagnostic Performance ◽

Virus Disease ◽

Vital Role ◽

Chest Ct ◽

Lung Involvement ◽

Test Results ◽

Rt Pcr ◽

Diagnostic Role ◽

Pcr Test

BACKGROUND AND OBJECTIVE: Role of chest CT in diagnosis of corona virus disease 2019 (COVID-19) has been controversial. The purpose of this study is to evaluate the diagnostic performance of chest CT when utilizing COVID-19 Reporting and Data System (CO-RADS). METHODOLOGY: Retrospective study including consecutive patients with positive SARS-CoV-2 RT-PCR test (initial or repeat test) and chest CT done in our institute between June and September 2020. Spectrum of CT ndings, CO-RADS score and 25 point CT severity score (CTSS) were recorded. RESULTS: A total of 300 consecutive patients with SARS-CoV-2 infection were included in the analysis. Out of the 168 patients who underwent CT prior to positive RT-PCR result, 125 (74.4%) had CO-RADS 3, 4 or 5 score on chest CT. 32 study patients (10.6%) had initial negative RT-PCR of which 24 (75%) had CO-RADS 4 or 5 score. Of the total patients with CO-RADS 3 to 5 score (227), 20 (8.8%) had severe lung involvement (CTSS 18-25), 83 (36.6%) had moderate lung involvement (CTSS 8-17) and 124 (54.6%) had mild lung involvement (CTSS 1-7). The mean CTSS was 7.9 with mean lobar score being higher in lower lobes (RLL=1.82, LLL=1.78) compared to the upper and middle lobes (RUL=1.61, RML=1.19, LUL=1.53). CONCLUSION:CT using CO-RADS scoring system has good diagnostic performance. In addition to assessing disease severity, it plays a vital role in triage of patients with suspected COVID-19 especially when there is limited availability of SARS-CoV-2 RT-PCR tests, delay in RT-PCR test results or in negative RT-PCR cases when there is high index of clinical suspicion.

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SARS-CoV-2: preliminary study of infected human nasopharyngeal tissue by high resolution microscopy

Virology Journal ◽

10.1186/s12985-021-01620-1 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Brian Mondeja ◽

Odalys Valdes ◽

Sonia Resik ◽

Ananayla Vizcaino ◽

Emilio Acosta ◽

...

Keyword(s):

High Resolution ◽

Control Sample ◽

Negative Control ◽

High Rate ◽

Apical Region ◽

The Novel ◽

Rt Pcr ◽

Crown Shape ◽

Novel Coronavirus ◽

High Resolution Microscopy

Abstract Background The novel coronavirus SARS-CoV-2 is the etiological agent of COVID-19. This virus has become one of the most dangerous in recent times with a very high rate of transmission. At present, several publications show the typical crown-shape of the novel coronavirus grown in cell cultures. However, an integral ultramicroscopy study done directly from clinical specimens has not been published. Methods Nasopharyngeal swabs were collected from 12 Cuban individuals, six asymptomatic and RT-PCR negative (negative control) and six others from a COVID-19 symptomatic and RT-PCR positive for SARS CoV-2. Samples were treated with an aldehyde solution and processed by scanning electron microscopy (SEM), confocal microscopy (CM) and, atomic force microscopy. Improvement and segmentation of coronavirus images were performed by a novel mathematical image enhancement algorithm. Results The images of the negative control sample showed the characteristic healthy microvilli morphology at the apical region of the nasal epithelial cells. As expected, they do not display virus-like structures. The images of the positive sample showed characteristic coronavirus-like particles and evident destruction of microvilli. In some regions, virions budding through the cell membrane were observed. Microvilli destruction could explain the anosmia reported by some patients. Virus-particles emerging from the cell-surface with a variable size ranging from 80 to 400 nm were observed by SEM. Viral antigen was identified in the apical cells zone by CM. Conclusions The integral microscopy study showed that SARS-CoV-2 has a similar image to SARS-CoV. The application of several high-resolution microscopy techniques to nasopharyngeal samples awaits future use.

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Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19)

Clinical Chemistry and Laboratory Medicine (CCLM) ◽

10.1515/cclm-2020-0285 ◽

2020 ◽

Vol 58 (7) ◽

pp. 1070-1076 ◽

Cited By ~ 179

Author(s):

Giuseppe Lippi ◽

Ana-Maria Simundic ◽

Mario Plebani

Keyword(s):

Diagnostic Accuracy ◽

Diagnostic Errors ◽

Laboratory Diagnosis ◽

Test Results ◽

Rt Pcr ◽

Viral Recombination ◽

Technical Issues ◽

Diagnostic Window ◽

Novel Coronavirus ◽

And Storage

AbstractA novel zoonotic coronavirus outbreak is spreading all over the world. This pandemic disease has now been defined as novel coronavirus disease 2019 (COVID-19), and is sustained by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As the current gold standard for the etiological diagnosis of SARS-CoV-2 infection is (real time) reverse transcription polymerase chain reaction (rRT-PCR) on respiratory tract specimens, the diagnostic accuracy of this technique shall be considered a foremost prerequisite. Overall, potential RT-PCR vulnerabilities include general preanalytical issues such as identification problems, inadequate procedures for collection, handling, transport and storage of the swabs, collection of inappropriate or inadequate material (for quality or volume), presence of interfering substances, manual errors, as well as specific aspects such as sample contamination and testing patients receiving antiretroviral therapy. Some analytical problems may also contribute to jeopardize the diagnostic accuracy, including testing outside the diagnostic window, active viral recombination, use of inadequately validated assays, insufficient harmonization, instrument malfunctioning, along with other specific technical issues. Some practical indications can hence be identified for minimizing the risk of diagnostic errors, encompassing the improvement of diagnostic accuracy by combining clinical evidence with results of chest computed tomography (CT) and RT-PCR, interpretation of RT-PCR results according to epidemiologic, clinical and radiological factors, recollection and testing of upper (or lower) respiratory specimens in patients with negative RT-PCR test results and high suspicion or probability of infection, dissemination of clear instructions for specimen (especially swab) collection, management and storage, together with refinement of molecular target(s) and thorough compliance with analytical procedures, including quality assurance.

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A blueprint for academic laboratories to produce SARS-CoV-2 quantitative RT-PCR test kits

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.015434 ◽

2020 ◽

Vol 295 (46) ◽

pp. 15438-15453 ◽

Cited By ~ 1

Author(s):

Samantha J. Mascuch ◽

Sara Fakhretaha-Aval ◽

Jessica C. Bowman ◽

Minh Thu H. Ma ◽

Gwendell Thomas ◽

...

Keyword(s):

Support Group ◽

Diagnostic Testing ◽

The Novel ◽

Rt Pcr ◽

Research Teams ◽

Environmental Testing ◽

Resource Limited ◽

Test Kit ◽

Institute Of Technology ◽

Novel Coronavirus

Widespread testing for the presence of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise, and/or instrumentation necessary to detect the virus by quantitative RT-PCR (RT-qPCR), the most robust, sensitive, and specific assay currently available. Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can replicate commercially available SARS-CoV-2 RT-qPCR test kits and backfill pipeline shortages. The Georgia Tech COVID-19 Test Kit Support Group, composed of faculty, staff, and trainees across the biotechnology quad at Georgia Institute of Technology, synthesized multiplexed primers and probes and formulated a master mix composed of enzymes and proteins produced in-house. Our in-house kit compares favorably with a commercial product used for diagnostic testing. We also developed an environmental testing protocol to readily monitor surfaces for the presence of SARS-CoV-2. Our blueprint should be readily reproducible by research teams at other institutions, and our protocols may be modified and adapted to enable SARS-CoV-2 detection in more resource-limited settings.

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