scholarly journals High-Throughput Transcription-mediated amplification (TMA), a real and consolidated alternative for the diagnosis of SARS-COV2. Review.

Author(s):  
FRANCISCO JAVIER GARCÍA-FERNÁNDEZ

Abstract The exceptional situation in which we have found ourselves since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified, which rapidly evolved into a global pandemic, translated into the need to incorporate the largest number of diagnostic tests to detect possible cases and contain the spread of the virus. The FDA authorized different trials using emergency procedures. One of the molecular assays adapted to the diagnosis of COVID19 is the transcription-mediated amplification (TMA) assay. We intend to answer the questions that are asked from a laboratory when a new technique is introduced. How does it work? Are your results comparable to gold standard techniques in terms of agreement and limit of detection? After the systematic review of the literature, an almost perfect concordance between the TMA and the RT-PCR was observed, taking into account the values of Cohen's kappa coefficient, positive percentage agreement, negative percentage agreement and global percentage agreement close to 100%. Regarding the concordance between the results obtained by TMA and the antigenic test, it presents a lower concordance, although it is true that the latter test is only optimal for the detection of SARS-CoV2 in a specific profile of patients. The literature shows that the TMA test has been used to study possible cases of reinfection. After analyzing the results, we concluded in the proven consolidation of TMA for the diagnosis and follow-up of SARS-COV2.

Medicinus ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. 31
Author(s):  
Aziza Ghanie Icksan ◽  
Muhammad Hafiz ◽  
Annisa Dian Harlivasari

<p><strong>Background : </strong>The first case of COVID-19 in Indonesia was recorded in March 2020. Limitation of reverse-transcription polymerase chain reaction (RT-PCR) has put chest CT as an essential complementary tool in the diagnosis and follow up treatment for COVID-19. Literatures strongly suggested that High-Resolution Computed Tomography (HRCT) is essential in diagnosing typical symptoms of COVID-19 at the early phase of disease due to its superior sensitivity  (97%) compared to chest x-ray (CXR).</p><p>The two cases presented in this case study showed the crucial role of chest CT with HRCT to establish the working diagnosis and follow up COVID-19 patients as a complement to RT-PCR, currently deemed a gold standard.<strong></strong></p>


2020 ◽  
Vol 21 (16) ◽  
pp. 5674
Author(s):  
Cyril Chik-Yan Yip ◽  
Siddharth Sridhar ◽  
Kit-Hang Leung ◽  
Anthony Chin-Ki Ng ◽  
Kwok-Hung Chan ◽  
...  

Sensitive molecular assays are critical for coronavirus disease 2019 (COVID-19) diagnosis. Here, we designed and evaluated two single-tube nested (STN) real-time RT-PCR assays, targeting SARS-CoV-2 RdRp/Hel and N genes. Both STN assays had a low limit of detection and did not cross react with other human coronaviruses and respiratory viruses. Using 213 initial respiratory specimens from suspected COVID-19 patients, the sensitivity of both the STN COVID-19-RdRp/Hel and the STN COVID-19-N assays was 100% (99/99), while that of the comparator non-nested N assay was 95% (94/99). Among 108 follow-up specimens from confirmed COVID-19 patients who tested negative by the non-nested COVID-19-RdRp/Hel assay, 28 (25.9%) were positive for SARS-CoV-2 by the STN COVID-19-RdRp/Hel or the STN COVID-19-N assay. To evaluate the performance of our novel STN assays in pooled specimens, we created four sample pools, with each pool consisting of one low positive specimen and 49 negative specimens. While the non-nested COVID-19-RdRp/Hel assay was positive in only one of four sample pools (25%), both of the STN assays were positive in two of four samples pools (50%). In conclusion, the STN assays are highly sensitive and specific for SARS-CoV-2 detection. Their boosted sensitivity offers advantages in non-traditional COVID-19 testing algorithms such as saliva screening and pooled sample screening during massive screening.


2021 ◽  
Vol 10 (1) ◽  
pp. 65-74
Author(s):  
Germán Enrique Arenas ◽  
Jesús De León Martínez ◽  
Marcela Negrete Vasquez ◽  
Mario Lora ◽  
Martín Carvajal ◽  
...  

Introduction: the Coronavirus disease 2019 (COVID-19) was declared as a global pandemic by the World Health Organization on March 11, 2020. The clinical presentation and severity of the disease has been described from its most typical symptoms, the common cold, pneumonia and respiratory distress syndrome, to the involvement of other organs and systems such such as the gastrointestinal, renal and cardiovascular. Case report: we describe the first case of COVID-19 diagnosed in Cartagena, Colombia, on March 11, 2020, and its uncommon clinic presentation, which was almost unknown at the time. An 85-year-old woman with week-long initial symptoms of nausea and occasional vomiting, with progression to diarrhea and a 38.5 oC fever during the last three days. The patient came from Oxford, UK, and she had been on a Caribbean cruise excursion since the end of February, 2020. Chest computed tomography showed ground glass opacities in both peripheral and central lung fields, multilobar and predominantly subpleural; without evidence of consolidation or pleural effusion. COVID-19 was confirmed three days after admission, when a RT-PCR molecular test performed on a nasopharyngeal swab sample tested positive for SARS-Cov-2 Conclusion: this first case of COVID-19 diagnosed in Cartagena occurred at a time when our health system was not prepared to face the pandemic. However, despite having manifested with a clinical that had not been described at the time, and thanks to the epidemiological, clinical and imaging data, the case could be adequately approached, diagnosed and treated according to the necessary and recommended measures at the time.


2022 ◽  
Author(s):  
Harsh Goel ◽  
Kashyap Shah ◽  
Janish Kothari ◽  
Timothy Daly ◽  
Pooja Saraiya ◽  
...  

Abstract Background: COVID-19 has caused an unprecedented global pandemic, with cardiovascular risk factors predicting outcomes. We investigated whether baseline trans-thoracic echocardiography could refine risk beyond clinical risk factors. Methods: Symptomatic COVID-19 positive (RT-PCR) adults across St Luke’s University Health Network between March 1st-October 31st 2021, with trans-thoracic echocardiography (TTE) within 15-180 days preceding COVID-19 positivity were selected. Demographic/clinical/echocardiographic variables were extracted from patients’ EHR and compared between groups stratified by disease severity. Logistic regression was used to identify independent predictors of hospitalization. Results: 192 patients were included. 87 (45.3%) required hospitalization, 34 (17.7%) suffered severe disease (need for ICU care/mechanical ventilation/in-hospital death). Age, co-morbidities, and several echocardiographic abnormalities were more prevalent in moderate-severe versus mild disease. On multivariate analysis, age (OR 1.039, 95% CI 1.011-1.067), coronary artery disease (OR 4.184, 95% CI 1.451-12.063), COPD (OR 6.886, 95% CI 1.396-33.959) and left atrial (LA) diameter ≥4.0cm (OR 2.379, 95% CI 1.031-5.493) predicted need for hospitalization. Model showed excellent discrimination (ROC AUC 0.809, 95% CI 0.746-0.873). Conclusion: Baseline LA enlargement independently predicts risk of hospitalization in COVID-19. When available, baseline LA enlargement could identify patients for 1) closer outpatient follow-up, and 2) counseling vaccine-hesitancy.


Author(s):  
Jingyi Ou ◽  
Mingkai Tan ◽  
Haolan He ◽  
Haiyan Tan ◽  
Jiewen Mai ◽  
...  

Background: In 2020, the current outbreak of Coronavirus Disease 2019(COVID-19) has constituted a global pandemic. But the question about the immune mechanism of patients with COVID-19 is unclear and cause particular concern to the world. Here, we launched a follow-up analysis of antibodies against SARS-CoV-2 of 192 COVID-19 patients, aiming to depict a kinetics profile of antibodies against SARS-CoV-2 and explore the related factors of antibodies expression against SARS-CoV-2 in COVID-19 patient. Methods: A total of 192 COVID-19 patients enrolled in the designated hospital of Guangzhou , Guangzhou Eighth People's Hospital, from January to February 2020 were selected as the study cohort. A cohort of 130 COVID-19 suspects who had been excluded from SARS-CoV-2 infected by negative RT-PCR result and 209 healthy people were enrolled in this study. Detection of IgM and IgG against SARS-CoV-2 were performed by Chemiluminescence immunoassay in different groups . Results: It has been found that the seroconversion time of IgM against SARS-CoV-2 in most patients was 5-10 days after the symptoms onset , and then rose rapidly, reaching a peak around 2 to 3 weeks, and the median peak concentration was 2.705 AU / mL. The peak of IgM maintained within one week, and then enters the descending channel. IgG seroconverted later than or synchronously with IgM, reaching peaks around 3 to 4 weeks.The median peak concentration was 33.998AU / ml,which was higher than that of IgM . IgM titers begins to gradually decrease after reaching the peak in the 4th week, after the 8th week, a majority of IgM in patient's serum started to turn negative. On the contrary, titers of IgG began to decline slightly after the fifth week, and more than 90% of results of patients were positive after 8 weeks. Additionally, the concentration of antibodies positively correlated with the severity of the disease and the duration of virus exist in host. Conclusion: We depict a kinetics profile of antibodies against SARS-CoV-2 in COVID-19 patients and found out that the levels of antibodies were related to the disease severity,age, gender and virus clearance or continuous proliferation of COVID-19 patients.


2020 ◽  
Vol 12 (03) ◽  
pp. 135-162 ◽  
Author(s):  
J. Terrence Jose Jerome ◽  
Francisco Mercier ◽  
Chaitanya S. Mudgal ◽  
Joan Arenas-Prat ◽  
Gustavo Vinagre ◽  
...  

AbstractWith a lot of uncertainty, unclear, and frequently changing management protocols, COVID-19 has significantly impacted the orthopaedic surgical practice during this pandemic crisis. Surgeons around the world needed closed introspection, contemplation, and prospective consensual recommendations for safe surgical practice and prevention of viral contamination. One hundred orthopaedic surgeons from 50 countries were sent a Google online form with a questionnaire explicating protocols for admission, surgeries, discharge, follow-up, relevant information affecting their surgical practices, difficulties faced, and many more important issues that happened during and after the lockdown. Ten surgeons critically construed and interpreted the data to form rationale guidelines and recommendations. Of the total, hand and microsurgery surgeons (52%), trauma surgeons (32%), joint replacement surgeons (20%), and arthroscopy surgeons (14%) actively participated in the survey. Surgeons from national public health care/government college hospitals (44%) and private/semiprivate practitioners (54%) were involved in the study. Countries had lockdown started as early as January 3, 2020 with the implementation of partial or complete lifting of lockdown in few countries while writing this article. Surgeons (58%) did not stop their surgical practice or clinics but preferred only emergency cases during the lockdown. Most of the surgeons (49%) had three-fourths reduction in their total patients turn-up and the remaining cases were managed by conservative (54%) methods. There was a 50 to 75% reduction in the number of surgeries. Surgeons did perform emergency procedures without COVID-19 tests but preferred reverse transcription polymerase chain reaction (RT-PCR; 77%) and computed tomography (CT) scan chest (12%) tests for all elective surgical cases. Open fracture and emergency procedures (60%) and distal radius (55%) fractures were the most commonly performed surgeries. Surgeons preferred full personal protection equipment kits (69%) with a respirator (N95/FFP3), but in the case of unavailability, they used surgical masks and normal gowns. Regional/local anesthesia (70%) remained their choice for surgery to prevent the aerosolized risk of contaminations. Essential surgical follow-up with limited persons and visits was encouraged by 70% of the surgeons, whereas teleconsultation and telerehabilitation by 30% of the surgeons. Despite the protective equipment, one-third of the surgeons were afraid of getting infected and 56% feared of infecting their near and dear ones. Orthopaedic surgeons in private practice did face 50 to 75% financial loss and have to furlough 25% staff and 50% paramedical persons. Orthopaedics meetings were cancelled, and virtual meetings have become the preferred mode of sharing the knowledge and experiences avoiding human contacts. Staying at home, reading, and writing manuscripts became more interesting and an interesting lifestyle change is seen among the surgeons. Unanimously and without any doubt all accepted the fact that COVID-19 pandemic has reached an unprecedented level where personal hygiene, hand washing, social distancing, and safe surgical practices are the viable antidotes, and they have all slowly integrated these practices into their lives. Strict adherence to local authority recommendations and guidelines, uniform and standardized norms for admission, inpatient, and discharge, mandatory RT-PCR tests before surgery and in selective cases with CT scan chest, optimizing and regularizing the surgeries, avoiding and delaying nonemergency surgeries and follow-up protocols, use of teleconsultations cautiously, and working in close association with the World Health Organization and national health care systems will provide a conducive and safe working environment for orthopaedic surgeons and their fraternity and also will prevent the resurgence of COVID-19.


2021 ◽  
Vol 14 ◽  
pp. 117954762110205
Author(s):  
Nader Salama ◽  
Saeed Blgozah

COVID-19 is a new global pandemic. It can affect multiple body systems and functions. However, the relationship between COVID-19 and male sexual activity did not yet get much consideration. Herein, we report the impact of COVID-19 on sexual function in 3 men who recovered from the disease. Compared with their condition before catching the infection, the men showed, in different degrees, a decline in all aspects of sexual function as assessed by the international index of erectile function. They started to develop premature ejaculation or exacerbate an already existing condition according to the premature ejaculation diagnostic tool scoring. Beck’s depression inventory revealed deterioration of the men’s moods up to severe depression. The sex-related hormones (testosterone-total and free, luteinizing hormone, follicle-stimulating hormone, prolactin, and estradiol) of these men were within normal levels. To the best of our knowledge, this is the first case report documenting deleterious changes in mood and several aspects of sexual functioning in males after recovery from the COVID-19 using validated measurement tools. Follow-up and psychological support of the recovered men may help mend their moods and consequently upgrade their sexual functioning.


Author(s):  
Cody Callahan ◽  
Rose A. Lee ◽  
Ghee Rye Lee ◽  
Kate Zulauf ◽  
James E. Kirby ◽  
...  

The urgent need for large-scale diagnostic testing for SARS-CoV-2 has prompted interest in sample-collection methods of sufficient sensitivity to replace nasopharynx (NP) sampling. Nasal-swab samples are an attractive alternative; however, previous studies have disagreed over how nasal sampling performs relative to NP sampling. Here, we compared nasal vs. NP specimens collected by healthcare workers in a cohort of individuals clinically suspected of COVID-19 as well as SARS-CoV-2 RT-PCR positive outpatients undergoing follow-up. We compared subjects being seen for initial evaluation vs. follow-up, two different nasal-swab collection protocols, and three different transport conditions, including traditional viral transport media (VTM) and dry swabs, on 307 total study participants. We compared categorical results and viral loads to those from standard NP swabs collected at the same time from the same patients. All testing was performed by RT-PCR on the Abbott SARS-CoV-2 RealTime EUA (limit of detection [LoD], 100 copies viral genomic RNA/mL transport medium). We found low concordance overall, with Cohen’s kappa of 0.49, with high concordance only for subjects with very high viral loads. We found medium concordance for testing at initial presentation (κ=0.68), and very low concordance for followup testing (κ=0.27). Finally, we show that previous reports of high concordance may have resulted from measurement using assays with sensitivity ≥1,000 copies/mL. These findings suggest nasal-swab testing be used for situations in which viral load is expected to be high, as we demonstrate that nasal-swab testing is likely to miss patients with low viral loads.


2021 ◽  
Author(s):  
Carolin Bier ◽  
Anke Edelmann ◽  
Kathrin Theil ◽  
Rolf Schwarzer ◽  
Maria Deichner ◽  
...  

Background. SARS-CoV-2 causes COVID-19, which can be fatal and is responsible for a global pandemic. Variants with increased transmissibility or the potential to evade immunity have emerged and represent a threat to global pandemic control. Variants of concern (VOC) can be identified by sequencing of viral RNA, or by more rapid methods for detection of subsets of signature mutations. Methods. We developed a multiplex, real-time RT-PCR assay (cobas SARS-CoV-2 Variant Set 1) for the qualitative detection and differentiation of three key SARS-CoV-2 mutations in the viral spike protein: del 69-70, E484K and N501Y. Analytical sensitivity and accuracy were evaluated at three testing sites using clinical specimens from patients infected with SARS-CoV-2 variants belonging to several different lineages, including B.1.1.7, B.1.351, and P.1. Results. The limit of detection for E484K was between 180 and 620 IU/mL for the three different isolates tested. For N501Y, the LOD was between 270 and 720 IU/mL (five isolates), while for del 69-70, it was 80 - 92 IU/mL (two isolates). Valid test results were obtained with all clinical specimens that were positive using routine diagnostic tests. Compared to sequencing (Sanger and next-generation), test results were 100% concordant at all three loci; no false positive or false negative results were observed. Conclusions. Data collected at three independent laboratories indicates excellent performance and concordance of cobas SARS-CoV-2 Variant Set 1 with sequencing. New sets of primers and probes that target additional loci can be rapidly deployed in response to the identification of other emerging variants.


2007 ◽  
Vol 177 (4S) ◽  
pp. 360-360
Author(s):  
Ana Agud ◽  
Maria J. Ribal ◽  
Lourdes Mengual ◽  
Mercedes Marin-Aguilera ◽  
Laura Izquierdo ◽  
...  

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