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Fulltext A RT-PCR assay for the detection of coronaviruses from four genera

Xiu L, Binder RA, Alarja NA, Kochek K, Coleman KK, Than ST, et al.

J Clin Virol, 2020 07;128:104391.
PMID: 32403008 DOI: 10.1016/j.jcv.2020.104391

BACKGROUND: During the past two decades, three novel coronaviruses (CoVs) have emerged to cause international human epidemics with severe morbidity. CoVs have also emerged to cause severe epidemics in animals. A better understanding of the natural hosts and genetic diversity of CoVs are needed to help mitigate these threats.
OBJECTIVE: To design and evaluate a molecular diagnostic tool for detection and identification of all currently recognized and potentially future emergent CoVs from the Orthocoronavirinae subfamily.
STUDY DESIGN AND RESULTS: We designed a semi-nested, reverse transcription RT-PCR assay based upon 38 published genome sequences of human and animal CoVs. We evaluated this assay with 14 human and animal CoVs and 11 other non-CoV respiratory viruses. Through sequencing the assay's target amplicon, the assay correctly identified each of the CoVs; no cross-reactivity with 11 common respiratory viruses was observed. The limits of detection ranged from 4 to 4 × 102 copies/reaction, depending on the CoV species tested. To assess the assay's clinical performance, we tested a large panel of previously studied specimens: 192 human respiratory specimens from pneumonia patients, 5 clinical specimens from COVID-19 patients, 81 poultry oral secretion specimens, 109 pig slurry specimens, and 31 aerosol samples from a live bird market. The amplicons of all RT-PCR-positive samples were confirmed by Sanger sequencing. Our assay performed well with all tested specimens across all sample types.
CONCLUSIONS: This assay can be used for detection and identification of all previously recognized CoVs, including SARS-CoV-2, and potentially any emergent CoVs in the Orthocoronavirinae subfamily.

Matched MeSH terms: Pneumonia, Viral/diagnosis*
Fulltext A call for a global COVID-19 Neuro Research Coalition

Winkler AS, Knauss S, Schmutzhard E, Leonardi M, Padovani A, Abd-Allah F, et al.

Lancet Neurol, 2020 06;19(6):482-484.
PMID: 32470416 DOI: 10.1016/S1474-4422(20)30150-2
Matched MeSH terms: Pneumonia, Viral/diagnosis*
Fulltext A novel strategy for community screening of SARS-CoV-2 (COVID-19): Sample pooling method

Lim KL, Johari NA, Wong ST, Khaw LT, Tan BK, Chan KK, et al.

PLoS One, 2020;15(8):e0238417.
PMID: 32857823 DOI: 10.1371/journal.pone.0238417

The rapid global spread of the coronavirus disease (COVID-19) has inflicted significant health and socioeconomic burden on affected countries. As positive cases continued to rise in Malaysia, public health laboratories experienced an overwhelming demand for COVID-19 screening. The confirmation of positive cases of COVID-19 has solely been based on the detection of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) using real-time reverse transcription polymerase chain reaction (qRT-PCR). In efforts to increase the cost-effectiveness and efficiency of COVID-19 screening, we evaluated the feasibility of pooling clinical Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens during nucleic acid extraction without a reduction in sensitivity of qRT-PCR. Pools of 10 specimens were extracted and subsequently tested by qRT-PCR according to the WHO-Charité protocol. We demonstrated that the sample pooling method showed no loss of sensitivity. The effectiveness of the pooled testing strategy was evaluated on both retrospective and prospective samples, and the results showed a similar detection sensitivity compared to testing individual sample alone. This study demonstrates the feasibility of using a pooled testing strategy to increase testing capacity and conserve resources, especially when there is a high demand for disease testing.

Matched MeSH terms: Pneumonia, Viral/diagnosis*
Fulltext A woman with fever and cough: coronavirus disease 2019

Lu YQ

Intern Emerg Med, 2020 Nov;15(8):1553-1554.
PMID: 32232784 DOI: 10.1007/s11739-020-02321-3
Matched MeSH terms: Pneumonia, Viral/diagnosis*
Fulltext Aerosol-generating procedures in thoracic surgery in the COVID-19 era in Malaysia

Sathiamurthy N, Balasubbiah N, Dharmaraj B

Asian Cardiovasc Thorac Ann, 2020 Oct;28(8):495-499.
PMID: 32787442 DOI: 10.1177/0218492320950898

BACKGROUND: The Covid-19 pandemic has caused changes in the surgical treatment of non-Covid patients, especially in thoracic surgery because most procedures are aerosol generating. Hospital Kuala Lumpur, where thoracic procedures are performed, was badly affected. We describe our experience in performing aerosol generating procedures safely in thoracic surgery during the Covid-19 era.
METHODS: Medical records of patients who underwent thoracic surgery from March 18, 2020 to May 17, 2020 were reviewed retrospectively. All patients undergoing thoracic surgery were tested for Covid-19 using the reverse transcriptase polymerase chain reaction method. Patients with malignancy were observed for 10 to 14 days in the ward after testing negative. The healthcare workers donned personal protective equipment for all the cases, and the number of healthcare workers in the operating room was limited to the minimum required.
RESULTS: A total of 44 procedures were performed in 26 thoracic surgeries. All of these procedures were classified as aerosol generating, and the mean duration of the surgery was 130 ± 43 minutes. None of the healthcare workers involved in the surgery were exposed or infected by Covid-19.
CONCLUSION: Covid-19 will be a threat for a long time and thoracic surgeons must continue to provide their services, despite having to deal with aerosol generating procedures, in the new normal. Covid-19 testing of all surgical candidates, using the reverse transcriptase polymerase chain reaction, donning full personal protective equipment for healthcare workers, and carefully planned procedures are among the measures suggested to prevent unnecessary Covid-19 exposure in thoracic surgery.

Matched MeSH terms: Pneumonia, Viral/diagnosis
Fulltext All together to Fight COVID-19

Momtazmanesh S, Ochs HD, Uddin LQ, Perc M, Routes JM, Vieira DN, et al.

Am J Trop Med Hyg, 2020 06;102(6):1181-1183.
PMID: 32323644 DOI: 10.4269/ajtmh.20-0281

Novel coronavirus disease (COVID-19), named a pandemic by the WHO, is the current global health crisis. National and international collaboration are indispensable for combating COVID-19 and other similar potential outbreaks. International efforts to tackle this complex problem have led to remarkable scientific advances. Yet, as a global society, we can and must take additional measures to fight this pandemic. Undoubtedly, our approach toward COVID-19 was not perfect, and testing has not been deployed fast enough to arrest the epidemic early on. It is critical that we revise our approaches to be more prepared for pandemics as a united body by promoting global cooperation and commitment.

Matched MeSH terms: Pneumonia, Viral/diagnosis
Fulltext An Overview of Deep Learning Techniques on Chest X-Ray and CT Scan Identification of COVID-19

Serena Low WC, Chuah JH, Tee CATH, Anis S, Shoaib MA, Faisal A, et al.

Comput Math Methods Med, 2021;2021:5528144.
PMID: 34194535 DOI: 10.1155/2021/5528144

Pneumonia is an infamous life-threatening lung bacterial or viral infection. The latest viral infection endangering the lives of many people worldwide is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19. This paper is aimed at detecting and differentiating viral pneumonia and COVID-19 disease using digital X-ray images. The current practices include tedious conventional processes that solely rely on the radiologist or medical consultant's technical expertise that are limited, time-consuming, inefficient, and outdated. The implementation is easily prone to human errors of being misdiagnosed. The development of deep learning and technology improvement allows medical scientists and researchers to venture into various neural networks and algorithms to develop applications, tools, and instruments that can further support medical radiologists. This paper presents an overview of deep learning techniques made in the chest radiography on COVID-19 and pneumonia cases.

Matched MeSH terms: Pneumonia, Viral/diagnosis
Fulltext Application of deep learning technique to manage COVID-19 in routine clinical practice using CT images: Results of 10 convolutional neural networks

Ardakani AA, Kanafi AR, Acharya UR, Khadem N, Mohammadi A

Comput Biol Med, 2020 06;121:103795.
PMID: 32568676 DOI: 10.1016/j.compbiomed.2020.103795

Fast diagnostic methods can control and prevent the spread of pandemic diseases like coronavirus disease 2019 (COVID-19) and assist physicians to better manage patients in high workload conditions. Although a laboratory test is the current routine diagnostic tool, it is time-consuming, imposing a high cost and requiring a well-equipped laboratory for analysis. Computed tomography (CT) has thus far become a fast method to diagnose patients with COVID-19. However, the performance of radiologists in diagnosis of COVID-19 was moderate. Accordingly, additional investigations are needed to improve the performance in diagnosing COVID-19. In this study is suggested a rapid and valid method for COVID-19 diagnosis using an artificial intelligence technique based. 1020 CT slices from 108 patients with laboratory proven COVID-19 (the COVID-19 group) and 86 patients with other atypical and viral pneumonia diseases (the non-COVID-19 group) were included. Ten well-known convolutional neural networks were used to distinguish infection of COVID-19 from non-COVID-19 groups: AlexNet, VGG-16, VGG-19, SqueezeNet, GoogleNet, MobileNet-V2, ResNet-18, ResNet-50, ResNet-101, and Xception. Among all networks, the best performance was achieved by ResNet-101 and Xception. ResNet-101 could distinguish COVID-19 from non-COVID-19 cases with an AUC of 0.994 (sensitivity, 100%; specificity, 99.02%; accuracy, 99.51%). Xception achieved an AUC of 0.994 (sensitivity, 98.04%; specificity, 100%; accuracy, 99.02%). However, the performance of the radiologist was moderate with an AUC of 0.873 (sensitivity, 89.21%; specificity, 83.33%; accuracy, 86.27%). ResNet-101 can be considered as a high sensitivity model to characterize and diagnose COVID-19 infections, and can be used as an adjuvant tool in radiology departments.

Matched MeSH terms: Pneumonia, Viral/diagnosis*
COVID-19 - How prepared are emergency departments in embracing the new norm?

Iqhbal KM, Ahmad NH

Med J Malaysia, 2020 09;75(5):585-586.
PMID: 32918431

No abstract provided.

Matched MeSH terms: Pneumonia, Viral/diagnosis
COVID-19 detected from targeted contact tracing, attempting to see the pattern in random happenings: early lessons in Malaysia

Ng BH, Andrea YLB, Nuratiqah NA, Faisal AH, Soo CI, Najma K, et al.

Med J Malaysia, 2020 09;75(5):582-584.
PMID: 32918430

The world feels strange as we face what is for most of us our first ever pandemic. The number of newly diagnosed cases rises daily in many parts of the world, and we are faced with the reality that there are still many things to learn about this new disease. We share here our experience of treating our first 199 COVID-19 patients in the Hospital Canselor Tuanku Muhriz, Pusat Perubatan Universiti Kebangsaan Malaysia (PPUKM).

Matched MeSH terms: Pneumonia, Viral/diagnosis*
Fulltext Call to Action: SARS-CoV-2 and CerebrovAscular DisordErs (CASCADE)

Abootalebi S, Aertker BM, Andalibi MS, Asdaghi N, Aykac O, Azarpazhooh MR, et al.

J Stroke Cerebrovasc Dis, 2020 Sep;29(9):104938.
PMID: 32807412 DOI: 10.1016/j.jstrokecerebrovasdis.2020.104938

BACKGROUND AND PURPOSE: The novel severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), now named coronavirus disease 2019 (COVID-19), may change the risk of stroke through an enhanced systemic inflammatory response, hypercoagulable state, and endothelial damage in the cerebrovascular system. Moreover, due to the current pandemic, some countries have prioritized health resources towards COVID-19 management, making it more challenging to appropriately care for other potentially disabling and fatal diseases such as stroke. The aim of this study is to identify and describe changes in stroke epidemiological trends before, during, and after the COVID-19 pandemic.
METHODS: This is an international, multicenter, hospital-based study on stroke incidence and outcomes during the COVID-19 pandemic. We will describe patterns in stroke management, stroke hospitalization rate, and stroke severity, subtype (ischemic/hemorrhagic), and outcomes (including in-hospital mortality) in 2020 during COVID-19 pandemic, comparing them with the corresponding data from 2018 and 2019, and subsequently 2021. We will also use an interrupted time series (ITS) analysis to assess the change in stroke hospitalization rates before, during, and after COVID-19, in each participating center.
CONCLUSION: The proposed study will potentially enable us to better understand the changes in stroke care protocols, differential hospitalization rate, and severity of stroke, as it pertains to the COVID-19 pandemic. Ultimately, this will help guide clinical-based policies surrounding COVID-19 and other similar global pandemics to ensure that management of cerebrovascular comorbidity is appropriately prioritized during the global crisis. It will also guide public health guidelines for at-risk populations to reduce risks of complications from such comorbidities.

Matched MeSH terms: Pneumonia, Viral/diagnosis
Fulltext Cardiovascular Disease and Use of Renin-Angiotensin System Inhibitors in COVID-19

Kow CS, Zaidi STR, Hasan SS

Am J Cardiovasc Drugs, 2020 Jun;20(3):217-221.
PMID: 32281055 DOI: 10.1007/s40256-020-00406-0

There is ongoing debate on the safety of renin-angiotensin system (RAS) inhibitors in COVID-19. Recently published studies highlight a potential relationship between cardiovascular disease (CVD) and COVID-19. This article aims to summarize the evidence on the use of RAS inhibitors in CVD patients with COVID-19, focusing on safety issues of the RAS inhibitors and their relationship with COVID-19.

Matched MeSH terms: Pneumonia, Viral/diagnosis
Challenges of Covid-19 testing

Tan GC, Cheong SK

Malays J Pathol, 2020 Apr;42(1):1.
PMID: 32342925

No abstract available.

Matched MeSH terms: Pneumonia, Viral/diagnosis*
Fulltext Clinical characteristics of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV2) patients in Hospital Tengku Ampuan Afzan

Soh TV, Dzawani M, Noorlina N, Nik F, Norazmi A

Med J Malaysia, 2020 09;75(5):479-484.
PMID: 32918413

BACKGROUND: The COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aims to describe the clinical characteristics of COVID-19 patients admitted to Hospital Tengku Ampuan Afzan (HTAA), Pahang, Malaysia and to identify the clinical and laboratory markers for severe disease, complications and virologic clearance according to clinical staging.

METHODS: This was a single-centre, retrospective, descriptive study. All COVID-19 patients admitted to HTAA from March 9 to April 15, 2020, were included in the study. Patients were categorised according to clinical staging. Data obtained from the medical report includes baseline characteristics of patients, comorbidities, presenting symptoms, laboratory findings, treatments, complications, and outcomes.

RESULTS: Of the total of 247 patients hospitalised, the majority consisted at clinical-stage 1 (43%) and stage 2 (39%) disease. Older patients, diabetes mellitus, hypertension, cardiovascular diseases, and chronic kidney disease were found more common among patients with severe disease. Fever was uncommon and the majority had normal haemoglobin levels, white cell counts, and platelet counts. C-reactive protein (CRP) was found statistically significant to predict pneumonia or hypoxia at a cut-off value of 14mg/L (sensitivity 73.8%, specificity 91.3%) and 50mg/L (sensitivity 100%, specificity 96.4%) respectively. Pneumonia was mostly diagnosed radiologically using chest radiography, especially among clinical stage 3. Acute kidney injury (AKI) was a significant complication, with 31% of clinical stage 3 and above developed AKI and 44% of them requiring haemodialysis. Median virologic clearance time was 15 days from onset of illness, and asymptomatic patients had longer clearance time.

CONCLUSION: COVID-19 presented with a wide spectrum of clinical patterns. CRP was a valuable predictor of severe disease. In this study risk and severity of acute kidney injury were found to be higher. A longer duration of virologic clearance was observed among the asymptomatic patients.

Matched MeSH terms: Pneumonia, Viral/diagnosis*
Diagnostic performance of COVID-19 serology assays

Zainol Rashid Z, Othman SN, Abdul Samat MN, Ali UK, Wong KK

Malays J Pathol, 2020 Apr;42(1):13-21.
PMID: 32342927

INTRODUCTION: The World Health Organization (WHO) declared COVID-19 outbreak as a world pandemic on 12th March 2020. Diagnosis of suspected cases is confirmed by nucleic acid assays with real-time PCR, using respiratory samples. Serology tests are comparatively easier to perform, but their utility may be limited by the performance and the fact that antibodies appear later during the disease course. We aimed to describe the performance data on serological assays for COVID-19.
MATERIALS AND METHODS: A review of multiple reports and kit inserts on the diagnostic performance of rapid tests from various manufacturers that are commercially available were performed. Only preliminary data are available currently.
RESULTS: From a total of nine rapid detection test (RDT) kits, three kits offer total antibody detection, while six kits offer combination SARS-CoV-2 IgM and IgG detection in two separate test lines. All kits are based on colloidal gold-labeled immunochromatography principle and one-step method with results obtained within 15 minutes, using whole blood, serum or plasma samples. The sensitivity for both IgM and IgG tests ranges between 72.7% and 100%, while specificity ranges between 98.7% to 100%. Two immunochromatography using nasopharyngeal or throat swab for detection of COVID-19 specific antigen are also reviewed.
CONCLUSIONS: There is much to determine regarding the value of serological testing in COVID-19 diagnosis and monitoring. More comprehensive evaluations of their performance are rapidly underway. The use of serology methods requires appropriate interpretations of the results and understanding the strengths and limitations of such tests.

Matched MeSH terms: Pneumonia, Viral/diagnosis*
Fulltext Diagnostic techniques for COVID-19 and new developments

Sheikhzadeh E, Eissa S, Ismail A, Zourob M

Talanta, 2020 Dec 01;220:121392.
PMID: 32928412 DOI: 10.1016/j.talanta.2020.121392

COVID-19 pandemic is a serious global health issue today due to the rapid human to human transmission of SARS-CoV-2, a new type of coronavirus that causes fatal pneumonia. SARS -CoV-2 has a faster rate of transmission than other coronaviruses such as SARS and MERS and until now there are no approved specific drugs or vaccines for treatment. Thus, early diagnosis is crucial to prevent the extensive spread of the disease. The reverse transcription-polymerase chain reaction (RT-PCR) is the most routinely used method until now to detect SARS-CoV-2 infections. However, several other faster and accurate assays are being developed for the diagnosis of COVID-19 aiming to control the spread of infection through the identification of patients and immediate isolation. In this review, we will discuss the various detection methods of the SARS-CoV-2 virus including the recent developments in immunological assays, amplification techniques as well as biosensors.

Matched MeSH terms: Pneumonia, Viral/diagnosis*
Fulltext Early experience with universal preoperative and pre-procedural screening for COVID-19 in low-risk pediatric surgical patients requiring general anesthesia

Sii CKS, Lee JA, Nah SA

Pediatr Surg Int, 2020 Dec;36(12):1407-1411.
PMID: 33068142 DOI: 10.1007/s00383-020-04760-7

PURPOSE: The COVID-19 pandemic has placed extraordinary demands on healthcare services worldwide. Some have reported increased viral transmission to healthcare workers during aerosol-generating procedures such as intubation. We report our experience with universal preoperative and preprocedural screening for COVID-19 in children requiring general anaesthesia with low risk of having the infection.
METHODS: This was a data review involving children aged

Matched MeSH terms: Pneumonia, Viral/diagnosis*
Fulltext Forecasting daily confirmed COVID-19 cases in Malaysia using ARIMA models

Singh S, Murali Sundram B, Rajendran K, Boon Law K, Aris T, Ibrahim H, et al.

J Infect Dev Ctries, 2020 09 30;14(9):971-976.
PMID: 33031083 DOI: 10.3855/jidc.13116

INTRODUCTION: The novel coronavirus infection has become a global threat affecting almost every country in the world. As a result, it has become important to understand the disease trends in order to mitigate its effects. The aim of this study is firstly to develop a prediction model for daily confirmed COVID-19 cases based on several covariates, and secondly, to select the best prediction model based on a subset of these covariates.
METHODOLOGY: This study was conducted using daily confirmed cases of COVID-19 collected from the official Ministry of Health, Malaysia (MOH) and John Hopkins University websites. An Autoregressive Integrated Moving Average (ARIMA) model was fitted to the training data of observed cases from 22 January to 31 March 2020, and subsequently validated using data on cases from 1 April to 17 April 2020. The ARIMA model satisfactorily forecasted the daily confirmed COVID-19 cases from 18 April 2020 to 1 May 2020 (the testing phase).
RESULTS: The ARIMA (0,1,0) model produced the best fit to the observed data with a Mean Absolute Percentage Error (MAPE) value of 16.01 and a Bayes Information Criteria (BIC) value of 4.170. The forecasted values showed a downward trend of COVID-19 cases until 1 May 2020. Observed cases during the forecast period were accurately predicted and were placed within the prediction intervals generated by the fitted model.
CONCLUSIONS: This study finds that ARIMA models with optimally selected covariates are useful tools for monitoring and predicting trends of COVID-19 cases in Malaysia.

Matched MeSH terms: Pneumonia, Viral/diagnosis
Fulltext Management of the dead during COVID-19 outbreak in Malaysia

Khoo LS, Hasmi AH, Ibrahim MA, Mahmood MS

Forensic Sci Med Pathol, 2020 09;16(3):463-470.
PMID: 32519316 DOI: 10.1007/s12024-020-00269-6

The emergence of a novel human coronavirus, SARS-CoV-2, causing severe respiratory tract infections in humans, is affecting all countries of the world and has become a global health concern. Since the virus was first identified in December 2019, the number of deaths have been propagating exponentially, causing countries across the world, including Malaysia, to increase emergency measures to combat the virus. Due to the fact that the COVID-19 pandemic does not discriminate its victims, it is of paramount importance to construct a plan for management of the dead for all suspected or confirmed COVID-19 cases, including the unidentified deceased, as an essential portion of the humanitarian forensic action approach. This document provides an overview on ways to maximize the local collective capacity from various government agencies to manage the dead based on the prevailing regulations and legislation in the country, in preparation for possible large scale deaths from this pandemic. The National Institute of Forensic Medicine Malaysia has improvised procedures and guidelines for management of the dead within the existing regulations in order to achieve a balance between medicolegal requirements and the safety of personnel managing the bodies of the deceased with suspected or confirmed COVID-19 infection; at the site of death, during transport, during postmortem procedures, storage and preparation before and during burial or cremation as well as environmental cleaning and disinfection, involving various agencies in the country. A form of temporary controlled burial is as an option to allow the reinvestigation of a decedent to help formally identify victims of the pandemic such as undocumented migrants or refugees who were previously not identified. Due to the different legal requirements and mortality rates between countries, there is no one-size-fits-all approach to the management of the dead. Whenever possible, every opportunity and assistance must be given to families to mourn their loved ones, even in times of crisis or an outbreak, in order to sustain an appropriate level of dignity and respect.

Matched MeSH terms: Pneumonia, Viral/diagnosis
Fulltext Nipah@20: Lessons Learned from Another Virus with Pandemic Potential

Gómez Román R, Wang LF, Lee B, Halpin K, de Wit E, Broder CC, et al.

mSphere, 2020 07 08;5(4).
PMID: 32641430 DOI: 10.1128/mSphere.00602-20

Nipah disease is listed as one of the WHO priority diseases that pose the greatest public health risk due to their epidemic potential. More than 200 experts from around the world convened in Singapore last year to mark the 20th anniversary of the first Nipah virus outbreaks in Malaysia and Singapore. Most of these experts are now involved in responding to the coronavirus disease 2019 (COVID-19) pandemic. Here, members of the Organizing Committee of the 2019 Nipah Virus International Conference review highlights from the Nipah@20 Conference and reflect on key lessons learned from Nipah that could be applied to the understanding of the COVID-19 pandemic and to preparedness against future emerging infectious diseases (EIDs) of pandemic potential.

Matched MeSH terms: Pneumonia, Viral/diagnosis

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