scholarly journals Practical laboratory considerations amidst the COVID-19 outbreak: early experience from Singapore

2020 ◽  
pp. jclinpath-2020-206563 ◽  
Author(s):  
Shaun S Tan ◽  
Benedict Yan ◽  
Sharon Saw ◽  
Chun Kiat Lee ◽  
Ai Teng Chong ◽  
...  
Keyword(s):  
Distress Syndrome ◽  
Early Experience ◽  
Turnaround Time ◽  
World Health ◽  
Health Ministry ◽  
Routine Testing ◽  
Reverse Transcription Pcr ◽  
Total Testing Process ◽  
Health Organization ◽  
Suspected Pneumonia

The coronavirus disease 2019 (COVID-19) is a zoonotic viral infection originating from Wuhan, China in December 2019. The World Health Organization has classified this pandemic as a global health emergency due to its virulent nature of transmission, which may lead to acute respiratory distress syndrome. Singapore’s health ministry has responded with enhanced surveillance of COVID-19 for all suspected pneumonia cases, further increasing the volume of testing via real-time reverse transcription PCR, as well as samples necessitating stringent infectious control. Collectively, this has implications on the total testing process, laboratory operations and its personnel due to biosafety concerns. Turnaround time for routine testing may also be affected. The aim of this article is to present our tertiary institution’s early experience with managing this emerging crisis and offer practical considerations for the preanalytical, analytical and postanalytical phases of laboratory testing in this cohort of patients.

scholarly journals Rapid and simultaneous identification of three mutations by the Novaplex™ SARS-CoV-2 Variants I Assay kit

2021 ◽  
Author(s):  
Wakaki Kami ◽  
Takeshi Kinjo ◽  
Wakako Arakaki ◽  
Hiroya Oki ◽  
Daisuke Motooka ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Cost Effective ◽  
Turnaround Time ◽  
World Health ◽  
Consensus Sequences ◽  
Reverse Transcription Pcr ◽  
Multiple Regions ◽  
Differential Identification ◽  
Health Organization ◽  
User Friendly

AbstractBackgroundThe emergence of SARS-CoV-2 variants has caused an unexpected rebound globally. The World Health Organization has listed three variants (B.1.1.7, B.1.351, and P.1) as variants of concern. To understand the epidemiology and thereby plan appropriate safety measures, differential identification of the variants is indeed critical.ObjectivesAlthough whole-genome sequencing is the gold standard for variant identification, it is time-consuming and relatively expensive. Therefore, a rapid, easy, and cost-effective platform targeting multiple regions of the genome is required. Here, we assessed the usefulness of the Novaplex™ SARS-CoV-2 Variants I Assay kit in identifying mutations in the variants.Study designWe retrospectively examined 30 stored nasal swabs from COVID-19-positive patients tested between November 2020 and March 2021. RNA extracted from these swabs was subjected to the commercial kit and real-time reverse transcription-PCR was performed. To determine the genome sequences of SARS-CoV-2 in the collected samples and deduce the consensus sequences among the identified variants, genome sequencing libraries were prepared and mapped to the reference genome.ResultsFour of the tested samples were determined as variants. Of them, two harbored both H69/V70 deletion and N501Y substitution, whereas two harbored E484K substitution alone.ConclusionsThe variant with E484K substitution alone (“R.1”) has been now categorized as a variant of interest in Japan. Additionally, the kit-based assay was found to be feasible, convenient, and user-friendly in identifying the abovementioned mutations with a turnaround time of only 2 hours.

scholarly journals A 3D-printed magnetic digital microfluidic diagnostic platform for rapid colorimetric sensing of carbapenemase-producing Enterobacteriaceae

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Pojchanun Kanitthamniyom ◽  
Pei Yun Hon ◽  
Aiwu Zhou ◽  
Mohammad Yazid Abdad ◽  
Zhi Yun Leow ◽  
...  
Keyword(s):  
Point Of Care ◽  
Resistance Mechanism ◽  
Turnaround Time ◽  
World Health ◽  
Colorimetric Sensing ◽  
Resource Limited ◽  
Reaction Chambers ◽  
Technological Platform ◽  
Health Organization ◽  
Digital Microfluidic

AbstractCarbapenemase-producing Enterobacteriaceae (CPE) are a group of drug-resistant Gram-negative pathogens that are classified as a critical threat by the World Health Organization (WHO). Conventional methods of detecting antibiotic-resistant pathogens do not assess the resistance mechanism and are often time-consuming and laborious. We have developed a magnetic digital microfluidic (MDM) platform, known as MDM Carba, for the identification of CPE by measuring their ability to hydrolyze carbapenem antibiotics. MDM Carba offers the ability to rapidly test CPE and reduce the amount of reagents used compared with conventional phenotypic testing. On the MDM Carba platform, tests are performed in droplets that function as reaction chambers, and fluidic operations are accomplished by manipulating these droplets with magnetic force. The simple droplet-based magnetic fluidic operation allows easy system automation and simplified hands-on operation. Because of the unique “power-free” operation of MDM technology, the MDM Carba platform can also be operated manually, showing great potential for point-of-care testing in resource-limited settings. We tested 27 bacterial isolates on the MDM Carba platform, and the results showed sensitivity and specificity that were comparable to those of the widely used Carba NP test. MDM Carba may shorten the overall turnaround time for CPE identification, thereby enabling more timely clinical decisions for better clinical outcomes. MDM Carba is a technological platform that can be further developed to improve diagnostics for other types of antibiotic resistance with minor modifications.

OBESITY IN SARS-COV-2 INFECTION: LITERATURE REVIEW

2021 ◽  
pp. 19-23
Author(s):  
Donizete Tavares Da Silva ◽  
Priscila De Sousa Barros Lima ◽  
Renato Sampaio Mello Neto ◽  
Gustavo Magalhães Valente ◽  
Débora Dias Cabral ◽  
...  
Keyword(s):  
Public Health ◽  
Acute Respiratory Distress Syndrome ◽  
Gastrointestinal Tract ◽  
Severe Acute Respiratory Syndrome ◽  
Distress Syndrome ◽  
Circulatory System ◽  
World Health ◽  
Global Public Health ◽  
The World ◽  
Health Organization

In March 2020, the World Health Organization (1) declared COVID-19 as a pandemic and a threat to global public health (2). The virus mainly affects the lungs and can cause acute respiratory distress syndrome (ARDS). In addition, coronavirus 2 severe acute respiratory syndrome (SARSCOV2) also has devastating effects on other important organs, including the circulatory system, brain, gastrointestinal tract, kidneys and liver

scholarly journals How to Control Covid-19 with a Nanobiotherapy?

2020 ◽  
Keyword(s):  
Intensive Care Unit ◽  
Immune Response ◽  
Acute Respiratory Distress Syndrome ◽  
Distress Syndrome ◽  
Multiple Organ ◽  
World Health ◽  
Shortness Of Breath ◽  
The World ◽  
Health Organization ◽  
Muscle Ache

The outbreak of emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) in China has been brought to global attention and declared a pandemic by the World Health Organization (WHO) on March 11, 2020. In a recent study of Nanshan Chen et al., on patients of Wuhan Jinyintan Hospital, Wuhan, China, from the 99 patients with SARSCoV-2 infection, 51% had chronic diseases and they had symptoms of fever (83%), cough (82%) shortness of breath (31%), muscle ache (11%), fatigue (9%), headache (8%), sore throat (5%), rhinorrhea (4%), chest pain (2%), diarrhea (2%), and nausea and vomiting (1%) [1, 2]. The majority of patients can recover, however, about 25% of patients will progress into severe complications including acute respiratory distress syndrome (ARDS), which may worsen rapidly into respiratory failure, need an intensive care unit (ICU) and even cause multiple organ failure [3]. Depending on the pathophysiological mechanisms supposed to be involved in the development of the various clinical forms of the disease, various types of treatment have been tested with varying degrees of success. We have developed a nanotherapy to block the entry of the virus into the host cell, to reduce its potential for replication and to regulate the immune response against the microbial aggressor [4].

scholarly journals COVID-19- or Tramadol-induced Seizure: A Differential Diagnosis in Young People

2020 ◽  
Vol 10 (4) ◽  
pp. 32009.1-32009.2
Author(s):  
Solmaz Nekoueifard ◽  
◽  
Mohammad Majidi ◽  
Keyword(s):  
Myocardial Infarction ◽  
Acute Kidney Injury ◽  
Differential Diagnosis ◽  
Acute Respiratory Distress Syndrome ◽  
Distress Syndrome ◽  
Kidney Injury ◽  
World Health ◽  
The World ◽  
Life Threatening ◽  
Health Organization

Coronavirus disease 2019 (COVID-19) was first declared in December 2019 from Wuhan, China [1, 2]. It then has been reported a pandemic in March 2020 by the World Health Organization [3]. Clinical features of COVID-19 are different from asymptomatic to mild to moderate symptoms, such as fever, headache, myalgia, sore throat, anosmia, cough, fatigue headache, hemoptysis, and dyspnea to the life-threatening complications, including shock, pneumonia, acute respiratory distress syndrome, myocarditis, myocardial infarction, acute kidney injury, multi-organ failure, and even death [1, 2].

scholarly journals Childbirth care: contributing to the debate on human development

2007 ◽  
Vol 15 (spe) ◽  
pp. 792-798 ◽  
Author(s):  
Cristina Maria Garcia de Lima Parada ◽  
Maria Antonieta de Barros Leite Carvalhaes
Keyword(s):  
Health Services ◽  
Health System ◽  
Human Development ◽  
Quality Care ◽  
Mortality Rates ◽  
World Health ◽  
Health Ministry ◽  
Public Resources ◽  
Health Organization ◽  
Childbirth Care

This study aimed to evaluate care during childbirth and neonatal development in the interior of São Paulo in order to support managers responsible for formulating public policies on human development and allocating public resources to the women's healthcare. This epidemiological study focused on the evaluation of health services based on the observation of the assistance delivered by the Single Health System in 12 maternities and 134 delivers. The Brazilian Health Ministry or World Health Organization standards were adopted for comparison. The results revealed problems related to the structure of some maternities, where some well-proven practices in normal childbirth are still little used, whereas other prejudicial or ineffective ones are routinely used. Reversing this picture is essential in order to offer humanized quality care to women with consequent reductions in maternal and neonatal mortality rates, in such a way that the region achieves the millennium goals established for improving human development.

scholarly journals A novel point mutation in the N gene of SARS-CoV-2 may affect the detection of the virus by RT-qPCR

2021 ◽  
Author(s):  
Mohammad Rubayet Hasan ◽  
Sathyavathi Sundararaju ◽  
Chidambaram Manickam ◽  
Faheem Mirza ◽  
Hamad Al-Hail ◽  
...  
Keyword(s):  
Viral Genome ◽  
Large Scale ◽  
Target Genes ◽  
Cytidine Deaminase ◽  
World Health ◽  
N Gene ◽  
Single Nucleotide ◽  
E Gene ◽  
Reverse Transcription Pcr ◽  
Health Organization

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, laboratory testing to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription PCR (RT-qPCR) has played a central role in mitigating the spread of the virus (1). Soon after the viral genome sequences were available, several RT-qPCR assays were developed and made available by World Health Organization (WHO) for public use (https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf). The primer and probe sequences for these assays were chosen from multiple target genes within the viral genome such as the E gene, RdRp gene, ORF1ab and N gene. Many commercial and laboratory-developed assays were developed for SARS-CoV-2 detection based on these primer and probe sequences. The large-scale sustained person-to-person transmission of SARS-CoV-2 has led to many mutational events, some of which may affect the sensitivity and specificity of available PCR assays (2). Recently, mutations in the E gene (C26340T) and N gene (C29200T) were reported affecting the detection of target genes by two commercial assays in 8 and 1 patients, respectively. Interestingly, both mutations are of C>T type, a common single nucleotide polymorphism (SNP) that may be associated with strong host cell mRNA editing mechanisms known as APOBEC cytidine deaminase (3, 4). Another study found a G to U substitution in position 29140 that affected the sensitivity of detection of N gene-based assays (5). Here we report a novel N gene mutation (C29200A) seen in 3 patients, which affected the detection of SARS-CoV-2 N gene by a commercial assay.

scholarly journals The Pandemic Hits Us Hard, but We Don’t Lose Hope

2021 ◽  
Vol 2 (1) ◽  
pp. 1-4
Author(s):  
Krisna Yuarno Phatama ◽  
Sholahuddin Rhatomy, MD ◽  
Asep Santoso ◽  
Nicolaas C. Budhiparama
Keyword(s):  
Acute Respiratory Distress Syndrome ◽  
Severe Acute Respiratory Syndrome ◽  
Respiratory Distress Syndrome ◽  
Respiratory Distress ◽  
World Health Organization ◽  
Distress Syndrome ◽  
World Health ◽  
Global Pandemic ◽  
New Variant ◽  
Health Organization

At the end of 2019, we faced a new variant of the coronavirus that can cause pneumonia and acute respiratory distress syndrome-like symptoms. It started in Wuhan, Hubei Province, China, and spread quickly to the whole world.This new virus is called Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and can manifest as a disease called coronavirus disease 2019 (COVID-19). On March 13th, 2020 World Health Organization (WHO) declared COVID-19 as a global pandemic, and the story of frightening pandemic begin.

scholarly journals Evaluation of WHO listed COVID-19 qPCR primers and probe in silico with 375 SERS-CoV-2 full genome sequences

2020 ◽  
Author(s):  
Derek Toms ◽  
Julang Li ◽  
Hugh Y. Cai
Keyword(s):  
In Silico ◽  
Sequence Data ◽  
World Health ◽  
Sequence Information ◽  
Genome Sequences ◽  
Qrt Pcr ◽  
Reverse Transcription Pcr ◽  
Successful Design ◽  
Pcr Assays ◽  
Health Organization

AbstractQuantitative reverse-transcription PCR (qRT-PCR) assays remains the gold standard for detection of the SARS-CoV-2 virus because of its sensitivity and specificity. However, successful design of qRT-PCR assays requires accurate viral genome sequences. With mutations accumulating as the virus is transmitted globally, we sought to compare current assays recommended by the World Health Organization with available SARS-CoV-2 genomic sequences in silico. While most sequences were conserved, there were notable mismatches, particularly in assays developed using early sequences when compared to more recent isolates. We recommend that any assay being evaluated for diagnostic tests be compared with prevalent sequence data from the region of proposed testing and that continued publicly accessible sequence information continue to be provided by the research community.

A New Method for Estimating the Incidence of Infectious Diseases

2021 ◽  
Author(s):  
Hamish McManus ◽  
Denton Callander ◽  
Jason Asselin ◽  
James McMahon ◽  
Jennifer F Hoy ◽  
...  
Keyword(s):  
Incidence Rates ◽  
World Health ◽  
Hiv Incidence ◽  
Routine Testing ◽  
Uniform Probability ◽  
Immunodeficiency Virus ◽  
Incidence Estimation ◽  
Baseline Incidence ◽  
Low Incidence ◽  
Health Organization

Abstract Ambitious World Health Organization targets for disease elimination require monitoring of epidemics using routine health data in settings of decreasing and low incidence. We evaluated two methods commonly applied to routine testing results to estimate incidence rates that assume uniform probability of infection between consecutive negative and positive tests based on: 1. the midpoint of this interval; and 2. a randomly selected point on this interval. We compared these with an approximation to the Poisson-binomial distribution which assigns partial incidence to time-periods based on the uniform probability of occurrence in these intervals. We assessed bias, variance and convergence of estimates using simulations of Weibull distributed failure times with systematically varied baseline incidence, and varying trend. We considered results for quarterly, half-yearly and yearly incidence estimation frequencies. We applied methods to assess human immunodeficiency virus (HIV) incidence in HIV-negative patients from the Treatment with Antiretrovirals and their Impact on Positive And Negative men study between 2012 and 2018. The Poisson-binomial method had reduced bias and variance at low levels of incidence and for increased estimation frequency, with increased consistency of estimation. Application of methods to real-world assessment of HIV incidence found decreased variance in Poisson-binomial model estimates, with observed incidence declining to levels where simulation results had indicated bias in midpoint and random-point methods.

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