scholarly journals A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades

2020 ◽  
Author(s):  
Md. Tanvir Islam ◽  
A. S. M. Rubayet Ul Alam ◽  
Najmuj Sakib ◽  
Md. Shazid Hasan ◽  
Tanay Chakrovarty ◽  
...  
Keyword(s):  
Low Income ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Epidemiological Surveillance ◽  
Low Income Countries ◽  
Amplification Refractory Mutation System ◽  
Pcr Assay ◽  
Maximum Resolution ◽  
Arms Pcr ◽  
Mutation System

SummaryTracing the globally circulating SARS-CoV-2 mutants is essential for the outbreak alerts and far-reaching epidemiological surveillance. The available technique to identify the phylogenetic clades through high-throughput sequencing is costly, time-consuming, and labor-intensive that hinders the viral genotyping in low-income countries. Here, we propose a rapid, simple and cost-effective amplification-refractory mutation system (ARMS)-based multiplex reverse-transcriptase PCR assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. This approach is applied on 24 COVID-19 positive samples as confirmed by CDC approved real-time PCR assay for SARS-CoV-2. Our multiplex PCR is designed in a mutually exclusive way to identify V-S and G-GH-GR clade variants separately. The pentaplex assay included all five variants and the quadruplex comprised of the triplex variants alongside either V or S clade mutations that created two separate subsets. The procedure was optimized in the primer concentration (0.2-0.6 µM) and annealing temperature (56-60°C) of PCR using 3-5 ng/µl cDNA template synthesized upon random- and oligo(dT)-primer based reverse transcription. The different primer concentration for the triplex and quadruplex adjusted to different strengths ensured an even amplification with a maximum resolution of all targeted amplicons. The targeted Sanger sequencing further confirmed the presence of the clade-featured mutations with another set of our designed primers. This multiplex ARMS-PCR assay is sample, cost-effective, and convenient that can successfully discriminate the circulating phylogenetic clades of SARS-CoV-2.

scholarly journals Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern

2022 ◽  
Author(s):  
Dongyan Xiong ◽  
Xiaoxu Zhang ◽  
Mengjuan Shi ◽  
Nuo Wang ◽  
Ping He ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Reverse Transcription ◽  
Cost Effective ◽  
Amplification Refractory Mutation System ◽  
Pcr Assay ◽  
High Quality ◽  
Reverse Transcription Pcr ◽  
Mutation System ◽  
The Common ◽  
Current Stage

The current stage of the pandemic, led by SARS-CoV-2 variants of concern (VOCs), underscores the necessity to develop a cost-effective and rapid molecular diagnosis assay to differentiate the VOCs. In this study, over 1 million SARS-CoV-2 genomic sequences of high quality from GISAID were analyzed and a network of the common mutations of the lineages was constructed.

scholarly journals Aptamer-Based Diagnostic Systems for the Rapid Screening of TB at the Point-of-Care

Diagnostics ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1352
Author(s):  
Darius Riziki Martin ◽  
Nicole Remaliah Sibuyi ◽  
Phumuzile Dube ◽  
Adewale Oluwaseun Fadaka ◽  
Ruben Cloete ◽  
...  
Keyword(s):  
Low Income ◽  
Point Of Care ◽  
Health Care Systems ◽  
Cost Effective ◽  
Rapid Screening ◽  
Low Income Countries ◽  
Sputum Smear ◽  
Diagnostic Systems ◽  
Molecular Tests ◽  
Rapid Tests

The transmission of Tuberculosis (TB) is very rapid and the burden it places on health care systems is felt globally. The effective management and prevention of this disease requires that it is detected early. Current TB diagnostic approaches, such as the culture, sputum smear, skin tuberculin, and molecular tests are time-consuming, and some are unaffordable for low-income countries. Rapid tests for disease biomarker detection are mostly based on immunological assays that use antibodies which are costly to produce, have low sensitivity and stability. Aptamers can replace antibodies in these diagnostic tests for the development of new rapid tests that are more cost effective; more stable at high temperatures and therefore have a better shelf life; do not have batch-to-batch variations, and thus more consistently bind to a specific target with similar or higher specificity and selectivity and are therefore more reliable. Advancements in TB research, in particular the application of proteomics to identify TB specific biomarkers, led to the identification of a number of biomarker proteins, that can be used to develop aptamer-based diagnostic assays able to screen individuals at the point-of-care (POC) more efficiently in resource-limited settings.

scholarly journals Amplification Refractory Mutation System – Polymerase Chain Reaction for Rapid Detection of rpoB Gene Mutations in Mycobacterium tuberculosis

2017 ◽  
Vol 5 (1) ◽  
pp. 81-85 ◽  
Author(s):  
Hemanta Kumari Chaudhary ◽  
Mitesh Shrestha ◽  
Prakash Chaudhary ◽  
Bal Hari Poudel
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Rpob Gene ◽  
Amplification Refractory Mutation System ◽  
Chain Reaction ◽  
Arms Pcr ◽  
Mutation System ◽  
Mdr Tb ◽  
Total Dna ◽  
Polymerase Chain ◽  
Rifampin Resistance

Multidrug-resistant tuberculosis (MDR-TB) has become a serious worldwide threat including in Nepal. MDR-TB refers to the pathological condition whereby Mycobacterium tuberculosis becomes resistant to the first line of drug treatment i.e. rifampin and isoniazid. Resistance to rifampin (RIF) is mainly caused by the mutations in the rpoB gene which codes for the β-subunit of RNA polymerase. In this study, Amplification Refractory Mutation System – Polymerase Chain Reaction (ARMS – PCR) technique has been used to detect mutations in the rpoB gene of Mycobacterium tuberculosis. Total DNA samples of 34 phenotypic MDR-TB were subjected to ARMS – PCR using three different codon specific primers (516, 526 and 531). These three codons occupy large portion of total mutation responsible for rifampin resistance. Out of the total DNA samples, all were bearing mutation in at least one of the three codons mentioned. Of those bearing mutation, the highest number had mutation in codon 531 (97.05 %) followed by codon 516 (17.64 %) and finally in codon 526 (11.76%) respectively. Hence, ARMS – PCR may be used as an alternative diagnostic technique for detection of rifampin resistance in Mycobacterium tuberculosis strains, especially for a developing country like Nepal.Int. J. Appl. Sci. Biotechnol. Vol 5(1): 81-85

scholarly journals P.028 Global surgery for pediatric hydrocephalus in the developing world: a review of the history, challenges, and future directions

2017 ◽  
Vol 44 (S2) ◽  
pp. S20-S20
Author(s):  
S Wang ◽  
RT Muir ◽  
BC Warf
Keyword(s):  
Low Income ◽  
Developing World ◽  
Pediatric Neurosurgery ◽  
Cost Effective ◽  
Global Surgery ◽  
Low Income Countries ◽  
Global Burden ◽  
Pediatric Hydrocephalus ◽  
Cost Effective Treatment ◽  
Education Gaps

Background: Pediatric hydrocephalus is one of the most common neurosurgical conditions and is a major contributor to the global burden of surgically treatable diseases. Methods: The authors conducted a literature review around the topic of pediatric hydrocephalus in the context of global surgery, the unique challenges to creating access to care in low-income countries, and current international efforts to address the problem. Results: Developing countries face the greatest burden of pediatric hydrocephalus due to high birth rates and greater risk of neonatal infections. This burden is related to more general global health challenges, including malnutrition, infectious diseases, maternal and perinatal risk factors, and education gaps. Unique challenges pertaining to the treatment of hydrocephalus in the developing world include a preponderance of postinfectious hydrocephalus, limited resources, and restricted access to neurosurgical care. In the 21st century, several organizations have established programs that provide hydrocephalus treatment and neurosurgical training in Africa, Central and South America, Haiti, and Southeast Asia. These international efforts have employed various models to achieve the goals of providing safe, sustainable, and cost-effective treatment. Conclusions: Broader commitment from the pediatric neurosurgery community, increased funding, public education, surgeon training, and ongoing surgical innovation will be needed to meaningfully address the global burden of untreated hydrocephalus.

scholarly journals Glucose 6 phosphate dehydrogenase deficiency and hemoglobinopathy in South Western Region Nepal: a boon or burden

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Narayan Gautam ◽  
Bhagwati Gaire ◽  
Trishna Manandhar ◽  
Bishnu P. Marasini ◽  
Niranjan Parajuli ◽  
...  
Keyword(s):  
Sickle Cell ◽  
G6pd Deficiency ◽  
Sickle Cell Trait ◽  
Amplification Refractory Mutation System ◽  
Cellulose Acetate Electrophoresis ◽  
Positive Trait ◽  
Arms Pcr ◽  
Phenotypic Method ◽  
Mutation System ◽  
Glucose 6 Phosphate Dehydrogenase

Abstract Objectives The study was carried out to optimize the phenotypic method to characterize the sickle cell trait (SCT), sickle cell anemia (SCA), and β-thalassemia (β-TT) suspected sample from tharu community of South Western province-5, Nepal. SCT and SCA were further evaluated by genotypic method employing amplification refractory mutation system (ARMS PCR). Moreover, Glucose 6 phosphate dehydrogenase (G6PD) was estimated in those hemoglobinopathy to observe its prevalence. The accurate and reliable method can play an important role in reduction of morbidity and mortality rate. Results The 100 suspected cases were subjected to phenotypic method adopting cellulose acetate electrophoresis and genotypic method using ARMS PCR which portraits (5%) SCA positive test showing HBS/HBS, (38%) SCT positive trait HBA/HBS and (36%) cases normal HBA/HBA. β-TT (21%) cases were confirmed by electropherogram. G6PD deficiency was observed in (40%) of SCA, (18.4%) of SCT, (4.8%) of β-TT and (2.8%) in normal cases. Increased G6PD were developed only in SCT (5.3%) and β-TT (4.8%). The study highlighted sickle cell disorder (SCD) and β-TT as the most common hemoglobinopathy coexisting with G6PD deficiency. Though hemoglobinopathy sometime could be protective in malaria but G6PD deficiency can cause massive hemolysis which may exacerbate the condition.

Improving life after stroke needs global efforts to implement evidence-based physical activity pathways

2019 ◽  
Vol 14 (5) ◽  
pp. 457-459 ◽  
Author(s):  
Frederike van Wijck ◽  
Julie Bernhardt ◽  
Sandra A Billinger ◽  
Marie-Louise Bird ◽  
Janice Eng ◽  
...  
Keyword(s):  
Physical Activity ◽  
Low Income ◽  
Best Practice ◽  
Recurrent Stroke ◽  
Cost Effective ◽  
Preliminary Evidence ◽  
Low Income Countries ◽  
Active Lifestyle ◽  
High Quality ◽  
The World

There is an urgent need to improve life after stroke across the world—especially in low-income countries—through methods that are effective, equitable and sustainable. This paper highlights physical activity (PA) as a prime candidate for implementation. PA reduces modifiable risk factors for first and recurrent stroke and improves function and activity during rehabilitation and following discharge. Preliminary evidence also indicates PA is cost-effective. This compelling evidence urgently needs to be translated into seamless pathways to enable stroke survivors across the world to engage in a more active lifestyle. Although more quality research is needed—particularly on how to optimize uptake and maintenance of PA—this should not delay implementation of high-quality evidence already available. This paper shares examples of best practice service models from low-, middle-, and high-income countries around the world. The authors call for a concerted effort to implement high-quality PA services to improve life after stroke for all.

scholarly journals Patent Buy-Outs for Global Disease Innovations for Low-and Middle-Income Countries

2006 ◽  
Vol 32 (2-3) ◽  
pp. 159-173 ◽  
Author(s):  
Kevin Outterson
Keyword(s):  
Low Income ◽  
Drug Price ◽  
Marginal Cost ◽  
Cost Effective ◽  
World Health ◽  
Low Income Countries ◽  
Significant Variable ◽  
Generic Competition ◽  
Middle Income ◽  
Cost Of Production

The World Health Organization’s CHOICE program analyzes the cost effectiveness of various health interventions related to the Millennium Development Goals. The program identifies the best strategies for improving health in low-income countries, using a standard set of methodological assumptions. These studies evaluate interventions in many areas, including child health and HIV/AIDS.For some of these treatments, drug costs are a significant variable: if the drug price doubles, the intervention becomes less cost effective. But if the drug price is reduced by 90%, then more therapies become affordable.Drug prices are uniquely susceptible to radical price reductions through generic competition. Patented pharmaceuticals may be priced at more than 30 times the marginal cost of production; the excess is the patent rent collected by the drug company while the patent and exclusive marketing periods remain. Patent rents are significant. AIDS drugs which sell for US$10,000 per person per year in the US are sold generically for less than US$200. If patented drugs could be sold at the marginal cost of production, cost effective treatments would become even more attractive, and other interventions would become affordable.

scholarly journals Multiplex amplification refractory mutation system PCR (ARMS-PCR) provides convenient method for differentiation of canine parvovirus vaccine and field strains

VirusDisease ◽  
2018 ◽  
Vol 29 (4) ◽  
pp. 565-568 ◽  
Author(s):  
Vikas Gupta ◽  
Vishal Chander ◽  
Soumendu Chakravarti ◽  
Gaurav Kumar Sharma ◽  
Javed Ahmed Malla ◽  
...  
Keyword(s):  
Convenient Method ◽  
Canine Parvovirus ◽  
Amplification Refractory Mutation System ◽  
Arms Pcr ◽  
Multiplex Amplification ◽  
Mutation System
Sign in / Sign up

Export Citation Format

Share Document