scholarly journals Detection of SARS CoV-2 reinfections by rapid inexpensive techniques

2021 ◽  
Author(s):  
Sherko Subhan Niranji ◽  
Sirwan M.A. Al-Jaf
Keyword(s):  
Developing Countries ◽  
Dna Sequences ◽  
Rapid Detection ◽  
Phylogenetic Analyses ◽  
Immunocompetent Patient ◽  
Clinical Samples ◽  
Specific Primers ◽  
Persistent Infections ◽  
The World ◽  
The Uk

Abstract Reinfections of SARS CoV-2 are rare in the world and it is difficult to be confirmed whether it is a reinfection or persistent infection. The most prominent factors used for differentiating the reinfections from persistent infections are whole genome sequencings and phylogenetic analyses that require times and funds, which may not be feasible in most developing countries. We previously developed rapid economical methods to identify both D614G and N501Y mutations in clinical samples using rRT PCR probes and endpoint PCR specific primers. Current study has found an immunocompetent patient with a SARS CoV-2 N501Y reinfection without comorbidities. The results suggested that the initial infection was due to a variant contained only D614G mutation while the reinfection was potentially as result of the UK variant contained three mutations confirmed by DNA sequences, including D614G, N501Y and A570D mutations. Seven cases of reinfections were also confirmed by these methods suggested that these techniques will support rapid detection of SARS CoV-2 reinfections in developing countries where sequencing tools are unavailable.

scholarly journals Identification of Porphyromonas gingivalis Strains by Heteroduplex Analysis and Detection of Multiple Strains

1999 ◽  
Vol 37 (12) ◽  
pp. 3906-3911 ◽  
Author(s):  
Eugene J. Leys ◽  
James H. Smith ◽  
Sharon R. Lyons ◽  
Ann L. Griffen
Keyword(s):  
Porphyromonas Gingivalis ◽  
Dna Sequences ◽  
Allelic Variation ◽  
Intergenic Spacer ◽  
Heteroduplex Analysis ◽  
Clinical Samples ◽  
Specific Primers ◽  
Intergenic Spacer Region ◽  
Species Specific ◽  
Multiple Strains

Heteroduplex analysis has been used extensively to identify allelic variation among mammalian genes. It provides a rapid and reliable method for determining and cataloging minor differences between two closely related DNA sequences. We have adapted this technique to distinguish among strains or clonal types of Porphyromonas gingivalis. The ribosomal intergenic spacer region (ISR) was amplified directly from a subgingival plaque sample by PCR with species-specific primers, avoiding the need for culturing the bacteria. The PCR products were then directly compared by heteroduplex analysis with known strains of P. gingivalis for identification. We identified 22 distinct but closely related heteroduplex types ofP. gingivalis in 1,183 clinical samples. Multiple strains were found in 34% of the samples in which P. gingivaliswas detected. Heteroduplex types were identified from these multistrain samples without separating them by culturing or molecular cloning. PCR with species-specific primers and heteroduplex analysis makes it possible to reliably and sensitively detect and identify strains ofP. gingivalis in large numbers of samples.

scholarly journals Rapid increase of SARS-CoV-2 variant B.1.1.7 detected in sewage samples from England between October 2020 and January 2021

2021 ◽  
Author(s):  
Thomas Wilton ◽  
Erika Bujaki ◽  
Dimitra Klapsa ◽  
Martin Fritzsche ◽  
Ryan Mate ◽  
...  
Keyword(s):  
Rapid Detection ◽  
Environmental Surveillance ◽  
The World ◽  
Human Immune Response ◽  
Human Immune ◽  
Amino Acid Mutations ◽  
The Uk ◽  
Multiple Amino Acid ◽  
Viral Sequences ◽  
Different Parts

AbstractSARS-CoV-2 variants with multiple amino acid mutations in the spike protein are emerging in different parts of the world raising concerns on their possible impact on human immune response to the virus and vaccine efficacy against them. Recently, a variant named lineage B.1.1.7 was detected and shown to be rapidly spreading across the UK since November 2020. As surveillance for these SARS-CoV-2 variants of concern (VOCs) becomes critical, we have investigated the use of environmental surveillance (ES) for the rapid detection and quantification of B.1.1.7 viruses in sewage as a way of monitoring its expansion that is independent on the investigation of identified clinical cases. B.1.1.7 mutations in viral sequences from sewage were first identified in a sample collected in London on 10th November 2020 and shown to rapidly increase in frequency to >95% in January 2021, in agreement with clinical data over the same period. We show that ES can provide an early warning of VOCs becoming prevalent in the population and that, as well as B.1.1.7, our method can potentially detect VOCs B.1.351 and P.1, first identified in South Africa and Brazil, respectively, and other viruses also carrying critical spike mutation E484K, known to have an effect on virus antigenicity.

scholarly journals Specific Primers for Rapid Detection of Microsporum audouinii by PCR in Clinical Samples

2006 ◽  
Vol 44 (12) ◽  
pp. 4336-4341 ◽  
Author(s):  
H. D. Roque ◽  
R. Vieira ◽  
S. Rato ◽  
M. Luz-Martins
Keyword(s):  
Rapid Detection ◽  
Clinical Samples ◽  
Specific Primers ◽  
Microsporum Audouinii

scholarly journals A simple and fast spectroscopy-based technique for Covid-19 diagnosis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Driss Lahlou Kitane ◽  
Salma Loukman ◽  
Nabila Marchoudi ◽  
Alvaro Fernandez-Galiana ◽  
Fatima Zahra El Ansari ◽  
...  
Keyword(s):  
Developing Countries ◽  
Multivariate Analysis ◽  
Spectroscopic Method ◽  
Rna Extraction ◽  
Limited Resources ◽  
Clinical Samples ◽  
Testing Time ◽  
Rt Pcr ◽  
The World ◽  
Testing Techniques

AbstractThe coronavirus pandemic, which appeared in Wuhan, China, in December 2019, rapidly spread all over the world in only a few weeks. Faster testing techniques requiring less resources are key in managing the pandemic, either to enable larger scale testing or even just provide developing countries with limited resources, particularly in Africa, means to perform tests to manage the crisis. Here, we report an unprecedented, rapid, reagent-free and easy-to-use screening spectroscopic method for the detection of SARS-CoV-2 on RNA extracts. This method, validated on clinical samples collected from 280 patients with quantitative predictive scores on both positive and negative samples, is based on a multivariate analysis of FTIR spectra of RNA extracts. This technique, in agreement with RT-PCR, achieves 97.8% accuracy, 97% sensitivity and 98.3% specificity while reducing the testing time post RNA extraction from hours to minutes. Furthermore, this technique can be used in several laboratories with limited resources.

scholarly journals The perioperative management of haemophilia: easier said than done Joint assessment in haemophilia – current physiotherapist practice in the UK

2014 ◽  
Vol 1 (3) ◽  
pp. 7-8 ◽  
Author(s):  
Madhuri S Kurdi ◽  
Ravikumar R Jadhav ◽  
Jaideep Ratkal ◽  
Jasvinder Kaur ◽  
H. R. Ashwini ◽  
...  
Keyword(s):  
Developing Countries ◽  
Blood Clotting ◽  
Perioperative Management ◽  
Bleeding Disorder ◽  
Haemophilia A ◽  
The World ◽  
Costs Of Treatment ◽  
The Uk ◽  
Joint Assessment

Abstarct Haemophilia is the oldest known rare genetic bleeding disorder that disrupts the blood clotting process. Although the level of haemophilia care has improved substantially, the problems of management in developing countries are poor awareness, high costs of treatment, inadequate diagnostic and coagulation screening facilities and scarce factor concentrates for therapy. We present here the problems in the perioperative management of a case of haemophilia A in India. It portrays the current picture of haemophilia management in many developing countries around the world.

scholarly journals Evaluation of two fluorescence immunoassays for the rapid detection of SARS-CoV-2 antigen—new tool to detect infective COVID-19 patients

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10801
Author(s):  
Lorena Porte ◽  
Paulette Legarraga ◽  
Mirentxu Iruretagoyena ◽  
Valeska Vollrath ◽  
Gabriel Pizarro ◽  
...  
Keyword(s):  
Rapid Detection ◽  
High Performance ◽  
Diagnostic Method ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Viral Loads ◽  
The World ◽  
Polymerase Chain ◽  
Potential Use

Background Real-Time Reverse-Transcription Polymerase Chain Reaction (RT-PCR) is currently the only recommended diagnostic method for SARS-CoV-2. However, rapid immunoassays for SARS-CoV-2 antigen could significantly reduce the COVID-19 burden currently weighing on laboratories around the world. Methods We evaluated the performance of two rapid fluorescence immunoassays (FIAs), SOFIA SARS Antigen FIA (Quidel Corporation, San Diego, CA, USA) and STANDARD F COVID-19 Ag FIA (SD Biosensor Inc., Gyeonggi-do, Republic of Korea), which use an automated reader. The study used 64 RT-PCR characterized clinical samples (32 positive; 32 negative), which consisted of nasopharyngeal swabs in universal transport medium. Results Of the 32 positive specimens, all from patients within 5 days of symptom onset, the Quidel and SD Biosensor assays detected 30 (93.8%) and 29 (90.6%) samples, respectively. Among the 27 samples with high viral loads (Ct ≤ 25), the two tests had a sensitivity of 100%. Specificity was 96.9% for both kits. Conclusion The high performance of the evaluated FIAs indicates a potential use as rapid and PCR-independent tools for COVID-19 diagnosis in early stages of infection. The excellent sensitivity to detect cases with viral loads above ~106 copies/mL (Ct values ≤ 25), the estimated threshold of contagiousness, suggests that the assays might serve to rapidly identify infective individuals.

scholarly journals A Panel of Diverse Pseudomonas aeruginosa Clinical Isolates for Research and Development

2021 ◽  
Author(s):  
Francois Lebreton ◽  
Erik Snesrud ◽  
Lindsey Hall ◽  
Emma Mills ◽  
Madeline Galac ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Pseudomonas Aeruginosa ◽  
Research And Development ◽  
Antibiotic Susceptibility ◽  
Antimicrobial Agents ◽  
Phylogenetic Analyses ◽  
New Drugs ◽  
World Health ◽  
Clinical Samples ◽  
The World

AbstractPseudomonas aeruginosa is a leading cause of community-acquired and hospital-acquired infections. Successful treatment is hampered by its remarkable ability to rapidly develop resistance to antimicrobial agents, mostly through mutation. In response, the World Health Organization listed carbapenem-resistant P. aeruginosa as a Priority 1 (Critical) pathogen for research and development of new treatments. A key resource in developing effective countermeasures is access to diverse and clinically relevant strains for testing. Herein we describe a panel of 100 diverse P. aeruginosa strains to support this endeavor.Whole genome sequencing was performed on 3,785 P. aeruginosa housed in our repository. Isolates were cultured from clinical samples collected from healthcare facilities around the world between 2003 and 2017. Core-genome multi-locus sequence typing and high-resolution SNP-based phylogenetic analyses were used to select a panel of 100 strains that captured the genetic diversity of this collection. Comprehensive antibiotic susceptibility testing was also performed using 14 clinically relevant antibiotics.This 100-strain diversity panel contained representative strains from 91 different sequence-types, including genetically distinct isolates from major epidemic clones ST-111, ST-235, ST-244, and ST-253. Seventy-one distinct antibiotic susceptibility profiles were identified ranging from pan-sensitive to pan-resistant. Known resistance alleles as well as the most prevalent mutations underlying the antibiotic susceptibilities were characterized for all isolates.This panel provides a diverse and comprehensive set of P. aeruginosa strains for use in developing solutions to antibiotic resistance. The isolates, and all available meta-data including genome sequences, are available to industry, academic institutions, federal and other laboratories at no additional cost.ImportancePseudomonas aeruginosa is one of the most important human pathogens and a leading target in the development of new drugs and therapeutics. This species displays a remarkable level of diversity and any potential therapeutic must contend with this characteristic to ensure it retains efficacy across different strains. To date, only limited panels of P. aeruginosa are available for testing, and none have been designed to capture the genetic diversity of the species. The panel described herein has been designed to address this shortcoming by providing a set of 100 distinct strains that greatly captures the diversity of the species. This panel will be of significant value to research groups working on this important pathogen, both for research purposes and in the development of new diagnostics and countermeasures.

scholarly journals Rapid detection of SARS CoV-2 N501Y mutation in clinical samples

2021 ◽  
Author(s):  
Sirwan M.A. Al-Jaf ◽  
Sherko Subhan Niranji
Keyword(s):  
South African ◽  
Low Cost ◽  
Clinical Samples ◽  
Conventional Pcr ◽  
Specific Primers ◽  
Vaccination Programs ◽  
Poor Countries ◽  
The Uk ◽  
And Control ◽  
Epidemiological Characteristics

Severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) variants poses major threats in increasing infectivity, transmission, mortality of Coronavirus Disease 2019 (Covid-19). Additionally, SARS CoV-2 variants resist antibody neutralizations or may abolish vaccine efficacies. Researches to develop economical and fast methods will support the developing or poor countries to challenge the Covid-19 pandemic via tracking common mutations that may help to deploy the vaccination programs and control the virus. Current study has developed a novel low-cost rapid technique, exploiting real time PCR probes and conventional PCR specific primers, to identify N501Y mutation, which was independently emerged in the UK, South African and Brazilian variants. Currently, these variants tend to spread to all over the world and seem to be more infectious, transmissible and fatal. This study helps tracking the N501Y mutation for understanding its clinical and epidemiological characteristics, in those countries where sequencing facilities are lacking or expensive. Further study should focus on other common mutations in the variants of concerns of SARS CoV-2.

scholarly journals A Diverse Panel of Clinical Acinetobacter baumannii for Research and Development

2020 ◽  
Vol 64 (10) ◽  
Author(s):  
Madeline R. Galac ◽  
Erik Snesrud ◽  
Francois Lebreton ◽  
Jason Stam ◽  
Michael Julius ◽  
...  
Keyword(s):  
Research And Development ◽  
Acinetobacter Baumannii ◽  
Antibiotic Susceptibility ◽  
Phylogenetic Analyses ◽  
Health Care Facilities ◽  
World Health ◽  
Clinical Samples ◽  
Resistant Organism ◽  
Content Type ◽  
The World

ABSTRACT Over the past two decades, Acinetobacter baumannii has emerged as a leading cause of nosocomial infections worldwide. Of particular concern are panresistant strains, leading the World Health Organization (WHO) to designate carbapenem-resistant A. baumannii as a priority 1 (critical) pathogen for research and development of new antibiotics. A key component in supporting this effort is accessibility to diverse and clinically relevant strains for testing. Here, we describe a panel of 100 diverse A. baumannii strains for use in this endeavor. Whole-genome sequencing was performed on 3,505 A. baumannii isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. Isolates were cultured from clinical samples at health care facilities around the world between 2001 and 2017. Core-genome multilocus sequence typing and high-resolution single nucleotide polymorphism (SNP)-based phylogenetic analyses were used to select a final panel of 100 strains that captured the genetic diversity of the collection. Comprehensive antibiotic susceptibility testing was also performed on all 100 isolates using 14 clinically relevant antibiotics. The final 100-strain diversity panel contained representative strains from 70 different traditional Pasteur scheme multilocus sequence types, including major epidemic clones. This diversity was also reflected in antibiotic susceptibility and antimicrobial resistance (AMR) gene content, with phenotypes ranging from pansensitive to panresistant, and over 100 distinct AMR gene alleles identified from 32 gene families. This panel provides the most diverse and comprehensive set of A. baumannii strains for use in developing solutions for combating antibiotic resistance. The panel and all available metadata, including genome sequences, will be available to industry and academic institutions and federal and other laboratories free of charge.

Searching for new Sources of growth. Are the Developing Countries Catching up with the Developed ones?

2015 ◽  
pp. 30-53
Author(s):  
V. Popov
Keyword(s):  
Developing Countries ◽  
Western Europe ◽  
Gdp Per Capita ◽  
The West ◽  
Catching Up ◽  
The Us ◽  
The World ◽  
Economic Divergence ◽  
Per Capita ◽  
Relative Standing

This paper examines the trajectory of growth in the Global South. Before the 1500s all countries were roughly at the same level of development, but from the 1500s Western countries started to grow faster than the rest of the world and PPP GDP per capita by 1950 in the US, the richest Western nation, was nearly 5 times higher than the world average and 2 times higher than in Western Europe. Since 1950 this ratio stabilized - not only Western Europe and Japan improved their relative standing in per capita income versus the US, but also East Asia, South Asia and some developing countries in other regions started to bridge the gap with the West. After nearly half of the millennium of growing economic divergence, the world seems to have entered the era of convergence. The factors behind these trends are analyzed; implications for the future and possible scenarios are considered.

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