scholarly journals Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 429 ◽  
Author(s):  
Cecilia Osunmakinde ◽  
Ramganesh Selvarajan ◽  
Timothy Sibanda ◽  
Bhekie Mamba ◽  
Titus Msagati
Keyword(s):  
Treatment Plant ◽  
Viral Metagenomics ◽  
Clinical Samples ◽  
Environmental Matrices ◽  
African Countries ◽  
Entire Genome ◽  
Detection And Identification ◽  
Key Issues ◽  
Environmental Milieu ◽  
Human Viruses

There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.

scholarly journals Using Small RNA Deep Sequencing Data to Detect Human Viruses

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Fang Wang ◽  
Yu Sun ◽  
Jishou Ruan ◽  
Rui Chen ◽  
Xin Chen ◽  
...  
Keyword(s):  
Small Rna ◽  
B Cell Lymphoma ◽  
Clinical Samples ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Detection And Identification ◽  
Small Rna Deep Sequencing ◽  
Human Viruses ◽  
First Time ◽  
Hiv 1

Small RNA sequencing (sRNA-seq) can be used to detect viruses in infected hosts without the necessity to have any prior knowledge or specialized sample preparation. The sRNA-seq method was initially used for viral detection and identification in plants and then in invertebrates and fungi. However, it is still controversial to use sRNA-seq in the detection of mammalian or human viruses. In this study, we used 931 sRNA-seq runs of data from the NCBI SRA database to detect and identify viruses in human cells or tissues, particularly from some clinical samples. Six viruses including HPV-18, HBV, HCV, HIV-1, SMRV, and EBV were detected from 36 runs of data. Four viruses were consistent with the annotations from the previous studies. HIV-1 was found in clinical samples without the HIV-positive reports, and SMRV was found in Diffuse Large B-Cell Lymphoma cells for the first time. In conclusion, these results suggest the sRNA-seq can be used to detect viruses in mammals and humans.

A Collaborative Approach to Upgrading to Limits of Technology at the York River Treatment Plant

2009 ◽  
Vol 4 (3) ◽  
Author(s):  
I. Venner ◽  
J. Husband ◽  
J. Noonan ◽  
A. Nelson ◽  
D. Waltrip
Keyword(s):  
Chesapeake Bay ◽  
Phase 1 ◽  
Treatment Plant ◽  
Cost Effective ◽  
Design Flow ◽  
Nutrient Reduction ◽  
York River ◽  
Hampton Roads ◽  
Key Issues ◽  
Virginia Department

In response to rapid population growth as well as to address the nutrient reduction goals for the Chesapeake Bay established by the Virginia Department of Environmental Quality (VDEQ), the Hampton Roads Sanitation District (HRSD) initiated the York River Treatment Plant (YRTP) Expansion Phase 1 project. The existing YRTP is a conventional step-feed activated sludge plant and is rated for an average daily design flow of 57 million liters per day (MLD). This project proposes to expand the existing treatment capacity to 114 MLD and to reduce the nutrients discharged to the York River, a tributary for the Chesapeake Bay. In order to meet the effluent limits set by the VDEQ, a treatment upgrade to limit of technology (LOT) or enhanced nutrient removal (ENR) was required. Malcolm Pirnie worked with HRSD and the VDEQ to develop and evaluate ENR process alternatives to achieve the required effluent limits with the goal of determining the most reliable and cost effective alternative to achieve the aggressive nutrient reduction goals. This paper will highlight the key issues in determining the most desirable treatment process considering both economic and non-economic factors.

scholarly journals Molecular Characterisation and Phylogenetic Analysis of Dermatophytic Fungi Isolated from Tinea Capitis in Northwest Nigeria Using Sequence of the 28S rRNA

2021 ◽  
Vol 12 (3) ◽  
pp. 646-655
Author(s):  
Hussain Yahaya Ungo-kore ◽  
Joseph Olorunmola Ehinmidu ◽  
Josiah Ademola Onaolapo ◽  
Olayeni Stephen Olonitola
Keyword(s):  
Phylogenetic Analysis ◽  
Tinea Capitis ◽  
28S Rdna ◽  
Clinical Samples ◽  
28S Rrna ◽  
Trichophyton Tonsurans ◽  
Detection And Identification ◽  
Microsporum Audouinii ◽  
Trichophyton Simii ◽  
Dermatophyte Species

The detection and identification of fungal DNA from clinical samples is one of the fundamental approaches in biomedicine. The incidence, distribution, and control of dermatophytes has progress significantly and the use of phylogenetic species concepts based on rRNA regions have enhanced the taxonomy of dermatophyte species; however, the use of 28S rDNA genes has certain limitations. This gene has been used in dermatophyte taxonomy with limited enumeration; we appraised the sequence disparity within and among groups of the species, the gene ranking in identification, phylogenetic analysis, and taxonomy of 32 strains of eight dermatophyte species. In this study, a set of primers was adopted to amplify the target followed by a partial sequencing of the rDNA. The utilization of a pairwise nucleotide differentiation, an affinity was observed among eight dermatophyte species, with disparity among species ranging from 0 to 197 base pair (bp). Intra-species bp differences were found within strains of Trichophyton eriotrephon, Trichophyton bullosum, Trichophyton simii (Trichophyton genus), Microsporum audouinii, and Trichophyton tonsurans (Microsporum and Trichophyton genus, respectively); however, only some strains of Trichophyton eriotrephon were found to be invariant having three genotypes. Trichophyton tonsurans exhibited most intra-species variability. The characterization and construction of a phylogenetic tree of 28S rDNA gene on dermatophyte species provide a bedrock of an additional finding of connections between species. However, 28S rRNA capture provides a novel method of effective and sensitive detection of dermatophytes lodged in human skin scale. We report for the first time the emergence of T. eriotrephon, T. bullosum, T. simii, T. benhamiae, and Ctenomyces serratus dermatophytes from Tinea capitis in Nigeria.

scholarly journals Validation and Implementation of a Diagnostic Algorithm for DNA Detection ofBordetella pertussis,B. parapertussis, andB. holmesiiin a Pediatric Referral Hospital in Barcelona, Spain

2018 ◽  
Vol 57 (1) ◽  
Author(s):  
Ana Valero-Rello ◽  
Desiree Henares ◽  
Lesly Acosta ◽  
Mireia Jane ◽  
Iolanda Jordan ◽  
...  
Keyword(s):  
Internal Control ◽  
Whooping Cough ◽  
Diagnostic Algorithm ◽  
Clinical Samples ◽  
Analytical Validation ◽  
Content Type ◽  
Detection And Identification ◽  
Ofbordetella Pertussis ◽  
Lower Limits

ABSTRACTThis study aimed to validate a comprehensive diagnostic protocol based on real-time PCR for the rapid detection and identification ofBordetella pertussis,Bordetella parapertussis, andBordetella holmesii, as well as its implementation in the diagnostic routine of a reference children’s hospital. The new algorithm included a triplex quantitative PCR (qPCR) targeting IS481gene (inB. pertussis,B. holmesii, and someBordetella bronchisepticastrains), pIS1001(B. parapertussis-specific) andrnaseP as the human internal control. Two confirmatory singleplex tests forB. pertussis(ptxA-Pr) andB. holmesii(hIS1001) were performed if IS481was positive. Analytical validation included determination of linear range, linearity, efficiency, precision, sensitivity, and a reference panel with clinical samples. Once validated, the new algorithm was prospectively implemented in children with clinical suspicion of whooping cough presenting to Hospital Sant Joan de Deu (Barcelona, Spain) over 12 months. Lower limits of detection obtained were 4.4, 13.9, and 27.3 genomic equivalents/ml of sample for IS481(onB. pertussis), pIS1001and hIS1001, and 777.9 forptxA-Pr. qPCR efficiencies ranged from 86.0% to 96.9%. Intra- and interassay variabilities were <3% and <5%, respectively. Among 566 samples analyzed,B. pertussis,B. holmesii, andB. parapertussiswere detected in 11.1%, 0.9% (only in females >4 years old), and 0.2% of samples, respectively. The new algorithm proved to be a useful microbiological diagnostic tool for whooping cough, demonstrating a low rate of other non-pertussisBordetellaspecies in our surveilled area.

scholarly journals Detection of Nocardia by 16S Ribosomal RNA Gene PCR and Metagenomic Next-Generation Sequencing (mNGS)

2022 ◽  
Vol 11 ◽  
Author(s):  
Juanjuan Ding ◽  
Bing Ma ◽  
Xupeng Wei ◽  
Ying Li
Keyword(s):  
16S Rrna ◽  
Ribosomal Rna ◽  
Human Herpesvirus ◽  
Antibiotic Sensitivity ◽  
Common Species ◽  
16S Ribosomal Rna ◽  
Clinical Samples ◽  
Klebsiella Pneumonia ◽  
Antimicrobial Drugs ◽  
Detection And Identification

In this study, the aim was to investigate the discriminatory power of molecular diagnostics based on mNGS and traditional 16S ribosomal RNA PCR among Nocardia species. A total of fourteen clinical isolates from patients with positive Nocardia cultures and clinical evidence were included between January 2017 and June 2020 in HeNan Provincial People’s Hospital. DNA extraction and 16S rRNA PCR were performed on positive cultures, and pathogens were detected by mNGS in these same samples directly. Among the 14 Nocardia isolates, four species were identified, and N. cyriacigeorgica (8 cases) is the most common species. Twelve of the 14 Nocardia spp. isolates were identified by the two methods, while two strains of N. cyriacigeorgica were not identified by mNGS. All tested isolates showed susceptibility to trimethoprim-sulfamethoxazole (SXT), amikacin and linezolid. Apart from Nocardia species, other pathogens such as Acinetobacter baumannii, Klebsiella pneumonia, Aspergillus, Enterococcus faecalis, Human herpesvirus, etc., were detected from the same clinical samples by mNGS. However, these different pathogens were considered as colonization or contamination. We found that it is essential to accurately identify species for determining antibiotic sensitivity and, consequently, choosing antibiotic treatment. 16S rRNA PCR was useful for identification of nocardial infection among species, while this technique needs the clinicians to make the pre-considerations of nocardiosis. However, mNGS may be a putative tool for rapid and accurate detection and identification of Nocardia, beneficial for applications of antimicrobial drugs and timely adjustments of medication.

scholarly journals Virus detection and identification in minutes using single-particle imaging and deep learning

2020 ◽  
Author(s):  
Nicolas Shiaelis ◽  
Alexander Tometzki ◽  
Leon Peto ◽  
Andrew McMahon ◽  
Christof Hepp ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Single Particle ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Clinical Samples ◽  
Promising Alternative ◽  
Detection And Identification ◽  
Particle Imaging ◽  
Single Particle Imaging

AbstractThe increasing frequency and magnitude of viral outbreaks in recent decades, epitomized by the current COVID-19 pandemic, has resulted in an urgent need for rapid and sensitive viral diagnostic methods. Here, we present a methodology for virus detection and identification that uses a convolutional neural network to distinguish between microscopy images of single intact particles of different viruses. Our assay achieves labeling, imaging and virus identification in less than five minutes and does not require any lysis, purification or amplification steps. The trained neural network was able to differentiate SARS-CoV-2 from negative clinical samples, as well as from other common respiratory pathogens such as influenza and seasonal human coronaviruses, with high accuracy. Single-particle imaging combined with deep learning offers a promising alternative to traditional viral diagnostic methods, and has the potential for significant impact.

Diagnosis of melioidosis: the role of molecular techniques

2021 ◽  
Vol 16 (4) ◽  
pp. 271-288
Author(s):  
Ian Gassiep ◽  
Delaney Burnard ◽  
Michelle J Bauer ◽  
Robert E Norton ◽  
Patrick N Harris
Keyword(s):  
Laboratory Diagnosis ◽  
Diagnostic Techniques ◽  
Molecular Techniques ◽  
Molecular Diagnostic ◽  
Clinical Samples ◽  
Molecular Diagnostic Techniques ◽  
Detection And Identification ◽  
Life Years ◽  
Culture Independent ◽  
Future Utility

Melioidosis is an emerging infectious disease with an estimated global burden of 4.64 million disability-adjusted life years per year. A major determinant related to poor disease outcomes is delay to diagnosis due to the fact that identification of the causative agent Burkholderia pseudomallei may be challenging. Over the last 25 years, advances in molecular diagnostic techniques have resulted in the potential for rapid and accurate organism detection and identification direct from clinical samples. While these methods are not yet routine in clinical practice, laboratory diagnosis of infectious diseases is transitioning to culture-independent techniques. This review article aims to evaluate molecular methods for melioidosis diagnosis direct from clinical samples and discuss current and future utility and limitations.

scholarly journals Studies of Genetic Relationships between Bovine, Caprine, Cervine, and Rangiferine Alphaherpesviruses and Improved Molecular Methods for Virus Detection and Identification

1999 ◽  
Vol 37 (5) ◽  
pp. 1247-1253 ◽  
Author(s):  
Carlos Ros ◽  
Sándor Belák
Keyword(s):  
Genetic Relationships ◽  
Bovine Herpesvirus ◽  
Clinical Samples ◽  
Enzyme Analysis ◽  
Amplification Efficiency ◽  
Sequence Alignments ◽  
Related Virus ◽  
Detection And Identification ◽  
Pcr Products ◽  
Herpesvirus 1

The glycoprotein B (gB) and D (gD) genes from five ruminant alphaherpesviruses, bovine herpesvirus 1 (BHV-1), bovine herpesvirus 5 (BHV-5), caprine herpesvirus 1 (CapHV-1), cervine herpesvirus 1, and rangiferine herpesvirus 1, were partially sequenced. The nucleotide sequence alignments revealed a highly conserved gB gene, with homologies ranging between 87.2 and 99.6%, and a more variable gD gene, with homologies ranging between 71.3 and 98.9%. The phylogenetic analysis of the gB and gD nucleotide and deduced amino acid sequences revealed that BHV-5 is the most closely related virus to the BHV-1 subtype 1 and BHV-1 subtype 2 cluster and that CapHV-1 is the most distantly related virus. The phylogenetic data showed a close relationship of all the studied viruses with suid herpesvirus 1. On the basis of sequence data for the gB gene, a nested PCR combined with restriction enzyme analysis (REA) of the PCR products was developed for the simultaneous detection and identification of the viruses that were studied. Nested primers from highly conserved sequence stretches were selected in order to amplify a region of 294 bp in all five viruses, and a subsequent REA of the PCR products allowed specific identification. A mimic molecule that served as an internal standard of the amplification efficiency was constructed. The practical diagnostic applicability of the assay was evaluated with clinical samples consisting of semen and organ specimens from experimentally infected animals.

scholarly journals Profile of the Spatial Distribution Patterns of the Human and Bacteriophage Virome in a Wastewater Treatment Plant Located in the South of Spain

Water ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2316
Author(s):  
Cristina García-Fontana ◽  
Alejandro Rodriguez-Sanchez ◽  
Barbara Muñoz-Palazon ◽  
Alejandro Gonzalez-Martinez ◽  
Maria Vela-Cano ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Wastewater Treatment Plants ◽  
Treatment Plant ◽  
Distribution Patterns ◽  
Conventional Activated Sludge ◽  
Typing Phage ◽  
Transmission Electron ◽  
Sequencing Studies ◽  
Microbial Characterization ◽  
Human Viruses

In wastewater treatment plants, most microbial characterization has focused on bacterial, archaeal, and fungal populations. Due to the difficult isolation, quantification, and identification of viruses, only a limited number of virome studies associated with wastewater treatment plants have been carried out. However, the virus populations play an important role in the microbial dynamics in wastewater treatment systems and the biosafety of effluents. In this work, the viral members present in influent wastewater, mixed liquor (aerobic bioreactor), excess sludge, and effluent water of a conventional activated sludge system for the treatment of urban wastewater were identified. Viral members were observed by transmission electron microscopy and studied through next-generation sequencing studies. The results showed the dominance of bacteriophages in the viral community in all samples, with the dominant viral phylotype classified as Escherichia coli O157 typing phage 7. Moreover, different human viruses, such as Cynomolgus cytomegalovirus and Gammaherpesvirus, were also detected.

scholarly journals Lassa Fever: Viral Replication, Disease Pathogenesis, and Host Immune Modulations

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 437
Author(s):  
Hinh Ly
Keyword(s):  
Lassa Fever ◽  
West African ◽  
Host Factors ◽  
Current Status ◽  
Special Issue ◽  
African Countries ◽  
Disease Pathogenesis ◽  
Virus Life Cycle ◽  
Key Issues ◽  
Made In

Despite major discoveries made in the last few decades about Lassa fever, there are still many unresolved key issues that hamper the development of effective vaccines and therapies against this deadly disease that is endemic in several West African countries. Some of these issues include the lack of a detailed understanding of the viral and participating host factors in completing the virus life cycle, in mediating disease pathogenesis or protection from disease, and in activating or suppressing host innate and cellular immunity against virus infection, as well as of the animal models required for testing vaccines and therapeutics. This Special Issue is devoted to understanding some of these important issues and to exploring the current status of the research and development in combating Lassa fever.

Sign in / Sign up

Export Citation Format

Share Document