scholarly journals First cases of Recombinant Noroviruses in Cameroon

2020 ◽  
pp. 1-6
Author(s):  
Akongnwi E Mugyia ◽  
◽  
Valentine N Ndze ◽  
Jane-Francis TK Akoachere ◽  
◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
New Orleans ◽  
Acute Gastroenteritis ◽  
Hospitalized Children ◽  
Rt Pcr ◽  
Recombination Activity ◽  
Common Cause ◽  
Dual Nomenclature ◽  
Generation Sequencing

Noroviruses have been reported as being a common cause of acute gastroenteritis both in children and adults worldwide. Genotyping and nomenclature of noroviruses was based on the partial capsid gene of the ORF2. Due to frequent reported recombination activities in the ORF1/ORF2 junction, a new dual nomenclature has been proposed based on genotyping of two genes – the capsid and polymerase genes. This study identified recombinant noroviruses circulating in Cameroon between 2010 and 2013. RT-PCR –based methods, next generation sequencing and phylogenetic analysis were used to genotype samples from hospitalized children. The combined RdRp/capsid dual genotype was determined for 19 GII strains including 5 RdRp genotypes (GII.P4, GII.P7, GII.P17, GII.P21, and GII.P31) and 5 capsid genotypes (GII.2, GII.3, GII.4, GII.6, GII.17). They had 17(89.5%) recombinants and 2 (112.5%) non recombinants. 17 were recombinants. The most prevalent noroviruses were GII.4 (76.5%) consisting of GII.4 Sydney [P31] (41.2%) and GII.4 Sydney [P4 New Orleans] (35.3%), followed by GII.6 [P7] (11.8%), GII.2 [P21] (5.9%) and GII.3 [P21] (5.9%). This is the first study of norovirus dual genotyping and recombinants in Cameroon. Recombination activity is high and contributes to ongoing evolution of circulating noroviruses in Cameroon.

scholarly journals Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal–oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication. Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1).

scholarly journals Next-generation sequencing and RT-PCR to identify a 32-day SARS-CoV-2 carrier

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Lingjie Song ◽  
Guibao Xiao ◽  
Ruixiang Tang ◽  
Xianqin Zhang ◽  
Zhan Gao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Rt Pcr ◽  
Generation Sequencing

scholarly journals Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

2021 ◽  
Author(s):  
Marcia Gumiel ◽  
Oscar M Rollano-Penaloza ◽  
Carmelo Peralta-Rivero ◽  
Leslie Tejeda ◽  
Valeria D. Palma Encinas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Theobroma Cacao ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Next Generation ◽  
Center Of Origin ◽  
Chloroplast Genomes ◽  
Geographical Locations ◽  
Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

scholarly journals Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1432
Author(s):  
Xavier Fernandez-Cassi ◽  
Sandra Martínez-Puchol ◽  
Marcelle Silva-Sales ◽  
Thais Cornejo ◽  
Rosa Bartolome ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acute Gastroenteritis ◽  
Clinical Analysis ◽  
Viral Metagenomics ◽  
Next Generation ◽  
Sequencing Data ◽  
Viral Pathogens ◽  
Viral Pathogen ◽  
Infectious Gastroenteritis ◽  
Generation Sequencing

Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery. Viral metagenomics in routine clinical settings has the potential to identify unexpected or novel variants of viral pathogens that cause gastroenteritis. In this study, 124 samples from acute gastroenteritis patients from 2012–2014 previously tested negative for common gastroenteritis pathogens were pooled by age and analyzed by next generation sequencing (NGS) to elucidate unidentified viral infections. The most abundant sequences detected potentially associated to acute gastroenteritis were from Astroviridae and Caliciviridae families, with the detection of norovirus GIV and sapoviruses. Lower number of contigs associated to rotaviruses were detected. As expected, other viruses that may be associated to gastroenteritis but also produce persistent infections in the gut were identified including several Picornaviridae members (EV, parechoviruses, cardioviruses) and adenoviruses. According to the sequencing data, astroviruses, sapoviruses and NoV GIV should be added to the list of viral pathogens screened in routine clinical analysis.

scholarly journals SARS-CoV-2 as a Trigger in the Development of Tourette’s-Like Symptoms: A Case Report

2021 ◽  
Author(s):  
Sabine Hazan ◽  
Sheldon Jordan
Keyword(s):  
Case Report ◽  
Next Generation Sequencing ◽  
Gut Microbiota ◽  
Dramatic Improvement ◽  
Next Generation ◽  
Rt Pcr ◽  
Gastrointestinal Microbiota ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing

Abstract Background: Reports have been surfacing surrounding CNS-associated symptoms in individuals affected by coronavirus disease 19 (COVID-19). Tourette syndrome is a neuropsychiatric disorder with usual onset in childhood. Gut microbiota can affect central physiology and function via the microbiota-gut-brain axis. The authors of this case report describe Tourette’s-like symptoms in a patient resulting from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection disrupting gut microbiota. Case Presentation: This case involves a 16-year-old female that developed acute onset Tourette’s-like symptoms along with neuropsychiatric symptoms after exposure to and infection from SARS-CoV-2. The patient had negative nasopharyngeal (NP) real-time reverse transcription-PCR (RT-PCR) tests for SARS-CoV-2 on five occasions from August of 2020 through June of 2021. The patient’s symptoms continued to worsen over the next six months until next-generation sequencing (NGS) revealed SARS-CoV-2 in her stool. Her treatment was adjusted as NGS revealed SARS-CoV-2 in her stool. Repair of the gastrointestinal microbiota, treatment with nutraceutical and pharmaceutical agents, as well as alterations in her surroundings resulted in dramatic improvement in the microbiome and a significant reduction of symptoms.Discussion: The use of (RT-PCR) testing to determine the presence or absence of SARS-CoV-2 may be inadequate and inaccurate for individuals that have been exposed to the virus. In addition, the impact of SARS-CoV-2 infection of the GI tract may cause significant havoc in the gut microbiota. Additional testing, eradication of infectious agents, as well as restoration of the gut microbiome are needed to effectively manage and treat this condition. The patient’s symptoms worsened over the next six months until next-generation sequencing (NGS) revealed SARS-CoV-2 in her stool and her treatment was adjusted. Treatment with nutraceuticals and alterations in her surroundings was followed by a more normal microbiome and a dramatic reduction in symptoms.

scholarly journals Next-Generation Sequencing-Based Detection of Common Bean Viruses in Wild Plants from Tanzania and Their Mechanical Transmission to Common Bean Plants

Plant Disease ◽  
2021 ◽  
Author(s):  
Beatrice Mwaipopo ◽  
Minna-Liisa Rajamäki ◽  
Neema Ngowi ◽  
Susan N’chimbi Msolla ◽  
P Njau ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Common Bean ◽  
Mosaic Virus ◽  
Viral Disease ◽  
Wild Plants ◽  
Next Generation ◽  
Rt Pcr ◽  
Bean Plants ◽  
Generation Sequencing ◽  
Common Bean Plants

Viral diseases are a major threat for common bean production. In recent surveys, >15 different viruses belonging to 11 genera were shown to infect common bean (Phaseolus vulgaris L.) in Tanzania. Management of viruses requires an understanding of how they survive from one season to the next. In this study, we explored the possibility that alternative host plants have a central role in the survival of common bean viruses. We used next-generation sequencing (NGS) techniques to sequence virus-derived small interfering RNAs, together with conventional reverse transcription-polymerase chain reaction (RT-PCR) to detect viruses in wild plants. Leaf samples for RNA extraction and NGS were collected from 1,430 wild plants around and within common bean fields in four agricultural zones in Tanzania. At least partial genome sequences of viruses potentially belonging to 25 genera were detected. The greatest virus diversity was detected in the eastern and northern zones, whereas wild plants in the Lake zone and especially in the southern highlands zone showed only a few viruses. RT-PCR analysis of all the collected plant samples confirmed the presence of yam bean mosaic virus and peanut mottle virus in wild legume plants. Of all viruses detected, only two viruses, cucumber mosaic virus and a novel bromovirus related to cowpea chlorotic mottle virus and brome mosaic virus, were mechanically transmitted from wild plants to common bean plants. The data generated in this study are crucial for development of viral disease management strategies and predicting crop viral disease outbreaks in different agricultural regions in Tanzania and beyond.

scholarly journals Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics

2020 ◽  
Vol 101 (12) ◽  
pp. 1280-1288
Author(s):  
Roozbeh Tahmasebi ◽  
Adriana Luchs ◽  
Kaelan Tardy ◽  
Philip Michael Hefford ◽  
Rory J. Tinker ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Low Income ◽  
Acute Gastroenteritis ◽  
Viral Gastroenteritis ◽  
Large Set ◽  
Next Generation ◽  
Genome Database ◽  
Detection Rates ◽  
Genome Data ◽  
Generation Sequencing

Human enteric adenovirus species F (HAdV-F) is one of the most common pathogens responsible for acute gastroenteritis worldwide. Brazil is a country with continental dimensions where continuous multiregional surveillance is vital to establish a more complete picture of the epidemiology of HAdV-F. The aim of the current study was to investigate the molecular epidemiology of HAdV-F using full-genome data in rural and low-income urban areas in northern Brazil. This will allow a genetic comparison between Brazilian and global HAdV-F strains. The frequency of HAdV-F infections in patients with gastroenteritis and molecular typing of positive samples within this period was also analysed. A total of 251 stool samples collected between 2010 and 2016 from patients with acute gastroenteritis were screened for HAdV-F using next-generation sequencing techniques. HAdV-F infection was detected in 57.8 % (145/251) of samples. A total of 137 positive samples belonged to HAdV-F41 and 7 to HAdV-F40. HAdV-F40/41 dual infection was found in one sample. Detection rates did not vary significantly according to the year. Single HAdV-F infections were detected in 21.9 % (55/251) of samples and mixed infections in 37.4 % (94/251), with RVA/HAdV-F being the most frequent association (21.5 %; 54/251). Genetic analysis indicated that the HAdV-F strains circulating in Brazil were closely related to worldwide strains, and the existence of some temporal order was not observed. This is the first large-scale HAdV-F study in Brazil in which whole-genome data and DNA sequence analyses were used to characterize HAdV-F strains. Expanding the viral genome database could improve overall genotyping success and assist the National Center for Biotechnology Information (NCBI)/GenBank in standardizing the HAdV genome records by providing a large set of annotated HAdV-F genomes.

scholarly journals Identification, Isolation, Propagation and Inactivation of SARS-CoV2 Isolated from Egypt

2020 ◽  
Author(s):  
M.G Seadawy ◽  
A.F Gad ◽  
M.F Elhoseny ◽  
B.El ELharty ◽  
M.D Shamel
Keyword(s):  
Next Generation Sequencing ◽  
Severe Acute Respiratory Syndrome ◽  
Gene Bank ◽  
Military Hospital ◽  
The Novel ◽  
Who Guidelines ◽  
Rt Pcr ◽  
Ssrna Virus ◽  
Inactivated Vaccines ◽  
Generation Sequencing

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 causes the novel pandemic Pneumonia disease. It is a positive single strand ssRNA virus that infect human. COVID-19 appeared in Egypt in Feb 2020. The samples were taken from patients with COVID-19 symptoms at military hospital in Egypt and transported to the main chemical laboratories under all the biosafety measures according to WHO guidelines. All samples were tested with RT-PCR. Positive samples were cultured using VeroE6 cell lines. The propagated virus was isolated and inactivated. The isolated virus was sequenced using next generation sequencing and submitted into gene bank. This study provides an isolation, propagation and inactivation methodology which is valuable for production of inactivated vaccines against SARS-CoV2 in Egypt.

scholarly journals The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7415
Author(s):  
An Huang ◽  
Shuo Liu ◽  
Haijun Li ◽  
Hongdi Luo ◽  
Qingyong Ni ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Control Region ◽  
Evolutionary Process ◽  
Tree Frog ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Mitogenome Sequence ◽  
Nd5 Gene ◽  
Generation Sequencing

The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases.

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