scholarly journals Two Different Strains of Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in North and South Osaka by Phylogenetic Analysis of Evolutionary Lineage: Evidence for Independent SFTSV Transmission

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 177
Author(s):  
Ryo Ikemori ◽  
Ikuko Aoyama ◽  
Tadahiro Sasaki ◽  
Hirono Takabayashi ◽  
Kazutoshi Morisada ◽  
...  
Keyword(s):  
Whole Genome ◽  
Evolutionary Lineage ◽  
First Case ◽  
Local Areas ◽  
Different Strains ◽  
Next Generation Sequencing Ngs ◽  
North And South ◽  
Severe Fever ◽  
Generation Sequencing ◽  
Japanese Group

Severe fever with thrombocytopenia syndrome (SFTS) is a novel tick-borne infectious disease, therefore, the information on the whole genome of the SFTS virus (SFTSV) is still limited. This study demonstrates a nearly whole genome of the SFTSV identified in Osaka in 2017 and 2018 by next-generation sequencing (NGS). The evolutionary lineage of two genotypes, C5 and J1, was identified in Osaka. The first case in Osaka belongs to suspect reassortment (L:C5, M:C5, S:C4), the other is genotype J1 (L: J1, M: J1, S: J1) according to the classification by a Japanese group. C5 was identified in China, indicating that C5 identified in this study may be transmitted by birds between China and Japan. This study revealed that different SFTSV genotypes were distributed in two local areas, suggesting the separate or focal transmission patterns in Osaka.

scholarly journals Utility of Whole-Genome Next-Generation Sequencing of Plasma in Identifying Opportunistic Infections in HIV/AIDS

2019 ◽  
Vol 13 (1) ◽  
pp. 7-11 ◽  
Author(s):  
Yang Zhou ◽  
Vagish Hemmige ◽  
Sudeb C. Dalai ◽  
David K. Hong ◽  
Kenneth Muldrew ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Opportunistic Infections ◽  
Case Series ◽  
Whole Genome ◽  
Next Generation ◽  
Invasive Procedures ◽  
First Case ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Hiv Aids

Background:AIDS-associated Opportunistic Infections (OIs) have significant morbidity and mortality and can be diagnostically challenging, requiring invasive procedures as well as a combination of culture and targeted molecular approaches.Objective:We aimed to demonstrate the clinical utility of Next-generation Sequencing (NGS) in pathogen identification; NGS is a maturing technology enabling the detection of miniscule amounts of cell-free microbial DNA from the bloodstream.Methods:We utilized a novel Next-generation Sequencing (NGS) test on plasma samples to diagnose a series of HIV-associated OIs that were diagnostically confirmed through conventional microbial testing.Results:In all cases, NGS test results were available sooner than conventional testing. This is the first case series demonstrating the utility of whole-genome NGS testing to identify OIs from plasma in HIV/AIDS patients.Conclusion:NGS approaches present a clinically-actionable, comprehensive means of diagnosing OIs and other systemic infections while avoiding the labor, expense, and delays of multiple tests and invasive procedures.

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 Detection of severe fever with thrombocytopenia syndrome virus and other viruses in cats via unbiased next-generation sequencing

2020 ◽  
pp. 104063872096750
Author(s):  
Yasuyuki Momoi ◽  
Aya Matsuu
Keyword(s):  
Next Generation Sequencing ◽  
Viral Infections ◽  
Nucleotide Sequencing ◽  
Plasma Samples ◽  
Next Generation ◽  
Dna Library ◽  
Immunodeficiency Virus ◽  
Next Generation Sequencing Ngs ◽  
Severe Fever ◽  
Generation Sequencing

We used unbiased next-generation sequencing (NGS) to detect unknown viruses in cats. Serum or plasma samples were obtained from clinically ill cats with suspected acute viral infections. Nucleic acid was extracted from serum or plasma samples to construct a complementary DNA library for NGS. Comprehensive nucleotide sequencing analyses enabled detection of the genomes of various viruses, including the severe fever with thrombocytopenia syndrome virus, feline immunodeficiency virus, feline morbillivirus, parvovirus, and Torque teno felis virus. Our findings indicate that comprehensive nucleotide analyses of serum or plasma samples can be used to detect infections with unknown viruses in cats.

scholarly journals Whole genome sequencing suggests transmission of Corynebacterium diphtheriae-caused cutaneous diphtheria in two siblings, Germany, 2018

2019 ◽  
Vol 24 (2) ◽  
Author(s):  
Anja Berger ◽  
Alexandra Dangel ◽  
Tilmann Schober ◽  
Birgit Schmidbauer ◽  
Regina Konrad ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Corynebacterium Diphtheriae ◽  
Whole Genome ◽  
Next Generation ◽  
Insect Bites ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

In September 2018, a child who had returned from Somalia to Germany presented with cutaneous diphtheria by toxigenic Corynebacterium diphtheriae biovar mitis. The child’s sibling had superinfected insect bites harbouring also toxigenic C. diphtheriae. Next generation sequencing (NGS) revealed the same strain in both patients suggesting very recent human-to-human transmission. Epidemiological and NGS data suggest that the two cutaneous diphtheria cases constitute the first outbreak by toxigenic C. diphtheriae in Germany since the 1980s.

scholarly journals Human Papillomavirus and the Development of Different Cancers

2016 ◽  
Vol 150 (3-4) ◽  
pp. 185-193 ◽  
Author(s):  
Ge Gao ◽  
David I. Smith
Keyword(s):  
Cervical Cancer ◽  
Squamous Cell Carcinomas ◽  
Human Papillomaviruses ◽  
Whole Genome ◽  
Physical Status ◽  
Cervical Cancers ◽  
Mate Pair ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Human papillomaviruses (HPV) are responsible for the development of almost all cervical cancers. HPV is also found in 85% of anal cancer and in 50% of penile, vulvar, and vaginal cancers, and they are increasingly found in a subset of head and neck cancers, i.e., oropharyngeal squamous cell carcinomas (OPSCC). The model for how HPV causes cancer is derived from several decades of study on cervical cancer, and it is just presumed that this model is not only completely valid for cervical cancer but for all other HPV-driven cancers as well. Next-generation sequencing (NGS) has now provided the necessary tools to characterize genomic alterations in cancer cells and can precisely determine the physical status of HPV in those cells as well. We discuss recent discoveries from different applications of NGS in both cervical cancer and OPSCCs, including whole-genome sequencing and mate-pair NGS. We also discuss what NGS studies have revealed about the different ways that HPV can be involved in cancer formation, specifically comparing cervical cancer and OPSCC.

scholarly journals An Update on Zoonotic Cryptosporidium Species and Genotypes in Humans

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3307
Author(s):  
Una Ryan ◽  
Alireza Zahedi ◽  
Yaoyu Feng ◽  
Lihua Xiao
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Molecular Detection ◽  
Epidemiological Studies ◽  
Cryptosporidium Species ◽  
Transmission Dynamics ◽  
Whole Genome ◽  
Zoonotic Pathogen ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The enteric parasite, Cryptosporidium is a major cause of diarrhoeal illness in humans and animals worldwide. No effective therapeutics or vaccines are available and therefore control is dependent on understanding transmission dynamics. The development of molecular detection and typing tools has resulted in the identification of a large number of cryptic species and genotypes and facilitated our understanding of their potential for zoonotic transmission. Of the 44 recognised Cryptosporidium species and >120 genotypes, 19 species, and four genotypes have been reported in humans with C. hominis, C. parvum, C. meleagridis, C. canis and C. felis being the most prevalent. The development of typing tools that are still lacking some zoonotic species and genotypes and more extensive molecular epidemiological studies in countries where the potential for transmission is highest are required to further our understanding of this important zoonotic pathogen. Similarly, whole-genome sequencing (WGS) and amplicon next-generation sequencing (NGS) are important for more accurately tracking transmission and understanding the mechanisms behind host specificity.

scholarly journals A20 Sample preparation for whole-genome next-generation sequencing (NGS) of hepatitis C virus (HCV) routine RNA samples

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
Julia Hillung ◽  
María Alma Bracho ◽  
Javier Pons Tamarit ◽  
Fernando González-Candelas
Keyword(s):  
Sample Preparation ◽  
Nucleic Acids ◽  
Blood Plasma ◽  
Reference Genome ◽  
Phylogenetic Analyses ◽  
Whole Genome ◽  
Library Preparation ◽  
Genome Sequences ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Next-generation sequencing (NGS) is a technique that can capture the variability of viral populations in transmission studies. The conventional sample preparation for NGS, based on amplicons, is a potential source of errors, derived from the variable affinity of specific primers for different viral variants and from irregular DNA polymerase efficiency. In this context, we propose a more reliable method for viral whole genome sample preparation, starting from nucleic acids obtained and stored with conventional procedures. Our goal was to obtain complete hepatitis C virus (HCV) genome sequences to subsequently perform extensive phylogenetic analyses. Additionally, we aimed to test the effectiveness of nuclease treatment used to remove contaminating host DNA. Nucleic acids were obtained from almost cell-free blood plasma of HCV-infected patients. As a source for Illumina library preparation, double-stranded cDNA was generated using random primers. The HCV genome was not amplified before library preparation, avoiding possible biases derived from unequal copying. To get rid of possible host contaminants in the samples, a DNase treatment step was added. Libraries were paired-end sequenced on the Illumina platform using MiSeq reagent kit v3. After conservative filtering of contaminant human reads by alignment with the human reference genome using Burrows-Wheeler Aligner (BWA), the remaining reads were mapped to the HCV reference genome using BWA. Primary maximum likelihood phylogenetic analyses were performed using ClustalW and IQTREE to infer the phylogenetic relationships of the sequenced samples in the context of complete genome sequences of the same genotype. NGS sample preparation method of HCV from blood plasma was established. Complete genome sequences of HCV could be obtained with variable coverage depending on the viral load of plasma samples. No significant reduction of host DNA proportion in DNase treated samples in comparison to the controls was observed. The new sequences clustered within the Los Alamos National Laboratory database-deposited HCV subtype 4d samples. The method can be used to obtain full-length sequences of HCV from nucleic acid samples not previously planned for NGS. No improvement was observed when DNase pre-treatment of nucleic acids extracted from blood plasma was performed.

scholarly journals Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia

2021 ◽  
Author(s):  
Wasfi Fares ◽  
Kais Ghedira ◽  
Mariem Gdoura ◽  
Anissa Chouikha ◽  
Sondes Haddad-Boubaker ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
High Genetic Diversity ◽  
Middle Income ◽  
Middle Income Countries ◽  
Transmission Period ◽  
Variant Detection ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The method of choice for SARS-CoV-2 variant detection is whole-genome sequencing using next-generation sequencing (NGS) technologies. Resources for this technology remain limited in many low- and middle-income countries, where it is not possible to perform whole-genome sequencing for representative numbers of SARS-CoV-2-positive cases.

Sign in / Sign up

Export Citation Format

Share Document