scholarly journals The epidemic of Q fever in 2018 to 2019 in Zhuhai city of China determined by metagenomic next-generation sequencing

2021 ◽  
Vol 15 (7) ◽  
pp. e0009520
Author(s):  
Mingxing Huang ◽  
Jinmin Ma ◽  
Jun Jiao ◽  
Chunna Li ◽  
Luan Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Q Fever ◽  
Quantitative Polymerase Chain Reaction ◽  
Clinical Information ◽  
Immunofluorescence Assay ◽  
Plasma Samples ◽  
Next Generation ◽  
Outbreak Period ◽  
Infection Source ◽  
Generation Sequencing

Q fever is a worldwide zoonosis caused by Coxiella burnetii (Cb). From January 2018 to November 2019, plasma samples from 2,382 patients with acute fever of unknown cause at a hospital in Zhuhai city of China were tested using metagenomic next-generation sequencing (mNGS). Of those tested, 138 patients (5.8%) were diagnosed with Q fever based on the presence of Cb genomic DNA detected by mNGS. Among these, 78 cases (56.5%) presented from Nov 2018 to Mar 2019, suggesting an outbreak of Q fever. 55 cases with detailed clinical information that occurred during the outbreak period were used for further analysis. The vast majority of plasma samples from those Cb-mNGS-positive patients were positive in a Cb-specific quantitative polymerase chain reaction (n = 38) and/or indirect immunofluorescence assay (n = 26). Mobile phone tracing data was used to define the area of infection during the outbreak. This suggested the probable infection source was Cb-infected goats and cattle at the only official authorized slaughterhouse in Zhuhai city. Phylogenic analysis based on genomic sequences indicated Cb strains identified in the patients, goat and cattle were formed a single branch, most closely related to the genomic group of Cb dominated by strains isolated from goats. Our study demonstrates Q fever was epidemic in 2018–2019 in Zhuhai city, and this is the first confirmed epidemic of Q fever in a contemporary city in China.

scholarly journals Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings

2021 ◽  
Vol 12 ◽  
Author(s):  
Tyler Dang ◽  
Irene Lavagi-Craddock ◽  
Sohrab Bodaghi ◽  
Georgios Vidalakis
Keyword(s):  
Next Generation Sequencing ◽  
Target Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
High Density ◽  
Poncirus Trifoliata ◽  
Next Generation ◽  
Developmental Processes ◽  
Wide Range ◽  
Generation Sequencing ◽  
Citrus Trees

Citrus dwarfing viroid (CDVd) induces stunting on sweet orange trees [Citrus sinensis (L.) Osbeck], propagated on trifoliate orange rootstock [Citrus trifoliata (L.), syn. Poncirus trifoliata (L.) Raf.]. MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play important roles in the regulation of tree gene expression. To identify miRNAs in dwarfed citrus trees, grown in high-density plantings, and their response to CDVd infection, sRNA next-generation sequencing was performed on CDVd-infected and non-infected controls. A total of 1,290 and 628 miRNAs were identified in stem and root tissues, respectively, and among those, 60 were conserved in each of these two tissue types. Three conserved miRNAs (csi-miR479, csi-miR171b, and csi-miR156) were significantly downregulated (adjusted p-value < 0.05) in the stems of CDVd-infected trees compared to the non-infected controls. The three stem downregulated miRNAs are known to be involved in various physiological and developmental processes some of which may be related to the characteristic dwarfed phenotype displayed by CDVd-infected C. sinensis on C. trifoliata rootstock field trees. Only one miRNA (csi-miR535) was significantly downregulated in CDVd-infected roots and it was predicted to target genes controlling a wide range of cellular functions. Reverse transcription quantitative polymerase chain reaction analysis performed on selected miRNA targets validated the negative correlation between the expression levels of these targets and their corresponding miRNAs in CDVd-infected trees. Our results indicate that CDVd-responsive plant miRNAs play a role in regulating important citrus growth and developmental processes that may participate in the cellular changes leading to the observed citrus dwarf phenotype.

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 Next Generation Sequencing of Tumor and Matched Plasma Samples: Identification of Somatic Variants in ctDNA From Ovarian Cancer Patients

2021 ◽  
Vol 11 ◽  
Author(s):  
Ana Barbosa ◽  
Pedro Pinto ◽  
Ana Peixoto ◽  
Joana Guerra ◽  
Manuela Pinheiro ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Next Generation Sequencing ◽  
Molecular Profiling ◽  
Post Treatment ◽  
Plasma Samples ◽  
Next Generation ◽  
Somatic Variant ◽  
Treatment Naïve ◽  
Ctdna Analysis ◽  
Generation Sequencing

Genetic testing to detect somatic alterations is usually performed on formalin-fixed paraffin-embedded tumor samples. However, tumor molecular profiling through ctDNA analysis may be particularly interesting with the emergence of targeted therapies for ovarian cancer (OC), mainly when tumor is not available and biopsy is not viable, also allowing representation of multiple neoplastic subclones. Using a custom panel of 27 genes, next-generation sequencing (NGS) was performed on tumor and matched plasma samples from 96 OC patients, which were combined in two groups (treatment naive and post-treatment). Overall, at least one somatic variant present in the tumor sample was also detected in the matched plasma sample in 35.6% of the patients, a percentage that increased to 69.6% of the treatment naive patients and 83.3% of those with stage IV disease, showing the potential of ctDNA analysis as an alternative to identify somatic variants in these patients, namely those that have predictive value for targeted therapy. In fact, of the two treatment-naive patients with somatic BRCA1 variants identified in tumor samples, in one of them we detected in ctDNA a BRCA1 somatic variant that was present in the tumor with a VAF of 53%, but not in the one that had a VAF of 5.4%. We also showed that ctDNA analysis has a complementary role to molecular unraveling of inter- and intra-tumor heterogeneity, as exemplified by one patient diagnosed with bilateral OC in which different somatic variants from both tumors were detected in ctDNA. Interestingly, as these bilateral tumors shared a rare combination of two of the three variants identified in ctDNA, we could conclude that these morphologically different tumors were clonally related and not synchronous independent neoplasias. Moreover, in the post-treatment group of patients with plasma samples collected after surgery, those with detectable somatic variants had poor prognosis when compared with patients with no detectable somatic variants, highlighting the potential of ctDNA analysis to identify patients at higher risk of recurrence. Concluding, this study demonstrated that somatic variants can be detected in plasma samples of a significant proportion of OC patients, supporting the use of NGS-based ctDNA testing for noninvasive tumor molecular profiling and to stratify patients according to prognosis.

scholarly journals Quadruplex qPCR for qualitative and quantitative analysis of the HIV-1 latent reservoir

2019 ◽  
Author(s):  
Christian Gaebler ◽  
Julio C. C. Lorenzi ◽  
Thiago Y. Oliveira ◽  
Lilian Nogueira ◽  
Victor Ramos ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Quantitative Polymerase Chain Reaction ◽  
Specific Antigen ◽  
Latent Reservoir ◽  
Next Generation ◽  
Sequencing Method ◽  
Generation Sequencing ◽  
Hiv 1 ◽  
Next Generation Sequencing Method

AbstractHIV-1 infection requires life-long therapy with anti-retroviral drugs due to the existence of a latent reservoir of transcriptionally inactive integrated proviruses. The goal of HIV-1 cure research is to eliminate or functionally silence this reservoir. To this end there are numerous ongoing studies to evaluate immunologic approaches including monoclonal antibody therapies. Evaluating the results of these studies requires sensitive and specific measures of the reservoir. Here we describe a relatively high throughput combined quantitative polymerase chain reaction (qPCR) and next generation sequencing method. Four different qPCR probes covering the packaging signal (PS), group-specific antigen (gag), polymerase (pol), and envelope (env) are combined in a single multiplex reaction to detect the HIV-1 genome in limiting dilution samples followed by sequence verification of individual reactions that are positive for combinations of any 2 of the 4 probes (Q4PCR). This sensitive and specific approach allows for an unbiased characterization of the HIV-1 latent reservoir.SummaryHIV-1 cure research seeks to decrease or eliminate the latent reservoir. The evaluation of such curative strategies requires accurate measures of the reservoir. Gaebler et al. describe a combined multicolor qPCR and next generation sequencing method that enables the sensitive and specific characterization of the HIV-1 latent reservoir.

Transcriptome (RNA next generation sequencing) for personalizing of cancer treatment: A correlation with previous clinical resistance.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e15046-e15046
Author(s):  
Manuel Sureda ◽  
Joseba Rebollo ◽  
Ramón González-Manzano ◽  
Elena Ma Martínez ◽  
Roman Rostagno ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Checkpoint Inhibitors ◽  
Metastatic Cancer ◽  
Alkylating Agents ◽  
Treatment Decision ◽  
Clinical Information ◽  
Next Generation ◽  
Clinical Resistance ◽  
Generation Sequencing

e15046 Background: RNA Next Generation Sequencing (transcriptome) is a potential useful tool to predict chemoresistance to available anticancer drug therapy. A correlation between previous clinical resistance and drug resistance profiling according to RNA NGS results has been studied. Methods: Since March 2018, whole transcriptome RNA NGS has been performed using Ion-Torrent GeneStudio S5 System in fresh-frozen biopsies obtained from tru-cut or surgical excision procedures from patients with resistant metastatic cancer. We have selected patients with clinically unequivocal drug resistance to previous therapies (tumor progressing to ongoing therapies or less than six months of stopped therapy). Drugs evaluated includes anthracyclines, alkylating agents (temozolomide), platinum derivatives, taxanes, TOPO 1 inhibitors (irinotecan and topotecan), antimetabolites (fluoropyrimidines, gemcitabine, methotrexate and pemetrexed), and more recently, immune checkpoint inhibitors. Results: A total of 111 procedures have been performed. In 64 patients an unequivocal clinical resistance to previous therapies could not be demonstrated, so the analyses has been performed in 47 patients with a number of different tumor histologies: colorectal cancer (13 patients), ovary/peritoneum (8), pancreas (4), NSCLC (4), breast (3), prostate (3), sarcoma (3), head and neck (2), uterus (2), kidney, bladder, cholangiocarcinoma, stomach and cervix (1 patient each). One hundred and fifty two drugs have been used in these patients (Median 3, Range 1 to 8) previous to the RNA NGS procedure. Resistance profile has been found in 120 out of 152 (78.9% of coincidence), and a favourable profile has been found in 32 (21%) previously used drugs, that could be re-used again in these patients. RNA NGS procedure gives additional information about drugs not previously used that helps in the treatment selection for the patients. Conclusions: Transcriptome provide drug resistance information that correlates in 78.9% of drugs with the previous clinical information. However, in 21% of the previously used drugs transcriptome informs as potentially active and could be tried again in subsequent therapies. Transcriptome (RNA sequencing) provides useful clinical information for treatment decision in the vast majority of pretreated cancer patients.

Evaluation of clonal hematopoiesis in late stage NSCLC using a next-generation sequencing panel targeting cancer genes.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 9050-9050 ◽  
Author(s):  
Stephanie J. Yaung ◽  
Frederike Fuhlbrück ◽  
Johnny Wu ◽  
Fergal Casey ◽  
Maureen Peterson ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Locally Advanced ◽  
Sequencing Analysis ◽  
Plasma Samples ◽  
Cancer Genes ◽  
Next Generation ◽  
Clonal Hematopoiesis ◽  
The Impact ◽  
Generation Sequencing

9050 Background: Somatic mutations derived from the expansion of clonal populations of blood cells (clonal hematopoiesis of indeterminate potential, or CHIP) may be detected in sequencing of cell-free DNA (cfDNA) samples. We evaluated the potential implications of CHIP in targeted sequencing of lung cancer plasma samples using matched peripheral blood mononuclear cells (PBMC) to identify CHIP. Methods: Samples were evaluated from OAK, a phase 3 trial of atezolizumab in locally advanced or metastatic NSCLC following failure with platinum-based therapy. 94 samples from Cycle 1 Day 1 (C1D1) plasma and matched PBMC were analyzed with the AVENIO ctDNA Surveillance Kit (For Research Use Only, not for use in diagnostic procedures), a 198-kb next-generation sequencing panel targeting cancer genes. Plasma samples from subsequent cycles of therapy (C2D1, C3D1, and C4D1) were also sequenced with the same panel. Using median input amounts of 22.8 ng cfDNA and 50 ng PBMC DNA, we obtained median deduplicated depths of 5413 and 5070, respectively. Results: In C1D1 cfDNA, a median of 120 single nucleotide variants were detected per sample, with 5.13% of variants not identified in matched PBMC (i.e., putative tumor-derived somatic variants) versus 94.87% of variants identified in matched PBMC (i.e., germline or CHIP variants). While the majority of PBMC-matched variants were SNPs with allele frequency (AF) around 50% or 100% as expected, there was a median of 1 (range 0-8) PBMC-matched cfDNA variants per sample with AF below 10%. Consistent with CHIP, the number of PBMC-matched cfDNA variants per subject below AF 10% were positively associated with age (p-value = 0.0145), and TP53 was the most frequently mutated gene. We found similar results in plasma samples from subsequent cycles. Conclusions: Plasma and PBMC sequencing analysis identified potential mutations derived from CHIP. However, 39% of cfDNA samples had zero potential CHIP mutations identified in the study, possibly due to the specific regions targeted by the AVENIO assay. While this study suggests that only a small percentage of variants detected by the AVENIO Surveillance panel in lung cancer are derived from CHIP, further studies are warranted to assess the impact and removal of these variants.

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