Molecular Genotyping of Human Rhinovirus by Using PCR and Sanger Sequencing

2014 ◽  
pp. 39-47 ◽  
Author(s):  
Wei Wang ◽  
Jing He ◽  
Yi Liu ◽  
Lei Xu ◽  
Wencai Guan ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Human Rhinovirus ◽  
Molecular Genotyping

scholarly journals Molecular epidemiology of rhinovirus among hospitalised patients, Singapore

2016 ◽  
Vol 31 (4) ◽  
Author(s):  
Chun Kiat Lee ◽  
Erik Wei Jun Low ◽  
Christian Benjamin George Highfield ◽  
Hong Kai Lee ◽  
Paul Tambyah Anantharajah ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Phylogenetic Reconstruction ◽  
Etiological Agent ◽  
Human Rhinovirus ◽  
Molecular Genotyping ◽  
Hospitalised Patients ◽  
The World ◽  
Study Population ◽  
Respiratory Specimens ◽  
Dominant Genotype

Human rhinovirus (HRV) is the most prevalent respiratory etiological agent in the world. Over 100 genotypes have been characterised using molecular genotyping techniques. Here, we characterised the molecular epidemiology of the circulating rhinoviruses among hospitalised patients in Singapore by sequencing 134 rhinovirus-positive respiratory specimens that were collected in the period between 2013 and 2015. Each sequence was assigned a genogroup and a genotype using the Enterovirus Genotyping Tool Version 0.1 and phylogenetic reconstruction, respectively. In this study, HRV-A (n=88) and HRV-C (n=38) were identified as the dominant genogroups in Singapore. HRV-A28 (n=7) was the dominant genotype in HRV-A while both HRVC2 (n=8) and HRV-C11 (n=8) were the dominant genotypes in HRV-C. HRV-B was observed to have the lowest number of positive detections in our study population (n=8). The result is interesting as another group had previously found HRV-B to be the second most common genogroup in Singapore after HRV-A.

scholarly journals Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis

Parasite ◽  
2020 ◽  
Vol 27 ◽  
pp. 24 ◽  
Author(s):  
Katelyn A. Houghton ◽  
Alexandre Lomsadze ◽  
Subin Park ◽  
Fernanda S. Nascimento ◽  
Joel Barratt ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Intestinal Parasite ◽  
Epidemiological Data ◽  
Amplicon Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Molecular Genotyping ◽  
Cyclospora Cayetanensis ◽  
Outbreak Investigations ◽  
Stool Specimens

Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in C. cayetanensis genomes. Four whole C. cayetanensis genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating C. cayetanensis into 19 new unique genotypes.

Successful in silico discovery of natural inhibitors for human rhinovirus coat protein

Planta Medica ◽  
2007 ◽  
Vol 73 (09) ◽  
Author(s):  
JM Rollinger ◽  
TM Steindl ◽  
K Anrain ◽  
EP Ellmerer ◽  
M Schmidtke ◽  
...  
Keyword(s):  
Coat Protein ◽  
In Silico ◽  
Human Rhinovirus ◽  
Natural Inhibitors

THE NUCLEAR FACTOR OF HEPATOCYTES 1β (HNF1β)–ASSOCIATED DISEASE. CLINIC, DIAGNOSTIC, TREATMENT (LITERATURE REVIEW AND CLINICAL OBSERVATION)

2019 ◽  
Vol 23 (2) ◽  
pp. 100-108
Author(s):  
S. V. Papizh ◽  
O. R. Piruzieva
Keyword(s):  
Sanger Sequencing ◽  
Clinical Observation ◽  
Liver Enzymes ◽  
Renal Ultrasound ◽  
Nuclear Factor ◽  
Hepatocyte Nuclear Factor ◽  
Renal Hypoplasia ◽  
Unilateral Renal Agenesis ◽  
Elevated Liver Enzymes ◽  
Medullary Nephrocalcinosis

Hepatocyte nuclear factor 1β (HNF1β)-associated disease is a rare autosomal dominant disease caused by various mutations in the HNF1β gene coding the hepatocyte nuclear factor 1β. HNF1β is a transcription factor that is critical for the development of kidney urogenital tract, pancreas, liver, brain, and parathyroid gland. Renal phenotype or HNF1β- nephropathy appeared to be extremely heterogenic: multicystic renal dysplasia, renal hypoplasia, unilateral renal agenesis, horseshoe kidney, atypical familial juvenile hyperuricemic nephropathy, urinary tract malformations and tubular dysfunction. Extrarenal phenotype of HNF1β-associated disease could be maturity-onset diabetes of the young (MODY), pancreatic atrophy and exocrine pancreatic dysfunction, elevated liver enzymes, neonatal cholestasis, congenital abnormalities of the genital tract, hyperparathyroidism, neurological symptoms. The multisystem phenotype makes clinical verification of the diagnosis extremely difficult. In this article, we present a clinical observation of a child with HNF1β – associated disease. The first clinical presentation of HNF1β-associated disease was ultrasound changes in the kidneys (hyperechogenic kidneys?), which were detected by prenatal ultrasonography in pregnancy. Renal ultrasound revealed polycystic kidney disease in the first days of life and bilateral medullary nephrocalcinosis by the age of three. The clinical examination showed a reduced renal function and developed Fanconi syndrome (glycosuria, low molecular proteinuria, hypophosphatemia, aminoaciduria, hyperuricosuria) in the first year of life. Also the child had a non-constant asymptomatic elevation of liver enzymes, hyperparathyroidism, osteoporosis. The diagnosis was confirmed by the results of next generation sequencing which revealed novel heterozygous mutation in exon 4 of the HNF1b gene (chr17: 36091813C>T), p.Cys273Tyr (c.818G>A). The identified mutation was validated by Sanger sequencing. Validation by Sanger sequencing did not reveal a chr17: 36091813C>T mutation in parents, which suggested the appearance of a mutation in the child de novo.

Rare Germline GLMN Variants Identified from Blue Rubber Bleb Nevus Syndrome Might Impact mTOR Signaling

2020 ◽  
Vol 22 (10) ◽  
pp. 675-682 ◽  
Author(s):  
Jie Yin ◽  
Zhongping Qin ◽  
Kai Wu ◽  
Yufei Zhu ◽  
Landian Hu ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Sanger Sequencing ◽  
Somatic Mutations ◽  
Venous Malformation ◽  
Underlying Disease ◽  
Mtor Signaling ◽  
Functional Effect ◽  
Germline Variants ◽  
Whole Exome

Backgrounds and Objective: Blue rubber bleb nevus syndrome (BRBN) or Bean syndrome is a rare Venous Malformation (VM)-associated disorder, which mostly affects the skin and gastrointestinal tract in early childhood. Somatic mutations in TEK have been identified from BRBN patients; however, the etiology of TEK mutation-negative patients of BRBN need further investigation. Method: Two unrelated sporadic BRBNs and one sporadic VM were firstly screened for any rare nonsilent mutation in TEK by Sanger sequencing and subsequently applied to whole-exome sequencing to identify underlying disease causative variants. Overexpression assay and immunoblotting were used to evaluate the functional effect of the candidate disease causative variants. Results: In the VM case, we identified the known causative somatic mutation in the TEK gene c.2740C>T (p.Leu914Phe). In the BRBN patients, we identified two rare germline variants in GLMN gene c.761C>G (p.Pro254Arg) and c.1630G>T(p.Glu544*). The GLMN-P254R-expressing and GLMN-E544X-expressing HUVECs exhibited increased phosphorylation of mTOR-Ser-2448 in comparison with GLMN-WTexpressing HUVECs in vitro. Conclusion: Our results demonstrated that rare germline variants in GLMN might contribute to the pathogenesis of BRBN. Moreover, abnormal mTOR signaling might be the pathogenesis mechanism underlying the dysfunction of GLMN protein.

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