scholarly journals Multiplex Detection of Rotavirus A, B, C, Norovirus GI and GII, Adenovirus, Astrovirus and Sapovirus in a Single PCR System in Stool Samples From Acute Diarrhea Children

2020 ◽  
Author(s):  
Wei Li ◽  
Weiwei Li ◽  
Ran Tao ◽  
Wenqing Xiang ◽  
Mingming Zhou ◽  
...  
Keyword(s):  
High Throughput ◽  
Acute Diarrhea ◽  
Cross Reaction ◽  
Melting Curve Analysis ◽  
Clinical Test ◽  
Rt Pcr ◽  
Rotavirus A ◽  
Diarrhea Virus ◽  
Intestinal Pathogens ◽  
Stool Samples

Abstract Background: Early and accurate identification of infection viruses among children can benefit the personalized medical treatment and management, and reduce the future occurrence of serious symptoms. Thus, it is critical to develop a high-throughput multiplex real-time RT-PCR method to improve the accuracy and efficiency in routine clinical lab tests. Here, we developed a RT-PCR combined with melting curve analysis (RRCMC) method for simultaneous detection of rotavirus A, B, C, norovirus GI and GII, adenovirus, astrovirus and sapovirus. Results: Stool samples were collected from 160 children with acute diarrhea and tested by RRCMC assay. A total of 71 patients were tested positive with norovirus, adenovirus or rotavirus. The RRCMC assay has high specificity. There is no internal cross-reaction through the 8 diarrhea viruses and no cross-reaction of other commonly intestinal pathogens and human genome. The detection limit was ranging from 1×102 to 1×105 copies/ml for each diarrhea virus. Conclusions: In conclusion, the RRCMC method is a suitable rapid clinical test for infection viruses, with the advantages of high-throughput, low cost, high sensitivity, and specificity.

Multiplex Detection of Rotavirus A, B, C, Norovirus GI and GII, Adenovirus, Astrovirus and Sapovirus in a Single PCR System in Stool Samples From Children With Acute Diarrhea

2021 ◽  
Author(s):  
Wei Li ◽  
Wei-wei Li ◽  
Lin Li ◽  
Lin He ◽  
Wen-qing Xiang ◽  
...  
Keyword(s):  
Acute Diarrhea ◽  
Simultaneous Detection ◽  
Melting Curve ◽  
Cross Reaction ◽  
Melting Curve Analysis ◽  
Clinical Test ◽  
Rotavirus A ◽  
Diarrhea Virus ◽  
Intestinal Pathogens ◽  
Stool Samples

Abstract We developed a RT-PCR combined with melting curve analysis (RRCMC) method for simultaneous detection of rotavirus A, B, C, norovirus GI and GII, adenovirus, astrovirus and sapovirus. Stool samples were collected from 160 children with acute diarrhea and tested by RRCMC assay. A total of 71 patients were tested positive with norovirus, adenovirus or rotavirus. The RRCMC assay has high specificity. There is no internal cross-reaction through the 8 diarrhea viruses and no cross-reaction of other commonly intestinal pathogens and human genome. The detection limit was ranging from 1×102 to 1×105 copies/ml for each diarrhea virus. In conclusion, the RRCMC method is a suitable rapid clinical test for infectious viruses, with the advantages of high-throughput, low cost, high sensitivity and specificity.

scholarly journals Diarrhea caused by rotavirus A, B, and C in suckling piglets from southern Brazil: molecular detection and histologic and immunohistochemical characterization

2018 ◽  
Vol 30 (3) ◽  
pp. 370-376 ◽  
Author(s):  
Paula R. Almeida ◽  
Elis Lorenzetti ◽  
Raquel S. Cruz ◽  
Tatiane T. Watanabe ◽  
Priscila Zlotowski ◽  
...  
Keyword(s):  
Virus Detection ◽  
Enteric Virus ◽  
Transmissible Gastroenteritis Virus ◽  
Southern Brazil ◽  
Rt Pcr ◽  
Viral Pathogen ◽  
Rotavirus A ◽  
Diarrhea Virus ◽  
Suckling Piglets ◽  
Transmissible Gastroenteritis

Rotavirus (RV) is an important viral pathogen causing diarrhea in piglets and other mammals worldwide. We describe 34 cases from 4 diarrheal outbreaks caused by RV in unvaccinated farrowing units in southern Brazil from 2011 to 2013. We performed autopsy, histologic examinations, bacterial culture, RV immunohistochemistry (IHC), and enteric virus detection through molecular assays for rotavirus A, B, and C, transmissible gastroenteritis virus, porcine epidemic diarrhea virus, sapovirus, norovirus, and kobuvirus. Histologically, villus atrophy (29 of 34) and epithelial vacuolation (27 of 34) occurred in all 4 outbreaks. Cell debris in the lamina propria occurred in 20 cases, mostly from outbreaks A (8 of 11), C (4 of 6), and D (7 of 11). IHC was positive for RV in 21 of 34 samples. RT-PCR was positive for RV in 20 of 30 samples; RV-C was the most frequently detected RV ( n = 17). Kobuvirus was detected in 11 samples, and, in 3 of them, there was single detection of this enteric virus.

scholarly journals Rotavirus genotyping in gastroenteritis cases of an infantile population from Western Brazilian Amazonia

2012 ◽  
Vol 45 (4) ◽  
pp. 520-522 ◽  
Author(s):  
Maria Sandra Moura Costa ◽  
Paulo Afonso Nogueira ◽  
Gleicienne Félix Magalhães ◽  
Paula Taquita ◽  
Luis André Mariúba ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Gel Electrophoresis ◽  
Polyacrylamide Gel Electrophoresis ◽  
Brazilian Amazon ◽  
Rt Pcr ◽  
Rotavirus A ◽  
Positive Stool ◽  
Group A ◽  
Stool Samples

INTRODUCTION: During the period from 2000 to 2002, 79 rotavirus-positive stool samples were collected from children presenting diarrhea in the Western Brazilian Amazon. METHODS: Molecular characterization of the G and P genotypes was performed using RT-PCR and electropherotyping analysis by polyacrylamide gel electrophoresis. RESULTS: A total of 59 samples were confirmed as group A rotavirus. A long electrophoretic profile was exhibited by the G1P[8], G3P[8], and G4P[8] genotypes. The G1P[8] genotype was found in greater proportion. The short electropherotype was exhibited only by G2 genotype strains. CONCLUSIONS: The proportion of the rotavirus genotypes observed was not different from that in other areas of Brazil. This study is the first genotyping of rotavirus in the Western Brazilian Amazon.

scholarly journals Use of dual priming oligonucleotide system-based multiplex RT-PCR assay to detect five diarrhea viruses in pig herds in South China

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guangbin Si ◽  
Jiawei Niu ◽  
Xia Zhou ◽  
Yongsheng Xie ◽  
Zhifei Chen ◽  
...  
Keyword(s):  
Detection Efficiency ◽  
Limit Of Detection ◽  
Transmissible Gastroenteritis Virus ◽  
Rt Pcr ◽  
Simple Method ◽  
Detection Rates ◽  
Rotavirus A ◽  
Diarrhea Virus ◽  
Dual Priming Oligonucleotide ◽  
Pcr Method

AbstractIn this study, a specific and simple method based on the dual priming oligonucleotide (DPO) system was developed to simultaneously detect transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine rotavirus A (PRV-A), porcine delta coronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), associated with the major enteric RNA viruses in pigs. The DPO system-based multiplex RT-PCR method simplified the primer design and did not require optimization of the annealing temperature. Specificity analysis revealed that the method could specifically detect TGEV, PEDV, PRV-A, PDCoV, and SADS-CoV without any cross-amplification of other circulating swine viruses. The limit of detection of the method was as low as 103–104 copies/μL plasmid of each virus. The method also had good repeatability, and obvious results were seen in three repeat experiments with an interval of 45 days. This optimized multiplex RT-PCR method was used to evaluate 181 clinical swine samples that were collected from four provinces of China between September 2016 and August 2018. The results showed that the positive detection rates of PEDV, PDCoV, SADS-CoV, PRV-A, and TGEV were 30.94% (56/181), 17.67% (32/181), 11.6% (21/181), 9.39% (17/181), and 0.55% (1/181), respectively. Mixed infection of two or more viruses was also common. The DPO system-based multiplex RT-PCR could be a useful tool for detecting enteric virus infections. This method has the advantages of easy operation, low cost, high detection efficiency, and short running time for early diagnosis in clinical cases.

scholarly journals Detection of C. difficile toxin as a model assay for performing fully automated high-throughput RT-PCR on clinical stool samples

2020 ◽  
Vol 172 ◽  
pp. 105882 ◽  
Author(s):  
Ulrich Eigner ◽  
Dominik Nörz ◽  
Svenja Reucher ◽  
Jan Furrer ◽  
Jingtao Sun ◽  
...  
Keyword(s):  
High Throughput ◽  
Rt Pcr ◽  
Stool Samples

scholarly journals Use of dual priming oligonucleotide system-based multiplex RT-PCR assay to detect five diarrhea viruses in pig herds in South China

2021 ◽  
Author(s):  
Guangbin Si ◽  
Jiawei Niu ◽  
Xia Zhou ◽  
Yongsheng Xie ◽  
Zhifei Chen ◽  
...  
Keyword(s):  
Detection Efficiency ◽  
Limit Of Detection ◽  
Transmissible Gastroenteritis Virus ◽  
Rt Pcr ◽  
Simple Method ◽  
Detection Rates ◽  
Rotavirus A ◽  
Diarrhea Virus ◽  
Dual Priming Oligonucleotide ◽  
Pcr Method

Abstract In this study, a specific and simple method based on the dual priming oligonucleotide (DPO) system was developed to simultaneously detect transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine rotavirus A (PRV-A), porcine delta coronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), associated with the major enteric RNA viruses in pigs. The multiplex RT-PCR method based on the DPO system simplified the primer design and did not require optimization of the annealing temperature. Specificity analysis revealed that the method could specifically detect TGEV, PEDV, PRV-A, PDCoV, and SADS-CoV without any cross-amplification of other circulating swine viruses. The limit of detection of the method was as low as 103–104 copies/μL plasmid of each virus. The method also had good repeatability, and obvious results were seen in three repeat experiments with an interval of 45 days. This optimized multiplex RT-PCR method was used to evaluate 181 clinical swine samples that were collected from four provinces of China between September 2016 and August 2018. The results showed that the positive detection rates of PEDV, PDCoV, SADS-CoV, PRV-A, and TGEV were 30.94% (56/181), 17.67% (32/181), 11.6% (21/181), 9.39% (17/181), and 0.55% (1/181), respectively. Mixed infection of two or more viruses was also common. The DPO system-based multiplex RT-PCR could be a useful tool for detecting enteric virus infections. This method has the advantages of easy operation, low cost, high detection efficiency, and short running time for early diagnosis in clinical cases.

Covid-19: A review of its clinical features, effects on gastrointestinal system and possibility of faecal transmission

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 623-627
Author(s):  
Kanishk K Adhit ◽  
Anjankar Ashish P ◽  
Siddhaarth K
Keyword(s):  
Clinical Presentation ◽  
Throat Swab ◽  
Respiratory Illness ◽  
Review Article ◽  
Gastrointestinal System ◽  
Rt Pcr ◽  
Significant Evidence ◽  
Stool Samples ◽  
High Possibility ◽  
Positive Results

In China, Wuhan in the province of China, COVID-19 a patient suffering from pneumonia was tested and to identify the cause, the throat swab of the patient was tested. On 7th January 2020 WHO declared the identification as COVID-19. And then it was proclaimed as a pandemic. It classically causes a respiratory illness presenting as a mild cough, fever and . However, several investigators have advocated the involvement of the gastrointestinal tract and liver in COVID-19 infection similar to other infections. Further research studies have shown results that are expanding the possibility of transmission because RT-PCR assessment has shown significant evidence for the presence of virus not only in samples but also in stool samples. Studies have shown that virus in stool samples have got positive results even after the illness has resolved, and two respiratory tests were done 24 hours after COVID-19 being tested negative. The review article the different findings of the clinical presentation of COVID-19. It sheds light on the effects of COVID-19 in the gastrointestinal system along with the reasons for the high possibility of transmission of COVID-19 through the route.

CLINICAL AND PARACLINICAL CHARACTERISTITICS OF ROTAVIRUS DIARRHEA IN CHILDREN LESS THAN 5 YEARS OLD IN PEDIATRIC DEPARTMENT OF BINH DINH GENERAL HOSPITAL

2013 ◽  
pp. 50-56
Author(s):  
Quoc Tinh Nguyen ◽  
Thi Cu Nguyen
Keyword(s):  
General Hospital ◽  
Acute Diarrhea ◽  
White Blood Cells ◽  
Blood Calcium ◽  
Pediatric Department ◽  
Rotavirus A ◽  
Initial Symptoms ◽  
Stool Specimens ◽  
The Mean ◽  
Rotavirus Diarrhea

Background: Diarrhea is a leading cause of morbidity and mortality in children in developing countries. Rotavirus is the most important factor cause of severe diarrhea and mortality in children, especially under 2 years. Objective: To study Clinical and paraclinical characteristitics of rotavirus diarrhea in children less than 5 years old in the Pediatric Department of Binh Dinh General Hospital. Methods: Cross observational study, 417 children from 2 months to 5 years old who were hospitalized for acute diarrhea without blood in stool in Pediatric Department of Binh Dinh general hospital, from 15/3/2012 to 14/3/2013. There were 228 patients with rotavirus - positive stool specimens and 189 patients with rotavirus - negative stool specimens. Tested for rotavirus A classification by agglutination techniques. Results: Percentage of Rotavirus diarrhea in children <5 years was 54.7%. The mean age of rotavirus diarrhea was 14.83 ± 9.08 tháng months. Ages with the highest cases of rotavirus diarrhea are 2 - 12 months: 48.2%. Rotavirrus diarrhea is experienced in every month but, the highest prevalence is experienced in the spring - summer) with 71,5%. Clinical characteristitics of rotavirus diarrhea: Vomit presents in 91,7% of cases. 32.9% of the initial symptoms of the disease is vomiting. Mean number of vomiting episodes per day: 7 ± 3.57 times, significantly higher compared with non-rotavirus acute diarrhea (p <0,01). Mean number of bowel movement per day: 10.61±4.18 times, mean duration of diarrhea: 6.66 ± 2.52 days. Younger children have higher frequency and duration of diarrhea compared to older children. Paraclinical characteristitics of rotavirus diarrhea: the mean number leukocyte: 9.74 ±3.61 (x 109/l). 2.2% with low blood sodium status; 8.8% with reduction in serum potassium concentration. 26.3% with low blood calcium and glucose status. Laboratory characteristics of stool: 8.8% with white blood cells in stool, 41.7% with carbohydrate in stool. Conclusion: Rotavirus accounting for 54.7% of the causes of diarrhea in children. Rotavirus diarrhea is experienced throughout the year but the highest prevalence is in the spring-summer. Prominent symptoms of the disease are vomiting and watery stool. Children <24 months experience higher frequency and duration of diarrhea compared to older age groups. Key words: Diarrhea, Rotavirus.

scholarly journals Etiological, epidemiological, and clinical features of acute diarrhea in China

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Li-Ping Wang ◽  
◽  
Shi-Xia Zhou ◽  
Xin Wang ◽  
Qing-Bin Lu ◽  
...  
Keyword(s):  
Clinical Features ◽  
Acute Diarrhea ◽  
Vibrio Parahaemolyticus ◽  
Bacterial Pathogens ◽  
Control Measures ◽  
Viral Pathogens ◽  
Rotavirus A ◽  
Positive Rate ◽  
Prevention And Control Measures ◽  
And Control

AbstractNational-based prospective surveillance of all-age patients with acute diarrhea was conducted in China between 2009‒2018. Here we report the etiological, epidemiological, and clinical features of the 152,792 eligible patients enrolled in this analysis. Rotavirus A and norovirus are the two leading viral pathogens detected in the patients, followed by adenovirus and astrovirus. Diarrheagenic Escherichia coli and nontyphoidal Salmonella are the two leading bacterial pathogens, followed by Shigella and Vibrio parahaemolyticus. Patients aged <5 years had higher overall positive rate of viral pathogens, while bacterial pathogens were more common in patients aged 18‒45 years. A joinpoint analysis revealed the age-specific positivity rate and how this varied for individual pathogens. Our findings fill crucial gaps of how the distributions of enteropathogens change across China in patients with diarrhea. This allows enhanced identification of the predominant diarrheal pathogen candidates for diagnosis in clinical practice and more targeted application of prevention and control measures.

scholarly journals Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 615
Author(s):  
Allen Wing-Ho Chu ◽  
Cyril Chik-Yan Yip ◽  
Wan-Mui Chan ◽  
Anthony Chin-Ki Ng ◽  
Dream Lok-Sze Chan ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
Rna Extraction ◽  
Nasopharyngeal Swab ◽  
Acid Extraction ◽  
Rt Pcr ◽  
Nucleic Acid Extraction ◽  
Suitable Alternative ◽  
Pcr Inhibitors ◽  
Pcr Targeting

SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFYTM) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS® easyMAG®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.

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