scholarly journals Molecular Characteristics of Rotavirus Isolated from a Diarrhea Outbreak in October 2008 in Bintuni Bay, Papua, Indonesia

2014 ◽  
Vol 5 ◽  
pp. VRT.S13555 ◽  
Author(s):  
Eka Pratiwi ◽  
Vivi Setiawaty ◽  
Rudi Hendro Putranto
Keyword(s):  
Genetic Material ◽  
Molecular Characteristics ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Viral Diarrhea ◽  
Severe Diarrhea ◽  
Laboratory Results ◽  
Vp7 Protein ◽  
Stool Specimens ◽  
Polymerase Chain

Background Viral diarrhea continues to be a health problem in Indonesia that often causes outbreaks; in particular, acute viral diarrhea in young children. Rotavirus is the leading cause of severe diarrhea in children under two years of age. This study aimed to determine the genotypes of rotavirus in Bintuni Bay, Papua. Methods Stool specimens from 15 patients were collected and analyzed for rotavirus using an enzyme immunosorbent assay (EIA) and reverse transcriptase-polymerase chain reaction (RT-PCR). Subsequently, we sequenced the genetic material of rotavirus positive samples by RT-PCR and analyzed the results using Mega-4 software. Results Two rotavirus serotypes were identified from the diarrhea outbreak in Bintuni, Papua in October 2008: serotype G1 with G1P[6] (50%) and G1P[8] (16.7%) strains, and serotype G2 with G2P[4] (23.3%) strain. Phylogenetic tree analyses of VP7 protein showed that rotavirus-infected diarrhea in Bintuni Bay, Papua at that time was dominated by the G1 serotype (83%). Conclusion The laboratory results showed that G1 serotype rotavirus was a cause of the outbreak of diarrhea in October 2008 in Bintuni, Papua.

Polymerase chain reaction amplification and typing of rotavirus in environmental samples

1995 ◽  
Vol 31 (5-6) ◽  
pp. 371-374 ◽  
Author(s):  
R. Gajardo ◽  
R. M. Pintó ◽  
A. Bosch
Keyword(s):  
Polymerase Chain Reaction ◽  
Environmental Samples ◽  
Polymerase Chain Reaction Amplification ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Group A ◽  
Reaction Amplification ◽  
Stool Specimens ◽  
Polymerase Chain

A reverse transcription polymerase chain reaction (RT-PCR) assay is described that has been developed for the detection and serotyping of group A rotavirus in stool specimens and concentrated and non-concentrated sewage specimens.

scholarly journals Evaluation of the Reverse Transcription-Polymerase Chain Reaction/Probe Test of Serum Samples and Immunohistochemistry of Skin Sections for Detection of Acute Bovine Viral Diarrhea Infections

2002 ◽  
Vol 14 (4) ◽  
pp. 303-307 ◽  
Author(s):  
Julia F. Ridpath ◽  
Sharon K. Hietala ◽  
Steve Sorden ◽  
John D. Neill
Keyword(s):  
Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Amplification ◽  
Clinical Signs ◽  
Bovine Viral Diarrhea ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Serum Samples ◽  
Viral Diarrhea ◽  
Persistent Infections ◽  
Polymerase Chain

Bovine viral diarrhea viruses (BVDV) cause both acute and persistent infections. While diagnostic tests have been designed to detect animals persistently infected (PI) with BVDV, the reliability of these tests in detecting acute BVDV infections is not known. It is also possible that acute BVDV infections may be confused with persistent infections in surveys for PI animals. In this study, 2 tests presently in use in diagnostic laboratories to test for PI animals, polymerase chain reaction amplification followed by probe hybridization (RT-PCR/probe) of serum samples and immunohistochemical detection of viral antigen in skin biopsies (IHC), were evaluated for their ability to detect acute BVDV infections. Sixteen colostrum-deprived, BVDV-free, and BVDV-antibody-free calves were infected with 6 different BVDV strains. Clinical signs, seroconversion, and virus isolation indicated that inoculated animals did replicate virus. Virus could be detected in 19% (3/16) of acutely infected animals by the RT-PCR/probe technique. No acutely infected animals were positive by IHC.

Increased detection of rotavirus using a real time reverse transcription-polymerase chain reaction (RT-PCR) assay in stool specimens from children with diarrhea

2004 ◽  
Vol 72 (3) ◽  
pp. 496-501 ◽  
Author(s):  
Xiaoli L. Pang ◽  
Bonita Lee ◽  
Nasim Boroumand ◽  
Barbara Leblanc ◽  
Jutta K. Preiksaitis ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Reverse Transcription ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Stool Specimens ◽  
Polymerase Chain

scholarly journals Epidemiology and genetic diversity of human parechoviruses circulating among children hospitalised with acute gastroenteritis in Pune, Western India: a 5-years study

2017 ◽  
Vol 146 (1) ◽  
pp. 11-18 ◽  
Author(s):  
P. R. PATIL ◽  
N. N. GANORKAR ◽  
V. GOPALKRISHNA
Keyword(s):  
Genetic Diversity ◽  
Acute Gastroenteritis ◽  
Clinical Manifestations ◽  
Western India ◽  
Vp1 Gene ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Predominant Genotype ◽  
Stool Specimens ◽  
Polymerase Chain

SUMMARYHuman parechoviruses (HPeVs) are known to cause various clinical manifestations including acute gastroenteritis. Although HPeV infections and their genotypes have been detected in human patients worldwide, no such reports are available from India to ascertain the association of HPeVs in acute gastroenteritis. The present study was conducted to determine the clinical features and genetic diversity of HPeVs detected in children hospitalised for acute gastroenteritis. Stool specimens (n= 979) collected from children aged ⩽5 years hospitalised for acute gastroenteritis in Pune, western India during January 2006–December 2010 were included. HPeV RNA was detected by reverse transcription-polymerase chain reaction (RT-PCR) (5′UTR) followed by genotyping using VP1 gene-based PCR and phylogenetic analysis. HPeV was detected in 13·9% (136/979) of the cases, co-infections with other enteric viruses were found in 43·4%. HPeV was more frequent in children ⩽1 year age with infections reported throughout the year. A total of 102/136 (75%) HPeV strains were genotyped, which comprised 13 different HPeV genotypes. Of these, HPeV1 was the most predominant genotype detected and phylogenetically clustered with the Harris strain which is rarely reported. The study documents circulation of heterogeneous HPeV genotypes. Two variant strains of HPeV4 and ‘RGD absent’ HPeV5 and 6 strains were also detected. This is the first report of HPeV with diversified genotypes identified in acute gastroenteritis patients from India.

scholarly journals Conjunctival polymerase chain reaction tests (RT-PCR) of COVID-19 patients in Shenyang, China

2021 ◽  
Vol 2 (1) ◽  
pp. 15-20
Author(s):  
Li Xu ◽  
Keyword(s):  
Polymerase Chain Reaction ◽  
Clinical Features ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Laboratory Results ◽  
Polymerase Chain

We report the laboratory results of conjunctival RT-PCR tests and some clinical features of these patients infected with COVID 19 in Shenyang, China

scholarly journals Evaluation of re-hospitalized COVID-19 patients in a hospital

2020 ◽  
Vol 66 (12) ◽  
pp. 1690-1695
Author(s):  
Ensar Durmus ◽  
Fatih Guneysu
Keyword(s):  
Emergency Service ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Negative Results ◽  
Laboratory Results ◽  
Training And Research ◽  
Unilateral Involvement ◽  
Polymerase Chain ◽  
University Training ◽  
Age Range

SUMMARY PURPOSE: This study intends to investigate the reasons for re-hospitalization, complaints, and prognoses of COVID-19 patients after being discharged. METHODS: COVID-19 patients who were re-hospitalized at the Sakarya University Training and Research Hospital were examined. Reverse transcriptase-polymerase chain reaction (RT-PCR), tomography and laboratory results, demographic characteristics, and prognostic results were recorded retrospectively. RESULTS: A total of 60 patients, including 26 males (43.3%) and 34 females (56.7%), with repeated admissions to the hospital for COVID-19 symptoms, were included in the study with a mean age of 56.9 (± 22.5) (median value = 61, age range = 3–88). The number of days of the second hospitalization was statistically significantly higher (p < 0.05). Patient age and number of days of hospitalization were strongly positively correlated (p < 0.01). A total of 11 patients (18%) had negative results in their first RT-PCR and subsequently tested positive in their second hospitalization. In addition, 10 (17.5%) of the patients who underwent thoracic tomography had unilateral involvement, 34 (59.6%) had bilateral involvement, and 13 (22.8%) had no significant results. Note that 4 (6.6%) of the patients re-hospitalized died in the hospital, while 56 (93.4%) were discharged once more. All of the four patients that died were female with a mean age of 81.5 years. CONCLUSION: Particularly patients with advanced age and comorbidities should be examined more carefully when discharged; if their complaints are repeated, they should be advised to quickly contact the emergency service.

scholarly journals Clinical Manifestations and Pregnancy Outcomes of Covid-19 in Indonesian Referral Hospital in Central Pandemic Area

2021 ◽  
Author(s):  
Muhammad Ilham Aldika Akbar ◽  
Khanizyah Erza Gumilar ◽  
Rino Andriya ◽  
Manggala Pasca Wardhana ◽  
Pungky Mulawardhana ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Pregnancy Outcomes ◽  
Clinical Manifestations ◽  
Referral Hospital ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Laboratory Findings ◽  
Cohort Design ◽  
Laboratory Results ◽  
Polymerase Chain

Objectives:. The data on clinical manifestations and pregnancy outcomes of pregnant women with COVID-19 are limited, particularly in developing countries. The aim of this study is to analyze the clinical manifestations and pregnancy outcomes in COVID-19 maternal cases in a large referral hospital in Indonesia Methods: The study used a prospective cohort design of all pregnant women with suspected COVID-19. Subjects were divided into COVID-19 and non COVID-19 group based on real-time polymerase chain reaction (RT-PCR) of SARS-CoV-2. The clinical characteristics, laboratory results, and pregnancy outcomes were then compared between both groups. Results: From 141 suspected maternal cases, 62 COVID-19 cases were confirmed (43.9%), while 79 suspected cases were found to be negative (56.1%). The clinical manifestations and laboratory findings between the two groups were not significantly different (p>0.05). However, the maternal mortality directly caused by COVID-19 was significantly higher compared to the non-COVID-19 group (8.3 vs 1.3%; p=0.044; OR 6.91, 95% CI: 0.79-60.81). Conclusions: The clinical manifestation and laboratory of suspected pregnant women with positive and negative RT-PCR COVID-19 result are similiar. However, within the Indonesian setting, COVID-19 strongly increases the risk of maternal death through both direct and indirect factors.

Diagnostic determination of Norovirus infection as one of the major causes of infectious diarrhea in HIV patients using a multiplex polymerase chain reaction assay

2019 ◽  
Vol 30 (6) ◽  
pp. 550-556 ◽  
Author(s):  
Siyuan Yang ◽  
Min Li ◽  
Jingwei Cheng ◽  
Gang Wan ◽  
Yunao Zhou ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Multiplex Polymerase Chain Reaction ◽  
Diagnostic Methods ◽  
Enterotoxigenic Escherichia Coli ◽  
Rt Pcr ◽  
Infectious Diarrhea ◽  
Chain Reaction ◽  
Hiv Patients ◽  
Stool Specimens ◽  
Polymerase Chain

Although infectious diarrhea is one of the most common complications in human immunodeficiency virus (HIV)-infected patients, robust diagnostic methods for determining potential pathogens are still limited in the clinic. Norovirus, a type of calicivirus, has been shown to be the most common cause of gastroenteritis. Here, we used multiplex polymerase chain reaction as a diagnostic tool to verify Norovirus as the diarrhea-related pathogen in HIV-infected patients with unknown etiological information. Stool specimens obtained from 81 HIV-infected patients with diarrhea were analyzed by BioFire FilmArray Gastrointestinal (GI) panel. Among 26 HIV-infected patients with unknown etiological information, we detected Norovirus in 14 stool specimens of these patients with 100% sensitivity and specificity as confirmed by reverse transcription polymerase chain reaction (RT-PCR), and one specimen showed both Norovirus and enterotoxigenic Escherichia coli infection. Among the remaining 55 patients with verified Clostridium difficile infection, nine patients also detected positive for Norovirus infection. In conclusion, using FilmArray GI panel and RT-PCR, we determined that Norovirus infection as one of the main pathogens responsible for diarrhea in HIV patients.

scholarly journals Comparison of Tests for Detection of Bovine Viral Diarrhea Virus in Diagnostic Samples

2007 ◽  
Vol 19 (4) ◽  
pp. 376-381 ◽  
Author(s):  
Misty A. Edmondson ◽  
M. Daniel Givens ◽  
Paul H. Walz ◽  
Julie A. Gard ◽  
David A. Stringfellow ◽  
...  
Keyword(s):  
Virus Isolation ◽  
Bovine Viral Diarrhea ◽  
Infected Cattle ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Diarrhea Virus ◽  
Viral Diarrhea ◽  
Polymerase Chain ◽  
Viral Diarrhea Virus ◽  
Level Of Agreement

Currently, a variety of tests are used to detect bovine viral diarrhea virus (BVDV) in persistently infected (PI) cattle. These tests include immunohistochemical staining (IHC), antigen capture enzyme-linked immunosorbent assay (ACE), virus isolation (VI), and reverse transcription-polymerase chain reaction (RT-PCR). However, a lack of methods standardization could compromise the ability to consistently identify animals infected with BVDV. This study evaluated the diagnostic proficiency of current methods for detecting BVDV in infected cattle using intra- and interlaboratory comparisons. Samples were collected from 4 animals more than 7 months of age (2 BVDV negative animals, a PI animal, and a PI animal that previously lacked detectable virus in serum as determined by VI). Samples were submitted to 23 participating diagnostic laboratories using the respective laboratory's standard submission protocol. Samples collected for submission included: 1) serum for ACE, RT-PCR, and VI; 2) whole blood for RT-PCR and VI; and 3) skin biopsies for ACE and IHC. The ACE performed on skin provided the greatest consistency in detecting positive samples and a perfect level of agreement among laboratories. Reverse transcription-polymerase chain reaction and IHC performed well by correctly identifying ≤85% of samples positive for BVDV. Virus isolation performed on serum yielded the lowest consistency in detecting positive samples and the lowest level of agreement. The level of agreement between laboratories for detecting BVDV in persistently infected cattle ranged from perfect to less than expected by chance. The variation between laboratories suggests a need for training opportunities in standardized laboratory protocols and proficiency testing.

scholarly journals Evaluation of urine SARS-COV-2 RT-PCR as a predictor of acute kidney injury and disease severity in patients with critical COVID-19

2021 ◽  
Vol 49 (5) ◽  
pp. 030006052110155
Author(s):  
Sérgio Pinto de Souza ◽  
Marcelo Augusto Duarte Silveira ◽  
Bruno Solano de Freitas Souza ◽  
Julia Barros Cabral ◽  
Erica Batista dos Santos Galvão de Melo ◽  
...  
Keyword(s):  
Respiratory Function ◽  
Cytopathic Effect ◽  
Severe Disease ◽  
Genetic Material ◽  
Kidney Injury ◽  
Disease Phenotype ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Viral Cytopathic Effect

Coronavirus disease 2019 (COVID-19) is an emerging infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which began as an outbreak in Wuhan, China and has spread rapidly across the globe. Although most infections are mild, patients with severe and critical COVID-19 infections face deterioration of respiratory function and may also have extrapulmonary manifestations, mostly affecting the kidney, digestive tract, heart, and nervous system. Here, we prospectively evaluated the presence of SARS-CoV-2 genetic material using reverse-transcription polymerase chain reaction in urine samples obtained from patients with COVID-19 receiving critical care. Among 51 included patients, we found higher serum creatinine levels, a longer hospital stay, and more frequent need for dialysis in urine-positive patients. These findings could suggest that, in predisposed patients, a direct viral cytopathic effect may contribute to a more severe disease phenotype.

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