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.

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.

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 Epidemiological profile and genetic diversity of sapoviruses (SaVs) identified in children suffering from acute gastroenteritis in Pune, Maharashtra, Western India, 2007–2011

2016 ◽  
Vol 145 (1) ◽  
pp. 106-114 ◽  
Author(s):  
N. LASURE ◽  
V. GOPALKRISHNA
Keyword(s):  
Genetic Diversity ◽  
Acute Gastroenteritis ◽  
Clinical Manifestations ◽  
Circulation Pattern ◽  
The Philippines ◽  
Western India ◽  
Faecal Samples ◽  
Severe Gastroenteritis ◽  
Sporadic Cases ◽  
Epidemiological Profile

SUMMARYSapoviruses (SaVs) are responsible for sporadic cases and outbreaks of acute gastroenteritis. Despite this, few studies in India have focused on the epidemiological investigation of SaV in cases of acute gastroenteritis. The aim of this study was to understand the molecular epidemiology, genetic diversity and clinical impact of SaV in diarrhoeic children from Pune, Western India. Between 2007 and 2011, a total of 985 faecal samples from diarrhoeic cases and non-diarrhoeic controls were collected and examined for the presence of SaV by nested RT–PCR. SaV was detected in 2·7% (21/778) of the cases and 1·9% (4/207) of the controls. We observed that the majority of SaV mono-infections caused severe gastroenteritis (67%) with clinical manifestations of diarrhoea (100%), vomiting (73%) and dehydration (80%). All known human SaV genogroups were detected in the study. At least eight genotypes were identified from cases and controls. Genogroups GIV and GV, along with genotypes GI.5, GII.4 and GII.6, were discovered for the first time in India. Two GII.4 study strains were found to be 98·5–99% identical, having a novel intra-genogroup recombinant (GII.1/GII.4) recently reported from the Philippines, suggesting probable evidence of recombination. The circulation pattern of SaV genotypes varied during the study period, with GII.1 being predominant in 2007 and 2009, GIV.1 in 2008, and GV.1 in 2011.

scholarly journals Molecular Epidemiology and Genetic Diversity of Norovirus in Young Children in Phnom Penh, Cambodia

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Kaewkanya Nakjarung ◽  
Ladaporn Bodhidatta ◽  
Pimmnapar Neesanant ◽  
Paphavee Lertsethtakarn ◽  
Orntipa Sethabutr ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Young Children ◽  
Real Time ◽  
Pediatric Hospital ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Phnom Penh ◽  
Stool Samples ◽  
Polymerase Chain ◽  
Predominant Strain

This study investigated the genetic diversity of noroviruses identified from a previous surveillance study conducted at the National Pediatric Hospital in Phnom Penh, Cambodia, from 2004 to 2006. In the previous study, 926 stool samples were collected from children aged 3–60 months with acute diarrhea (cases) and without diarrhea (controls) with reported 6.7% of cases and 3.2% of controls being positive for norovirus. The initial norovirus diagnostic assay was performed with real-time reverse transcription-polymerase chain reaction (real-time RT PCR) which also distinguished between genogroups I and II (GI and GII). Norovirus infection was most commonly detected in children aged 12–23 months in both cases and controls. Norovirus Genotyping Tool and phylogenetic analysis of partial sequences of the 3′ end of the RNA-dependent RNA Polymerase (RdRp) and the capsid domain region were employed to assign genotypes of the norovirus strains. GII.4 was the most predominant capsid genotype detected at 39.5% followed by GII.6 at 14.9%. The GII.4 Hunter 2004 variant was the predominant strain detected. Six RdRP/capsid recombinants including GII.P7/GII.6, GII.P7/GII.14, GII.P7/GII.20, GII.P12/GII.13, GII.P17/GII.16, and GII.P21/GII.3 were also identified. This study of norovirus infection in young children in Cambodia suggests genetic diversity of norovirus as reported worldwide.

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.

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.

scholarly journals Deteksi transmisi virus dengue pada nyamuk wild Aedes Aegypti betina di Kota Manado

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Grace Trovancia ◽  
Angle Sorisi ◽  
Josef S.B. Tuda
Keyword(s):  
Polymerase Chain Reaction ◽  
Aedes Aegypti ◽  
Dengue Virus ◽  
Reverse Transcription ◽  
Clinical Manifestations ◽  
Virus Transmission ◽  
Survey Study ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

Abstract: Dengue hemorrhagic fever is an acute disease with clinical manifestations of hemorrhage caused by dengue virus infection. Manado is endemic dengue. Dengue virus has the ability to maintain its existence in nature through horizontal and vertical transmission. There are several ways to detect the dengue virus by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and immunohistochemistry Streptavidin Biotin Peroxidase Complex (ISBPC). This research aims to determine the wild Aedes aegypti population in Manado and to detect dengue virus in wild mosquito Aedes aegypti by ISBPC methods. This was a descriptive survey study with a cross sectional design to describe the transmission of dengue virus in wild mosquito Aedes aegypti in the city of Manado. The results showed that there were 5 wild Aedes aegypti mosquitoes positive for dengue virus, and 36 wild Aedes aegypti mosquitoes negative containing dengue virus. Conclusion: Of the 41 samples immunohistochemistry tested, 5 samples showed dengue virus transmission in wild mosquito Aedes aegypti in Manado which is a positive possibility of horizontal transmission.Keywords: detection of dengue virus, transmission, wild Aedes aegypti, Manado. Abstrak: Demam berdarah dengue adalah suatu penyakit akut dengan manifestasi klinis perdarahan yang disebabkan oleh infeksi virus dengue. Manado merupakan daerah endemis demam berdarah. Virus dengue memiliki kemampuan untuk mempertahankan keberadaannya di alam melalui transmisi horizontal dan vertikal. Ada beberapa cara untuk mendeteksi virus dengue yaitu Reverse Transcription-Polymerase Chain Reaction (RT-PCR) dan imunohistokimia Streptavidin Biotin Peroxidase Complex (SBPC). Penelitian ini bertujuan untuk mengetahui populasi nyamuk wild Aedes aegypti di Kota Manado dan mendeteksi virus dengue pada nyamuk wild Aedes aegypti dewasa menggunakan metode imunohistokimia streptavidin biotin peroxidase complex (ISBPC). Jenis penelitian ialah survei deskriptif dengan desain potong lintang untuk mengetahui gambaran transmisi virus dengue pada nyamuk wild Aedes aegypti betina di Kota Manado. Hasil pene;itian mendapatkan 5 nyamuk wild Aedes aegypti positif mengandung virus dengue, dan 36 nyamuk wild Aedes aegypti negatif mengandung virus dengue. Simpulan: Berdasarkan hasil penelitian dapat disimpulkan bahwa dari 41 sampel yang telah diuji imunohistokimia, 5 sampel gambaran transmisi virus dengue pada nyamuk wild Aedes aegypti betina di Kota Manado yang kemungkinan transmisi horizontal adalah positif. Kata kunci: deteksi virus dengue, transmisi, wild Aedes aegypti, Manado.

Molecular Epidemiology of Human Sapovirus Among Children with Acute Gastroenteritis in Western Canada

2021 ◽  
Author(s):  
Ran Zhuo ◽  
Xiaofeng Ding ◽  
Stephen B. Freedman ◽  
Bonita E. Lee ◽  
Samina Ali ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Acute Gastroenteritis ◽  
Western Canada ◽  
High Detection Rate ◽  
High Genetic Diversity ◽  
Predominant Genotype ◽  
Significant Difference ◽  
Stool Specimens ◽  
Capsid Protein Vp1 ◽  
Predominant Strain

Objectives: Sapovirus is increasingly recognized as an important cause of acute gastroenteritis (AGE) worldwide, however studies of prevalence, genetic diversity and strain-specific clinical implications have been scarce. Methods: To fill this knowledge gap, we used reverse transcription real-time PCR and sequencing of the partial major capsid protein VP1 gene to analyze stool specimens and rectal swabs obtained from 3347 children with AGE and 1355 asymptomatic controls (all <18 years old) collected between December 2014 and August 2018 in Alberta, Canada. Results: Sapovirus was identified in 9.5% (317/3347) of the children with AGE and 2.9% of controls. GI.1 (36%) was the predominant genotype identified, followed by GI.2 (18%), GII.5 (8%) and GII.3 (6%). Rare genotypes GII.1, GII.2, GV.1, GII.4, GIV.1, GI.3 and GI.7 were also seen. Sapovirus was detected year-round, peaking during the winter months of November to January. The exception was the 2016-2017 season when GI.2 overtook GI.1 as the predominant strain with a high detection rate persisting into April. We did not observe significant difference in the severity of gastroenteritis by genogroup or genotype. Repeated infection by sapovirus of different genogroups occurred in three controls who developed AGE later. Conclusions: Our data suggests that sapovirus is a common cause of AGE in children with high genetic diversity.

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 Development and Application of an RT-PCR to Differentiate the Prevalent NA-PRRSV Strains in China

2017 ◽  
Vol 11 (1) ◽  
pp. 66-72 ◽  
Author(s):  
Yanlin Li ◽  
Guobiao Ji ◽  
Xiaodong Xu ◽  
Juan Wang ◽  
Yingying Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Rna Detection ◽  
Highly Pathogenic ◽  
Genotype 2 ◽  
Polymerase Chain ◽  
Virus Strains ◽  
Highly Pathogenic Prrsv ◽  
Reverse Transcript

Background: PRRSV features with genetic diversity and high mutation which leads to the emergence of a multiple of circulating virus strains with different virulence. North American (genotype 2) PRRSV (NA-PRRSV) can be divided into classical PRRSV (C-PRRSV), highly pathogenic PRRSV (HP-PRRSV), and NADC30-like PRRSV (NL-PRRSV) according to their genomic characteristics and pathogenicity. So far, the above three subtypes of NA-PRRSV are now circulating in China. Objective and Method: In this study, a reverse transcript polymerase chain reaction (RT-PCR) was established to simultaneously differentiate three subtypes of NA-PRRSV. The established RT-PCR can be applied to PRRSV-infected samples originated from both supernatant of cell culture and pig tissues and showed specificity exclusively to PRRSV. The sensitivity of RT-PCR showed the minimum RNA detection was 0.04ng/µl. Result and Conclusion: The established RT-PCR was next used to differentiate the subtypes of 29 NA-PRRSV isolated in 2016 and the results showed that HP-PRRSV is still the dominant circulating virus strain in the presence of NADC30-like PRRSV in Henan province.

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