scholarly journals A tightly clustered hepatitis E virus genotype 1a is associated with endemic and outbreak infections in Bangladesh

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255054
Author(s):  
Trang Nguyen Hoa ◽  
Saif Ullah Munshi ◽  
Khanh Nguyen Ngoc ◽  
Chau Le Ngoc ◽  
Thanh Tran Thi Thanh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
T Cell ◽  
Hepatitis E Virus ◽  
Genetic Relatedness ◽  
Hepatitis E ◽  
Immunoglobulin M ◽  
Whole Genome Sequence ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
Genotype 1A

Background Hepatitis E virus (HEV) infection is endemic in Bangladesh and there are occasional outbreaks. The molecular characteristics and pathogenesis of endemic and outbreak HEV strains are poorly understood. We compared the genetic relatedness and virulence associated mutations of endemic HEV strains with outbreak strains. Methods We analyzed systematically collected serum samples from HEV immunoglobulin M (IgM) positive patients attended at Bangabandhu Sheikh Mujib Medical University, Dhaka from August 2013 to June 2015. HEV RNA positive samples were subjected to whole genome sequencing. Genotype and subtype of the strains were determined by phylogenetic analysis. Virulence associated mutations e.g. acute viral hepatitis (AVH), fulminant hepatic failure (FHF), chronic hepatitis, ribavirin treatment failure (RTF), B and T cell neutralization epitopes were determined. Results 92 HEV immunoglobulin M (IgM) antibody positive plasma samples (43 in 2013–2014 and 49 in 2014–2015) were studied. 77.1% (70/92) of the samples were HEV RNA positive. A 279 bp open reading frame (ORF) 2 and ORF 3 sequence was obtained from 54.2% (38/70) of the strains. Of these 38 strains, whole genome sequence (WGS) was obtained from 21 strains. In phylogenetic analysis of 38 (279 bp) sequence all HEV sequences belonged to genotype 1 and subtype 1a. Further phylogenetic analysis of 21 HEV WGS, Bangladeshi HEV sequences clustered with genotype 1a sequences from neighboring countries. Within genotype 1a cluster, Bangladesh HEV strains formed a separate cluster with the 2010 HEV outbreak strains from northern Bangladesh. 80.9 to 100% of the strains had A317T, T735I, L1120I, L1110F, P259S, V1479I, G1634K mutations associates AVH, FHF and RTF. Mutations in T cell recognition epitope T3, T5, T7 was observed in 76.1%, 100% and 100% of the strains respectively. Conclusion Strains of HEV genotype 1a are dominant in Bangladesh and are associated with endemic and outbreak of HEV infection. HEV isolates in Bangladesh have high prevalence of virulence associated mutations and mutation which alters antigenicity to B and T cell epitopes.

Hepatitis E virus-induced primary cutaneous CD30(+) T cell lymphoproliferative disorder

2017 ◽  
Vol 67 (6) ◽  
pp. 1334-1339 ◽  
Author(s):  
Vincent Mallet ◽  
Julie Bruneau ◽  
Julien Zuber ◽  
Cécile Alanio ◽  
Stéphanie Leclerc-Mercier ◽  
...  
Keyword(s):  
T Cell ◽  
Lymphoproliferative Disorder ◽  
Hepatitis E Virus ◽  
Hepatitis E

Performance of a new rapid test for detecting anti-hepatitis E virus immunoglobulin M in immunocompetent and immunocompromised patients

2015 ◽  
Vol 70 ◽  
pp. 101-104 ◽  
Author(s):  
Florence Abravanel ◽  
Sébastien Lhomme ◽  
Sabine Chapuy-Regaud ◽  
Jean-Marie Peron ◽  
Laurent Alric ◽  
...  
Keyword(s):  
Hepatitis E Virus ◽  
Rapid Test ◽  
Hepatitis E ◽  
Immunoglobulin M ◽  
Immunocompromised Patients

scholarly journals Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 183 ◽  
Author(s):  
Tohru Suzuki ◽  
Yoshihiro Otake ◽  
Satoko Uchimoto ◽  
Ayako Hasebe ◽  
Yusuke Goto
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Molecular Characterization ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Wild Ruminant ◽  
Genome Sequence Analysis ◽  
Genomic Characterization

Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.

Consecutive evaluation of immunoglobulin M and G antibodies against hepatitis E virus

1996 ◽  
Vol 31 (6) ◽  
pp. 818-822 ◽  
Author(s):  
Wel-Min Ke ◽  
De Tan ◽  
Jian-Guo Li ◽  
Satoru Izumi ◽  
Yoshitake Shinji ◽  
...  
Keyword(s):  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Immunoglobulin M

scholarly journals Identification and Characterization of Mycobacterium tuberculosis Beijing Genotype Strain SBH163, Isolated in Sabah, Malaysia

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Jaeyres Jani ◽  
Siti Fatimah Abu Bakar ◽  
Zainal Arifin Mustapha ◽  
Chin Kai Ling ◽  
Roddy Teo ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequence ◽  
Beijing Genotype ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
Content Type ◽  
Identification And Characterization ◽  
Insight Into ◽  
Malaysian Borneo

This is a report on the whole-genome sequence of Mycobacterium tuberculosis strain SBH163, which was isolated from a patient in the Malaysian Borneo state of Sabah. This report provides insight into the molecular characteristics of an M. tuberculosis Beijing genotype strain related to strains from Russia and South Africa.

Study of a hepatitis E virus outbreak involving drinking water and sewage contamination in Shimla, India, 2015–2016

2019 ◽  
Vol 113 (12) ◽  
pp. 789-796 ◽  
Author(s):  
Anuradha S Tripathy ◽  
Meenal Sharma ◽  
Avinash R Deoshatwar ◽  
Prasad Babar ◽  
Rakesh Bharadwaj ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Water Samples ◽  
Hepatitis E Virus ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Hepatitis E ◽  
Rt Pcr ◽  
Oral Transmission ◽  
Sewage Contamination ◽  
Current Outbreak

Abstract Background Hepatitis E, caused by hepatitis E virus (HEV), accounts for 50% of acute hepatitis cases in India. We report an outbreak of hepatitis E in Shimla, India, in 2015–2016. Methods ICMR-National Institute of Virology (NIV), Pune, received two batches of water samples from Shimla in January 2016 to test for the presence of enterically transmitted hepatitis viruses. Subsequently, 57 icterus patients were tested for various markers of hepatotropic viruses, i.e. anti-HEV IgM/IgG, anti-hepatitis A virus (anti-HAV) IgM/IgG antibodies and HEV RNA. Water samples were screened for HEV and HAV RNA followed by phylogenetic analysis. Results Overall, 48/57 patients availing municipal water had evidence of HEV infection, detected by serology and RT-PCR. All the water samples tested positive for HEV and HAV RNA, while the patients were negative for anti-HAV IgM antibody, indicating no recent HAV infection. Phylogenetic analysis confirmed the aetiological agent of the current outbreak to be HEV genotype 1. Conclusions Serology and RT-PCR confirmed HEV as the aetiology of the outbreak. The absence of new cases of hepatitis A, despite the presence of HAV in the water supply, could be due to previously acquired immunity. Sewage contamination of water leading to faecal-oral transmission of HEV still remains a concern, thus emphasising the need for a vaccination/control strategy.

scholarly journals Prevalence and phylogenetic analysis of hepatitis E virus in pigs, wild boars, roe deer, red deer and moose in Lithuania

2018 ◽  
Vol 60 (1) ◽  
Author(s):  
Ugne Spancerniene ◽  
Juozas Grigas ◽  
Jurate Buitkuviene ◽  
Judita Zymantiene ◽  
Vida Juozaitiene ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis E Virus ◽  
Red Deer ◽  
Roe Deer ◽  
Hepatitis E ◽  
Wild Boars

scholarly journals Full Genomic Characterization of a Lentogenic Newcastle Disease Virus Isolated from Farm-Reared Ostriches (Struthio camelus) in Northwest China

2017 ◽  
Vol 5 (6) ◽  
Author(s):  
Shanhui Ren ◽  
Chongyang Wang ◽  
Xiaolong Gao ◽  
Xue Zhang ◽  
Xiangwei Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Newcastle Disease Virus ◽  
Disease Virus ◽  
Newcastle Disease ◽  
Northwest China ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Struthio Camelus ◽  
Genomic Characterization

ABSTRACT To our knowledge, our study is the first to report the whole-genome sequence of an ostrich-origin Newcastle disease virus (NDV) isolate, abbreviated as Ostrich/SX-01/06. Phylogenetic analysis revealed that this isolate belongs to the subgenotype c in class II. The identification of the complete genome will provide useful information regarding ostrich diseases, especially NDV.

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