scholarly journals Species A Rotavirus (RVA) Isolated from Sewage in Nigeria, 2014: Close Genetic Relatedness of Partial G, P, and NSP4 Gene Sequences Encoding G1 with Cogent Genes of Other Asian and African Rotaviruses

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Babatunde Olanrewaju Motayo ◽  
Johnson Adekunle Adeniji ◽  
Adedayo Omotayo Faneye
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genetic Relatedness ◽  
Molecular Characteristics ◽  
Nsp4 Gene ◽  
Limited Information ◽  
Gene Sequences ◽  
Monophyletic Cluster ◽  
Group A ◽  
Vp7 Gene

Rotavirus has been identified as a major cause of gastroenteritis in Nigeria. There is limited information on the intragenotype diversity of Nigerian rotavirus isolates. We therefore investigated the molecular characteristics of some rotavirus gene sequences detected in sewage from Nigeria. Seven sewage samples, out of a total of 68, tested positive for rotavirus RNA (10.3%). Genotype G1P[4]was the most common genotype (5 isolates) and one isolate for genotypes G1P[8] and G3P[6]. Phylogenetic analysis of the partial VP7 gene of 3 G1P[4]isolates analyzed identified them as genotype G1 Lineage 2 along with Chinese strains with 99.1% to 100% amino acid similarity. Amino acid substitutions D-97→E and S-147→D/N were observed within the 7-1a and 7-2 domains of VP7 gene among the study G1P4 isolates in reference to vaccine strain RotaTeq®. Phylogenetic analysis of the G3P[6]study isolate identified it as genotype G3 Lineage 3, forming a monophyletic cluster with 100% bootstrap value with other West African strains G3 isolates. Phylogenetic analysis of GIP[4]VP4 genes identified them as P4 Lineage 5, while 3 NSP4 gene sequences belonged to genotype E1, while 1 belonged to E2. The results from this study represent phylogenetic analysis of partial gene sequences of environmental group A rotavirus (RVA) isolates from Nigeria.

scholarly journals Molecular Characteristics and Phylogenetic Analysis of Short Beak and Dwarfism Syndrome-Related Novel Goose Parvovirus

2021 ◽  
Author(s):  
Yonglin Li ◽  
Jingyu Jia ◽  
Qingling Mi ◽  
Yufeng Li ◽  
Yuehua Gao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Point Mutations ◽  
Molecular Characteristics ◽  
Structural Protein ◽  
Common Amino Acid ◽  
Separate Branch ◽  
Goose Parvovirus ◽  
Cherry Valley Duck ◽  
Short Beak

Abstract Short beak and dwarfism syndrome (SBDS) emerged in cherry valley duck flocks in China in 2015, and novel goose parvovirus (NGPV) was proved to be the etiological agent of SBDS. To date, whether SBDS-related NGPV isolates possess common molecular characteristics remains unknown. In this study, three new NGPV strains (namely, SDHT16, SDJN19, and SDLC19) were isolated from diseased ducks showing typical SBDS and successfully passaged in embryonated goose or cherry valley duck embryo. The whole genomes of three NGPV strains shared 98.9%–99.7% homologies between each other but showed slightly lower homologies (95.2%–96.1%) with the classical GPV strains. A total of 16 common amino acid point mutations were produced in the VP1 proteins of six NGPV strains (SDHT16, SDJN19, SDLC19, QH, JS1, and SDLC01) compared with the classical Chinese GPV strains, among which nine amino acid sites were identical to the European GPV strain B. The non-structural protein Rep1 of the six NGPV strains generated 12 common amino acid mutations compared with the classical GPV strains. The phylogenetic analysis indicated that the Chinese NGPV strains clustered with the European SBDS-related NGPV strains, forming a separate branch, distinct from the group formed by the classical GPV strains. Taken together, the present study unveils the common molecular characteristics of the NGPV isolates and directs the conclusion that the Chinese NGPV isolates probably originate from a common ancestor with the European SBDS-related NGPV.

scholarly journals Detection and molecular characterization of reassortant DS-1-like G1P [8] strains of rotavirus A

2017 ◽  
Vol 62 (2) ◽  
pp. 91-96
Author(s):  
O. V. Morozova ◽  
T. A. Sashina ◽  
N. A. Novikova
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequences ◽  
Mutation Rates ◽  
Molecular Characteristics ◽  
Viral Gastroenteritis ◽  
Rotavirus A ◽  
Group A Rotaviruses ◽  
Group A ◽  
First Time

Group A rotaviruses (RVA) are the main cause of viral gastroenteritis in children worldwide. In this study we provide the molecular characteristics of reassortant DS-1-like G1P[8] RVA strains detected in Russia for the first time. Previously, such reassortant strains were detected in Japan and Thailand. The G1P[8] RVAs with DS-1-like short electropherotype RNA-PAGE were isolated from children hospitalised with an acute gastroenteritis during the 2013-2014 period. The DS-1-like G1P[8] strains accounted for 2.6% of all RVA strains detected continuously throughout the season. A phylogenetic analysis was made on the basis of the established nucleotide sequences of genes VP7, VP8* (VP4), VP6 and NSP4. The Nizhny Novgorod strains belong to G1-I and G1-II alleles of VP7 gene and to P[8]-3 allele of VP4. According to their VP6 sequences, two Russian samples clustered with the reassortant strains isolated in Japan, Thailand and Australia and two other strains were phylogenetically close to the typical G2P[4] DS-1-like RVA. Nucleotide sequences of G1P[8] strains that belong to NSP4 gene form a separate cluster from G3P[8] DS-1-like rotaviruses detected in Thailand and Australia. The RVA alleles included in Rotarix and RotaTeq vaccine strains were clustered separately from the studied reassortant RVAs. On the grounds of phylogenetic analysis we assume a polyphyletic origin of reassortants between Wa- and DS-1-like strains. Mutation rates evaluated by Bayesian inference in clusters with reassortant RVA strains were 1.004Е-3 (VP7), 1.227E-3 (VP4), 3.909E-4 (VP6), and 4.014Е-4 (NSP4). Analysis of tMRCA showed relatively contemporary origin of alleles DS-1-like G1P[8] rotaviruses: VP7 - 1998 (G1-I) and 1981 (G1-II), VP4 - 1998, VP6 - 1994, NSP4 - 1979.

scholarly journals Prevalence and molecular characteristics of rotaviruses from Polish turkey flocks between 2008 and 2011

2013 ◽  
Vol 57 (4) ◽  
pp. 461-465 ◽  
Author(s):  
Katarzyna Domańska-Blicharz ◽  
Anna Jacukowicz ◽  
Zenon Minta
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Geographical Origin ◽  
Molecular Characteristics ◽  
Nsp4 Gene ◽  
Group Affiliation ◽  
Pcr Assay ◽  
Distinct Subgroup ◽  
Commercial Turkey ◽  
European Group

Abstract Between 2008 and 2011, commercial turkey flocks in Poland were examined for the presence of rotaviruses. Ten faecal swabs from each of 207 turkey flocks (turkeys aged one to 19 weeks) were collected in different regions of the country and tested using a PCR assay that targeted the NSP4 gene. The prevalence of rotavirus was 20.3% in the flocks tested. Phylogenetic analysis revealed a clear division into groups dependent on geographical origin of the analysed viruses. All Polish rotaviruses belonged to the European group. However, they were found to be genetically variable based on the sequence analysis. The most frequently identified rotaviruses belonged to RV-1 subgroup and two of them formed a distinct subgroup of RV-2. Rotaviruses were detected in healthy and enteric turkeys. The observed amino acid changes probably did not affect the group affiliation, nor the pathogenecity of the studied rotavirus strains.

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.

scholarly journals Phylogenetic analysis of partial VP7 gene of the emerging human group A rotavirus G12 strains circulating in Tunisia

2017 ◽  
Vol 66 (2) ◽  
pp. 112-118 ◽  
Author(s):  
Amal Moussa ◽  
Mouna Ben Hadj Fredj ◽  
Meriam BenHamida-Rebaï ◽  
Imene Fodha ◽  
Noureddine Boujaafar ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Human Group ◽  
Group A Rotavirus ◽  
Group A ◽  
Vp7 Gene

An Outbreak of ESBL-producing Klebsiella pneumoniae in an Iranian Referral Hospital: Epidemiology and Molecular Typing

2019 ◽  
Vol 19 (1) ◽  
pp. 46-54 ◽  
Author(s):  
Shima Mahmoudi ◽  
Babak Pourakbari ◽  
Aliakbar Rahbarimanesh ◽  
Mohammad Reza Abdosalehi ◽  
Keyghobad Ghadiri ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Nosocomial Infections ◽  
Molecular Typing ◽  
Genetic Relatedness ◽  
Referral Hospital ◽  
Limited Information ◽  
Hospital Epidemiology ◽  
Rapd Pcr ◽  
Published Report ◽  
Random Amplification

Introduction: Klebsiella pneumoniae is a common cause of nosocomial infections; however, there is limited information in Iran regarding nosocomial outbreaks due to extended-spectrum β–lactamase (ESBL) producing K pneumoniae strains, particularly using molecular methods. The present study focused on the molecular mechanism of ESBL resistance and genetic relatedness in K. pneumoniae isolates causing nosocomial infections in an Iranian referral hospital. Material and Methods: This study evaluated the antimicrobial resistance and molecular epidemiology of K. pneumoniae causing nosocomial infections in children between October 2013 and March 2014. The ESBL detection was carried out for all the isolates by the CLSI method and PCR was carried out for the detection of the blaSHV, blaTEM, and blaCTX-M genes among ESBL-producing K. pneumonia. Molecular typing of the K. pneumoniae was performed using random amplification of polymorphic DNA-polymerase chain reaction (RAPD-PCR). Results: A total of 30 isolates of K. pneumoniae were used for epidemiological analysis. High rates of resistance to cefotaxime (n=29, 97%), cefazolin (n=29, 97%), cefepime (n=25, 83%) and gentamicin (n=23, 77%) were observed. A total of 29 strains (97%) produced ESBLs. The frequency of blaSHV, blaCTX-M and blaTEM genes among these isolates was 83% (n=25), 70% (n=21) and 57% (n=17), respectively. Surprisingly 11 isolated (37%) carried blaSHV, blaCTX-M and blaTEM genes simultaneously. Moreover, the concurrent presence of “blaSHV and blaCTX-M” and “blaSHV and blaTEM” was seen in 8 (27%) and 4 (13%) isolates, respectively. RAPDPCR analyses revealed that K. pneumoniae isolates belonged to 2 RAPD-PCR types among which one cluster counted for 28 isolates. Conclusion: To our knowledge, this is the first published report of a nosocomial outbreak of ESBL-producing K. pneumoniae in children in Iran. Although the epidemiology of nosocomial infections with ESBL-producing organisms has not yet been explored in depth in Iran, our findings suggest that ESBL-producing organisms are already an established public health threat in our country.

scholarly journals Clinical and Molecular Characteristics and Outcome of Cystic Partially Differentiated Nephroblastoma and Cystic Nephroma: A Narrative Review of the Literature

Cancers ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 997
Author(s):  
Sophie E. van Peer ◽  
Corine J. H. Pleijte ◽  
Ronald R. de Krijger ◽  
Marjolijn C. J. Jongmans ◽  
Roland P. Kuiper ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Genetic Testing ◽  
Renal Tumor ◽  
Molecular Characteristics ◽  
Extensive Literature ◽  
Cystic Nephroma ◽  
Limited Information ◽  
Review Of The Literature ◽  
Genetic Characteristics ◽  
Excellent Outcome

In children presenting with a predominantly cystic renal tumor, the most likely diagnoses include cystic partially differentiated nephroblastoma (CPDN) and cystic nephroma (CN). Both entities are rare and limited information on the clinical and molecular characteristics, treatment, and outcome is available since large cohort studies are lacking. We performed an extensive literature review, in which we identified 113 CPDN and 167 CN. The median age at presentation for CPDN and CN was 12 months (range: 3 weeks–4 years) and 16 months (prenatal diagnosis–16 years), respectively. No patients presented with metastatic disease. Bilateral disease occurred in both entities. Surgery was the main treatment for both. Two/113 CPDN patients and 26/167 CN patients had previous, concomitant, or subsequent other tumors. Unlike CPDN, CN was strongly associated with somatic (n = 27/29) and germline (n = 12/12) DICER1-mutations. Four CPDN patients and one CN patient relapsed. Death was reported in six/103 patients with CPDN and six/118 CN patients, none directly due to disease. In conclusion, children with CPDN and CN are young, do not present with metastases, and have an excellent outcome. Awareness of concomitant or subsequent tumors and genetic testing is important. International registration of cystic renal tumor cohorts is required to enable a better understanding of clinical and genetic characteristics.

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

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