scholarly journals Phylogenetic Analysis of European Brown Hare Syndrome Virus Strains from Poland (1992–2004)

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1999
Author(s):  
Andrzej Fitzner ◽  
Ewa Kwit ◽  
Wiesław Niedbalski ◽  
Ewelina Bigoraj ◽  
Andrzej Kęsy ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Single Amino Acid ◽  
Brown Hare ◽  
European Brown Hare ◽  
Genetic Groups ◽  
Vp60 Gene ◽  
European Brown Hare Syndrome ◽  
Virus Strains

European brown hare syndrome (EBHS) is lethal to several species of free-living hares worldwide. The genetic characterization of its virus (EBHSV) strains in European circulation and epidemiological knowledge of EBHSV infections is not yet complete. The study determined the nucleotide sequences of the genomes of EBHSV strains from Poland and analyzed their genetic and phylogenetic relationships to a group of hare lagoviruses. The genome of five virus strains detected in Poland between 1992 and 2004 was obtained by RT-PCR and sequencing of the obtained amplicons. The genetic relationships of the EBHSV strains were analyzed using the full genome and VP60 gene sequences. Additionally, the amino acid sequence of the VP60 gene was analyzed to identify mutations specific to recognized EBHSV subgroups. Partial amplification of the virus open reading frame (ORF)1 and ORF2 regions obtained nearly complete nucleotide genome sequences of the EBHSV strains. Phylogenetic analysis placed them in a GII.1 cluster with other European strains related to nonpathogenic hare caliciviruses. VP60 gene analysis allocated these EBHSV strains to the G1.2, G2.2–2.3 or G3 virus genetic groups. The amino acid sequence differences in the entire genome ranged from 1.1 to 2.6%. Compared to a reference French EBHSV-GD strain, 22 variable amino acid sites were identified in the VP60 region of the Polish strains, but only six were in VP10. Single amino acid changes appeared in different sequence positions among Polish and other European virus strains from different genetic groups, as well as in VP10 sequences of nonpathogenic hare caliciviruses. The results of the study showed a high genetic homogeneity of EBHSV strains from Poland despite their different location occurrence and initial detection times. These strains are also phylogenetically closely related to other EBHSV strains circulating in Europe, likely confirming the slow evolutionary dynamics of this lagovirus species.

scholarly journals NEW VARIANTS OF EUROPEAN BROWN HARE SYNDROME VIRUS STRAINS IN FREE-RANGING EUROPEAN BROWN HARES (LEPUS EUROPAEUS) FROM SLOVAKIA

2007 ◽  
Vol 43 (1) ◽  
pp. 89-96 ◽  
Author(s):  
Kai Frölich ◽  
Jörns Fickel ◽  
Arne Ludwig ◽  
Dietmar Lieckfeldt ◽  
Wolf Jürgen Streich ◽  
...  
Keyword(s):  
Lepus Europaeus ◽  
Brown Hare ◽  
European Brown Hare ◽  
European Brown Hare Syndrome ◽  
Free Ranging ◽  
Virus Strains

Development of a RT-PCR for the Detection of European Brown Hare Syndrome Virus

2011 ◽  
Vol 271-273 ◽  
pp. 410-416 ◽  
Author(s):  
Yang Ze Xiao ◽  
Li Rui Li ◽  
Yin Wang ◽  
Xue Ping Yao ◽  
Xue Qing Han ◽  
...  
Keyword(s):  
Pasteurella Multocida ◽  
Brown Hare ◽  
Rt Pcr ◽  
European Brown Hare ◽  
Vp60 Gene ◽  
Specificity And Sensitivity ◽  
Overlap Extension ◽  
Pcr Method ◽  
European Brown Hare Syndrome

To develop the reverse transcriptase polymerase chain reaction (RT-PCR) for the detection of European brown hare syndrome virus (EBHSV), 3 specific primers and 9 overlapping oligo primers were designed to amplify a fragment of 335 nucleotides from the genome of EBHSV according to the genome sequences published in GenBank, and a 359 bp DNA fragment of the capsid protein(VP60)gene of EBHSV was synthesized in vitro by using overlap extension PCR to construct the recombinant plasmids pGM-T-EBHSV, then the RT-PCR method was described through the optimization of reaction conditions, sensitivity and specificity tests. Results showed the RT-PCR method was supplied for the detection of EBHSV with good specificity and sensitivity. The sensitivity of the RT-PCR could reach about 50 copies of cloned viral genomic fragments (pGM-T-EBHSV), and no amplifications for RHDV, Pasteurella multocida, E.coliandSalmonellafrom rabbits detection by this approach.

scholarly journals Phylogenetic analysis and predicted functional effect of protein mutations of E6 and E7 HPV16 strains isolated in Indonesia

2015 ◽  
Vol 24 (4) ◽  
pp. 197-205
Author(s):  
Dwi Wulandari ◽  
Lisnawati Rachmadi ◽  
Tjahjani M. Sudiro
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Asian American ◽  
Protein Function ◽  
Single Amino Acid ◽  
Hpv16 E6 ◽  
E6 And E7 ◽  
Neutral Mutations

Background: E6 and E7 are oncoproteins of HPV16. Natural amino acid variation in HPV16 E6 can alter its carcinogenic potential. The aim of this study was to analyze phylogenetically E6 and E7 genes and proteins of HPV16 from Indonesia and predict the effects of single amino acid substitution on protein function. This analysis could be used to reduce time, effort, and research cost as initial screening in selection of protein or isolates to be tested in vitro or in vivo.Methods: In this study, E6 and E7 gene sequences were obtained from 12 samples of  Indonesian isolates, which  were compared with HPV16R (prototype) and 6 standard isolates in the category of European (E), Asian (As), Asian-American (AA), African-1 (Af-1), African-2 (Af-2), and North American (NA) branch from Genbank. Bioedit v.7.0.0 was used to analyze the composition and substitution of single amino acids. Phylogenetic analysis of E6 and E7 genes and proteins was performed using Clustal X (1.81) and NJPLOT softwares. Effects of single amino acid substitutions on protein function of E6 and E7 were analysed by SNAP.Results: Java variants and isolate ui66* belonged to European branch, while the others belonged to Asian and African branches. Twelve changes of amino acids were found in E6 and one in E7 proteins. SNAP analysis showed two non neutral mutations, i.e. R10I and C63G in E6 proteins. R10I mutations were found in Af-2 genotype (AF472509) and Indonesian isolates (Af2*), while C63G mutation was found only in Af2*.Conclusion: E6 proteins of HPV16 variants were more variable than E7. SNAP analysis showed that only E6 protein of African-2 branch had functional differences compared to HPV16R.

scholarly journals Characterization of a Novel Plasmid-Mediated Cephalosporinase (CMY-9) and Its Genetic Environment in an Escherichia coli Clinical Isolate

2002 ◽  
Vol 46 (8) ◽  
pp. 2427-2434 ◽  
Author(s):  
Yohei Doi ◽  
Naohiro Shibata ◽  
Keigo Shibayama ◽  
Kazunari Kamachi ◽  
Hiroshi Kurokawa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Gene Cassette ◽  
Single Amino Acid ◽  
Common Region ◽  
Class 1 Integron ◽  
Class 1 ◽  
The Common ◽  
High Level

ABSTRACT An Escherichia coli strain, HKYM68, which showed resistance to broad-spectrum cephalosporins was isolated from a sputum specimen in Japan. The high-level resistance of the strain to ceftazidime, cefpirome, and moxalactam was carried by a self-transferable plasmid. The β-lactamase gene responsible for the resistance was cloned and sequenced. The deduced amino acid sequence of this gene product, CMY-9, had a single amino acid substitution (E85D), the residue reported to be part of the recognition site for the R1 side chain of β-lactams, compared with the amino acid sequence of CMY-8 and also had 78% identity with the amino acid sequence of CepH, a chromosomal cephalosporinase of Aeromonas hydrophila. A sul1-type class 1 integron containing an aacA1-orfG gene cassette was identified upstream of bla CMY-9 and ended with a truncated 3′ conserved segment. The following 2.1 kb was almost identical to the common region of integrons In6 and In7 and the integron of pSAL-1, except that orf513 encoding a putative transposase was identified instead of orf341 due to addition of a single nucleotide. bla CMY-9 was closely located downstream of the end of the common region. These observations are indicative of the exogenous derivation of bla CMY-9 from some environmental microorganisms such as aeromonads.

The genetic analysis of new Polish strains of European brown hare syndrome virus

2014 ◽  
Vol 17 (2) ◽  
pp. 353-355
Author(s):  
E. Kwit ◽  
M. Chrobocińska ◽  
Z. Grądzki ◽  
Ł. Jarosz ◽  
B. Majer-Dziedzic ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Phylogenetic Position ◽  
Brown Hare ◽  
Gene Encoding ◽  
European Brown Hare ◽  
Close Relationship ◽  
Provinces Of Poland ◽  
Pcr Method ◽  
European Brown Hare Syndrome ◽  
Hare Population

Abstract In this paper we describe recently occurring outbreaks of European brown hare syndrome (EBHS) in a captive hare population. The aim of our study was to evaluate the phylogenetic position of detected Polish strains compared to other European strains of EBHSV. Investigations were undertaken in hares from different provinces of Poland. Liver or spleen samples were tested for viral RNA using the RT-nested PCR method and the products were subsequently sequenced. The genetic analysis was based on the fragment of gene encoding viral capsid protein; it revealed a high homology and close relationship between Polish and European EBHSV strains isolated between 2001 and 2011

Morphologic and Immunohistochemical Characterization of the Hepatic Lesions Associated with European Brown Hare Syndrome

1994 ◽  
Vol 31 (3) ◽  
pp. 327-334 ◽  
Author(s):  
D. Gavier-Widén
Keyword(s):  
Fatty Degeneration ◽  
Lepus Europaeus ◽  
Coagulation Necrosis ◽  
Brown Hare ◽  
Electron Microscopic ◽  
European Brown Hare ◽  
European Brown Hare Syndrome ◽  
Hepatic Lesions ◽  
Living Adult

Liver lesions were studied in 40 free-living adult European brown hares ( Lepus europaeus) and varying hares ( Lepus timidus) of both sexes that had died in Sweden with the viral infection European brown hare syndrome (EBHS). The lesions were characterized by their histopathologic, immunohistochemical, and electron microscopic findings. Periportal to massive coagulation necrosis was a distinctive feature of EBHS. Lytic necrosis, inflammation, fatty degeneration, and cholangitis occurred variably. Accumulation of basophilic granules in the cytoplasm of hepatocytes was commonly observed; these lesions corresponded ultrastructurally to mitochondrial calcification. Viral antigen was revealed in the cytoplasm and nucleus of hepatocytes and in the cytoplasm of macrophages.

Amino acid sequence of a basic aspartate-49-phospholipase A2 from Trimeresurus flavoviridis venom and phylogenetic analysis of Crotalinae venom phospholipases A2

Toxicon ◽  
2005 ◽  
Vol 46 (2) ◽  
pp. 185-195 ◽  
Author(s):  
Takahito Chijiwa ◽  
Kazuki Abe ◽  
Tomohisa Ogawa ◽  
Nikolai N. Nikandrov ◽  
Shosaku Hattori ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Phospholipase A2 ◽  
Phospholipases A2 ◽  
Trimeresurus Flavoviridis
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