scholarly journals TBEV Subtyping in Terms of Genetic Distance

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1240
Author(s):  
Andrei A. Deviatkin ◽  
Galina G. Karganova ◽  
Yulia A. Vakulenko ◽  
Alexander N. Lukashev
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Species Level ◽  
Quantitative Criterion ◽  
Tick Borne Encephalitis ◽  
Everyday Work ◽  
Phylogenetic Grouping ◽  
Tick Borne Encephalitis Virus

Currently, the lowest formal taxon in virus classification is species; however, unofficial lower-level units are commonly used in everyday work. Tick-borne encephalitis virus (TBEV) is a species of mammalian tick-borne flaviviruses that may cause encephalitis. Many known representatives of TBEV are grouped into subtypes, mostly according to their phylogenetic relationship. However, the emergence of novel sequences could dissolve this phylogenetic grouping; in the absence of strict quantitative criterion, it may be hard to define the borders of the first TBEV taxonomic unit below the species level. In this study, the nucleotide/amino-acid space of all known TBEV sequences was analyzed. Amino-acid sequence p-distances could not reliably distinguish TBEV subtypes. Viruses that differed by less than 10% of nucleotides in the polyprotein-coding gene belonged to the same subtype. At the same time, more divergent viruses were representatives of different subtypes. According to this distance criterion, TBEV species may be divided into seven subtypes: TBEV-Eur, TBEV-Sib, TBEV-FE, TBEV-2871 (TBEV-Ob), TBEV-Him, TBEV-178-79 (TBEV-Bkl-1), and TBEV-886-84 (TBEV-Bkl-2).

scholarly journals Spontaneous Mutations Restore the Viability of Tick-Borne Encephalitis Virus Mutants with Large Deletions in Protein C

2003 ◽  
Vol 77 (1) ◽  
pp. 443-451 ◽  
Author(s):  
Regina M. Kofler ◽  
Agnes Leitner ◽  
Gabriel O'Riordain ◽  
Franz X. Heinz ◽  
Christian W. Mandl
Keyword(s):  
Amino Acid ◽  
Protein C ◽  
Deletion Mutant ◽  
Hydrophobic Interactions ◽  
Encephalitis Virus ◽  
Sequence Element ◽  
Hydrophobic Domain ◽  
Large Deletions ◽  
Tick Borne Encephalitis ◽  
Tick Borne Encephalitis Virus

ABSTRACT The capsid protein, C, of tick-borne encephalitis virus has recently been found to tolerate deletions up to a length of 16 amino acid residues that partially removed the central hydrophobic domain, a sequence element conserved among flaviviruses which may be crucial for virion assembly. In this study, mutants with deletion lengths of 19, 21, 27, or 30 residues, removing more or all of this hydrophobic domain, were found to yield viable virus progeny, but this was without exception accompanied by the emergence of additional mutations within protein C. These point mutations or sequence duplications were located downstream of the engineered deletion and generally increased the hydrophobicity, suggesting that they may compensate for the loss of the central hydrophobic domain. Two of the second-site mutations, together with the corresponding deletion, were introduced into a wild-type genetic backbone, and the analysis of these “double mutants” provided direct evidence that the viability of the deletion mutant indeed depended on the presence of the second-site mutation. Our results corroborate the notion that hydrophobic interactions of protein C are essential for the assembly of infectious flavivirus particles but rule out the possibility that individual residues of the central hydrophobic domain are absolutely required for infectivity. Furthermore, the double mutants were found to be highly attenuated and capable of inducing a protective immune response in mice at even lower inoculation doses than the previously characterized 16-amino-acid-residue deletion mutant, suggesting that the combination of large deletions and second-site mutations may be a superior way to generate safe, attenuated flavivirus vaccine strains.

scholarly journals Genetic Mapping of Rabies Virus in Dogs as a Basis for Disease Control

2016 ◽  
Vol 10 (1) ◽  
Author(s):  
Muharam Saepulloh ◽  
R. M. Abdul Adji
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Phylogenetic Relationship ◽  
Rabies Virus ◽  
Virus Isolate ◽  
Protein Gene ◽  
Genetic Characteristics ◽  
Nucleoprotein Gene ◽  
N Protein

The purpose of this study was to determine the genetic characteristics of rabies virus based on phylogenetic relationship among rabies virus in various regions in Indonesia. The amino acid sequence of the nucleoprotein gene of rabies virus isolate from Banten (RV/Banten01/dog/2007),Makasar (RV/MKS-26/dog/2010), Bukit Tinggi (RV/BKT-52/dog/2009 and RV/BKT-58/dog/2009), Medan (RV/Medan27/dog/2007)andBali(RV/Bali-1/dog/2009;RV/Bali-2/dog/2009;RV/Bali-3/dog/2009),Indonesiawasdetermined.TheseisolatesshowedahighdegreeofhomologyamongIndonesianisolateswhichreached100%.Meanwhile,thelevelofhomologybetweenrabiesvirusisolatesfromcatsrabiesvirusisolatesfromdogsreached97%.ResultsofphylogeneticanalysisusingtheaminoacidsequencesoftheNgenesshowedthatallofIndonesianrabiesvirusisolateswerecloselyrelatedtorabiesvirusesfromChinathanthosefromThailand,Laos,Burma,andVietnamwhichgeograficallycloser to Indonesia. Data obtained from the phylogenetic analysis is expected to trace the source of rabies spread and thepossibility to create a vaccines which more suitable with rabies virus that spreads in Indonesia. Based on the phylogenetic relationship analysisusing the amino acid sequence of the rabies virus N protein gene showed that all of rabies virus isolated from Indonesian regions share a highhomology with others ranging from 97-100%..Key words: sequencing, rabies, nucleoprotein gene (N), homology

scholarly journals Functional Analysis of Potential Carboxy-Terminal Cleavage Sites of Tick-Borne Encephalitis Virus Capsid Protein

2007 ◽  
Vol 82 (5) ◽  
pp. 2218-2229 ◽  
Author(s):  
Sabrina Schrauf ◽  
Petra Schlick ◽  
Tim Skern ◽  
Christian W. Mandl
Keyword(s):  
Amino Acid ◽  
Capsid Protein ◽  
Protein C ◽  
Terminal Region ◽  
Encephalitis Virus ◽  
Viral Protease ◽  
Tick Borne Encephalitis ◽  
Carboxy Terminal Region ◽  
Tick Borne Encephalitis Virus ◽  
Carboxy Terminal

ABSTRACT The mature capsid protein C of flaviviruses is generated through the proteolytic cleavage of the precursor polyprotein by the viral NS2B/3 protease. This cleavage is a prerequisite for the subsequent processing of the viral surface protein prM, and the concerted progression of these events plays a key role in the process of the assembly of infectious virions. Protein C of tick-borne encephalitis virus (TBEV) contains two amino acid sequence motifs within the carboxy-terminal region that match the canonical NS2B/3 recognition site. Site-specific mutagenesis in the context of the full-length TBEV genome was used to investigate the in vivo cleavage specificity of the viral protease in this functionally important domain. The results indicate that the downstream site is necessary and sufficient for efficient cleavage and virion assembly; in contrast, the upstream site is dispensable and placed in a structural context that renders it largely inaccessible to the viral protease. Mutants with impaired C-prM cleavage generally exhibited a significantly increased cytotoxicity. In spite of the clear preference of the protease for only one of the two naturally occurring motifs, the enzyme was unexpectedly tolerant to both the presence of a noncanonical threonine residue at position P2 and the position of cleavage relative to the adjacent internal prM signal sequence. The insertion of three amino acid residues downstream of the cleavage site did not change the viral phenotype. Thus, this study further illuminates the specificity of the TBEV protease and reveals that the carboxy-terminal region of protein C has a remarkable functional flexibility in its role in the assembly of infectious virions.

scholarly journals Molecular Genetic Analysis of the Complete Genome of Tick-Borne Encephalitis Virus (Siberia Subtype): Modern Kolarovo-2008 Isolate

2011 ◽  
pp. 44-48 ◽  
Author(s):  
E. V. Chausov ◽  
V. A. Ternovoy ◽  
E. V. Protopopova ◽  
S. N. Konovalova ◽  
Yu. V. Kononova ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Complete Genome ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Encephalitis Virus ◽  
Nucleotide Sequence Analysis ◽  
Tick Borne Encephalitis ◽  
Tick Borne Encephalitis Virus ◽  
Siberian Subtype

Determined is the complete genome sequence of Kolarovo-2008 strain (Siberia subtype) of Tick-borne encephalitis virus (TBEV), isolated from a tick in the suburbs of the Tomsk city. Nucleotide sequence analysis testifies of the fact that the level of genetic differences within the Siberian subtype of TBEV amounts to 10 % of the nucleotide sequence and to 7 % of amino-acid sequence for certain virus genes. 3'-HTO of the genome of Siberian subtype has the highest rate of variability and the homology level ranging from 65 to 97 %. Kolarovo-2008 and Vasilchenko (isolated in Novosibirsk in 1969) strains have the highest level of genome homology. The level of dissimilarity between the two Tomsk strains is substantially higher: the total number of amino-acid substitutions in Tomsk Zausaev and Kolarovo-2008 strains equals to 124, and 3'HTO level of homology is 79 %. Identified genetic variability of the Siberian subtype of TBEV is of a great importance for further development and enhancement of tick-borne encephalitis virus diagnostics.

scholarly journals Amino acid changes responsible for attenuation of virus neurovirulence in an infectious cDNA clone of the Oshima strain of Tick-borne encephalitis virus

2004 ◽  
Vol 85 (4) ◽  
pp. 1007-1018 ◽  
Author(s):  
Daisuke Hayasaka ◽  
Tamara S. Gritsun ◽  
Kentarou Yoshii ◽  
Tomotaka Ueki ◽  
Akiko Goto ◽  
...  
Keyword(s):  
Cell Culture ◽  
Amino Acid ◽  
Cdna Clone ◽  
Infectious Clone ◽  
Encephalitis Virus ◽  
Infectious Cdna Clone ◽  
Amino Acid Substitutions ◽  
Parent Virus ◽  
Tick Borne Encephalitis ◽  
Tick Borne Encephalitis Virus

A stable full-length infectious cDNA clone of the Oshima strain of Tick-borne encephalitis virus (Far-Eastern subtype) was developed by a long high-fidelity RT-PCR and one-step cloning procedure. The infectious clone (O-IC) had four amino acid substitutions and produced smaller plaques when compared with the parent Oshima 5-10 strain. Using site-directed mutagenesis, the substitutions were reverted to restore the parent virus sequence (O-IC-pt). Although genetically identical, parent virus Oshima 5-10 and virus recovered from O-IC-pt demonstrated some biological differences that are possibly explained by the presence of quasispecies with differing virulence characteristics within the original virus population. These observations may have implications for vaccines based on modified infectious clones. It was also demonstrated that the amino acid substitution E-S40→P at position 40 in the envelope (E) glycoprotein was responsible for plaque size reduction, reduced infectious virus yields in cell culture and reduced mouse neurovirulence. Additionally, two amino acid substitutions in the non-structural (NS)5 protein (virus RNA-dependent RNA polymerase) NS5-V378→A and NS5-R674→K also contributed to attenuation of virulence in mice, but did not demonstrate a noticeable biological effect in baby hamster kidney cell culture. Comparative neurovirulence tests revealed how the accumulation of individual mutations (E-S40→P, NS5-V378→A and NS5-R674→K) can result in the attenuation of a virus.

Sign in / Sign up

Export Citation Format

Share Document