scholarly journals Comparative molecular and genetic characterization of rabies viruses (Rabies lyssavirus, Lyssavirus, Rhabdoviridae) circulated in the Russian Federation in 1985–2016

2020 ◽  
Vol 65 (1) ◽  
pp. 41-48
Author(s):  
O. N. Zaykova ◽  
T. V. Grebennikova ◽  
M. A. Losich ◽  
A. L. Elakov ◽  
A. M. Gulyukin ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Epidemiology ◽  
Rabies Virus ◽  
Russian Federation ◽  
Amino Acid Sequences ◽  
Phylogenetic Study ◽  
Human Populations ◽  
Human Beings ◽  
The Russian Federation ◽  
Virus Isolates

Introduction. Rabies caused by the neurotropic virus of the genus Lyssavirus, Rhabdoviridae family, which infects all warm-blooded vertebrates including human beings. The homology level of the amino acid sequences for Lyssaviruses nucleoprotein reaches 78–93%.Aim – study the genetic diversity and molecular epidemiology of Lyssaviruses circulated in the Russian Federation in 1985–2016.Material and methods. 54 isolates of rabies virus isolated from animals, and 2 isolates from humans, 4 vaccine strains of rabies virus: RV-97, ERA, Shchelkovo 51, ERAG333 used in phylogenetic study. Phylogenetic analysis was performed using Genbank data on genome fragments of 73 rabies virus isolates and 9 EBLV-1 isolates. DNASTAR V.3.12, Bio Edit 7.0.4.1 and MEGA v.10.0.5, Primer Premier 5 programs have been used.Results. Comparative molecular genetic analysis of genomes fragments of 130 Lissaviruses, isolated on the territory of the RF, Ukraine in 1985-2016, vaccine strains of rabies virus, showed their distribution by geographical feature. Comparison of the nucleoprotein fragments of the rabies virus isolates with vaccine strains revealed 4 marker mutations: V56I (Eurasian group), L/V95W (Central group), D101N/S/T, and N/G106D. Phylogenetic analysis of the isolate «Juli», isolated from a human bitten by a bat proved his belonging to the European Bat lyssavirus-1a.Discussion. Study of the molecular epidemiology of rabies within the Russian Federation allows for the genotyping of the viruses and helps to study the hidden mechanisms of rabies infection in animal and human populations, and to characterize vaccine strains, including during oral vaccination.Conclusion. Further study of the molecular epidemiology of rabies within the Russian Federation and the countries bordering it is important.

scholarly journals Genetic analysis of nucleotide sequences of neuraminidase gene of highly pathogenic avian influenza A/H5N8 virus isolates recovered in the Russian Federation in 2020

2021 ◽  
pp. 301-307
Author(s):  
P. B. Akshalova ◽  
N. G. Zinyakov ◽  
A. V. Andriyasov ◽  
P. D. Zhestkov ◽  
Z. B. Nikonova ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Influenza Virus ◽  
Avian Influenza ◽  
Russian Federation ◽  
Highly Pathogenic Avian Influenza ◽  
Nucleotide Sequences ◽  
Highly Pathogenic ◽  
Pathogenic Avian Influenza ◽  
The Russian Federation ◽  
Virus Isolates

Avian influenza is a highly dangerous viral disease that causes huge economic damage to poultry farming. Currently, highly virulent influenza virus with N8 neur- aminidase subtype is quite often detected in populations of domestic and wild birds in various countries of the world. The article provides data on complete nucleotide sequences of the neuraminidase gene of highly pathogenic avian influenza virus isolates recovered in the second half of 2020 from pathological material received from four regions of the Russian Federation. The conducted research showed that the subtype of the isolated virus was N8. According to the phylogenetic analysis, isolates of N8 virus belong to group 8C.4. During the phylogenetic analysis of the neuraminidase, we also took into account data on hemagglutinin classification, according to which H5N8 virus isolates belong to a widespread clade 2.3.4.4. Viruses of the clade were first registered in 2010 in China and they have been circulating up to now. The paper also provides data of a comparative analysis of nucleotide sequences of the studied isolates and the isolates from the international GenBank and GISAID databases, recovered in other countries from 2007 to 2020. During the analysis of the amino acid sequence of the studied isolates, no substitutions were found in the positions that affect resistance to neuraminidase inhibitors. The complete nucleotide sequences of the neuraminidase gene of the avian influenza virus subtype N8 (isolates A/domestic goose/OMSK/1521-1/2020, A/duck/Chelyabinsk/1207-1/2020, A/duck/Saratov/1578-2/2020, A/goose/Tatarstan/1730-2/2020) are published in the international GenBank and GISAID databases. Based on the analysis of the nucleotide sequences of the studied isolates, the article shows gradual evolution of the N8 subtype virus.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

Molecular epidemiology of rabies virus isolates in Uganda

2010 ◽  
Vol 147 (1) ◽  
pp. 135-138 ◽  
Author(s):  
Shinji Hirano ◽  
Takuya Itou ◽  
Hisashi Shibuya ◽  
Yoshito Kashiwazaki ◽  
Takeo Sakai
Keyword(s):  
Molecular Epidemiology ◽  
Rabies Virus ◽  
Virus Isolates

scholarly journals Features of developing SARS-CoV-2 nucleocapsid protein population-based seroprevalence during the first wave of the COVID-19 epidemic in the Russian Federation

2021 ◽  
Vol 11 (2) ◽  
pp. 297-323
Author(s):  
A. Yu. Popova ◽  
E. E. Andreeva ◽  
E. A. Babura ◽  
S. V. Balakhonov ◽  
N. S. Bashketova ◽  
...  
Keyword(s):  
Russian Federation ◽  
Serum Antibody ◽  
Geographic Region ◽  
Primary Data ◽  
Reproductive Number ◽  
Federal State ◽  
Human Populations ◽  
Cross Sectional ◽  
Age Related ◽  
The Russian Federation

The novel coronavirus (SARS-CoV-2) pandemic, dubbed COVID-19, has become one of the most serious challenges for human populations in the vast majority of countries worldwide. Rapid spreading and increased mortality related to it required new approaches to manage epidemic processes on a global scale. One of such approaches was based on analyzing SARS-CoV-2 seroprevalence associated with COVID-19. Our aim was to summarize the results on assessing seroprevalence to the SARS-CoV-2 nucleocapsid antigen (Nc) in residents from 26 regions of the Russian Federation, carried out during the first wave of the COVID-19 epidemic.Materials and methods. Seroprevalence distribution was examined in 26 model regions of the Russian Federation according to the unified method developed by the Rospotrebnadzor with the participation of the Federal State Institution Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology. Such approach implied formation of a group of volunteer subjects in model geographic region who were tested by ELISA for anti-Nc serum antibody level in peripheral blood. Analyzed primary data obtained in separate regions were either accepted for publication or released.Results. The current paper finalizes the data obtained in all 26 regions of the Russian Federation. The total SARS-CoV-2 seroprevalence was 19.5 (10.0–25.6)% with the maximum and minimum value found in the Kaliningrad Region and the Republic of Crimea, respectively (50.2% vs. 4.3%). A pattern of age-related seroprevalence distribution indicates insignificant predominance of seroprevalence among subjects of 1–17 years old: 22.1 (13.1–31.8)%. Among COVID-19 convalescents positive for SARS-CoV Nc antibodies it reached 60.0 (40.0–73.3)%. The number of contact persons comprised 6285 subjects or 8.5% of total volunteer cohort, with the level of seroprevalence reaching up to 25.3 (17.95–35.8)%. A direct correlation was revealed between levels of seroprevalence in convalescent and contact volunteers. In addition, the reproductive number for SARS-CoV was calculated comprising 5.8 (4.3–8.5) suggesting that one convalescent subject can infect at least 4 healthy individuals. A high level of asymptomatic forms of COVID-19 among seropositive subjects was confirmed empirically comprising up to 93.6 (87.1–94.9)%.Conclusion. A single cross-sectional study performed during 2020 June–August timeframe allowed to assess pattern of sex- and agerelated COVID-19 seroprevalence for general population in 26 Russian Federation regions. The data obtained may serve as a basis for the longitudinal cohort investigation with serial subject sampling. The timing and duration of study will be determined by dynamics of ongoing COVID-19 epidemic.

scholarly journals Molecular Epidemiology of Rabies Virus Isolates in India

2006 ◽  
Vol 44 (9) ◽  
pp. 3218-3224 ◽  
Author(s):  
T. Nagarajan ◽  
B. Mohanasubramanian ◽  
E. V. Seshagiri ◽  
S. B. Nagendrakumar ◽  
M. R. Saseendranath ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Rabies Virus ◽  
Virus Isolates
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