scholarly journals Waterborne Outbreak of Acute Gastroenteritis Caused by Recombinant Norovirus GII.P7–GII.6 in Khabarovsk in 2019

2020 ◽  
pp. 50-54
Author(s):  
LV Butakova ◽  
EYu Sapega ◽  
OE Trotsenko ◽  
TA Zaytseva ◽  
TN Karavyanskaya ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Acute Gastroenteritis ◽  
Molecular Genetic ◽  
Disease Onset ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Contaminated Water ◽  
Rt Pcr ◽  
Waterborne Outbreak ◽  
Causative Agents

Background: Noroviruses are common causative agents of acute gastroenteritis worldwide. Person-to-person transmission is the dominant transmission route for norovirus infection but contaminated water also often leads to outbreaks. Objectives: Our purpose was to do epidemiologic and molecular genetic analyses of waterborne norovirus infection outbreak among children in Khabarovsk in 2019. Materials and methods: Clinical and water samples were screened for the presence of norovirus RNA using real-time RT-PCR detection kit. The norovirus nucleotide sequences were determined by Sanger sequencing. The obtained sequences were subjected to a phylogenetic analysis. Results: In July 2019, 34 children developed acute gastroenteritis in Khabarovsk. The epidemiologic investigation showed that on the eve of the disease onset all patients played and bathed in a pedestrian fountain complex. A molecular genetic analysis of 18 biological samples from children with acute gastroenteritis and a water sample from the fountain revealed a recombinant norovirus GII.P7-GII.6. We established a 100.0% identity of all obtained nucleotide sequences to each other. A phylogenetic analysis of ORF2 partial sequences showed that the capsid protein of the Khabarovsk GII.P7-GII.6 strains belonged to the variant GII.6a. Conclusions: Contaminated water in the pedestrian interactive fountain complex was the most likely cause of the norovirus infection outbreak among children in Khabarovsk in 2019 associated with the lack of proper maintenance and regular disinfection measures.

Morphological and molecular identification of some species of nematode of the family Protostrongylidae Leiper, 1926

2016 ◽  
Vol 3 (4) ◽  
pp. 454-461
Author(s):  
Салахутдинов ◽  
I. Salakhutdinov ◽  
Рузиев ◽  
B. Ruziev ◽  
Каримова ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Digital Camera ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Genetic Identification ◽  
Mountain Area ◽  
Phylogenetic Relations ◽  
The Family

Objective of research: conducting morphological and molecular-genetic identification and studying phylogenetic relations between protostrongylids. Materials and methods: helminthological material was collected from wild (Capra sibirica, C. falconeri, Ovis vignei and O. ammon) and domestic hollow horned ruminants (C. hircus and O. aries), and land mollusks of the family Xeropicta in the piedmont and mountain area of Uzbekisan. The morphology of protostrongylids was studied using the methods of Boev (1975) and Anderson (1978). To identify the nematode type we used temporary preparations treated with glycerol. The first-stage larvae were investigated by examination of fecal samples from animals taking into account the length, tail form and body size. To study the morphology of the third-stage protostrongylid larvae the feet of infected mollusks Xeropicta candaсharica were separated and placed into the artificial gastric juice where the cap was destroyed and the infected larvae were eliminated. After determination of species belonging of mature and larval nematodes the material was stored in separate test-tubes with distilled water under the low temperature (- 20 ºС) or in 70 % Ethanol for the molecular analysis. We used microscopes ML 2000 with a digital camera and Olympus CX3. DNA extraction, amplification and sequencing were performed with an automated sequencer. Phylogenetic analysis was conducted using the software Clustal X 2.0. Phylogenetic trees were created by the Neighbor–Joining method. Nucleotide sequences ITS-2 regions of species Protostrongylus rufescens (EU018485), P. shiozawai (AB478249), Ortostrongylus macrotis (EU018483), Cystocaulus ocreatus (EU018481) and Umingmakstrongylus pallikuukensis (AY648409) received from the NCBI GenBank were used in phylogenetic analysis. Results and discussion: Four species of adult protostrongylid nematodes: Protostrongylus rufescens, P. hobmaieri, Spiculocaulus leuckarti and Cystocaulus ocreatus were determined. DNA from four species of mature protostrongylids and larvae was amplified by using ITS-2 regions. Amplificate dimension of nematodes P. rufescens and P. hobmaieri was 380 base pairs (b.p.), S. leuckarti – 388, C. ocreatus – 399 b.p. According to the results of phylogenetic analysis and comparison of nucleotide sequences, five protostrongylid species were found in animals of the Caprinae subfamily: P. rufescens, P. hobmaieri, Protostrongylus sp., S. leuckarti and C. ocreatus. The morphological and molecular-genetic analysis of detected nematodes enables the precise identification.

NOROVIRUS GENOTYPES THAT CAUSED CASES OF ACUTE GASTROENTERITIS IN THE KHABAROVSK REGION

2018 ◽  
pp. 52-56 ◽  
Author(s):  
L.V. Butakova ◽  
E.Yu. Sapega ◽  
O.E. Trotsenko ◽  
T.A. Zaytseva ◽  
T.N. Karavyanskaya ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Study ◽  
Acute Gastroenteritis ◽  
Molecular Genetic ◽  
Nucleotide Sequences ◽  
Molecular Genetic Study ◽  
Variant Type ◽  
Sequencing Method ◽  
Sporadic Cases ◽  
Sporadic Acute Gastroenteritis

Noroviruses are the leading etiologic cause of outbreaks and sporadic cases of acute gastroenteritis worldwide. The objective of research was to study the genotypes of noroviruses, that caused outbreaks and sporadic incidence of norovirus infection in the Khabarovsk region in 2015-2018. The analysis of outbreaks due to norovirus infection in the Khabarovsk Region in 2015-2018 was performed. The molecular genetic study of samples from 60 patients from three norovirus outbreaks in the Khabarovsk Region and from 164 children with sporadic acute gastroenteritis in Khabarovsk region was performed. Genotype of noroviruses was determined by sequencing method, phylogenetic analysis of the obtained nucleotide sequences was carried out. The norovirus genotypes GII.17, GII.4 Sydney_2012 and GII.6 had caused the outbreaks of norovirus infection in the Khabarovsk region in 2015-2018. Sporadic cases of acute gastroenteritis in children in Khabarovsk in 2016 were due to GII.4 Sydney_2012, GII.3 and GII.6 norovirus genotypes. Detection of the GII.4 Sydney_2012 strain in both outbreaks and sporadic norovirus infection cases in the Khabarovsk region in 2016 evidenced of active circulation of this variant type during this period. The genotype GII.6 had been identified in Khabarovsk from 2016 to 2018.

scholarly journals Use of the method of phylogenetic analysis in an epidemiological investigation in case of HIV infection in pediatric practice

2021 ◽  
Vol 13 (1) ◽  
pp. 106-114
Author(s):  
S. P. Kruglyak ◽  
V. O. Kotova ◽  
E. I. Miroshnichenko ◽  
O. A. Skaly ◽  
E. S. Makhno ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Hiv Infection ◽  
Phylogenetic Trees ◽  
Comparison Group ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Likelihood Method ◽  
Epidemiological Investigation

The aim of the study is to study the main pathways and risk factors for HIV infection in a child, to establish a probable source of infection for a child, as well as to exclude the possibility of criminal or nosocomial infection.Materials and methods. At the first stage, an epidemiological investigation was conducted. Next, a molecular genetic analysis of two blood plasma samples studied (child and mother) and a comparison group were used, in which 18 nucleotide sequences of HIV-1 variants were used, obtained from patients living in the Primorsky Region, and 8 characterized nucleotide sequences additionally taken from GenBank international database. Distance calculation and phylogenetic analysis were performed by constructing phylogenetic trees using the Maximum Likelihood method using the GTR evolution model.Research results. The data obtained indicate that the nucleotide sequence from the child is most similar to the nucleotide sequence from the mother (potential source) and reliably grouped on the phylogenetic tree, forming a common cluster that is different from the samples of the comparison group. This indicates the likelihood of an epidemiological link between HIV infections in the mother and her child.Conclusion. According to the results of this study, we can conclude that the child is infected from an HIV-infected mother, approximately at the age of a child older than 4 years old, when he received the last negative test result for HIV markers.

scholarly journals Molecular genetic analysis of some North African barley germplasms

2017 ◽  
Vol 109 (2) ◽  
pp. 187
Author(s):  
Reda Gaafar ◽  
Mai Allam ◽  
Rasha Sabry ◽  
Mahmoud Saker
Keyword(s):  
Rapd Markers ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
North African ◽  
Rt Pcr ◽  
Breeding Selection ◽  
High Level ◽  
Barley Genotypes ◽  
Selection Of ◽  
Selection Of Resistance

<p>Isozyme and RAPD markers were used to characterize 29 barley accessions, which were collected from North Africa. In addition, resistance gene sequences were employed to develop molecular markers using RT-PCR approach. High level of polymorphism was found with both RAPD and isozyme markers, where RAPD showed that 60 % of amplified bands were polymorphic. Peroxidase showed three polymorphic loci (7 allelic bands). Isozymes cluster analysis successfully separated the barley accessions into three geographically distinct groups. RAPD investigation demonstrated that Egyptian accessions were grouped into two obvious groups. Moreover, the Tunisian accessions showed no distinct clustering, while high dissimilarities were revealed by the Algerian accessions. In the RT-PCR, from six primer pairs selected, primer pair AF092524P1P2 successfully amplified two specific amplicons of approximately (340 &amp; 220 bp) and (360 &amp; 270 bp), respectively in two Egyptian barley genotypes (El-Awamah and Awlad-Ali). One primer pair DN988165P1P2 gave only one specific amplicon in both barley genotypes of 250 and 270 bp, respectively. The markers developed could be used in improving barley crop by assisting in breeding selection of resistance genotypes.</p>

scholarly journals Molecular genetic analysis of variant phenotypes of the ABO blood group system

Blood ◽  
1996 ◽  
Vol 88 (7) ◽  
pp. 2732-2737 ◽  
Author(s):  
K Ogasawara ◽  
R Yabe ◽  
M Uchikawa ◽  
N Saitou ◽  
M Bannai ◽  
...  
Keyword(s):  
Blood Group ◽  
Molecular Genetic ◽  
Nonsynonymous Substitution ◽  
Single Strand Conformation Polymorphism ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Activity Level ◽  
Blood Group System ◽  
Nucleotide Substitutions ◽  
Group System

ABO is clinically the most important blood group system in transfusion medicine and includes many variant phenotypes. To understand the molecular genetic basis of this polymorphic system, we have analyzed genomic DNAs obtained from Japanese individuals possessing variant ABO phenotypes including A2, Ax, Ael, cis-AB, Bx, and Bel. By polymerase chain reaction-single-strand conformation polymorphism (SSCP) and nucleotide sequence analyses, we identified 11 different alleles. These alleles had nucleotide sequences different from those of the previously described 13 different alleles responsible for the common ABO phenotypes. Analysis of the nucleotide sequences of the alleles responsible for those variant phenotypes showed that the amino acid residues at position 266 and 268 may be crucial for transferase specificity, whereas those at positions 214, 216, 223, 291, and 352 may be critical for the activity level. Nine of the 11 alleles, responsible for the A2, Ax, Ael, cis-AB, Bx, and Bel phenotypes, were presumed to be generated from common ABO alleles by single nucleotide mutations such as nonsynonymous substitution, deletion, or insertion. Two other alleles, responsible for the A2 and Ael phenotypes, may have originated by recombination, gene conversionlike events or accumulation of nucleotide substitutions. Our data indicate that different alleles could cause the same ABO variant phenotypes, and that these alleles do not necessarily belong to a single evolutionary lineage.

scholarly journals Primary synovial sarcoma of the heart: a cytogenetic and molecular genetic analysis combining RT-PCR and COBRA-FISH of a case with a complex karyotype

2004 ◽  
Vol 17 (11) ◽  
pp. 1434-1439 ◽  
Author(s):  
Hans Martin Hazelbag ◽  
Károly Szuhai ◽  
Hans J Tanke ◽  
Carla Rosenberg ◽  
Pancras C W Hogendoorn
Keyword(s):  
Genetic Analysis ◽  
Synovial Sarcoma ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Complex Karyotype ◽  
Rt Pcr

scholarly journals The refinement of species affiliation of some click beetles (Coleoptera: Elateridae) based on the molecular genetic analysis

2021 ◽  
Vol 101 (1) ◽  
pp. 14-19
Author(s):  
T.M. Bragina ◽  
◽  
D.T. Konysbayeva ◽  
M.M. Rulyeva ◽  
M.A. Bobrenko ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Dna Sequences ◽  
Sandy Loam ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Time Data ◽  
Click Beetles ◽  
Gene Coi ◽  
University Of Oslo

The article is devoted to data on the approbation of modern methods and the refinement of species affiliation of soil-inhabiting larvae of click beetles (wireworm) based on the molecular genetic analysis (DNAbarcoding). For the first time, data obtained on the complete identity of certain DNA sequences of a number of species of click beetles living in the Kostanay Region (Kazakhstan) — dangerous pests of agricultural crops. At the same time, the World genetic bank (GenBank) did not find identical DNA sequences of decoded DNA nucleotide sequences for a number of studied specimens. The basis for this study was the materials collected in 2018 in the subzone of ordinary black earth on sandy loam soils (Mendykarinsky district). The selection of larvae was carried out by the method of standard soil-zoological samples. The fixation and storage of the selected click beetles larvae was carried out according to the method of preparing samples for molecular genetic analysis with fixation in 96 % alcohol. After the classic identification of the taxonomic position of the collected specimens, the species were identified by genetic analysis on the nucleotide sequence of the cytochrome C oxidase I subunit gene (COI). The assembly and decoding of the DNA nucleotide sequences of the studied samples were carried out using the programs «Codon Code Aligner» and «MEGA-X». As a result of the work carried out in the DNA laboratory of the Museum of Natural History (University of Oslo, Norway), it was possible to identify the complete identity of the DNA sequences of several mass species of click beetles, while a number of decoded DNA sequences of model specimens were absent in the genetic bank, which requires replenishment in it with new data.

scholarly journals Molecular genetic analysis of the strain Leningrad-16 used for the production of measles vaccine

2020 ◽  
Vol 97 (2) ◽  
pp. 182-189
Author(s):  
Georgy M. Ignatyev ◽  
Alena V. Atrasheuskaya ◽  
Lidiya L. Sukhanova ◽  
Elena S. Sidorenko ◽  
Nina A. Netesova
Keyword(s):  
Vaccine Strain ◽  
Measles Virus ◽  
Restriction Analysis ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Rt Pcr ◽  
Virus Genotype ◽  
Molecular Genetic Study ◽  
Production Stages ◽  
Pcr Method

Aim. To study the genetic stability of the measles virus strain Leningrad-16 (L-16) used for the production of vaccine at JSC NPO Mikrogen.Materials and methods. A series of production and sowing strains of L-16 (JSC NPO Mikrogen), ready-made series of measles vaccines from various manufacturers, and the strain of measles virus genotype D6 were studied. Molecular genetic study of the strains was performed using RT-PCR followed by restriction analysis and sequencing.Results. The complete genome sequences of the production and sowing strains of L-16 that are used for vaccine production were obtained. The sequence of the vaccine strain was deposited in GenBank. Strain L-16 was confirmed to be genetically stable. The obtained data demonstrated the possibility of using the RT-PCR method with subsequent restriction analysis to confirm the authenticity of the vaccine strain L-16 in finished mono and three component vaccines.Conclusion. The results of the study suggest the applicability of the molecular genetic methods to confirm the authenticity of the studied strains not only at the production stages, but also in the finished series of vaccines.

scholarly journals An Outbreak of Gastroenteritis Associated with a Novel GII.8 Sapovirus Variant-Transmitted by Vomit in Shenzhen, China, 2019

2020 ◽  
Author(s):  
Yuxiao Yan ◽  
Yuan Li ◽  
Shi Wen ◽  
Miao Jin ◽  
Xiangyu Kong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Factor Analysis ◽  
Acute Gastroenteritis ◽  
Single Factor ◽  
Shenzhen City ◽  
Novel Variant ◽  
Causative Agents ◽  
Single Factor Analysis ◽  
Independent Branch

Abstract Human Sapovirus (SaVs) has been reported as one of the causative agents of acute gastroenteritis worldwide. We investigated an outbreak of SaV that affected 428 students of a primary school during spring activities from 24th February to 11th March 2019 in Shenzhen city, China. The single factor analysis showed that the students which saw others vomiting in classroom or playground, saw vomitus less than 1.5 meters are susceptible (P < 0.05). Seven of eleven fecal samples from patients were positive for GII.8 SaV genotype. In this study, we obtained the genome sequence of a sapovirus GII.8 strain SZ08 comprehensively analyzed the genetic diversity. The phylogenetic analysis showed that the GII.8 strain SZ08 formed an independent branch and became a novel variant of GII.8 genotype.

scholarly journals Detection of Rickettsial DNA in Ticksin Irkutsk Region

2015 ◽  
Vol 14 (6) ◽  
pp. 43-46 ◽  
Author(s):  
N. . Yakovchitc ◽  
E. . Bondarenko ◽  
R. . Adelshin ◽  
O. . Melnikova ◽  
E. . Vershinin ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Citrate Synthase ◽  
Nucleotide Sequences ◽  
Surface Proteins ◽  
Rt Pcr ◽  
Rickettsia Species ◽  
Test Systems ◽  
Haemaphysalis Concinna ◽  
Irkutsk Region ◽  
Pcr Test

Individually 470 Dermacentor nuttalli and 46 Haemaphysalis concinna ticks collected in Irkutsk Region were analyzed using RT-PCR test systems. Rickettsia contamination of D. nuttalli was 82,3% including 1,3% of the ticks with R. sibirica DNA. H. concinna ticks were infected by rickettsia to 8,7% and the detected DNA in 6,5% of cases belonged to R. heilongjiangensis. PCR results were confirmed by phylogenetic analysis of the nucleotide sequences of three gene fragments: citrate synthase (gltA) and ompA and ompB surface proteins. Thus, circulation of two Rickettsia species pathogenic to humans was determined at the examined area.

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