Molecular epidemiology and evolution of coxsackievirus A9

Microbiology ◽  
2000 ◽  
Vol 81 (5) ◽  
pp. 1361-1372 ◽  
Author(s):  
Juhana Santti ◽  
Heli Harvala ◽  
Leena Kinnunen ◽  
Timo Hyypiä
Keyword(s):  
Genetic Relationships ◽  
Amino Acid Sequences ◽  
Sequencing Analysis ◽  
Nonstructural Proteins ◽  
Geographical Regions ◽  
Coxsackievirus A9 ◽  
Phylogenetic Grouping ◽  
Grouping Pattern ◽  
Arginine Glycine Aspartic Acid ◽  
Phylogenetic Lineages

Genetic relationships between 35 clinical isolates of coxsackievirus A9 (CAV9), collected during the last five decades from different geographical regions, were investigated by partial sequencing. Analysis of a 150 nucleotide sequence at the VP1/2A junction region identified 12 CAV9 genotypes. While most of the strains within each genotype showed geographical clustering, the analysis also provided evidence for long-range importation of virus strains. Phylogenetic analysis of a longer region around the VP1/2A junction (approximately 390 nucleotides) revealed that the designated genotypes actually represented phylogenetic lineages. The phylogenetic grouping pattern of the isolates in the analysis of the VP4/VP2 region was similar to that obtained in the VP1/2A region whereas analysis of the 3D region indicated a strikingly different grouping, which suggests that recombination events may occur in the region encoding the nonstructural proteins. Analysis of the deduced amino acid sequences of the VP1 polypeptide demonstrated that the RGD (arginine-glycine-aspartic acid) motif, implicated in the interaction of the virus with integrin, was fully conserved among the isolates.

scholarly journals Recombination Events and Conserved Nature of Receptor Binding Motifs in Coxsackievirus A9 Isolates

Viruses ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 68 ◽  
Author(s):  
Eero Hietanen ◽  
Petri Susi
Keyword(s):  
Clinical Data ◽  
Receptor Binding ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Sequence Evolution ◽  
Vp1 Gene ◽  
Nonstructural Proteins ◽  
Rgd Motif ◽  
Coxsackievirus A9 ◽  
Vp1 Capsid Protein

Coxsackievirus A9 (CVA9) is an enterically transmitted enterovirus and one of the most pathogenic type among human enteroviruses. CVA9 isolates use a distinctive RGD (Arg-Gly-Asp) motif within VP1 capsid protein that defines its ability to bind to integrin receptor(s) for cellular entry. To investigate CVA9 evolution and pathogenicity, genetic relationships and recombination events were analyzed between 54 novel clinical isolates of CVA9, as well as 21 previously published full length CVA9 sequences from GenBank. Samples were investigated by partial sequencing of the novel VP1 and 3Dpol genes, as well as including the corresponding areas from GenBank sequences. Phylogenetic analyses were combined with clinical data in a further attempt to analyze whether sequence evolution reflects CVA9 pathogenicity in the phylogenies. Furthermore, VP1 gene was also analyzed for receptor binding sites including the RGD motif and the putative heparan sulfate (HS) site. Analysis of the 559-nucleotide-long VP1 sequences identified six clades. Although most of the strains within each clade showed geographical clustering, the grouping pattern of the isolates in the analysis of the VP1 gene was strikingly different from grouping of 3Dpol, which suggests that recombination events may have occurred in the region encoding the nonstructural proteins. Inclusion of clinical data did not provide any evidence of symptom based phylogenetic clustering of CVA9 isolates. Amino acid sequence analysis of the VP1 polypeptide demonstrated that the RGD motif was fully conserved among the isolates while the putative HS binding site was only found in one isolate. These data suggest that integrin binding is essential for virus tropism, but do not explain the symptom repertoire.

scholarly journals Nucleotide Sequence and Genetic Structure of a Novel Carbaryl Hydrolase Gene (cehA) from Rhizobium sp. Strain AC100

2002 ◽  
Vol 68 (3) ◽  
pp. 1220-1227 ◽  
Author(s):  
Masayuki Hashimoto ◽  
Mitsuru Fukui ◽  
Kouichi Hayano ◽  
Masahito Hayatsu
Keyword(s):  
Nucleotide Sequence ◽  
Insertion Sequence ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Homology Search ◽  
Sequencing Analysis ◽  
Terminal Sequence ◽  
Homologous Sequences ◽  
Naphthyl Acetate ◽  
Reading Frames

ABSTRACT Rhizobium sp. strain AC100, which is capable of degrading carbaryl (1-naphthyl-N-methylcarbamate), was isolated from soil treated with carbaryl. This bacterium hydrolyzed carbaryl to 1-naphthol and methylamine. Carbaryl hydrolase from the strain was purified to homogeneity, and its N-terminal sequence, molecular mass (82 kDa), and enzymatic properties were determined. The purified enzyme hydrolyzed 1-naphthyl acetate and 4-nitrophenyl acetate indicating that the enzyme is an esterase. We then cloned the carbaryl hydrolase gene (cehA) from the plasmid DNA of the strain and determined the nucleotide sequence of the 10-kb region containing cehA. No homologous sequences were found by a database homology search using the nucleotide and deduced amino acid sequences of the cehA gene. Six open reading frames including the cehA gene were found in the 10-kb region, and sequencing analysis shows that the cehA gene is flanked by two copies of insertion sequence-like sequence, suggesting that it makes part of a composite transposon.

scholarly journals Phylogenetic and histological variation in avipoxviruses isolated in South Africa

2013 ◽  
Vol 94 (10) ◽  
pp. 2338-2351 ◽  
Author(s):  
Kristy Offerman ◽  
Olivia Carulei ◽  
Tertius A. Gous ◽  
Nicola Douglass ◽  
Anna-Lise Williamson
Keyword(s):  
South Africa ◽  
South African ◽  
Immune Cell ◽  
Genetic Relationships ◽  
Industry Analysis ◽  
The South ◽  
Mesodermal Cell ◽  
Gross Pathology ◽  
Branching Patterns ◽  
Phylogenetic Grouping

Thirteen novel avipoxviruses were isolated from birds from different regions of South Africa. These viruses could be divided into six groups, according to gross pathology and pock appearance on chick chorioallantoic membranes (CAMs). Histopathology revealed distinct differences in epidermal and mesodermal cell proliferation, as well as immune cell infiltration, caused by the different avipoxviruses, even within groups of viruses causing similar CAM gross pathology. In order to determine the genetic relationships among the viruses, several conserved poxvirus genetic regions, corresponding to vaccinia virus (VACV) A3L (fpv167 locus, VACV P4b), G8R (fpv126 locus, VLTF-1), H3L (fpv140 locus, VACV H3L) and A11R–A12L (fpv175–176 locus) were analysed phylogenetically. The South African avipoxvirus isolates in this study all grouped in clade A, in either subclade A2 or A3 of the genus Avipoxvirus and differ from the commercial fowlpox vaccines (subclade A1) in use in the South African poultry industry. Analysis of different loci resulted in different branching patterns. There was no correlation between gross morphology, histopathology, pock morphology and phylogenetic grouping. There was also no correlation between geographical distribution and virus phenotype or genotype.

scholarly journals Isolation and identification of a novel human parechovirus

2004 ◽  
Vol 85 (2) ◽  
pp. 391-398 ◽  
Author(s):  
Miyabi Ito ◽  
Teruo Yamashita ◽  
Hideaki Tsuzuki ◽  
Naokazu Takeda ◽  
Kenji Sakae
Keyword(s):  
Vero Cells ◽  
Amino Acid Sequences ◽  
Human Enterovirus ◽  
Nucleotide Identity ◽  
Aichi Virus ◽  
Human Parechovirus ◽  
Isolation And Identification ◽  
Respiratory Illnesses ◽  
C Terminus ◽  
Arginine Glycine Aspartic Acid

A cytopathic agent (A308/99) was isolated using Vero cells from a stool specimen of a 1-year-old patient with transient paralysis. The agent was approximately 28 nm in diameter with a distinct ultrastructure resembling the virus particle of an enterovirus. It could not be neutralized by antisera against human picornaviruses such as human enterovirus, Aichi virus or human parechovirus. The virion contained three capsid proteins with molecular masses of 38, 30·3 and 30 kDa. Determination of the complete nucleotide sequence of A308/99 revealed that the nucleotide and deduced amino acid sequences were closely related to those of human parechoviruses. When 11 regions encoding the structural and non-structural proteins were compared, A308/99 had between 75 and 97 % and 73 and 97 % nucleotide identity with human parechovirus type 1 (HPeV-1) and type 2 (HPeV-2), respectively. The most distinctive divergence was seen in VP1, which had 74·5 % and 73·1 % nucleotide identity with HPeV-1 and HPeV-2, respectively. Viruses related to A308/99 were also isolated from three patients with gastroenteritis, exanthema or respiratory illnesses. A308/99 and these other three isolates had no arginine–glycine–aspartic acid (RGD) motif, which is located near the C terminus of VP1 in HPeV-1 and HPeV-2. A seroepidemiological study revealed that the prevalence of A308/99 antibodies was low (15 %) among infants but became higher with age, reaching more than 80 % by 30 years of age. These observations indicate that A308/99 is genetically close to, but serologically and genetically distinct from, HPeV-1 and HPeV-2 and accordingly can be classified as third serotype of human parechovirus.

Discovery and genome characterization of a new Nepovirus infecting grapevine

Plant Disease ◽  
2020 ◽  
Author(s):  
Maher Al Rwahnih ◽  
Olufemi Joseph Alabi ◽  
Min Sook Hwang ◽  
Tongyan Tian ◽  
Dimitre Mollov ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Virus Transmission ◽  
Amino Acid Sequences ◽  
Molecular Characteristics ◽  
Vitis Vinifera L ◽  
Sequencing Analysis ◽  
Biological Index ◽  
Chenopodium Amaranticolor ◽  
Sequence Contigs

In 2012, dormant canes of a proprietary wine grape (Vitis vinifera L.) accession were included in the collection of the University of California-Davis Foundation Plant Services. No virus-like symptoms were elicited when bud chips from propagated own-rooted canes of the accession were graft-inoculated onto a panel of biological index grape varieties. However, chlorotic ring symptoms were observed on sap inoculated Chenopodium amaranticolor Coste & A. Rein and C. quinoa Willd. plants, indicating the presence of a mechanically transmissible virus. Transmission electron microscopy of virus preps from symptomatic C. quinoa revealed spherical, non-enveloped virions of ~27 nm in diameter. And nepovirus-like haplotypes of sequence contigs were detected in both the source grape accession and recipient C. quinoa plants using high throughput sequencing analysis. A novel bipartite nepovirus-like genome was assembled from these contigs and the termini of each RNA segment were verified by RACE assays. The RNA1 (7,186-nt) of the virus encode a large polyprotein P1 of 231.1 kDa while the RNA2 (4,460-nt) also encode a large polyprotein P2 of 148.9 kDa. Each of the polyadenylated RNA segment is flanked by 5′- (RNA1=156-nt; RNA2=170-nt) and 3′- (RNA1=834-nt; RNA2=261-nt) untranslated region sequences that shared >90% identities between their corresponding sequences. Maximum-likelihood phylogenetic analyses of the conserved Pro-Pol amino acid sequences of Secoviridae species revealed the clustering of the new virus within the nepovirus clade. Considering its biological and molecular characteristics, and based on current criteria, we propose that the novel virus, named as grapevine nepovirus A (GNVA), be assigned as a member of the genus Nepovirus.

Characterization ofDicrocoelium dendriticumisolates from small ruminants in Shaanxi Province, north-western China, using internal transcribed spacers of nuclear ribosomal DNA

2013 ◽  
Vol 89 (1) ◽  
pp. 124-129 ◽  
Author(s):  
Q.Q. Bian ◽  
G.H. Zhao ◽  
Y.Q. Jia ◽  
Y.Q. Fang ◽  
W.Y. Cheng ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Small Ruminants ◽  
Internal Transcribed Spacers ◽  
Shaanxi Province ◽  
Western China ◽  
Nuclear Ribosomal Dna ◽  
Specific Sequence ◽  
Sheep And Goats ◽  
Rdna Sequences ◽  
Geographical Regions

AbstractThe genetic variations in internal transcribed spacers (ITS) spanning ITS-1, 5.8S and ITS-2 rDNA ofDicrocoelium dendriticum, isolated from sheep and goats in four geographical regions in Shaanxi province, were examined. The lengths of ITS-1, 5.8S and ITS-2 rDNA sequences forD. dendriticumwere 749 bp, 161 bp and 234 bp, respectively. Intra-specific sequence variations ofD. dendriticumwere 0–0.5% for ITS-1 and 0–1.3% for ITS-2 rDNA, while the inter-specific variations among species in genusDicrocoeliumin ITS-2 rDNA were 3.4–12.3%. Phylogenetic analysis based on sequences of ITS-2 rDNA showed that allD. dendriticumisolates in the present study were grouped with referenceD. dendriticumisolates from sheep and goats, andD. dendriticumisolates from cattle and Japanese serow were clustered in a sister clade. However, the phylogenetic tree could not reveal geographically genetic relationships ofD. dendriticumisolates in different origins and hosts. These findings provided basic information for further study of molecular epidemiology and control ofD. dendriticuminfection in Shaanxi province as well as in the world.

scholarly journals Prevalence and Molecular Characterization of Tetracycline Resistance in Enterococcus Isolates from Food

2004 ◽  
Vol 70 (3) ◽  
pp. 1555-1562 ◽  
Author(s):  
Geert Huys ◽  
Klaas D'Haene ◽  
Jean-Marc Collard ◽  
Jean Swings
Keyword(s):  
Tetracycline Resistance ◽  
Recipient Strain ◽  
Sequencing Analysis ◽  
Evolutionary Modeling ◽  
Phenotypic Resistance ◽  
Homology Groups ◽  
Filter Mating ◽  
Gene Filter ◽  
Phylogenetic Lineages

ABSTRACT In the present study, a collection of 187 Enterococcus food isolates mainly originating from European cheeses were studied for the phenotypic and genotypic assessment of tetracycline (TC) resistance. A total of 45 isolates (24%) encompassing the species Enterococcus faecalis (n = 33), E. durans (n = 7), E. faecium (n = 3), E. casseliflavus (n = 1), and E. gallinarum (n = 1) displayed phenotypic resistance to TC with MIC ranges of 16 to 256 μg/ml. Eight of these strains exhibited multiresistance to TC, erythromycin, and chloramphenicol. By PCR detection, TC resistance could be linked to the presence of the tet(M) (n = 43), tet(L) (n = 16), and tet(S) (n = 1) genes. In 15 isolates, including all of those for which the MIC was 256 μg/ml, both tet(M) and tet(L) were found. Furthermore, all tet(M)-containing enterococci also harbored a member of the Tn916-Tn1545 conjugative transposon family, of which 12 erythromycin-resistant isolates also contained the erm(B) gene. Filter mating experiments revealed that 10 E. faecalis isolates, 3 E. durans isolates, and 1 E. faecium isolate could transfer either tet(M), tet(L), or both of these genes to E. faecalis recipient strain JH2-2. In most cases in which only tet(M) was transferred, no detectable plasmids were acquired by JH2-2 but instead all transconjugants contained a member of the Tn916-Tn1545 family. Sequencing analysis of PCR amplicons and evolutionary modeling showed that a subset of the transferable tet(M) genes belonged to four sequence homology groups (SHGs) showing an internal homology of ≥99.6%. Two of these SHGs contained tet(M) mosaic structures previously found in Tn916 elements and on Lactobacillus and Neisseria plasmids, respectively, whereas the other two SHGs probably represent new phylogenetic lineages of this gene.

scholarly journals Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

2015 ◽  
Vol 71 (1) ◽  
pp. 81-95 ◽  
Author(s):  
Hoda Moradkhani ◽  
Ali Ashraf Mehrabi ◽  
Alireza Etminan ◽  
Alireza Pour-Aboughadareh
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Issr Marker ◽  
D Genome ◽  
Ploidy Levels ◽  
Marker Data ◽  
Geographical Regions ◽  
High Level

AbstractThe aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions ofAegilopsandTriticumspecies with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA) revealed that 81% (ISSR) and 84% (SSR) of variability was partitioned among individuals within populations. Comparing the genetic diversity ofAegilopsandTriticumaccessions, based on genetic parameters, shows that genetic variation ofAe. crassaandAe. tauschiispecies are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA) for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA), also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

scholarly journals Characterization of the complete mitochondrial genomes of two sibling species of parasitic roundworms, Haemonchus contortus and Teladorsagia circumcincta.

2020 ◽  
Author(s):  
Nikola Palevich ◽  
Paul Haydon Maclean ◽  
Young-Jun Choi ◽  
Makedonka Mitreva
Keyword(s):  
New Zealand ◽  
High Resolution ◽  
Haemonchus Contortus ◽  
Animal Health ◽  
Small Ruminants ◽  
Population Connectivity ◽  
Amino Acid Sequences ◽  
Strain Level ◽  
Teladorsagia Circumcincta ◽  
Geographical Regions

Abstract Background Haemonchus contortus and Teladorsagia circumcincta are among the two most pathogenic internal parasitic nematodes infecting small ruminants, such as sheep and goats, and are a global animal health issue. Accurate identification and delineation of Haemonchidae species is essential for development of diagnostic and control strategies with high resolution for Trichostrongyloidea infection in ruminants. Here, we describe in detail and compare the complete mitochondrial (mt) genomes of the New Zealand H. contortus and T. circumcincta field strains to improve our understanding of species- and strain-level evolution in these closely related roundworms. Methods In the present study, we performed extensive comparative bioinformatics analyses on the recently sequenced complete mt genomes of the New Zealand H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP field strains. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), Maximum Likelihood (ML) and Maximum Parsimony (MP).Results The AT-rich mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP are 14,001 bp (A+T content of 77.4 %) and 14,081 bp (A+T content of 77.3 %) in size, respectively. All 36 of the typical nematode mt genes are transcribed in the forward direction in both species and comprise of 12 protein-encoding genes (PCGs), 2 ribosomal RNA (rrn) genes, and 22 transfer RNA (trn) genes. The secondary structures for the 22 trn genes and two rrn genes differ between H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP, however the gene arrangements of both are consistent with other Trichostrongylidea sequenced to date. Conclusions Comparative analyses of the complete mitochondrial nucleotide sequences, PCGs, A+T rich and non-coding repeat regions of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP further reinforces the high levels of diversity and gene flow observed among Trichostrongylidea, and supports their potential as ideal markers for strain-level identification from different hosts and geographical regions with high resolution for future studies. The complete mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP presented here provide useful novel markers for further studies of the meta-population connectivity and the genetic mechanisms driving evolution in nematode species.

scholarly journals The Phylogenetic Analysis of Cimex hemipterus (Hemiptera: Cimicidae) Isolated from Different Regions of Iran Using Cytochrome Oxidase Subunit I Gene

2020 ◽  
Author(s):  
Awat Samiei ◽  
Mousa Tavassoli ◽  
Karim Mardani
Keyword(s):  
Dna Sequencing ◽  
Cytochrome Oxidase ◽  
Blood Feeding ◽  
Coi Gene ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Bed Bugs ◽  
Geographical Regions ◽  
Dna Sequencing Analysis ◽  
I Gene

Background: Bedbugs are blood feeding ectoparasites of humans and several domesticated animals. There are scar­city of information about the bed bugs population throughout Iran and only very limited and local studies are availa­ble. The aim of this study is to assess the phylogenetic relationships and nucleotide diversity using partial sequences of cytochrome oxidase I gene (COI) among the populations of tropical bed bugs inhabiting Iran. Methods: The bedbugs were collected from cities located in different geographical regions of Iran. After DNA ex­traction PCR was performed for COI gene using specific primers. Then DNA sequencing was performed on PCR products for the all 15 examined samples. Results: DNA sequencing analysis showed that the all C. hemipterus samples were similar, despite the minor nu­cleotide variations (within the range of 576 to 697bp) on average between 5 and 10 Single nucleotide polymorphisms (SNPs). Subsequently, the results were compared with the database in gene bank which revealed close similarity and sequence homology with other C. hemipterus from other parts of the world. Conclusion: In conclusion, this study has demonstrated the ability of the COI gene to differentiate between the C. hemipterus populations from a few different locations in Iran. The current research is the first report of phylogenetic and genetic species diversity analysis conducted on C. hemipterus in Iran. These results provided basic information for further studies of molecular epidemiology, public health and pest control operators in Iran.

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