scholarly journals Molecular Characteristics and Phylogenetic Analysis of Short Beak and Dwarfism Syndrome-Related Novel Goose Parvovirus

2021 ◽  
Author(s):  
Yonglin Li ◽  
Jingyu Jia ◽  
Qingling Mi ◽  
Yufeng Li ◽  
Yuehua Gao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Point Mutations ◽  
Molecular Characteristics ◽  
Structural Protein ◽  
Common Amino Acid ◽  
Separate Branch ◽  
Goose Parvovirus ◽  
Cherry Valley Duck ◽  
Short Beak

Abstract Short beak and dwarfism syndrome (SBDS) emerged in cherry valley duck flocks in China in 2015, and novel goose parvovirus (NGPV) was proved to be the etiological agent of SBDS. To date, whether SBDS-related NGPV isolates possess common molecular characteristics remains unknown. In this study, three new NGPV strains (namely, SDHT16, SDJN19, and SDLC19) were isolated from diseased ducks showing typical SBDS and successfully passaged in embryonated goose or cherry valley duck embryo. The whole genomes of three NGPV strains shared 98.9%–99.7% homologies between each other but showed slightly lower homologies (95.2%–96.1%) with the classical GPV strains. A total of 16 common amino acid point mutations were produced in the VP1 proteins of six NGPV strains (SDHT16, SDJN19, SDLC19, QH, JS1, and SDLC01) compared with the classical Chinese GPV strains, among which nine amino acid sites were identical to the European GPV strain B. The non-structural protein Rep1 of the six NGPV strains generated 12 common amino acid mutations compared with the classical GPV strains. The phylogenetic analysis indicated that the Chinese NGPV strains clustered with the European SBDS-related NGPV strains, forming a separate branch, distinct from the group formed by the classical GPV strains. Taken together, the present study unveils the common molecular characteristics of the NGPV isolates and directs the conclusion that the Chinese NGPV isolates probably originate from a common ancestor with the European SBDS-related NGPV.

scholarly journals Mechanism of Metronidazole Resistance inHelicobacter pylori: Comparison of the rdxA Gene Sequences in 30 Strains

2000 ◽  
Vol 44 (8) ◽  
pp. 2207-2210 ◽  
Author(s):  
Nadia Maggi Solcà ◽  
Marco Valerio Bernasconi ◽  
Jean-Claude Piffaretti
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Amino Acid ◽  
Resistant Strain ◽  
Point Mutations ◽  
Housekeeping Genes ◽  
Amino Acid Substitutions ◽  
Metronidazole Resistance ◽  
Nucleotide Mutation ◽  
Nucleotide Insertion

ABSTRACT The rdxA gene of 30 independently isolatedHelicobacter pylori strains was sequenced. A comparison of the rdxA sequences revealed a higher percentage of amino acid substitutions in the corresponding protein than in other housekeeping genes. Out of 122 point mutations, 41 were missense and 4 were nonsense. A resistant strain with a nucleotide insertion in therdxA sequence was also found. With the exception of the point mutations and the insertion generating a stop signal, no particular nucleotide mutation or amino acid substitution could be associated to metronidazole resistance. Moreover, phylogenetic analysis of the 30 nucleotide sequences did not demonstrate specific clusters associated with the resistance phenotype.

scholarly journals Mobuck virus genome sequence and phylogenetic analysis: identification of a novel Orbivirus isolated from a white-tailed deer in Missouri, USA

2014 ◽  
Vol 95 (1) ◽  
pp. 110-116 ◽  
Author(s):  
Elyse Cooper ◽  
Srivishnupriya Anbalagan ◽  
Patricia Klumper ◽  
Gail Scherba ◽  
Randy R. Simonson ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Clinical Signs ◽  
Amino Acid Identity ◽  
Virus Genome ◽  
The Novel ◽  
Structural Protein ◽  
Middle Point ◽  
Wide Range ◽  
Haemorrhagic Disease

The genus Orbivirus includes a diverse group of segmented dsRNA viruses that are transmitted via arthropods, have a global distribution and affect a wide range of hosts. A novel orbivirus was co-isolated with epizootic haemorrhagic disease virus (EHDV) from a white-tailed deer (Odocoileus virginianus) exhibiting clinical signs characteristic of EHDV. Using antiserum generated against EHDV, a pure isolate of the novel non-cytopathic orbivirus was obtained in Aedes albopictus cell culture. Genomic sequencing and phylogenetic analysis of predicted ORFs showed that eight of the ten ORFs were most homologous to Peruvian horse sickness virus (PHSV), with amino acid identities of 44.3–73.7 %. The remaining two ORFs, VP3 and VP5, were most similar to Middle Point orbivirus (35.9 %) and Yunnan orbivirus (59.8 %), respectively. Taxonomic classification of orbiviruses is largely based on homology of the major subcore structural protein VP2(T2), encoded by segment 2 for mobuck virus. With only 69.1 % amino acid identity to PHSV, we propose mobuck virus as the prototype of a new species of Orbivirus.

scholarly journals Species A Rotavirus (RVA) Isolated from Sewage in Nigeria, 2014: Close Genetic Relatedness of Partial G, P, and NSP4 Gene Sequences Encoding G1 with Cogent Genes of Other Asian and African Rotaviruses

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Babatunde Olanrewaju Motayo ◽  
Johnson Adekunle Adeniji ◽  
Adedayo Omotayo Faneye
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genetic Relatedness ◽  
Molecular Characteristics ◽  
Nsp4 Gene ◽  
Limited Information ◽  
Gene Sequences ◽  
Monophyletic Cluster ◽  
Group A ◽  
Vp7 Gene

Rotavirus has been identified as a major cause of gastroenteritis in Nigeria. There is limited information on the intragenotype diversity of Nigerian rotavirus isolates. We therefore investigated the molecular characteristics of some rotavirus gene sequences detected in sewage from Nigeria. Seven sewage samples, out of a total of 68, tested positive for rotavirus RNA (10.3%). Genotype G1P[4]was the most common genotype (5 isolates) and one isolate for genotypes G1P[8] and G3P[6]. Phylogenetic analysis of the partial VP7 gene of 3 G1P[4]isolates analyzed identified them as genotype G1 Lineage 2 along with Chinese strains with 99.1% to 100% amino acid similarity. Amino acid substitutions D-97→E and S-147→D/N were observed within the 7-1a and 7-2 domains of VP7 gene among the study G1P4 isolates in reference to vaccine strain RotaTeq®. Phylogenetic analysis of the G3P[6]study isolate identified it as genotype G3 Lineage 3, forming a monophyletic cluster with 100% bootstrap value with other West African strains G3 isolates. Phylogenetic analysis of GIP[4]VP4 genes identified them as P4 Lineage 5, while 3 NSP4 gene sequences belonged to genotype E1, while 1 belonged to E2. The results from this study represent phylogenetic analysis of partial gene sequences of environmental group A rotavirus (RVA) isolates from Nigeria.

scholarly journals Molecular characterization of the viral structural protein genes in the first outbreak of dengue virus type 2 in Hunan Province, inland China in 2018

2020 ◽  
Author(s):  
Jiaoqiong Guan ◽  
Zhanlong He ◽  
Meng Qin ◽  
Xialin Deng ◽  
Jun Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Protein Binding ◽  
Causative Agent ◽  
Binding Sites ◽  
Selection Pressure ◽  
Hunan Province ◽  
Structural Protein ◽  
Protein Binding Sites ◽  
Dengue Outbreak

Abstract Background: An unexpected dengue outbreak occurred in the Hunan Province in 2018. This is the first dengue outbreak in this area of inland China, and 172 cases were reported. Methods: To verify the causative agent of this outbreak and investigate gene characterization, the structural protein C/prM/E genes of viruses isolated from local residents were sequenced followed by mutation and phylogenetic analysis. The recombination, selection pressure, potential secondary structure and three-dimensional structure analysis were also performed. Results: Phylogenetic analysis revealed that all epidemic strains were classified as the cosmopolitan DENV-2 genotype, closest to the Zhejiang strain (MH010629, 2017) and then Malaysia strain (KJ806803, 2013). Compared with the DENV-2SS, 151 base substitutions were found in 89 sequences of isolates, which resulted in 20 non-synonymous mutations, of which 17 mutations existed among all samples (two in capsid protein, six in prM/M, and nine in envelope proteins). Moreover, amino acid substitutions at 602th (E322:Q→H) and 670th (E390: N→S) may enhance virulence of the epidemic strains. One new DNA-binding site and five new protein binding sites were observed. Two polynucleotide-binding sites and seven protein binding sites were lost compared with DENV-2SS. Meanwhile, five changes were found in helix regions. Minor changes were observed in helical transmembrane and disordered regions. The 429th amino acid of E proteins was switch from histamine (positively charged) to asparagines (neutral) in all 89 isolate strains. No recombination events or positive selection pressure sites were observed. To our knowledge, this study is the first one to analyze the genetic characteristics of epidemic strain in the first dengue outbreak in Hunan Province, inland China. Conclusions: The causative agent is likely to come from Zhejiang Province, a neighbouring Province where dengue fever broke out in 2017. This study may help to understand the intrinsic geographical relatedness of DENV-2 and contributes to further research on pathogenicity and vaccine development.

scholarly journals Primary structure of a structural protein from the cuticle of the migratory locust, Locusta migratoria

1986 ◽  
Vol 236 (3) ◽  
pp. 713-720 ◽  
Author(s):  
P Højrup ◽  
S O Andersen ◽  
P Roepstorff
Keyword(s):  
Amino Acid ◽  
Primary Structure ◽  
Locusta Migratoria ◽  
Protein A ◽  
Complete Sequence ◽  
Amino Acid Residues ◽  
Structural Protein ◽  
Migratory Locust ◽  
Common Amino Acid ◽  
Conserved Sequence

The complete amino acid sequence of a structural protein isolated from pharate cuticle of the locust Locusta migratoria was determined. The protein has an unusual amino acid composition: 42% of the residues are alanine and only 14 of the 20 common amino acid residues are present. The primary structure consists of regions enriched in particular amino acid residues. The N-terminal region and a region close to the C-terminus are enriched in glycine. The rest of the protein is dominated by alanine, except for two short regions enriched in hydrophilic residues. Almost all the proline residues are situated in the alanine-rich regions in a conserved sequence ‘A-A-P-A/V’. An internal duplication has taken place covering most of the protein except for the glycine-rich regions. Owing to the unusual features of the protein a combination of automated Edman degradations and plasma-desorption m.s. was used to determine the complete sequence. The protein does not show sequence homology to other proteins, but proteins divided into regions enriched in the same kind of amino acid residues have been isolated from other insect structures.

Genetic characterization and phylogenetic analysis of Novel Duck-Origin Goose Parvovirus in Anhui Province, Eastern China

2021 ◽  
Author(s):  
Yong Wang ◽  
Jianfei Sun ◽  
Da Zhang ◽  
Xu Guo ◽  
Wenhao Shen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Sequencing ◽  
Phylogenetic Trees ◽  
Genetic Characterization ◽  
Eastern China ◽  
Anhui Province ◽  
Muscovy Duck ◽  
Goose Parvovirus ◽  
Short Beak ◽  
Muscovy Duck Parvovirus

Abstract Recently, a novel duck-origin goose parvovirus (N-GPV) was reported to cause short beak and dwarfism syndrome in ducks. In this study, we performed complete genome sequencing and analyzed three different duck-derived parvoviruses that infected different breeds of ducks. Phylogenetic trees based on gene sequences indicated that they were classical goose parvovirus (C-GPV), Muscovy duck parvovirus (MDPV), and N-GPV, respectively. Furthermore, potential recombination events were found. These results improve our understanding of the diversity of duck-derived parvoviruses in the Anhui province, eastern China, and provide a reference for the prevention of associated diseases.

Structural protein reorganization and fold emergence investigated through amino acid sequence permutations

Amino Acids ◽  
2014 ◽  
Vol 47 (1) ◽  
pp. 147-152
Author(s):  
Giovanni Minervini ◽  
Alessandro Masiero ◽  
Emilio Potenza ◽  
Silvio C. E. Tosatto
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Structural Protein

scholarly journals HLA-DRB1 Alleles Associated with Lower Leishmaniasis Susceptibility Share Common Amino Acid Polymorphisms and Epitope Binding Repertoires

Vaccines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 270
Author(s):  
Nicky de Vrij ◽  
Pieter Meysman ◽  
Sofie Gielis ◽  
Wim Adriaensen ◽  
Kris Laukens ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cell Epitope ◽  
Human Leukocyte ◽  
Leishmania Species ◽  
Hla Polymorphism ◽  
Common Amino Acid ◽  
Binding Core ◽  
Epitope Discovery ◽  
Epitope Binding ◽  
The Impact

Susceptibility for leishmaniasis is largely dependent on host genetic and immune factors. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors for leishmaniasis, little is known regarding the mechanisms that underpin these associations. To better understand this underlying functionality, we first collected all known leishmaniasis-associated HLA variants in a thorough literature review. Next, we aligned and compared the protection- and risk-associated HLA-DRB1 allele sequences. This identified several amino acid polymorphisms that distinguish protection- from risk-associated HLA-DRB1 alleles. Subsequently, T cell epitope binding predictions were carried out across these alleles to map the impact of these polymorphisms on the epitope binding repertoires. For these predictions, we used epitopes derived from entire proteomes of multiple Leishmania species. Epitopes binding to protection-associated HLA-DRB1 alleles shared common binding core motifs, mapping to the identified HLA-DRB1 amino acid polymorphisms. These results strongly suggest that HLA polymorphism, resulting in differential antigen presentation, affects the association between HLA and leishmaniasis disease development. Finally, we established a valuable open-access resource of putative epitopes. A set of 14 HLA-unrestricted strong-binding epitopes, conserved across species, was prioritized for further epitope discovery in the search for novel subunit-based vaccines.

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