scholarly journals Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7214 ◽  
Author(s):  
Dongliang Fei ◽  
Yaxi Guo ◽  
Qiong Fan ◽  
Haoqi Wang ◽  
Jiadi Wu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Close Association ◽  
Phylogenetic Analyses ◽  
Apis Cerana ◽  
Nucleotide Identity ◽  
Structural Protein ◽  
Accession Number ◽  
Sequence Comparisons ◽  
Deformed Wing Virus ◽  
Recombination Detection

Background Deformed wing virus (DWV) is one of many viruses that infect honeybees and has been extensively studied because of its close association with honeybee colony collapse that is induced by Varroa destructor. However, virus genotypes, sequence characteristics, and genetic variations of DWV remain unknown in China. Methods Two DWV strains were isolated from Jinzhou and Qinhuangdao cities in China, and were named China1-2017 (accession number: MF770715) and China2-2018 (accession number: MH165180), respectively, and their complete genome sequences were analyzed. To investigate the phylogenetic relationships of the DWV isolates, a phylogenetic tree of the complete open reading frame (ORF), structural protein VP1, and non-structural protein 3C+RdRp of the DWV sequences was constructed using the MEGA 5.0 software program. Then, the similarity and recombinant events of the DWV isolated strains were analyzed using recombination detection program (RDP4) software and genetic algorithm for recombination detection (GARD). Results The complete genomic analysis showed that the genomes of the China1-2017 and China2-2018 DWV strains consisted of 10,141 base pairs (bp) and 10,105 bp, respectively, and contained a single, large ORF (China1-2017: 1,146–9,827 bp; China2-2018: 1,351–9,816 bp) that encoded 2,894 amino acids. The sequences were compared with 20 previously reported DWV sequences from different countries and with sequences of two closely related viruses, Kakugo virus (KV) and V. destructor virus-1. Multiple sequence comparisons revealed a nucleotide identity of 84.3–96.7%, and identity of 94.7–98.6% in amino acids between the two isolate strains and 20 reference strains. The two novel isolates showed 96.7% nucleotide identity and 98.1% amino acid identity. The phylogenetic analyses showed that the two isolates belonged to DWV Type A and were closely related to the KV-2001 strain from Japan. Based on the RDP4 and GARD analyses, the recombination of the China2-2018 strain was located at the 4,266–7,507 nt region, with Korea I-2012 as an infer unknown parent and China-2017 as a minor parent, which spanned the entire helicase ORF. To the best of our knowledge, this is the first study to the complete sequence of DWV isolated from Apis cerana and the possible DWV recombination events in China. Our findings are important for further research of the phylogenetic relationship of DWVs in China with DWV strains from other countries and also contribute to the understanding of virological properties of these complex DWV recombinants.

scholarly journals Phylogenetic Analysis of Deformed Wing Virus Genotypes from Diverse Geographic Origins Indicates Recent Global Distribution of the Virus

2007 ◽  
Vol 73 (11) ◽  
pp. 3605-3611 ◽  
Author(s):  
Olga Berényi ◽  
Tamás Bakonyi ◽  
Irmgard Derakhshifar ◽  
Hemma Köglberger ◽  
Gražyna Topolska ◽  
...  
Keyword(s):  
New Zealand ◽  
Nucleic Acid ◽  
United Arab Emirates ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
Structural Protein ◽  
Deformed Wing Virus ◽  
Reverse Transcription Pcr ◽  
Geographic Origins

ABSTRACT Honeybees originating from 10 different countries (Austria, Poland, Germany, Hungary, Slovenia, Nepal, Sri Lanka, the United Arab Emirates, Canada, and New Zealand) located on four continents were analyzed for the presence of deformed wing virus (DWV) nucleic acid by reverse transcription-PCR. Two target regions within the DWV genome were selected for PCR amplification and subsequent sequencing, i.e., a region within the putative VP2 and VP4 structural-protein genes and a region within the RNA helicase enzyme gene. DWV nucleic acid was amplified from 34 honeybee samples representing all the above-mentioned countries with the notable exception of New Zealand. The amplification products were sequenced, and phylogenetic analyses of both genomic regions were performed independently. The phylogenetic analyses included all sequences determined in this study as well as previously published DWV sequences and the sequences of two closely related viruses, Kakugo virus (KGV) and Varroa destructor virus 1 (VDV-1). In the sequenced regions, the DWV genome turned out to be highly conserved, independent of the geographic origins of the honeybee samples: the partial sequences exhibited 98 to 99% nucleotide sequence identity. Substitutions were most frequently observed at the same positions in the various DWV sequences. Due to the high level of sequence conservation, no significant clustering of the samples in the phylogenetic trees could be identified. On the other hand, the phylogenetic analyses support a genetic segregation of KGV and VDV-1 from DWV.

scholarly journals Genome analysis and phylogenetic characterization of two deformed wing virus strains from Apis cerana in Vietnam

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9911
Author(s):  
Ha T. Thu ◽  
Nguyen T.K. Lien ◽  
Pham T. Lanh ◽  
Bui T.T. Duong ◽  
Nguyen T. Hoa ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Sequence Alignment ◽  
Apis Cerana ◽  
Deformed Wing Virus ◽  
Reading Frame ◽  
Phylogenetic Characterization ◽  
South Vietnam ◽  
Nucleotide Sequence Alignment ◽  
Significant Difference

Background Deformed wing virus (DWV) is a virulent virus that causes honeybee disease. DWV can exist as a latent infection in honeybees, outbreak into epidemics, and cause serious damage to beekeeping cross the world, including Vietnam. Methods The two DWV strains circulating in Vietnamese honeybee, Apis cerana, were first isolated from adult honeybees in North Vietnam (DWV-NVN) and South Vietnam (DWV-SVN). Their complete nucleotide sequences were determined, aligned, and compared with other DWV strains. Results The two Vietnamese DWV strains comprised 10,113 bp and contained a large single open reading frame (ORF) of 2,893 amino acids, initiating at nucleotide 1,130 and terminating at nucleotide 9,812. Multiple nucleotide sequence alignment between these two DWV-VN strains and DWV strains in A. mellifera was performed. The DWV-VN strains showed a low genetic identity (from 91.4% to 92.0%) with almost of these strains, but lower identities (89.2% and 89.4%) with UK2 and (89.6%) with the China2 strain. Low identities (91.7% and 91.9%) were also observed between the China3 strain (in A. cerana) and the DWV-VN strains, respectively. The deduced amino acid sequence alignment showed high genetic similarities (97.0%–97.9%) when the USA1, Chile, Italy1, France, UK1, UK2, Japan, Korea2, China1, China2 and China3 strains were compared to the DWV-VN strains. This ratio was 96.7% and 96.8% when the Korea1 strain was compared to the DWV-SVN and DWV-NVN strains, respectively. Numerous amino acid substitutions were identified in the L, VP3, and RdRp sequences. Notably, we observed six substitutions positioned at amino acids 27 (E > I), 98 (S > T), 120 (A > V), 153 (M > T), 170 (D > F), and 174 (Y > F) in the L protein, two amino acid changes at positions 980 (S > A) and 1032 (E > T) in VP3, and one amino acid change at position 2627 (R > C) unique to the DWV-VN strains. Phylogenetic analysis based on complete genome sequences, RdRp sequences and Simplot analysis indicated that there was a significant difference between DWV-VN strains in A. cerana and DWV strains in A. mellifera. The results suggested that the genetic variations of the DWV-VN strains in A. cerana help them to adapt geographical conditions and may lead to change the viral pathogenicity of DWV-VN strains.

scholarly journals Identification of two distinct genotypes of hepatitis E virus in a Japanese patient with acute hepatitis who had not travelled abroad

2002 ◽  
Vol 83 (8) ◽  
pp. 1931-1940 ◽  
Author(s):  
Masaharu Takahashi ◽  
Tsutomu Nishizawa ◽  
Akira Yoshikawa ◽  
Shin Sato ◽  
Norio Isoda ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nucleotide Sequence ◽  
Acute Hepatitis ◽  
Hepatitis E Virus ◽  
Phylogenetic Analyses ◽  
Hepatitis E ◽  
The United States ◽  
Nucleotide Identity ◽  
Single Patient ◽  
Entire Genome

Two distinct hepatitis E virus (HEV) isolates, designated HE-JI3 and HE-JI4, were identified in a single patient with acute hepatitis in Japan, who had not travelled abroad. The HEV load of HE-JI3 at admission was 102 copies/ml, but that of HE-JI4 was tenfold higher at 103 copies/ml. The viraemia of HE-JI4 persisted for up to 16 days from admission, whereas HE-JI3 disappeared at 9 days after admission. The entire nucleotide sequence of the HE-JI4 isolate and partial nucleotide sequences of open reading frames (ORFs) 1 and 2 of the HE-JI3 isolate were determined. The full-length nucleotide sequence of HE-JI4 consisted of 7171 nucleotides excluding the poly(A) tail and contained ORF1 encoding 1684 amino acids, ORF2 encoding 671 amino acids and ORF3 encoding 114 amino acids. Sequence and phylogenetic analyses of the HEV genomes indicated that HE-JI4 was most closely related to an HEV isolate (T1) of genotype IV with the same strategy for translation of ORF2 and ORF3, but which differed from it by 16·5% over the entire genome. The HE-JI3 isolate showed the highest nucleotide identity (88·6–95·1%) to the genotype III HEVs, having higher identity to human and swine HEV isolates from the United States (US1, US2 and swUS1) than to those reported thus far from Japan (JRA1 and swJ570). The two co-infecting strains of HE-JI3 and HE-JI4 identified from the single patient shared only 80·1% nucleotide identity. These results indicate that multiple genotypes of HEV co-circulate in Japan, and that genotype IV comprises a remarkably heterogeneous group of HEVs.

scholarly journals Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1103-1115 ◽  
Author(s):  
Hongguang Shao ◽  
Zhijian Tu
Keyword(s):  
Phylogenetic Analyses ◽  
Mosquito Species ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Sequence Comparisons ◽  
Wide Range ◽  
Multiple Copies ◽  
Catalytic Motif ◽  
Open The Doors ◽  
Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

scholarly journals Identification and functional characterization of two bamboo FD gene homologs having contrasting effects on shoot growth and flowering

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Smritikana Dutta ◽  
Anwesha Deb ◽  
Prasun Biswas ◽  
Sukanya Chakraborty ◽  
Suman Guha ◽  
...  
Keyword(s):  
Large Scale ◽  
Forest Ecology ◽  
Phylogenetic Analyses ◽  
Functional Characterization ◽  
Constitutive Expression ◽  
Transcript Level ◽  
In Planta ◽  
Mobility Shift ◽  
Vegetative Development ◽  
Sequence Comparisons

AbstractBamboos, member of the family Poaceae, represent many interesting features with respect to their fast and extended vegetative growth, unusual, yet divergent flowering time across species, and impact of sudden, large scale flowering on forest ecology. However, not many studies have been conducted at the molecular level to characterize important genes that regulate vegetative and flowering habit in bamboo. In this study, two bamboo FD genes, BtFD1 and BtFD2, which are members of the florigen activation complex (FAC) have been identified by sequence and phylogenetic analyses. Sequence comparisons identified one important amino acid, which was located in the DNA-binding basic region and was altered between BtFD1 and BtFD2 (Ala146 of BtFD1 vs. Leu100 of BtFD2). Electrophoretic mobility shift assay revealed that this alteration had resulted into ten times higher binding efficiency of BtFD1 than BtFD2 to its target ACGT motif present at the promoter of the APETALA1 gene. Expression analyses in different tissues and seasons indicated the involvement of BtFD1 in flower and vegetative development, while BtFD2 was very lowly expressed throughout all the tissues and conditions studied. Finally, a tenfold increase of the AtAP1 transcript level by p35S::BtFD1 Arabidopsis plants compared to wild type confirms a positively regulatory role of BtFD1 towards flowering. However, constitutive expression of BtFD1 had led to dwarfisms and apparent reduction in the length of flowering stalk and numbers of flowers/plant, whereas no visible phenotype was observed for BtFD2 overexpression. This signifies that timely expression of BtFD1 may be critical to perform its programmed developmental role in planta.

scholarly journals Characteristics of 29 novel atypical solute carriers of major facilitator superfamily type: evolutionary conservation, predicted structure and neuronal co-expression

Open Biology ◽  
2017 ◽  
Vol 7 (9) ◽  
pp. 170142 ◽  
Author(s):  
Emelie Perland ◽  
Sonchita Bagchi ◽  
Axel Klaesson ◽  
Robert Fredriksson
Keyword(s):  
Lipid Bilayers ◽  
Markov Models ◽  
Phylogenetic Analyses ◽  
Molecular Transport ◽  
Major Facilitator Superfamily ◽  
Proximity Ligation Assay ◽  
Sequence Comparisons ◽  
Altered Expression ◽  
Solute Carriers ◽  
Major Facilitator

Solute carriers (SLCs) are vital as they are responsible for a major part of the molecular transport over lipid bilayers. At present, there are 430 identified SLCs, of which 28 are called atypical SLCs of major facilitator superfamily (MFS) type. These are MFSD1, 2A, 2B, 3, 4A, 4B, 5, 6, 6 L, 7, 8, 9, 10, 11, 12, 13A, 14A and 14B; SV2A, SV2B and SV2C; SVOP and SVOPL; SPNS1, SPNS2 and SPNS3; and UNC93A and UNC93B1. We studied their fundamental properties, and we also included CLN3, an atypical SLC not yet belonging to any protein family (Pfam) clan, because its involvement in the same neuronal degenerative disorders as MFSD8. With phylogenetic analyses and bioinformatic sequence comparisons, the proteins were divided into 15 families, denoted atypical MFS transporter families (AMTF1-15). Hidden Markov models were used to identify orthologues from human to Drosophila melanogaster and Caenorhabditis elegans . Topology predictions revealed 12 transmembrane segments (for all except CLN3), corresponding to the common MFS structure. With single-cell RNA sequencing and in situ proximity ligation assay on brain cells, co-expressions of several atypical SLCs were identified. Finally, the transcription levels of all genes were analysed in the hypothalamic N25/2 cell line after complete amino acid starvation, showing altered expression levels for several atypical SLCs.

scholarly journals Capsid Assembly is Regulated by Amino Acid Residues Asparagine 47 and 48 in The VP2 Protein of Porcine Parvovirus

2020 ◽  
Author(s):  
Jucai Wang ◽  
Yunchao Liu ◽  
Yumei Chen ◽  
Teng Zhang ◽  
Aiping Wang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Vaccine Development ◽  
Acid Sites ◽  
Site Directed Mutagenesis ◽  
Porcine Parvovirus ◽  
Capsid Assembly ◽  
Structural Protein ◽  
Native Page ◽  
Vp2 Protein

Abstract Background: Porcine parvovirus (PPV) is a major cause of reproductive failure in swine, and has caused huge losses throughout the world. Viral protein 2 (VP2) of PPV is a major structural protein that can self-assemble into virus-like particles (VLP) with hemagglutination (HA) activity. In order to identify the essential residues involved in the mechanism of capsid assembly and to further understand the function of HA, we analyzed a series of deletion mutants and site-directed mutations within the N-terminal of VP2 in the Escherichia coli (E. coli) system. Results: Our results showed that deletion of first 47 amino acids from the N-terminal of VP2 protein did not affect capsid assembly, and further truncation to residue 48 Asparagine (Asn, N) caused detrimental effects. Site-directed mutagenesis experiments demonstrated that residue 47Asn reduced the assembly efficiency of PPV VLP, while residue 48Asn destroyed the stability, hemagglutination, and self-assembly characteristics of the PPV VP2 protein. These findings indicated that the residues 47Asn and 48Asn are important amino acid sites to capsid assembly and HA activity. Results from Native PAGE inferred that macromolecular polymers were critical intermediates of the VP2 protein during the capsid assembly process. Site-directed mutation at 48Asn did not affect the association of monomers to form into oligomers, but destroyed the ability of oligomers to assemble into macromolecular particles, influencing both capsid assembly and HA activity. Conclusions: These results demonstrated that PPV capsid assembly is a complex process that is regulated by amino acids 47Asn and 48Asn, which are located at the N-terminal of VP2 and closely related to the association of macromolecular particles. Our findings provide valuable information on the mechanisms of PPV capsid assembly and the possibility of chimeric VLP vaccine development by replacing as much as 47 amino acids at the N-terminal of VP2 protein.

scholarly journals Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov

2019 ◽  
Author(s):  
Cristina Merla ◽  
Carla Rodrigues ◽  
Virginie Passet ◽  
Marta Corbella ◽  
Harry A. Thorpe ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Type Strain ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Klebsiella Oxytoca ◽  
Mass Spectrometry Analysis ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Single Strain ◽  
Spectrometry Analysis

AbstractKlebsiella oxytoca causes opportunistic human infections and post-antibiotic haemorrhagic diarrhoea. This Enterobacteriaceae species is genetically heterogeneous and is currently subdivided into seven phylogroups (Ko1 to Ko4, Ko6 to Ko8). Here we investigated the taxonomic status of phylogroups Ko3 and Ko4. Genomic sequence-based phylogenetic analyses demonstrate that Ko3 and Ko4 formed well-defined sequence clusters related to, but distinct from, Klebsiella michiganensis (Ko1), Klebsiella oxytoca (Ko2), K. huaxiensis (Ko8) and K. grimontii (Ko6). The average nucleotide identity of Ko3 and Ko4 were 90.7% with K. huaxiensis and 95.5% with K. grimontii, respectively. In addition, three strains of K. huaxiensis, a species so far described based on a single strain from a urinary tract infection patient in China, were isolated from cattle and human faeces. Biochemical and MALDI-ToF mass spectrometry analysis allowed differentiating Ko3, Ko4 and Ko8 from the other K. oxytoca species. Based on these results, we propose the names Klebsiella spallanzanii for the Ko3 phylogroup, with SPARK_775_C1T (CIP 111695T, DSM 109531T) as type strain, and Klebsiella pasteurii for Ko4, with SPARK_836_C1T (CIP 111696T, DSM 109530T) as type strain. Strains of K. spallanzanii were isolated from human urine, cow faeces and farm surfaces, while strains of K. pasteurii were found in faecal carriage from humans, cows and turtles.Accession numbersThe nucleotide sequences generated in this study were deposited in ENA and are available through the INSDC databases under accession numbers MN091365 (SB6411T = SPARK775C1T), MN091366 (SB6412 T = SPARK836C1T) and MN104661 to MN104677 (16S rRNA), MN076606 to MN076643 (gyrA and rpoB), and MN030558 to MN030567 (blaOXY). Complete genomic sequences were submitted to European Nucleotide Archive under the BioProject number PRJEB15325.AbbreviationsANI, average nucleotide identity; HCCA, a-cyano-4-hydroxycinnamic acid; isDDH, in silico DNA-DNA hybridization; SCAI, Simmons citrate agar with inositol; MALDI57 ToF MS: Matrix-assisted laser desorption/ionization time of flight mass spectrometry

scholarly journals Molecular analysis of the dengue virus type 1 and 2 in Brazil based on sequences of the genomic envelope-nonstructural protein 1 junction region

2004 ◽  
Vol 46 (3) ◽  
pp. 145-152 ◽  
Author(s):  
Cecília Luiza S. Santos ◽  
Maria Anice M. Sallum ◽  
Peter G. Foster ◽  
Iray Maria Rocco
Keyword(s):  
Sequence Data ◽  
Nonstructural Protein ◽  
Phylogenetic Analyses ◽  
Decomposition Analysis ◽  
Structural Protein ◽  
Network Graph ◽  
Junction Region ◽  
Split Decomposition ◽  
Genotype Iii ◽  
Nonstructural Protein 1

The genomic sequences of the Envelope-Non-Structural protein 1 junction region (E/NS1) of 84 DEN-1 and 22 DEN-2 isolates from Brazil were determined. Most of these strains were isolated in the period from 1995 to 2001 in endemic and regions of recent dengue transmission in São Paulo State. Sequence data for DEN-1 and DEN-2 utilized in phylogenetic and split decomposition analyses also include sequences deposited in GenBank from different regions of Brazil and of the world. Phylogenetic analyses were done using both maximum likelihood and Bayesian approaches. Results for both DEN-1 and DEN-2 data are ambiguous, and support for most tree bipartitions are generally poor, suggesting that E/NS1 region does not contain enough information for recovering phylogenetic relationships among DEN-1 and DEN-2 sequences used in this study. The network graph generated in the split decomposition analysis of DEN-1 does not show evidence of grouping sequences according to country, region and clades. While the network for DEN-2 also shows ambiguities among DEN-2 sequences, it suggests that Brazilian sequences may belong to distinct subtypes of genotype III.

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