Genome-scale molecular and phylogenetic characterization of Middle Point orbiviruses from Australia

2021 ◽  
Vol 102 (12) ◽  
Author(s):  
Kalpana Agnihotri ◽  
Jane Oakey ◽  
Craig Smith ◽  
Richard Weir ◽  
Alyssa Pyke ◽  
...  
Keyword(s):  
Core Protein ◽  
Phylogenetic Analyses ◽  
Sequence Information ◽  
Mosquito Vector ◽  
Middle Point ◽  
Phylogenetic Characterization ◽  
Ongoing Surveillance ◽  
Genome Scale ◽  
Full Length Genome

Middle Point orbivirus (MPOV) is an Australian arbovirus, belongs to the Yunnan orbivirus species found in China. First detected and reported from Beatrice Hill, Northern Territory (NT), MPOV has to date, only been exclusively reported from the NT, Australia. Whilst genetic characterization of MPOV has been previously described, only restricted to sequence information for segments 2 and 3 coding core protein VP2 and outer capsid protein VP3, respectively. This study presents for the first time nearly full-length genome sequences of MPOV, which represent 24 isolates collected over a span of more than 20 years from 1997 to 2018. Whilst the majority of isolates were sampled at Beatrice Hill, NT where MPOV is most frequently isolated, this report also describes the first two isolations of MPOV from Queensland (QLD), Australia. One of which is the first non-bovine isolate obtained from the mosquito vector Aedes vittiger. We further compared these MPOV sequences with known sequences of the Yunnan orbivirus and other known orbivirus sequences of mosquito origin found in Australia. The phylogenetic analyses indicate the Australian MPOV sequences are more closely related to each other than other known sequences of Yunnan orbivirus. Furthermore, MPOV sequences are closely related to sequences from the Indonesian isolate JKT-8650. The clustering of Australian sequences in the phylogenetic tree suggests the monophyletic lineage of MPOV circulating in Australia. Further, ongoing surveillance is required to assess the existence and prevalence of this or other yet undetected lineages of MPOV and other orbiviruses in Australia.

scholarly journals Genetic characterization of the Wyeomyia group of orthobunyaviruses and their phylogenetic relationships

2012 ◽  
Vol 93 (5) ◽  
pp. 1023-1034 ◽  
Author(s):  
Rashmi Chowdhary ◽  
Craig Street ◽  
Amelia Travassos da Rosa ◽  
Marcio R. T. Nunes ◽  
Kok Keng Tee ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Whole Genome Sequence ◽  
Interferon Response ◽  
Sequence Information ◽  
History Of ◽  
Group Members ◽  
Genome Sequence Information ◽  
Genome Reassortment

Phylogenetic analyses can give new insights into the evolutionary history of viruses, especially of viruses with segmented genomes. However, sequence information for many viral families or genera is still limited and phylogenies based on single or short genome fragments can be misleading. We report the first genetic analysis of all three genome segments of Wyeomyia group viruses Wyeomyia, Taiassui, Macaua, Sororoca, Anhembi and Cachoeira Porteira (BeAr328208) in the genus Orthobunyavirus of the family Bunyaviridae. In addition, Tucunduba and Iaco viruses were identified as members of the Wyeomyia group. Features of Wyeomyia group members that distinguish them from other viruses in the Bunyamwera serogroup and from other orthobunyaviruses, including truncated NSs sequences that may not counteract the host’s interferon response, were characterized. Our findings also suggest genome reassortment within the Wyeomyia group, identifying Macaua and Tucunduba viruses as M-segment reassortants that, in the case of Tucunduba virus, may have altered pathogenicity, stressing the need for whole-genome sequence information to facilitate characterization of orthobunyaviruses and their phylogenetic relationships.

scholarly journals Characterization of an Isolate of Citrus Concave Gum-Associated Virus from Apples in China and Development of an RT-RPA Assay for the Rapid Detection of the Virus

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2239
Author(s):  
Zhen Liu ◽  
Zhenfei Dong ◽  
Binhui Zhan ◽  
Shifang Li
Keyword(s):  
Reverse Transcription ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
The United States ◽  
Polymerase Chain Reaction Method ◽  
Large Scale Testing ◽  
Bright Stripe ◽  
Full Length Genome

Apple (Malus domestica) fruits exhibiting bright stripe symptoms were identified in Weihai City, Shandong Province, China. To investigate the virome in the apple samples, the method of high throughput sequencing (HTS) was used to identify the viruses. It was found that the sequence of citrus concave gum-associated virus (CCGaV) was involved in the apple transcriptome dataset. The full-length genome of the CCGaV-Weihai isolate contained two segments, the RNA1 was 6674 nt in size containing a conserved RNA-dependent RNA polymerase (RdRp), and the RNA2 was ambisense, 2706 nt in length, encoding a movement protein (MP) and a coat protein (CP). Sequence alignment and phylogenetic analyses indicated that CCGaV-Weihai was more closely related to CCGaV-H2799 isolated from the apple host in the United States and distantly related to CCGaV-CGW2 from Citrus sinensis in Italy, indicating a possibly geographical and host differentiation of CCGaV isolates. This was the first identification and characterization of CCGaV infecting apples in China. Additionally, a rapid and sensitive reverse transcription recombinase polymerase amplification (RT-RPA) assay technique was established for CCGaV detection in apple plants. The RT-RPA of CCGaV was not affected by other common viruses in apple plants and is about 10-fold more sensitive than the conventional reverse transcription polymerase chain reaction method, which can be used in large-scale testing.

scholarly journals The ompA Gene in Chlamydia trachomatis Differs in Phylogeny and Rate of Evolution from Other Regions of the Genome

2006 ◽  
Vol 74 (1) ◽  
pp. 578-585 ◽  
Author(s):  
Brian W. Brunelle ◽  
George F. Sensabaugh
Keyword(s):  
Chlamydia Trachomatis ◽  
Membrane Protein ◽  
Outer Membrane ◽  
Outer Membrane Protein ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Phylogenetic Characterization ◽  
Tissue Tropisms

ABSTRACT Strains of Chlamydia trachomatis are classified into serovars based on nucleotide sequence differences in ompA, the gene that encodes the major outer membrane protein. Phylogenetic characterization of strains based on ompA, however, results in serovar groupings that are inconsistent with the distinguishing features of C. trachomatis pathobiology, e.g., tissue tropisms and disease presentation. We have compared nucleotide sequences at multiple sites distributed around the chlamydial genome from 18 strains representing 16 serovars; sampled regions included genes encoding housekeeping enzymes (totaling 2,073 bp), intergenic noncoding segments (1,612 bp), and a gene encoding a second outer membrane protein (porB; 1,023 bp), with the ompA sequence (1,194 bp) used for reference. These comparative analyses revealed substantial variation in nucleotide substitution patterns among the sampled regions, with average pairwise sequence differences ranging from 0.15% for the housekeeping genes to 12.1% for ompA. Phylogenetic characterization of the sampled genomic sequences yielded a strongly supported tree that divides the strains into groupings consistent with C. trachomatis biology and which has a topology quite distinct from the ompA tree. This phylogenetic incongruity can be accounted for by recombination of the ompA gene between different genomic backgrounds. We found, however, no evidence of recombination within or between any of the sampled regions around the C. trachomatis genome apart from ompA. Parallel analysis of published sequence data on four members of the pmp gene family are consistent with the phylogenetic analyses reported here.

scholarly journals Genetic and phylogenetic characterization of genome segments 2 and 6 of bluetongue virus isolates in Japan from 1985 to 2008

2012 ◽  
Vol 93 (7) ◽  
pp. 1465-1473 ◽  
Author(s):  
Hiroaki Shirafuji ◽  
Tohru Yanase ◽  
Tomoko Kato ◽  
Makoto Yamakawa
Keyword(s):  
Bluetongue Virus ◽  
Phylogenetic Analyses ◽  
Control Measures ◽  
Asia Pacific ◽  
Segment Length ◽  
Genetic Characteristics ◽  
Phylogenetic Characterization ◽  
Partial Correlations ◽  
Different Origins

This study conducted genetic and phylogenetic analyses of genome segments 2 and 6 (Seg-2 and Seg-6), which encode serotype-specific structural proteins of the outer capsid, of bluetongue virus (BTV) isolated in Japan from 1985 to 2008. The Japanese strains of BTV were clearly sorted into six groups by several genetic characteristics of Seg-2, including segment length, ORF length and 5′- and 3′-terminal sequences, and were identified as serotypes 2, 3, 9, 12, 16 and 21 by phylogenetic comparisons with Seg-2 of reference and field strains of serotypes 1–24. In contrast, phylogenetic comparisons of Seg-6 also revealed some variations among the Japanese strains and partial correlations of the serotypes between the Japanese strains and the reference or field strains. Thus, the results revealed that at least six serotypes of BTV were isolated in Japan and that there were some variations in the genetic and phylogenetic characteristics of Seg-2 and Seg-6 among the Japanese strains, suggesting that BTV of several different origins has appeared sporadically in Japan. These data will be beneficial for understanding BTV epidemiology and taking better control measures against bluetongue in Japan and its neighbouring countries in the Asia-Pacific region.

scholarly journals First complete genome sequence and molecular characterization of Canine morbillivirus isolated in Central Brazil

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Vivaldo Gomes da Costa ◽  
Marielena Vogel Saivish ◽  
Priscila Gomes de Oliveira ◽  
Abelardo Silva-Júnior ◽  
Marcos Lázaro Moreli ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Canine Distemper Virus ◽  
Phylogenetic Analyses ◽  
Domestic Dogs ◽  
Molecular Characteristics ◽  
Central Brazil ◽  
West Region ◽  
Glycosylation Sites ◽  
Full Length Genome

AbstractThe Brazilian regions are still highly endemic areas for Canine morbillivirus [canine distemper virus (CDV)]. However, little is known regarding the genetic variability of the strain circulating in several Brazilian regions. Here, we report the first full-length genome and molecular characterization of CDV isolated from domestic dogs in the Brazilian Center-West region. Sequence alignment and phylogenetic analyses based on deduced amino acid and nucleotide sequences showed that the isolated strain is characterized as the South America-I/Europe genotype. However, it segregates into a CDV subgenotype branch. Interestingly, both H and F proteins have a gain of a potential N-glycosylation sites compared to the Onderstepoort vaccine strain. Therefore, this study provides a reference to further understand the epidemic and molecular characteristics of the CDV in Brazil.

scholarly journals Physiological, Ecological, and Phylogenetic Characterization of Stappia, a Marine CO-Oxidizing Bacterial Genus

2006 ◽  
Vol 73 (4) ◽  
pp. 1266-1276 ◽  
Author(s):  
Carolyn F. Weber ◽  
Gary M. King
Keyword(s):  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Membrane Lipid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Bisphosphate Carboxylase ◽  
Phylogenetic Characterization ◽  
Metabolic Versatility ◽  
Wide Range

ABSTRACT Bacteria play a major role in marine CO cycling, yet very little is known about the microbes involved. Thirteen CO-oxidizing Stappia isolates obtained from existing cultures, macroalgae, or surf samples representing geographically and ecologically diverse habitats were characterized using biochemical, physiological, and phylogenetic approaches. All isolates were aerobic chemoorganotrophs that oxidized CO at elevated (1,000 ppm) and ambient-to-subambient concentrations (<0.3 ppm). All contained the form I (OMP) coxL gene for aerobic CO dehydrogenase and also the form II (BMS) putative coxL gene. In addition, some strains possessed cbbL, the large subunit gene for ribulose-1,5-bisphosphate carboxylase/oxygenase, suggesting the possibility of lithotrophic or mixotrophic metabolism. All isolates used a wide range of sugars, organic acids, amino acids, and aromatics for growth and grew at salinities from 5 to 45 ppt. All but one isolate denitrified or respired nitrate. Phylogenetic analyses based on 16S rRNA gene sequences indicated that several isolates could not be distinguished from Stappia aggregata and contributed to a widely distributed species complex. Four isolates (of strains GA15, HI, MIO, and M4) were phylogenetically distinct from validly described Stappia species and closely related genera (e.g., Ahrensia, Pannonibacter, Pseudovibrio, and Roseibium). Substrate utilization profiles, enzymatic activity, and membrane lipid composition further distinguished these isolates and supported their designations as new Stappia species. The observed metabolic versatility of Stappia likely accounts for its cosmopolitan distribution and its ability to contribute to CO cycling as well as other important biogeochemical cycles.

scholarly journals Characterization of Tomato yellow spot virus, a novel tomato-infecting begomovirus in Brazil

2007 ◽  
Vol 42 (9) ◽  
pp. 1335-1343 ◽  
Author(s):  
Renata Faier Calegario ◽  
Sávio de Siqueira Ferreira ◽  
Eduardo Chumbinho de Andrade ◽  
Francisco Murilo Zerbini
Keyword(s):  
Host Range ◽  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Datura Stramonium ◽  
Sweet Pepper ◽  
Yellow Spot ◽  
Spot Virus ◽  
Sequence Comparisons ◽  
Full Length Genome

The objective of this work was the biological and molecular characterization of a begomovirus detected in São Joaquim de Bicas, Minas Gerais, Brazil, named TGV-[Bi2], by determining its host range, complete nucleotide sequence and phylogenetic relationships with other begomoviruses. Biological characterization consisted of a host range study using either sap inoculation or particle bombardment as inoculation methods. The yellow spot virus can infect plants in Solanaceae and Amaranthaceae, including economically importat crops as sweet pepper, and weeds as Datura stramonium and Nicotiana silvestris. For the molecular characterization, the full-length genome (DNA-A and DNA-B) was amplified, cloned and completely sequenced. Sequence comparisons and phylogenetic analyses indicated that TGV-[Bi2] constitutes a novel begomovirus species named Tomato yellow spot virus (ToYSV), closely related to Sida mottle virus (SiMoV).

scholarly journals Phylogenetic Characterization of a Novel Insect-Specific Flavivirus Detected in a Culex Pool, Collected from Assam, India

Intervirology ◽  
2015 ◽  
Vol 58 (3) ◽  
pp. 149-154 ◽  
Author(s):  
Sibnarayan Datta ◽  
Reji Gopalakrishnan ◽  
Soumya Chatterjee ◽  
Vijay Veer
Keyword(s):  
Direct Detection ◽  
Nonstructural Protein ◽  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
Specific Primers ◽  
Phylogenetic Characterization ◽  
Dna And Rna ◽  
Indian State ◽  
Mosquito Pool

Objective: We report the phylogenetic characterization of a unique flavivirus sequence detected in a wild Culex tritaeniorhynchus mosquito pool, collected from the northeast Indian state of Assam. Methods: DNA and RNA were extracted from field-collected mosquito pools. Extracts were subjected to PCR and reverse transcriptase PCR amplification using universal and type-specific primers for direct detection of flavivirus-specific viral nucleic acids. An amplified flavivirus nonstructural protein 5 (NS5) genetic region was sequenced and BLAST searched, and phylogenetic analyses performed with reference sequences retrieved from GenBank. Results: Phylogenetic analyses revealed the sequence to be related to insect-specific flaviviruses (ISFs) of the genus Flavivirus, family Flaviviridae. Despite being related to the Palm Creek virus (PCV; an ISF very recently reported from Northern Australia), the present sequence (provisionally named Assam virus) was found to be highly divergent from PCV and other ISF sequences available in GenBank. The partial NS5 sequence analysis demonstrated low nucleotide sequence identity (66-77%) with known ISFs reported from other parts of the globe. Conclusion: Findings of this study suggest the presence of a candidate novel ISF - the first to be reported from India.

scholarly journals Molecular and Phylogenetic Characterization of Novel Papillomaviruses Isolated from Oral and Anogenital Neoplasms of Japanese Macaques (Macaca fuscata)

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 630
Author(s):  
Lucijan Skubic ◽  
Lea Hošnjak ◽  
Jeannette P. Staheli ◽  
Michael R. Dyen ◽  
Rebecca M. Ducore ◽  
...  
Keyword(s):  
Macaca Fuscata ◽  
Phylogenetic Analyses ◽  
Japanese Macaques ◽  
Genomic Region ◽  
Malignant Neoplasms ◽  
Regulatory Sequences ◽  
Phylogenetic Characterization ◽  
Viral Loads ◽  
Molecular Features

Papillomaviruses (PVs) are a diverse group of host species-specific DNA viruses, etiologically linked with various benign and malignant neoplasms of cutaneous and mucosal epithelia. Here, we describe the detection and characterization of the first two PVs naturally infecting Japanese macaques (Macaca fuscata), including the determination of their etiological association(s) with the development of original neoplasms. The molecular and phylogenetic analyses were performed on complete genome sequences of Macaca fuscata PV types 1 (MfuPV1) and 2 (MfuPV2), which were completely sequenced in samples of a malignant oral tumor and benign anogenital neoplasm of Japanese macaques, respectively. Subsequently, two type-specific quantitative real-time PCRs were developed to estimate viral loads of MfuPV1 and MfuPV2 and to evaluate their etiological roles. The in silico molecular analyses revealed that both viral genomes encode characteristic PV proteins with conserved functional domains and have a non-coding genomic region with regulatory sequences to regulate and complete the viral life cycle. However, additional experimental evidence is needed to finally confirm the presence and biological functionality of the molecular features of both novel PVs. While MfuPV1, together with PVs identified in other macaques, is classified into the Alphapapillomavirus (Alpha-PV) species 12, MfuPV2 is most likely a representative of the novel viral species within the Alpha-PV genus. Their relatively high viral loads suggest that both PVs are etiologically linked with the development of the original neoplasms.

Phylogenetic Analysis and Molecular Characterization of Xanthium sibiricum Using DNA Barcoding, PCR-RFLP, and Specific Primers

Planta Medica ◽  
2017 ◽  
Vol 83 (11) ◽  
pp. 946-953 ◽  
Author(s):  
Salvatore Tomasello ◽  
Günther Heubl
Keyword(s):  
Phylogenetic Analyses ◽  
Sequence Information ◽  
Diagnostic Pcr ◽  
Specific Pcr ◽  
Xanthium Sibiricum ◽  
Pcr Rflp ◽  
Allele Specific ◽  
Nuclear Its ◽  
Specific Restriction

AbstractThe fruits of Xanthium sibiricum have been widely used in traditional Chinese medicine for the treatment of nasal sinusitis and headaches. The genus Xanthium (cocklebur) is a taxonomically complex genus. Different taxonomic concepts have been proposed, some including several species, others lumping the different taxa in a few extremely polymorphic species. Due to the morphological similarities between species, the correct authentication of X. sibiricum is very difficult. Therefore, we established a polymerase chain reaction-restriction fragment length polymorphism method and diagnostic PCR based on nuclear internal transcribed spacer and chloroplast trnQ-rps16 barcodes to differentiate X. sibirium from related species.Results from the phylogenetic analyses based on sequence information from four marker regions (plastidal psbA-trnH and trnQ-rps16 and nuclear ITS and D35) support those taxonomic concepts accepting a reduced number of species, as four to five major clades are revealed in the phylogenetic reconstructions. X. sibiricum, together with some accessions from closely related taxa, is always supported as monophyletic, constituting a well-defined genetic entity. Allele-specific primer pairs for ITS and trnQ-rps16 were designed to amplify diagnostic products from the genomic DNA of X. sibiricum. Specific PCR in combination with digestion using the restriction enzyme MseI allowed for the identification of X. sibiricum by producing specific restriction patterns. The results demonstrate that the applied techniques provide effective and accurate authentication of X. sibiricum.

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