scholarly journals A Novel Bunyavirus Discovered in Oriental Shrimp (Penaeus chinensis)

2021 ◽  
Vol 12 ◽  
Author(s):  
Xuan Dong ◽  
Tao Hu ◽  
Yanbei Ren ◽  
Fanzeng Meng ◽  
Chen Li ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Genomic Diversity ◽  
Brown Spot ◽  
Taqman Probe ◽  
Glycoprotein Precursor ◽  
N Protein ◽  
Penaeus Chinensis ◽  
Reverse Transcription Quantitative Pcr ◽  
Pcr Method ◽  
Oriental Shrimp

Herein, we describe a novel bunyavirus, oriental wenrivirus 1 (OWV1), discovered in moribund oriental shrimp (Penaeus chinensis) collected from a farm in China in 2016. Like most bunyaviruses, OWV1 particles were enveloped, spherical- to ovoid-shaped, and 80–115 nm in diameter. However, its genome was found to comprise four segments of (-)ssRNA. These included an L RNA segment (6,317 nt) encoding an RNA-directed RNA polymerase (RdRp) of 2,052 aa, an M RNA segment (2,978 nt) encoding a glycoprotein precursor (GPC) of 922 aa, an S1 RNA segment (1,164 nt) encoding a nucleocapsid (N) protein of 243 aa, and an S2 RNA segment (1,382 nt) encoding a putative non-structural (NSs2) protein of 401 aa. All the four OWV1 RNA segments have complementary terminal decanucleotides (5′-ACACAAAGAC and 3′-UGUGUUUCUG) identical to the genomic RNA segments of uukuviruses and similar to those of phleboviruses and tenuiviruses in the Phenuiviridae. Phylogenetic analyses revealed that the RdRp, GPC, and N proteins of OWV1 were closely related to Wēnzhōu shrimp virus 1 (WzSV-1) and Mourilyan virus (MoV) that infect black tiger shrimp (P. monodon). Phylogenetic analyses also suggested that OWV1 could be classified into a second, yet to be established, species of the Wenrivirus genus in the Phenuiviridae. These wenriviruses also clustered with Wenling crustacean virus 7 from shrimps and bunya-like brown spot virus from white-clawed crayfish. Of note there were no homologs of the NSs2 of OWV1 and MoV/WzSV-1 in GenBank, and whether other crustacean phenuiviruses also possess a similar S2 RNA segment warrants further investigation. In addition, we established a TaqMan probe-based reverse-transcription quantitative PCR method for detection of OWV1, and it was detected as 1.17 × 102—1.90 × 107 copies/ng-RNA in gills of 23 out of 32 P. chinensis samples without an obvious gross sign. However, the discovery of OWV1 highlights the expanding genomic diversity of bunyaviruses.

scholarly journals Two New Haplotypes of Bartonella sp. Isolated from Lipoptena fortisetosa (Diptera: Hippoboscidae) in SE Poland

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 485
Author(s):  
Katarzyna Bartosik ◽  
Weronika Maślanko ◽  
Alicja Buczek ◽  
Marek Asman ◽  
Joanna Witecka ◽  
...  
Keyword(s):  
Potential Role ◽  
Roe Deer ◽  
Phylogenetic Analyses ◽  
Rpob Gene ◽  
Molecular Characteristics ◽  
Broad Host Range ◽  
South Eastern ◽  
Se Poland ◽  
Pcr Method ◽  
The Subject

Insects of the genus Lipoptena are parasitic arthropods with a broad host range. Due to the type of parasitism (hematophagy), their potential role as vectors of pathogens, i.e., Bartonella sp., Anaplasma phagocytophilum, Rickettsia spp., and Borrelia burgdorferi is considered. As the range of their occurrence has been changing dynamically in recent years and infestations of humans have increasingly been reported, these organisms are now the subject of numerous studies. Our research aimed to present the molecular characteristics of Bartonella sp. detected in Lipoptena fortisetosa parasitizing wild cervids in south-eastern Poland. Adults of Lipoptena spp. were collected from carcasses of roe deer and red deer between spring and autumn in 2013. The PCR method was used to detect Bartonella sp. in the insects. We report two new haplotypes of the rpoB gene of Bartonella sp. isolated from L. fortisetosa feeding on wild cervids in south-eastern Poland and the presence of this invasive ectoparasitic species in the studied area since 2013. Phylogenetic analyses of newly obtained Bartonella sp. haplotypes confirmed their unique position on the constructed tree and network topology. The rpoB gene sequences found belonging to lineage B support the view that this phylogenetic lineage represents a novel Bartonella species.

scholarly journals Characterization of a New Orthotospovirus from Chilli Pepper in Yunnan Province, China

Plant Disease ◽  
2020 ◽  
Vol 104 (4) ◽  
pp. 1175-1182
Author(s):  
Kuanyu Zheng ◽  
Tsung-Chi Chen ◽  
Kuo Wu ◽  
Ya-Chi Kang ◽  
Shyi-Dong Yeh ◽  
...  
Keyword(s):  
Yunnan Province ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Pepper Plant ◽  
Necrosis Virus ◽  
Chilli Pepper ◽  
N Protein ◽  
Reverse Transcription Pcr ◽  
High Amino Acid ◽  
Groundnut Bud Necrosis Virus

Chilli pepper (Capsicum annuum L.) is one of the most important crops in Yunnan Province, China. An orthotospovirus isolate 14YV855 was isolated from a diseased chilli pepper plant exhibiting yellow ringspots and necrosis on leaves in Shiping County, Honghe Hani and Yi Autonomous Prefecture, Yunnan Province in 2014. The complete genome sequence of 14YV855 was determined. The small, medium, and large RNAs are 3,428, 4,781, and 8,917 nucleotides long, respectively. The complete nucleocapsid (N) protein of 14YV855 shares a high amino acid identity of 84.8 to 89.9% to that of Capsicum chlorosis virus (CaCV), Groundnut bud necrosis virus (GBNV), Watermelon bud necrosis virus (WBNV), and Watermelon silver mottle virus (WSMoV), which is slightly less than the 90% identity threshold for the demarcation of new Orthotospovirus sp. Phylogenetic analyses revealed that the N protein and RNA-dependent RNA polymerase of 14YV855 are the most related to WSMoV, while the NSs, NSm, and Gn/Gc proteins are similar to those of GBNV. As expected, 14YV855 is serologically related to CaCV, GBNV, WBNV, and WSMoV when the monoclonal antibody against the N protein of WSMoV was used; however, 14YV855 can be distinguished from other orthotospoviruses by reverse-transcription PCR using the specific primers. Our results indicate that 14YV855 is a new Orthotospovirus sp. belonging to the WSMoV serogroup and is provisionally named Chilli yellow ringspot virus.

scholarly journals Pathogenicity and a TaqMan Real-Time PCR for Specific Detection of Pantoea allii, a Bacterial Pathogen of Onions

Plant Disease ◽  
2019 ◽  
Vol 103 (12) ◽  
pp. 3031-3040 ◽  
Author(s):  
Shabnam Rahimi-Khameneh ◽  
Sanni Hsieh ◽  
Renlin Xu ◽  
Tyler J. Avis ◽  
Sean Li ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Phylogenetic Analyses ◽  
Similarity Index ◽  
Taqman Probe ◽  
Economic Losses ◽  
In Planta ◽  
Pcr Assay ◽  
Blind Test ◽  
Reliable Detection

Bacterial diseases of onion are reported to cause significant economic losses. Pantoea allii Brady, one of the pathogens causing the center rot on onions, has not yet been reported in Canada. We report the pathogenicity of P. allii on commercially available Canadian green onions (scallions). All P. allii-inoculated plants, irrespective of the inoculum concentration, exhibited typical leaf chlorotic discoloration on green onion leaves, which can reduce their marketability. Reisolation of P. allii from infected scallion tissues and reidentification by sequencing and phylogenetic analyses of the leuS gene suggest that the pathogen can survive in infected tissues 21 days after inoculation. This is the first report of P. allii as a potential pathogen of green onions. This study also reports the development and validation of a TaqMan real-time PCR assay targeting the leuS gene for reliable detection of P. allii in pure cultures and in planta. A 642-bp leuS gene fragment was targeted because it showed high nucleotide diversity and positively correlated with genome-based average nucleotide identity with respect to percent similarity index and identity of Pantoea species. The assay specificity was validated using 61 bacterial and fungal strains. Under optimal conditions, the selected primers and FAM-labeled TaqMan probe were specific for the detection of nine reference P. allii strains by real-time PCR. The 52 strains of other Pantoea spp. (n = 25), non-Pantoea spp. (n = 20), and fungi/oomycetes (n = 7) tested negative (no detectable fluorescence). Onion tissues spiked with P. allii, naturally infested onion bulbs, greenhouse infected green onion leaf samples, as well as an interlaboratory blind test were used to validate the assay specificity. The sensitivities of a 1-pg DNA concentration and 30 CFU are comparable to previously reported real-time PCR assays of other bacterial pathogens. The TaqMan real-time PCR assay developed in this study will facilitate reliable detection of P. allii and could be a useful tool for screening onion imports or exports for the presence of this pathogen.

scholarly journals DESAIN IN SILICO DNA PROBE PENDETEKSI MUTASI DAERAH RESISTENSI QUINOLON Gen gyrA DAN gyrB Mycobacterium tuberculosis

2019 ◽  
Vol 7 (2) ◽  
pp. 44
Author(s):  
Tasya Pramiswari ◽  
Jennifer Tamara ◽  
Ni Made Febrianti ◽  
Sagung Chandra Yowani
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Therapy Resistance ◽  
Dna Probe ◽  
Gyrb Gene ◽  
Taqman Probe ◽  
Probe Design ◽  
Gyra Gene ◽  
Mdr Tb ◽  
Pcr Method ◽  
Two Stages

Fluoroquinolone (FQ) is the main drug used in MDR-TB therapy resistance to FQ can cause death and increase the risk of treatment failure in MDR-TB patients. Mutations in gyrA gene and gyrB gene from Mycobacterium tuberculosis are responsible for the occurrence of FQ resistance. The highest mutation of gyrA gene in QRDR was found in codon 94, while mutations in gyrB gene was found in codon 500. M. Tuberculosis which resistant to FQ can be detected using the Real Time Polymerase Chain Reaction (RT-PCR) method with DNA probe.                                                                                                                                                                                                                             This study will design the nucleotide sequence of the TaqMan type probe using the Clone Manager Suite 9.2 program. The results of the DNA probe design were then analyzed in two stages, which is based on the probe criteria in general and based on the TaqMan probe labeling criteria. The design of the mutant probe DNA using the program produced 1 probe for Asp94Ala specific mutations in the gyrA gene and 33 probes for Asp500Ala specific mutations in the gyrB gene. After being analyzed by the two criteria, it was obtained the A94MA1 probe with the 5 '-TCGATCTACGCCAGCCTGGT-3' sequence and B500MA12 probe with the order of 5 '-TACCACAAGCTCGTGCTGATGGC-3'. The results of these probes meet both criteria and can be used to detect mutations in codon 94 gyrA genes and codons 500 gyrB genes of  Mycobacterium tuberculosis.

scholarly journals Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Isaiah Paolo A. Lee ◽  
Cheryl P. Andam
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Clusters ◽  
Genomic Diversity ◽  
Ecological Niches ◽  
Cronobacter Sakazakii ◽  
Type Vi Secretion System ◽  
Accessory Gene ◽  
Pan Genome ◽  
Accessory Genes ◽  
Mannose Metabolism

Abstract Background Cronobacter sakazakii is an emerging opportunistic bacterial pathogen known to cause neonatal and pediatric infections, including meningitis, necrotizing enterocolitis, and bacteremia. Multiple disease outbreaks of C. sakazakii have been documented in the past few decades, yet little is known of its genomic diversity, adaptation, and evolution. Here, we analyzed the pan-genome characteristics and phylogenetic relationships of 237 genomes of C. sakazakii and 48 genomes of related Cronobacter species isolated from diverse sources. Results The C. sakazakii pan-genome contains 17,158 orthologous gene clusters, and approximately 19.5% of these constitute the core genome. Phylogenetic analyses reveal the presence of at least ten deep branching monophyletic lineages indicative of ancestral diversification. We detected enrichment of functions involved in proton transport and rotational mechanism in accessory genes exclusively found in human-derived strains. In environment-exclusive accessory genes, we detected enrichment for those involved in tryptophan biosynthesis and indole metabolism. However, we did not find significantly enriched gene functions for those genes exclusively found in food strains. The most frequently detected virulence genes are those that encode proteins associated with chemotaxis, enterobactin synthesis, ferrienterobactin transporter, type VI secretion system, galactose metabolism, and mannose metabolism. The genes fos which encodes resistance against fosfomycin, a broad-spectrum cell wall synthesis inhibitor, and mdf(A) which encodes a multidrug efflux transporter were found in nearly all genomes. We found that a total of 2991 genes in the pan-genome have had a history of recombination. Many of the most frequently recombined genes are associated with nutrient acquisition, metabolism and toxin production. Conclusions Overall, our results indicate that the presence of a large accessory gene pool, ability to switch between ecological niches, a diverse suite of antibiotic resistance, virulence and niche-specific genes, and frequent recombination partly explain the remarkable adaptability of C. sakazakii within and outside the human host. These findings provide critical insights that can help define the development of effective disease surveillance and control strategies for Cronobacter-related diseases.

Detection of Sesame Seed DNA in Foods Using Real-Time PCR

2007 ◽  
Vol 70 (4) ◽  
pp. 1033-1036 ◽  
Author(s):  
JENNIFER L. BRZEZINSKI
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Sesame Seed ◽  
Food Products ◽  
Taqman Probe ◽  
2S Albumin ◽  
Sesame Seeds ◽  
Baked Goods ◽  
Pcr Method ◽  
Seed Dna

The detection of potentially allergenic foods, such as sesame seeds, in food products is a major concern for the food-processing industry. A real-time PCR method was designed to determine if sesame seed DNA is present in food products. The PCR reaction amplifies a 66-bp fragment of the sesame seed 2S albumin gene, which is detected with a sesame-specific, dual-labeled TaqMan probe. This reaction will not amplify DNA derived from other seeds present in baked goods, such as pumpkin, poppy, and sunflower seeds. Additionally, this assay will not cross-react with DNA from several tree nut species, such as almond, Brazil nut, cashew, hazelnut, and walnut, as well as four varieties of peanut. This assay is sensitive enough to detect 5 pg of purified sesame seed DNA, as well as sesame seed DNA in a spiked wheat cracker sample.

scholarly journals Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants

2020 ◽  
Vol 8 (11) ◽  
pp. 1679
Author(s):  
Valentina Méndez ◽  
Miryam Valenzuela ◽  
Francisco Salvà-Serra ◽  
Daniel Jaén-Luchoro ◽  
Ximena Besoain ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Phylogenetic Analyses ◽  
Plant Diseases ◽  
Genomic Diversity ◽  
Clavibacter Michiganensis ◽  
Tomato Plants ◽  
Clavibacter Michiganensis Subsp ◽  
Genomic Analyses ◽  
Encoding Genes ◽  
Genomic Similarity

The genus Clavibacter has been associated largely with plant diseases. The aims of this study were to characterize the genomes and the virulence factors of Chilean C. michiganensis subsp. michiganensis strains VL527, MSF322 and OP3, and to define their phylogenomic positions within the species, Clavibacter michiganensis. VL527 and MSF322 genomes possess 3,396,632 and 3,399,199 bp, respectively, with a pCM2-like plasmid in strain VL527, with pCM1- and pCM2-like plasmids in strain MSF322. OP3 genome is composed of a chromosome and three plasmids (including pCM1- and pCM2-like plasmids) of 3,466,104 bp. Genomic analyses confirmed the phylogenetic relationships of the Chilean strains among C.michiganensis subsp. michiganensis and showed their low genomic diversity. Different virulence levels in tomato plants were observable. Phylogenetic analyses of the virulence factors revealed that the pelA1 gene (chp/tomA region)—that grouped Chilean strains in three distinct clusters—and proteases and hydrolases encoding genes, exclusive for each of the Chilean strains, may be involved in these observed virulence levels. Based on genomic similarity (ANIm) analyses, a proposal to combine and reclassify C. michiganensis subsp. phaseoli and subsp. chilensis at the species level, as C. phaseoli sp. nov., as well as to reclassify C. michiganensis subsp. californiensis as the species C. californiensis sp. nov. may be justified.

scholarly journals Broad-spectrum detection of papillomaviruses in bovine teat papillomas and healthy teat skin

2004 ◽  
Vol 85 (8) ◽  
pp. 2191-2197 ◽  
Author(s):  
Tomoko Ogawa ◽  
Yoshimi Tomita ◽  
Mineyuki Okada ◽  
Kuniko Shinozaki ◽  
Hiroko Kubonoya ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Broad Spectrum ◽  
Phylogenetic Analyses ◽  
Genomic Diversity ◽  
Bovine Papillomavirus ◽  
Subclinical Infection ◽  
Healthy Skin ◽  
Sequence Alignments ◽  
Spectrum Detection

To investigate the prevalence of bovine papillomavirus (BPV) in bovine papilloma and healthy skin, DNA extracted from teat papillomas and healthy teat skin swabs was analysed by PCR using the primer pairs FAP59/FAP64 and MY09/MY11. Papillomavirus (PV) DNA was detected in all 15 papilloma specimens using FAP59/FAP64 and in 8 of the 15 papilloma specimens using MY09/MY11. In swab samples, 21 and 8 of the 122 samples were PV DNA positive using FAP59/FAP64 and MY09/MY11, respectively. Four BPV types (BPV-1, -3, -5 and -6), two previously identified putative BPV types (BAA1 and -5) and 11 putative new PV types (designated BAPV1 to -10 and BAPV11MY) were found in the 39 PV DNA-positive samples. Amino acid sequence alignments of the putative new PV types with reported BPVs and phylogenetic analyses of the putative new PV types with human and animal PV types showed that BAPV1 to -10 and BAPV11MY are putative new BPV types. These results also showed the genomic diversity and extent of subclinical infection of BPV.

scholarly journals The Virulence of S. marcescens Strains Isolated From Contaminated Blood Products Is Divergent in the C. elegans Infection Model

2021 ◽  
Vol 12 ◽  
Author(s):  
Alexander Diamandas ◽  
Mikhail R. Razon ◽  
Sandra Ramirez-Arcos ◽  
Ann Karen C. Brassinga
Keyword(s):  
Blood Donation ◽  
Phylogenetic Analyses ◽  
Bursaphelenchus Xylophilus ◽  
Human Infection ◽  
Genomic Diversity ◽  
Multi Drug Resistance ◽  
Clinical Strain ◽  
Infection Model ◽  
Pinewood Nematode ◽  
Environmental Strain

Bacterial contamination of platelet concentrates (PCs) can occur during blood donation or PC processing, necessitating routine screening to identify contaminated products in efforts to prevent adverse transfusion reactions in recipient patients. Serratia marcescens is a common bacterial contaminant, and its resilient nature coupled with genetic promiscuity imbue this environmental bacterium with resistance to disinfectants and antibiotics enhancing bacterial virulence. In this study, we aim to understand adaptive survival mechanisms through genetic characterization of two S. marcescens strains, CBS11 and CBS12, isolated from PCs by Canadian Blood Services. Genomic analyses of the two strains indicated that CBS11 has one chromosome and one plasmid (pAM01), whereas CBS12 has no plasmids. Phylogenetic analyses show that CBS11 and CBS12 are non-clonal strains, with CBS11 clustering closely with clinical strain CAV1492 and less so with environmental strain PWN146, and CBS12 clustering with a clinical strain AR_0027. Interestingly, pAM01 was most closely related to PWN146p1, a plasmid found in S. marcescens PWN146 strain associated with pinewood nematode Bursaphelenchus xylophilus. Lastly, the genomic diversity of CBS11 and CBS12 was not reflected in the antibiotic resistance profiles as they were remarkably similar to one another, but was reflected in the virulence phenotypes assessed in the Caenorhabditis elegans nematode infection model, with CBS11 being more virulent then CBS12. Taken together, we suggest that S. marcescens environmental isolates that feature evolutionary diverse genomics are better equipped to adapt and thrive in varied environments, such as that of PCs, and therefore is as much of a concern as multi-drug resistance for human infection potential.

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