scholarly journals Paramyxo- and Coronaviruses in Rwandan Bats

2019 ◽  
Vol 4 (3) ◽  
pp. 99 ◽  
Author(s):  
Wanda Markotter ◽  
Marike Geldenhuys ◽  
Petrus Jansen van Vuren ◽  
Alan Kemp ◽  
Marinda Mortlock ◽  
...  
Keyword(s):  
Morphological Identification ◽  
Related Sequence ◽  
Genetic Database ◽  
Reverse Transcription Pcr ◽  
Fruit Bat ◽  
Pcr Assays ◽  
Study Sites ◽  
Positive Results ◽  
High Diversity ◽  
Horseshoe Bats

A high diversity of corona- and paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of corona- and paramyxoviral RNA using reverse transcription PCR assays. Positive results were further characterized by DNA sequencing and phylogenetic analysis. In addition to morphological identification of bat species, we also did molecular confirmation of species identities, contributing to the known genetic database available for African bat species. We detected a novel Betacoronavirus in two Geoffroy’s horseshoe bats (Rhinolophus clivosus) bats. We also detected several different paramyxoviral species from various insectivorous bats. One of these viral species was found to be homologous to the genomes of viruses belonging to the Jeilongvirus genus. Additionally, a Henipavirus-related sequence was detected in an Egyptian rousette fruit bat (Rousettus aegyptiacus). These results expand on the known diversity of corona- and paramyxoviruses and their geographical distribution in Africa.

scholarly journals Performance evaluation of ImmunoCAP® ISAC 112: a multi-site study

2017 ◽  
Vol 55 (4) ◽  
Author(s):  
Marianne van Hage ◽  
Peter Schmid-Grendelmeier ◽  
Chrysanthi Skevaki ◽  
Mario Plebani ◽  
Walter Canonica ◽  
...  
Keyword(s):  
South African ◽  
Low Frequency ◽  
Specific Ige ◽  
High Concentration ◽  
Serum Samples ◽  
Site Analysis ◽  
Calibration Sample ◽  
Clustering And Classification ◽  
Study Sites ◽  
Positive Results

Abstract Background: After the re-introduction of ImmunoCAP Methods: The study was carried out at 22 European and one South African site. Microarrays from different batches, eight specific IgE (sIgE) positive, three sIgE negative serum samples and a calibration sample were sent to participating laboratories where assays were performed according to the manufacturer’s instructions. Results: For both the negative and positive samples results were consistent between sites, with a very low frequency of false positive results (0.014%). A similar pattern of results for each of the samples was observed across the 23 sites. Homogeneity analysis of all measurements for each sample were well clustered, indicating good reproducibility; unsupervised hierarchical clustering and classification via random forests, showed clustering of identical samples independent of the assay site. Analysis of raw continuous data confirmed the good accuracy across the study sites; averaged standardized, site-specific ISU-E values fell close to the center of the distribution of measurements from all sites. After outlier filtering, variability across the whole study was estimated at 25.5%, with values of 22%, 27.1% and 22.4% for the ‘Low’, ‘Moderate to High’ and ‘Very High’ concentration categories, respectively. Conclusions: The study shows a robust performance of the ImmunoCAP

scholarly journals Detection of mycoplasma contamination in cell substrates using reverse transcription-PCR assays

2010 ◽  
Vol 110 (1) ◽  
pp. 54-60 ◽  
Author(s):  
M. Peredeltchouk ◽  
S.A. Wilson David ◽  
B. Bhattacharya ◽  
D.V. Volokhov ◽  
V. Chizhikov
Keyword(s):  
Reverse Transcription ◽  
Mycoplasma Contamination ◽  
Reverse Transcription Pcr ◽  
Pcr Assays

scholarly journals Molecular detection of vector borne pathogens in anemic and thrombocytopenic dogs in southern Brazil

2018 ◽  
Vol 27 (4) ◽  
pp. 505-513 ◽  
Author(s):  
Anna Cláudia Baumel Mongruel ◽  
Priscila Ikeda ◽  
Keyla Carstens Marques de Sousa ◽  
Jyan Lucas Benevenute ◽  
Margarete Kimie Falbo ◽  
...  
Keyword(s):  
18S Rrna ◽  
Molecular Detection ◽  
Phylogenetic Analyses ◽  
Southern Brazil ◽  
Conventional Pcr ◽  
Pathogenic Potential ◽  
Vector Borne ◽  
Pcr Assays ◽  
Etiological Agents ◽  
Positive Results

Abstract Arthropod-borne pathogens are medically important because of their ability to cause diseases in their hosts. The purpose of this study was to detect the occurrence of Ehrlichia spp., piroplasmids and Hepatozoon spp. in dogs with anemia and thrombocytopenia in southern Brazil. EDTA-whole blood was collected from 75 domestic dogs presenting anemia or/and thrombocytopenia from Guarapuava, state of Paraná, Brazil. DNA samples were subjected to conventional PCR assays for Ehrlichia spp. (dsb), piroplasmids (18S rRNA) and Hepatozoon spp. (18S rRNA), followed by sequencing and phylogenetic analyses. Among the 75 dogs, one (1.33%) was positive for Hepatozoon sp. and six (8%) were positive for piroplasmids in 18S rRNA cPCR assays. None of the dogs showed positive results in Ehrlichia spp.-cPCR targeting dsb gene. The phylogenetic analyses revealed that three piroplasm sequences were clustered with Rangellia vitalii, while one sequence was grouped with B. vogeli. The only sequence obtained from Hepatozoon spp.-PCR protocol was pooled with H. canis. Therefore, there is urgent need for differential molecular diagnosis of the two piroplasm species cited as etiological agents in clinical cases of canine hemoparasitic diseases, given the higher pathogenic potential of R. vitalii than of B. vogeli.

scholarly journals KEANEKARAGAMAN DAN KEKERABATAN LALAT BUAH (DIPTERA: TEPHRITIDAE) DI KALIMANTAN SELATAN BERDASARKAN KARAKTER MORFOLOGI DAN MOLEKULAR (RAPD-PCR DAN SEKUENSING DNA)

2013 ◽  
Vol 13 (2) ◽  
pp. 192-202
Author(s):  
M Indar Pramudi ◽  
Retno Dyah Puspitarini ◽  
Bambang Tri Rahardjo
Keyword(s):  
Dna Sequencing ◽  
Base Pair ◽  
Morphological Analysis ◽  
Fruit Fly ◽  
Fruit Flies ◽  
Morphological Identification ◽  
Bactrocera Carambolae ◽  
Rapd Pcr ◽  
Study Sites ◽  
Group B

Diversity and phylogeny of fruit fly (Diptera: Tephritidae) in South Kalimantan based on morphology and molecular (RAPD-PCR and DNA sequencing). Seven species of fruit fly was known by morphological identification. The fruit flies were found from  trapping with methyl eugenol and fruit collecting at all study sites in South Kalimantan. The results showed that as much as 17  plants were infected by fruit fly. Dendrogram based on morphological identification analyzed by using UPGMA with MEGA 4 program consisted in a group consisting of 5 sub-groups. Bactrocera carambolae and Bactrocera papayae of morphology were still a closely related fruit fly at 0.935. Whereas, based on RAPD result analized by UPGMA using 20 character of DNA based, showed that out of seven species consisted 2 groups, 1st group were B. umbrosa,  B. occipitalis and sub-group of B. latifrons. The second group consists of sub-groups B.carambolae, B. papaya, sub-group B. albistrigata and B. cucurbitae. The results of dendrogram from sequencing DNA fruit fly analysis comprised one of group and three sub-groups. The first sub-groups were B. papayae, B. carambolae, B. occipitalis, B.latifrons. The second subgroup were B. cucurbitae and B. umbrosa. While B. albistrigata separate but still one group with another fruit flies. The results of DNA sequencing showed that there were a homology of the seven species of the fruit fly i.e at 83 base pair / bp (C), 101 bp (T), 265 bp (G), 420 bp (A), 432 bp (T), 600 bp (A ). The length of the base pair for B. occipitalis, B. cucurbitae, B. albistrigata, B. carambolae, B. papayae, B. latifrons were respectively 615, 898, 570.969, 898 and 615 bp. The results of morphological analysis and RAPD methods showed difference in the distribution of groups and sub-groups. But based on morphologycal and DNA identification seven species of fruit flies found were all same as the genebank.

scholarly journals Nationwide survey reveals high diversity of Fusarium species and related mycotoxins in Brazilian rice: 2014 and 2015 harvests

2019 ◽  
Author(s):  
Gláucia Mara Moreira ◽  
Camila Primieri Nicolli ◽  
Larissa Bitencourt Gomes ◽  
Claudigo Ogoshi ◽  
Klaus K. Scheuermann ◽  
...  
Keyword(s):  
Fusarium Species ◽  
Nationwide Survey ◽  
Morphological Identification ◽  
Mycotoxin Contamination ◽  
Country Level ◽  
Species Complexes ◽  
Three Samples ◽  
The Status ◽  
Concentration Levels ◽  
High Diversity

Ninety three samples of rice were obtained from research and commercial plots at eight rice-producing regions of Brazil and analyzed for the presence of Fusarium species and 14 mycotoxins. A total of 352 isolates belonging to Fusarium genus were obtained from 85 % of the samples. These were assigned to four species complexes (SC) based on morphological identification. The most frequent SC detected was F. incarnatum-equiseti (FIESC, 32.4 %) followed by F. fujikuroi (FFSC, 26.1 %), F. graminearum (FGSC, 24.7 %) and F. chlamydosporum (FCSC, 16.8 %). FGSC was limited geographically and dominant in the southern subtropical production regions while the others occurred in all regions, particularly FIESC, the most widespread among them. The samples were individually contaminated with three to eight mycotoxins. The most common mycotoxins detected were zearalenone (ZEA), beauvericin, and acetylated forms of deoxynivalenol (AcDON). Other toxins included enniatins, T-2, HT-2, DON, neosolaniol and moniliformin. The concentration levels were all below the Brazilian promulgated limits established only for DON (< 750 ppb), and ZEA (< 100 ppb) with one exception for the latter. Most toxins were found in both the husk and flour fractions, but AcDON tended to concentrate more in the husk. Our survey extends considerable our knowledge of the Fusarium complexes infecting rice and provides an update on the status of rice mycotoxin contamination at the country level, which can be considered generally safe. However, attention should be paid to the widespread contamination of beauvericin.

scholarly journals Multicenter Comparison of PCR Assays for Detection of Human Herpesvirus 8 DNA in Semen

1999 ◽  
Vol 37 (5) ◽  
pp. 1298-1301 ◽  
Author(s):  
Philip E. Pellett ◽  
Thomas J. Spira ◽  
Omar Bagasra ◽  
Chris Boshoff ◽  
Lawrence Corey ◽  
...  
Keyword(s):  
Artificial Insemination ◽  
Human Herpesvirus ◽  
Population Based ◽  
Human Herpesvirus 8 ◽  
Hiv Positive ◽  
Assay Sensitivity ◽  
Herpesvirus 8 ◽  
Immunodeficiency Virus ◽  
Pcr Assays ◽  
Positive Results

Reported prevalences of human herpesvirus 8 (HHV-8) (Kaposi’s sarcoma-associated herpesvirus) in semen have ranged widely. This is possibly due to differences in assay sensitivity, geographic or population-based differences in the true presence of the virus in semen, and PCR contamination. This study assessed interlaboratory sensitivity and reproducibility in the analysis of blinded experimental panels, each consisting of 48 specimens and being composed of semen specimens from different healthy artificial-insemination donors (n = 30) and human immunodeficiency virus (HIV)-infected patients (n = 7) plus positive (n = 4) and negative (n = 7) controls. The experimental panels analyzed in each laboratory were identical except for being independently coded. Of 10 experiments done in five laboratories, 5 experiments from three laboratories had evidence of PCR contamination; all instances of contamination were in the context of nested PCR procedures. In the experiments with no false-positive results, HHV-8 DNA was detected in three (8%) of the 37 semen specimens (two from artificial-insemination donors and one from an HIV-positive patient) but in only 3 (1.6%) of the 184 PCRs in which these specimens were analyzed. This suggests that HHV-8 DNA is present in semen at concentrations that can be too low to allow its consistent detection. This study emphasizes the importance of performing blinded, multi-institution experiments to provide a coherent basis for comparing results and to motivate standardization of methods.

scholarly journals Comparison of commercial realtime reverse transcription PCR assays for the detection of SARS-CoV-2

2020 ◽  
Vol 129 ◽  
pp. 104510 ◽  
Author(s):  
Zsófia Iglói ◽  
Margareta leven ◽  
Zain Abdel-Karem Abou-Nouar ◽  
Babette Weller ◽  
Veerle Matheeussen ◽  
...  
Keyword(s):  
Reverse Transcription ◽  
Reverse Transcription Pcr ◽  
Pcr Assays

DNA barcoding reveals CITES-listed species among Taiwanese government-seized chelonian specimens

Genome ◽  
2018 ◽  
Vol 61 (8) ◽  
pp. 615-624 ◽  
Author(s):  
Chia-Hao Chang ◽  
Wei-Yu Dai ◽  
Ting-Yu Chen ◽  
An-Hsin Lee ◽  
Hsuan-Yi Hou ◽  
...  
Keyword(s):  
Law Enforcement ◽  
Dna Barcoding ◽  
Species Delimitation ◽  
Accurate Method ◽  
Morphological Identification ◽  
Biological Processes ◽  
Mitochondrial Cytochrome ◽  
Law Enforcement Agencies ◽  
Genetic Database ◽  
Reference Sequences

Compared to traditional morphological identification, DNA barcoding—molecular identification based on sequencing of a segment of mitochondrial cytochrome c oxidase subunit I (COI)—provides a shortcut to authenticating chelonian identifications. Here, we selected 63 government-seized chelonian specimens deposited at Taipei Zoo for DNA barcoding analysis. DNA barcoding and subsequent phylogenetic analysis successfully authenticated 36 chelonian species, including five that are listed in CITES Appendix I. Approximately 90% (57/63) of the specimens were successfully authenticated by our molecular approach, but lack or error of BOLD reference sequences, biological processes such as hybridization, and uncertain species delimitation all reduced the accuracy of DNA barcoding. To increase the accuracy of DNA barcoding, Taipei Zoo will continue to enrich the BOLD database and also establish a genetic database, to include additional genetic markers, by using government-seized chelonian specimens. A fast and accurate method to authenticate seized samples could assist law enforcement agencies to prosecute criminals and restrict illegal exploitation of wild chelonian resources.

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