scholarly journals Astrovirus in Reunion Free-tailed Bat (Mormopterus francoismoutoui)

2019 ◽  
Author(s):  
Léa Joffrin ◽  
Axel O. G. Hoarau ◽  
Erwan Lagadec ◽  
Patrick Mavingui ◽  
Camille Lebarbenchon
Keyword(s):  
Genetic Diversity ◽  
Rna Viruses ◽  
Mammalian Species ◽  
Rdrp Gene ◽  
Chain Reaction ◽  
Rna Dependent Rna Polymerase ◽  
Nested Polymerase Chain Reaction ◽  
High Genetic Diversity ◽  
Partial Rdrp ◽  
Polymerase Chain

AbstractAstroviruses (AstVs) are RNA viruses responsible for infection of a large diversity of avian and mammalian species, including bats, livestock, and humans. We investigated AstV infection in a free-tailed bat species, Mormopterus francoismoutoui, endemic to Reunion Island. A total of 190 guano samples were collected in a maternity colony during 19 different sampling sessions, between June 2016 and June 2017. Biological material was tested for the presence of the AstV RNA-dependent RNA-polymerase (RdRp) gene with a pan-AstV semi-nested polymerase chain reaction assay. In total, 15 guano samples (7.9%) tested positive, with high genetic diversity of the partial RdRp gene sequences among positive samples. A phylogenetic analysis further revealed that the detected viruses were genetically related to AstVs reported in reptiles, dogs, and pigs, but did not cluster with AstVs commonly found in bats. Although more investigation need to be conducted to assess the level of infected bats in the studied population, our findings suggest that Reunion free-tailed bats are exposed to AstV, and that cross-species transmission may occur with other hosts sharing the same habitat.

scholarly journals Astrovirus in Reunion Free-Tailed Bat (Mormopterus francoismoutoui)

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1524
Author(s):  
Léa Joffrin ◽  
Axel O. G. Hoarau ◽  
Erwan Lagadec ◽  
Marie Köster ◽  
Riana V. Ramanantsalama ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rna Viruses ◽  
Mammalian Species ◽  
Rdrp Gene ◽  
Chain Reaction ◽  
Rna Dependent Rna Polymerase ◽  
Nested Polymerase Chain Reaction ◽  
High Genetic Diversity ◽  
Partial Rdrp ◽  
Polymerase Chain

Astroviruses (AstVs) are RNA viruses infecting a large diversity of avian and mammalian species, including bats, livestock, and humans. We investigated AstV infection in a free-tailed bat species, Mormopterus francoismoutoui, endemic to Reunion Island. A total of 380 guano samples were collected in a maternity colony during 38 different sampling sessions, from 21 June 2016 to 4 September 2018. Each sample was tested for the presence of the AstV RNA-dependent RNA-polymerase (RdRp) gene using a pan-AstV semi-nested polymerase chain reaction assay. In total, 27 guano samples (7.1%) tested positive, with high genetic diversity of the partial RdRp gene sequences among positive samples. Phylogenetic analysis further revealed that the detected viruses were genetically related to AstVs reported in rats, reptiles, dogs, and pigs, but did not cluster with AstVs commonly found in bats. Although more investigations need to be conducted to assess the prevalence of infected bats in the studied population, our findings show that Reunion free-tailed bats are exposed to AstVs, and suggest that cross-species transmission may occur with other hosts sharing the same habitat.

scholarly journals Genetic diversity of Ehrlichia ruminantium strains in Cameroon

2014 ◽  
Vol 81 (1) ◽  
Author(s):  
Seraphine N. Esemu ◽  
Roland N. Ndip ◽  
Lucy M. Ndip
Keyword(s):  
Genetic Diversity ◽  
Deoxyribonucleic Acid ◽  
Amino Acid Level ◽  
Gene Products ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Ehrlichia Ruminantium ◽  
Polymerase Chain ◽  
Study Sites ◽  
Partial Fragment

In order to investigate the extent of genetic diversity among Ehrlichia ruminantium strains in Cameroon, a partial fragment (800 bp) of the E. ruminantium map1 gene was amplified by nested polymerase chain reaction in 121 of 156 E. ruminantium pCS20-positive DNA samples extracted from ticks and cattle collected from two ranches. Deoxyribonucleic acid sequencing of the map1 gene products indicated the presence of at least 21 genotypes at the nucleotide level and 16 genotypes at the amino acid level circulating within the study sites. Some of the genotypes were identical to Antigua (U50830), Blaaukrans (AF368000) or UmBanein (U50835), whilst the others were new genotypes. Twenty-four representative sequences were deposited in GenBank and given accession numbers JX477663 – JX477674 (for sequences of tick origin) and JX486788 – JX486799 (for sequences of cattle origin). Knowledge of E. ruminantium strain diversity could be important in understanding the epidemiology of heartwater

scholarly journals CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2

2020 ◽  
Author(s):  
João Carneiro ◽  
Catarina Gomes ◽  
Cátia Couto ◽  
Filipe Pereira
Keyword(s):  
Genetic Diversity ◽  
False Negative ◽  
Virus Detection ◽  
Pcr Primers ◽  
Screening Tests ◽  
Testing Methods ◽  
Novel Mutations ◽  
Chain Reaction ◽  
High Genetic Diversity ◽  
Polymerase Chain

AbstractThe ability to detect the SARS-CoV-2 in a widespread epidemic is crucial for screening of carriers and for the success of quarantine efforts. Methods based on real-time reverse transcription polymerase chain reaction (RT-qPCR) and sequencing are being used for virus detection and characterization. However, RNA viruses are known for their high genetic diversity which poses a challenge for the design of efficient nucleic acid-based assays. The first SARS-CoV-2 genomic sequences already showed novel mutations, which may affect the efficiency of available screening tests leading to false-negative diagnosis or inefficient therapeutics. Here we describe the CoV2ID (http://covid.portugene.com/), a free database built to facilitate the evaluation of molecular methods for detection of SARS-CoV-2 and treatment of COVID-19. The database evaluates the available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Updated sequences alignments are used to constantly verify the theoretical efficiency of available testing methods. Detailed information on available detection protocols are also available to help laboratories implementing SARS-CoV-2 testing.

Using a Polymerase Chain Reaction as a Complementary Test to Improve the Detection of Dermatophyte Fungus in Nails

2014 ◽  
Vol 104 (3) ◽  
pp. 233-237 ◽  
Author(s):  
María José Iglesias Sánchez ◽  
Ana María Pérez Pico ◽  
Félix Marcos Tejedor ◽  
María Jesús Iglesias Sánchez ◽  
Raquel Mayordomo Acevedo
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Classical Method ◽  
Clinical Manifestations ◽  
Culture Method ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Traditional Procedure ◽  
Polymerase Chain

Background Dermatomycoses are a group of pathologic abnormalities frequently seen in clinical practice, and their prevalence has increased in recent decades. Diagnostic confirmation of mycotic infection in nails is essential because there are several pathologic conditions with similar clinical manifestations. The classical method for confirming the presence of fungus in nail is microbiological culture and the identification of morphological structures by microscopy. Methods We devised a nested polymerase chain reaction (PCR) that amplifies specific DNA sequences of dermatophyte fungus that is notably faster than the 3 to 4 weeks that the traditional procedure takes. We compared this new technique and the conventional plate culture method in 225 nail samples. The results were subjected to statistical analysis. Results We found concordance in 78.2% of the samples analyzed by the two methods and increased sensitivity when simultaneously using the two methods to analyze clinical samples. Now we can confirm the presence of dermatophyte fungus in most of the positive samples in just 24 hours, and we have to wait for the result of culture only in negative PCR cases. Conclusions Although this PCR cannot, at present, substitute for the traditional culture method in the detection of dermatophyte infection of the nails, it can be used as a complementary technique because its main advantage lies in the significant reduction of time used for diagnosis, in addition to higher sensitivity.

Detection of hepatitis “C” virus in formalin-fixed liver tissue by nested polymerase chain reaction

1992 ◽  
Vol 37 (4) ◽  
pp. 310-314 ◽  
Author(s):  
Richard Sallie ◽  
Anne Rayner ◽  
Bernard Portmann ◽  
A. L. W. F. Eddleston ◽  
Roger Williams
Keyword(s):  
Polymerase Chain Reaction ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Liver Tissue ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Polymerase Chain ◽  
Formalin Fixed

scholarly journals A PCR-based Assay for Distinguishing between A1 and A2 Mating Types of Phytophthora capsici

2017 ◽  
Vol 142 (4) ◽  
pp. 260-264
Author(s):  
Ping Li ◽  
Dong Liu ◽  
Min Guo ◽  
Yuemin Pan ◽  
Fangxin Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mating Type ◽  
Phytophthora Capsici ◽  
Mating Types ◽  
Sequence Repeat ◽  
Chain Reaction ◽  
Plant Parasite ◽  
Dna Fragment ◽  
Polymerase Chain ◽  
Microsatellite Diversity

Sexual reproduction in the plant parasite Phytophthora capsici Leonian requires the interaction of two distinct mating types, A1 and A2. Co-occurrence of these mating types can enhance the genetic diversity of P. capsici and alter its virulence or resistance characteristics. Using an intersimple sequence repeat (ISSR) screen of microsatellite diversity, we identified, cloned, and sequenced a novel 1121-base pair (bp) fragment specific to the A1 mating type of P. capsici. Primers Pcap-1 and Pcap-2 were designed from this DNA fragment to specifically detect the A1 mating type. Polymerase chain reaction (PCR) using these primers amplified an expected 997-bp fragment from known A1 mating types, but yielded a 508-bp fragment from known A2 mating types. This PCR-based assay could be adapted to accurately and rapidly detect the co-occurrence of A1 and A2 P. capsici mating types from field material.

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