scholarly journals Detection and phylogenetic analysis of porcine enteric calicivirus, genetically related to the Cowden strain of sapovirus genogroup III, in Brazilian swine herds

2008 ◽  
Vol 28 (1) ◽  
pp. 82-86 ◽  
Author(s):  
Aline F. Barry ◽  
Alice F. Alfieri ◽  
Amauri A. Alfieri
Keyword(s):  
Phylogenetic Analysis ◽  
Polymerase Gene ◽  
High Similarity ◽  
Rt Pcr ◽  
Pcr Assay ◽  
High Prevalence ◽  
Cowden Strain ◽  
Dna Fragment ◽  
Swine Herds ◽  
Rna Polymerase Gene

Sapovirus of the Caliciviridae family is an important agent of acute gastroenteritis in children and piglets. The Sapovirus genus is divided into seven genogroups (G), and strains from the GIII, GVI and GVII are associated with infections in swine. Despite the high prevalence in some countries, there are no studies related to the presence of porcine enteric sapovirus infections in piglets in Brazil. In the present study, 18 fecal specimens from piglets up to 28 days were examined to determine the presence of sapovirus genome by RT-PCR assay, using primers designed to amplify a 331 bp segment of the RNA polymerase gene. In 44.4% (8/18) of fecal samples, an amplified DNA fragment was obtained. One of these fragments was sequenced and submitted to molecular and phylogenetic analysis. This analysis revealed high similarity, with nucleotides (87%) and amino acids (97.8%), to the Cowden strain, the GIII prototype of porcine enteric calicivirus. This is the first description of sapovirus in Brazilian swine herds.

Detection and characterisation of hepatitis E virus in naturally infected swine in Croatia

2013 ◽  
Vol 61 (4) ◽  
pp. 517-528 ◽  
Author(s):  
Zoran Lipej ◽  
Dinko Novosel ◽  
Lea Vojta ◽  
Besi Roić ◽  
Miljenko Šimpraga ◽  
...  
Keyword(s):  
Hepatitis E Virus ◽  
Age Groups ◽  
Hepatitis E ◽  
Health Concern ◽  
Rt Pcr ◽  
Animal Reservoir ◽  
Naturally Occurring ◽  
High Prevalence ◽  
Swine Herds ◽  
Bile Samples

Hepatitis E is a viral zoonotic disease infecting swine worldwide. Since pigs represent a likely animal reservoir for the hepatitis E virus, the epidemiology of naturally occurring hepatitis E was investigated in Croatian swine herds. Nearly all tested animals were seropositive for antibodies against the hepatitis E virus (55/60, 91.7%). Active infection was detected in all age groups by RT-PCR of viral RNA in serum (8/60, 13.3%) and bile samples (3/37, 8.1%), which was further confirmed by histopathological findings of characteristic lesions in the livers of the infected animals. Three new strains of hepatitis E virus were isolated from Croatian pig herds. Phylogenetic analysis using median-joining networks clustered those Croatian strains with isolates from various parts of the world, indicating their likely origin in international trade. Similarity to human isolates implies a zoonotic potential of Croatian strains, which raises a public health concern, especially in the light of the high prevalence of hepatitis E in the herds studied.

scholarly journals Cherry virus A infecting cherries and plums in the Czech Republic – Short communication

2013 ◽  
Vol 40 (No. 1) ◽  
pp. 37-39 ◽  
Author(s):  
D. Šafářová ◽  
M. Navrátil ◽  
F. Paprštein ◽  
T. Candresse ◽  
A. Marais
Keyword(s):  
Phylogenetic Analysis ◽  
Czech Republic ◽  
Sweet Cherry ◽  
Short Communication ◽  
Rt Pcr ◽  
Pcr Assay ◽  
The Czech Republic ◽  
Germplasm Collections ◽  
Sweet Cherries

 The presence of Cherry virus A (CVA) in the germplasm collections of sweet cherries and plums was studied. CVA was detected using the specific RT-PCR assay in six of eight sweet cherry and one of four plum cultivars. Specifity of amplicons and distant position of cherry and non-cherry isolates was verified by sequencing and phylogenetic analysis. Results indicate that the cherry landraces and cultivars could be infected by CVA more than it has been assumed.

Caraparu virus (group C Orthobunyavirus): sequencing and phylogenetic analysis based on the conserved region 3 of the RNA polymerase gene

Virus Genes ◽  
2007 ◽  
Vol 35 (3) ◽  
pp. 681-684 ◽  
Author(s):  
Cintia Lopes de Brito Magalhães ◽  
Bárbara Resende Quinan ◽  
Renata Franco Vianna Novaes ◽  
João Rodrigues dos Santos ◽  
Erna Geessien Kroon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Polymerase ◽  
Polymerase Gene ◽  
Virus Group ◽  
Conserved Region ◽  
Rna Polymerase Gene

scholarly journals Co-Circulation and Excretion Dynamics of Diverse Rubula- and Related Viruses in Egyptian Rousette Bats from South Africa

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 37 ◽  
Author(s):  
Marinda Mortlock ◽  
Muriel Dietrich ◽  
Jacqueline Weyer ◽  
Janusz T. Paweska ◽  
Wanda Markotter
Keyword(s):  
South Africa ◽  
Temporal Dynamics ◽  
Virus Transmission ◽  
Sample Type ◽  
Limited Extent ◽  
Human Pathogens ◽  
Polymerase Gene ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Viral Excretion

The Egyptian rousette bat (Rousettus aegyptiacus) has previously been implicated as the natural host of a zoonotic rubulavirus; however, its association with rubulaviruses has been studied to a limited extent. Urine, spleen, and other organs collected from the R. aegyptiacus population within South Africa were tested with a hemi-nested RT-PCR assay targeting a partial polymerase gene region of viruses from the Avula- and Rubulavirus genera. Urine was collected over a 14-month period to study the temporal dynamics of viral excretion. Diverse rubulaviruses, including viruses related to human mumps and parainfluenza virus 2, were detected. Active excretion was identified during two peak periods coinciding with the host reproductive cycle. Analysis of additional organs indicated co-infection of individual bats with a number of different putative rubulaviruses, highlighting the limitations of using a single sample type when determining viral presence and diversity. Our findings suggest that R. aegyptiacus can harbor a range of Rubula- and related viruses, some of which are related to known human pathogens. The observed peaks in viral excretion represents potential periods of a higher risk of virus transmission and zoonotic disease spill-over.

scholarly journals Molecular Detection and Epidemiology of Sapporo-Like Viruses

2000 ◽  
Vol 38 (2) ◽  
pp. 530-536 ◽  
Author(s):  
Jan Vinjé ◽  
Hanneke Deijl ◽  
Reina van der Heide ◽  
David Lewis ◽  
Kjell-Olof Hedlund ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
First Generation ◽  
Amino Acid Identity ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Three Samples ◽  
New Genotype ◽  
Complete Capsid ◽  
Single Primer ◽  
Distinct Genetic Cluster

Sapporo-like viruses (SLVs) are associated with acute gastroenteritis in humans. Due to a limited supply of available reagents for diagnosis, little is known about the incidence and pathogenicity of these viruses. We have developed a first-generation generic reverse transcriptase (RT) PCR assay based on a single primer pair targeting the RNA polymerase gene. With this assay, 55 (93%) of the 59 stool specimens collected in a 10-year period of time (1988 to 1998) and containing typical caliciviruses by electron microscopy tested positive and could be confirmed by Southern hybridization. By phylogenetic analysis, most SLV strains could be classified into one of the three recently described genotypes. However, three samples clustered separately, forming a potential new genotype. We sequenced the complete capsid gene of one of the strains in this cluster: Hu/SLV/Stockholm/97/SE. Alignment of the capsid sequences showed 40 to 74% amino acid identity among strains of the different clusters. Phylogenetic analysis of the aligned sequences confirmed the placing of Hu/SLV/Stockholm/97/SE into a new distinct genetic cluster. This is the first report on the development of a broadly reactive RT-PCR assay for the detection of SLVs.

scholarly journals Phylogenetic relationships among rhabdoviruses inferred using the L polymerase gene

2005 ◽  
Vol 86 (10) ◽  
pp. 2849-2858 ◽  
Author(s):  
H. Bourhy ◽  
J. A. Cowley ◽  
F. Larrous ◽  
E. C. Holmes ◽  
P. J. Walker
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Pcr Amplification ◽  
Polymerase Gene ◽  
Rt Pcr ◽  
Degenerate Primers ◽  
The Family ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Vector Borne

RNA viruses of the family Rhabdoviridae include arthropod-borne agents that infect plants, fish and mammals, and also include a variety of non-vector-borne mammalian viruses. Herein is presented a molecular phylogenetic analysis, the largest undertaken to date, of 56 rhabdoviruses, including 20 viruses which are currently unassigned or assigned as tentative species within the Rhabdoviridae. Degenerate primers targeting a region of block III of the L polymerase gene were defined and used for RT-PCR amplification and sequencing. A maximum-likelihood phylogenetic analysis of a 158-residue L polymerase amino acid sequence produced an evolutionary tree containing the six recognized genera of the Rhabdoviridae and also enabled us to identify four more monophyletic groups of currently unclassified rhabdoviruses that we refer to as the ‘Hart Park’, ‘Almpiwar’, ‘Le Dantec’ and ‘Tibrogargan’ groups. The broad phylogenetic relationships among these groups and genera also indicate that the evolutionary history of rhabdoviruses was strongly influenced by mode of transmission, host species (plant, fish or mammal) and vector (orthopteran, homopteran or dipteran).

scholarly journals Analysis of Genetic Diversity of Russian Sour Cherry Plum pox virus Isolates Provides Evidence of a New Strain

Plant Disease ◽  
2018 ◽  
Vol 102 (3) ◽  
pp. 569-575 ◽  
Author(s):  
Sergei Chirkov ◽  
Anna Sheveleva ◽  
Peter Ivanov ◽  
Alexander Zakubanskiy
Keyword(s):  
Phylogenetic Analysis ◽  
Sour Cherry ◽  
Plum Pox Virus ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Illumina Hiseq ◽  
Environmental Distribution ◽  
Amino Acid Levels ◽  
Virus Isolates ◽  
Sequence Identities

Plum pox virus (PPV) exists as a complex of nine strains adapted to different Prunus hosts. Unusual PPV isolates that do not belong to the known cherry-adapted strains were discovered on sour cherry in Russia. Here, two complete genomes of isolates Tat-2 and Tat-4 were determined by sequencing on the Illumina HiSeq 2500 platform. Both were composed of 9,792 nucleotides, excluding the poly(A) tail, with the organization typical of PPV and had 99.4 and 99.7% identity between each other at the nucleotide and amino acid levels. The sequence identities between Tat-2/Tat-4 and known PPV strains ranged from 77.6 to 83.3% for genomic RNA and from 80.0 to 93.8% for polyprotein. Phylogenetic analysis placed Tat-2 and Tat-4 in a separate clade, distinct from the C and CR strains. Three more Tat-2/Tat-4-like isolates were detected in local cherry plantings using the newly developed, specific RT-PCR assay. Based on the phylogenetic analysis, sequence identities, and environmental distribution, Tat-2, Tat-4, and related isolates represent a new cherry-adapted PPV strain for which the name PPV-CV (Cherry Volga) is proposed.

scholarly journals The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey

2020 ◽  
Author(s):  
Karamese Murat ◽  
Ozgur Didem ◽  
Tarhan Ceyda ◽  
Dik Altintas Susamber ◽  
Caliskan Okan ◽  
...  
Keyword(s):  
Epidemiologic Studies ◽  
Screening Tests ◽  
Gene Fragment ◽  
Polymerase Gene ◽  
Rt Pcr ◽  
Rna Dependent Rna Polymerase ◽  
Final Study ◽  
The World ◽  
Study Population ◽  
Rna Polymerase Gene

ABSTRACTCOVID-19, is caused by SARS-CoV-2, has been started on December/2019 in Wuhan/China and spread all over the world. We analyzed RT-PCR results of 10,000 cases from April-2 to May-30, 2020 in three neighbor cities located on the Eastern of Turkey. The final study population was 7853 cases after excluded screening tests. RT-PCR were performed to detect the SARS-CoV-2-specific RdRp (RNA-dependent-RNA-polymerase) gene fragment. The number of total positive samples out of 7853 were 487; however, the number of non-repeating positive patient was 373 (4.8%). The cough and fever were the most common symptoms in positive cases. The epidemiologic studies should be performed about the prevalence of SARS-CoV-2 infection to better understand the effect of the virus all over the world.

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