scholarly journals Molecular analysis of Peste des Petits Ruminants Virus from outbreak in Turkey during 2010-2012

2019 ◽  
Vol 70 (3) ◽  
pp. 1617
Author(s):  
A. SAIT ◽  
S.B. DAGALP
Keyword(s):  
Sequence Analysis ◽  
Partial Sequence ◽  
N Gene ◽  
Peste Des Petits Ruminants ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Nucleotide Level ◽  
F Gene ◽  
Pcr Targeting ◽  
Lineage Iv

The aim of the study is to determine the epizootiology of Peste des petits ruminants (PPR) in Turkey during 2010-2012, using molecular genotyping. Samples of blood (n=193), swab (n=7) and tissue (n=374) were collected from sheep (n=473) and goats (n=101) suspected of having PPRV infection from an outbreak in 50 provinces of Turkey during 2010–2012. These samples (n=574) were tested using reverse transcription polymerase chain reaction (RT-PCR) and real-time reverse transcriptionpolymerase chain reaction (RT-qPCR) targeting selected parts of the fusion (F) and the nucleocapsid (N) genes. Positivity ratios were 35.5%, 39.3%, and 44.4% with regards to RT-PCR targeting the F and the N genes, and RT-Qpcr targeting the latter gene (N), respectively. The overall positivity rate was 45.8%. For sequence analyses, F-gene (n=53) and N-gene (n=60) positive samples representing different provinces were selected. After phylogenetic analysis, the circulating PPRV was located in lineage IV according to two gene regions. The F-gene partial sequence analysis at the nucleotide level showed 98.2-100% resemblence among 53 for F-gene, and 97.9-98.9% and 91.3-92.4% to Turkey2000 and Nigeria75/1 sequences, respectively. The N-gene partial sequence analysis at the nucleotide level showed 94.2-100% resemblence among 60 for N-gene, and 94.2-98.3% and 89.3-90.9% to Turkey2000 and Nigeria75/1 sequences, respectively. The result of this study indicates that PPRV infection is enzootic in Turkey, and belongs to the lineage IV, which is present in three haplogroup. The phylogenic analysis indicates the spread of the virus is associated with unauthorized movement of stock.

scholarly journals Epidemiology and molecular characterization of re-emerged virulent strains of Peste des Petits Ruminants virus among sheep in Kassala State, Eastern Sudan

2021 ◽  
Vol 74 (1) ◽  
Author(s):  
Fatima A. Saeed ◽  
Mohammed M.Gumaa ◽  
Sana A.Abdelaziz ◽  
Khalid A. Enan ◽  
Selma K. Ahmed ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Protein Gene ◽  
Small Ruminants ◽  
Partial Sequence ◽  
N Gene ◽  
Enzyme Linked Immunosorbent Assay ◽  
Peste Des Petits Ruminants ◽  
Rt Pcr ◽  
Lineage Iv ◽  
Eastern Sudan

Abstract Background Peste des Petits Ruminants (PPR) is a severe contagious viral disease, which mainly affects small ruminants. PPR is caused by a Morbillivirus that belongs to the family Paramyxoviridae. In this study 12 suspected PPR outbreaks among sheep and goats were investigated in four localities in Kassala State, Eastern Sudan, during 2015—2017. The causative agent was confirmed by a Sandwich Enzyme-Linked Immunosorbent Assay (sELISA), and a Reverse Transcription Polymerase Chain Reaction (RT-PCR) targeting a partial sequence of nucleocapsid protein gene (N- gene) and a partial sequence of fusion protein gene (F- gene). Sequencing and phylogenetic analysis were carried out on six N- gene based RT-PCR products selected from two outbreaks occurred on border and inner localities of Kassala State to determine the circulating lineages of PPRV strains. Identity percentages were determined between isolates in this study and previous Sudanese, and other (African and Asian) isolates which clustered along with them. Results Out of 30 samples, 22 (73.3%) were positive using sandwich ELISA. From 22 s ELISA positive samples, 17 (77.3%) were positive by Ngene based RT-PCR and only 7(43.8%) out of 16 positive samples by N gene based RT-PCR were positive using Fgene based RT-PCR. The sequencing and phylogenetic analysis confirmed involvement of the lineage IV of PPRV in outbreaks among small ruminants in Kassala State and high identity percentage between our isolates and previous Sudanese and other (African and Asian) isolates. Conclusions The present study demonstrates that genetic relationship between PPRV strains circulating in sheep in Kassala State, Eastern Sudan, and PPRV strains characterized as lineage IV in neighboring African countries such as Eretria,Ethiopia, Egypt, and other Asian countries

scholarly journals Molecular Epidemiology of Peste Des Petits Ruminants Cases Associated with Abortion in Sheep and Goat in Marmara Region of Turkey, 2018

2020 ◽  
Vol 40 (04) ◽  
pp. 494-498
Author(s):  
Zuleyha Pestil
Keyword(s):  
Sequence Analysis ◽  
Molecular Epidemiology ◽  
Experimental Infection ◽  
Epidemiological Data ◽  
Marmara Region ◽  
Peste Des Petits Ruminants ◽  
Rt Pcr ◽  
Etiologic Agents ◽  
The Relationship ◽  
Lineage Iv

The aim of this study was to investigate the molecular epidemiology of peste des petits ruminants (PPR) infections associated with abortion in sheep and goat samples from the Marmara region of Turkey during 2018. The study was carried out from 116 sheep and 26 goat abortion cases. PPR virus (PPRV) detection in these samples was performed using real-time RT-PCR (Q-RT-PCR). Then, sequence analysis was performed from PPRV positive samples. Q-RT-PCR results demonstrated that 12 (10.34%) out of 116 sheep abortion samples and 3 (11.53%) out of 26 goat abortion samples were positive for PPRV genome. The sequence results of RT-PCR positive products revealed that the viruses causing the cases belong to lineage IV. Furthermore, molecular analysis showed that present cases were not related to PPRV vaccine strains or its mutants. Marmara region, where this study was conducted, is a neighbour of European countries such as Bulgaria and Greece. The first PPR cases in Europe were reported from Bulgaria at the beginning of 2018 and subsequently, other cases also reported before are mentioned in the present study. This study provides valuable information to understand the epidemiology of recently emerged PPRV cases in Europe and Turkey. Furthermore, because of the prevalence of PPRV in abortion samples in this study, these results suggest that PPRV may be one of the possible etiologic agents of abortions in sheep and goat. However, for clarification of the relationship between abortion and PPRV, there is need more robust epidemiological data and experimental infection studies

scholarly journals Verification and diagnostic evaluation of the RealStar® Middle East respiratory syndrome coronavirus (N gene) reverse transcription-PCR kit 1.0

2019 ◽  
Vol 14 (11) ◽  
pp. 941-948 ◽  
Author(s):  
Leonie-Sophie Hecht ◽  
Angeles Jurado-Jimenez ◽  
Markus Hess ◽  
Hussein El Halas ◽  
Gregor Bochenek ◽  
...  
Keyword(s):  
Middle East ◽  
Reverse Transcription ◽  
Diagnostic Procedure ◽  
Middle East Respiratory Syndrome ◽  
Diagnostic Evaluation ◽  
N Gene ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Confirmatory Assay ◽  
Pcr Targeting

Aim: We report the diagnostic evaluation of a confirmatory reverse transcription-PCR (RT-PCR) kit targeting the Middle East respiratory syndrome coronavirus (MERS-CoV) N gene. Material & methods: 33 patient samples from two collections sites in Riyadh, Saudi Arabia, which were pre-characterized via real-time RT-PCR targeting MERS-CoV orf1a and upE, and were tested using the MERS-CoV N gene, as a confirmatory assay. This diagnostic procedure follows a two-step diagnostics scheme, recommended by the WHO. Results: 18/33 samples tested positive, 11/33 tested negative for MERS-CoV RNA and 2/33 showed uncertain results. Conclusion: The results suggest, that the RealStar® MERS-CoV (N gene) RT-PCR kit 1.0 can be considered a suitable and reliable confirmatory assay in combination with the RealStar MERS-CoV RT-PCR kit 1.0 according to the diagnostic scheme recommended by WHO.

scholarly journals Genetic Characterization of a Novel Mutant of Peste Des Petits Ruminants Virus Isolated fromCapra ibexin China during 2015

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Zixiang Zhu ◽  
Xiaocui Zhang ◽  
Gulizhati Adili ◽  
Jiong Huang ◽  
Xiaoli Du ◽  
...  
Keyword(s):  
Genomic Sequences ◽  
Economic Losses ◽  
N Gene ◽  
Peste Des Petits Ruminants ◽  
Capra Ibex ◽  
V Protein ◽  
First Time ◽  
Lineage Iv ◽  
New Mutations

Peste des petits ruminants virus (PPRV) is the causative agent of peste des petits ruminants (PPR). The spread of PPR often causes severe economic losses. Therefore, special attention should be paid to the surveillance of PPR emergence, spread, and geographic distribution. Here we describe a novel mutant of PPRV China/XJBZ/2015 that was isolated fromCapra ibexin Xinjiang province in China 2015. The sequence analysis and phylogenetic assessment indicate that China/XJBZ/2015 belongs to lineage IV, being closely related to China/XJYL/2013 strain. Interestingly, the V protein sequence of China/XJBZ/2015 showed lower homology with other Chinese PPRVs isolated during 2013 to 2014 (94%~95%), whereas it shared 100% identity with three Tibet strains isolated in China 2007. The 3′ UTR, V gene, and C gene were determined to be highly variable. Besides, 29 PPR genomic sequences available in GenBank were analyzed in this study. It is the first time to use PPRV genomic sequences to classify the different lineages which confirmed the lineage clustering of PPRVs using N gene 255 bp fragments and F gene 322 bp fragments. In conclusion, our findings indicate that the PPRVs continue to evolve in China, and some new mutations have emerged.

scholarly journals Identification of Encephalomyocarditis Virus in Clinical Samples by Reverse Transcription-PCR Followed by Genetic Typing Using Sequence Analysis

1998 ◽  
Vol 36 (12) ◽  
pp. 3463-3467 ◽  
Author(s):  
H. Vanderhallen ◽  
F. Koenen
Keyword(s):  
Sequence Analysis ◽  
Reverse Transcription ◽  
Molecular Techniques ◽  
Encephalomyocarditis Virus ◽  
Clinical Samples ◽  
Nucleotide Sequence Analysis ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Field Samples ◽  
Pcr Targeting

The objective of the present study was to gain a better understanding of the epidemiology of encephalomyocarditis virus (EMCV) infections in pigs by applying molecular techniques. The diagnostic potential of a reverse transcription-PCR (RT-PCR) targeting 286 nucleotides at the 3′ end of the gene which encodes the viral polymerase was assessed with experimental and field samples. In addition, the use of the amplified sequences for an epidemiological study was evaluated. The heart was clearly shown to be the most suitable organ. The detection limit was determined to be 1 viral particle in 100 mg of heart tissue. The sensitivity and specificity of the assay on the basis of the results obtained in this study were 94 and 100%, respectively. Phylogenetic analysis of the amplified sequences classified EMCVs in two distinct lineages. Group A consists of the reference strain ATCC 129B, all isolates collected between 1991 and 1994 in Belgium in association with reproductive failure, and all Greek isolates. All Belgian isolates collected since the first isolation of EMCV in relation to myocardial failure in fatteners in Belgium group together with the isolates from Cyprus (1996 and 1997), Italy (1986 to 1996), and France (1995) in group B irrespective of their pathogenicity. The analyzed part of the 3D gene differed by 13.0% between Groups A and B. In contrast to the sequence homogeneity of the Belgian isolates collected between 1991 and 1994, molecular diversity, which ranged between 0 and 2%, was observed among the Belgian isolates collected in 1995 and 1996. Among all Greek isolates the diversity ranged between 1 and 8%. However, this diversity does not seem to reflect geographical links between the outbreaks. A RT-PCR for the rapid and specific diagnosis of EMCV in a variety of clinical samples followed by nucleotide sequence analysis proved to be valuable for molecular epidemiological studies.

scholarly journals Validation of real-time polymerase chain reaction versus conventional polymerase chain reaction for diagnosis of brucellosis in cattle sera

2021 ◽  
Vol 14 (1) ◽  
pp. 144-154
Author(s):  
Nour H. Abdel-Hamid ◽  
Eman I. M. Beleta ◽  
Mohamed A. Kelany ◽  
Rania I. Ismail ◽  
Nadia A. Shalaby ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Roc Curve ◽  
Diagnostic Performance ◽  
Rt Pcr ◽  
Conventional Pcr ◽  
Chain Reaction ◽  
Serum Samples ◽  
Polymerase Chain ◽  
Pcr Targeting ◽  
Pcr Techniques

Background and Aim: Different polymerase chain reaction (PCR) techniques have and are still being used for the direct detection of Brucella DNA in serum samples of different animal species and humans without being validated or properly validated, resulting in discrepancies. Thus, this study aimed to evaluate the diagnostic performance of the TaqMan Real- Time-PCR (RT-PCR) targeting the bcsp31 gene versus conventional PCR for the accurate diagnosis of brucellosis at the genus level in cattle sera. Materials and Methods: One hundred and eighty-four serum samples were collected from bacteriologically positive and negative cows with ages ranging from 1 to 5 years old at some infected private farms in the Nile Delta under quarantine measures as well as brucellosis free farms. These samples were classified into four groups after serological diagnosis and investigated by TaqMan RT-PCR and conventional PCR targeting the IS711 gene for Brucella DNA detection. The diagnostic performance characteristics of both PCR techniques were estimated considering the bacteriological results as a gold standard. Results: TaqMan RT-PCR revealed superiority over conventional PCR; it was able to detect Brucella DNA in 95% (67/70) and 89% (25/28) of the cattle sera samples belonging to Group 1 (serologically and bacteriologically positive) and Group 2 (serologically negative but bacteriologically positive), respectively. On evaluating the diagnostic performance, TaqMan RT-PCR showed superior diagnostic sensitivity (93.9%), diagnostic specificity (88.4%), performance index (182.3), almost perfect kappa agreement (0.825±0.042), strong positive correlation (r=0.826), high accuracy based on the receiver operating characteristic (ROC) curve, and area under the ROC curve (0.911) at p<0.05 and CI of 95%. Conclusion: A cattle serum sample is not the metric of choice for targeting Brucella genomic DNA by conventional PCR. The time-saving and rapid TaqMan RT-PCR method revealed a better diagnostic performance in the detection of Brucella DNA in cattle sera. Such performance offered by TaqMan RT-PCR may be considered a step toward the possibility of using such technology in the direct differentiation between Brucella-infected and -vaccinated cattle immunized by smooth vaccines from cattle sera using primers specific for such vaccines.

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