scholarly journals Comparison of genes as target for molecular diagnosis of peste des petits ruminants in goats

2013 ◽  
Vol 29 (2) ◽  
pp. 56-62 ◽  
Author(s):  
AR Bhuiyan ◽  
MM Rahman ◽  
JA Begum ◽  
MR Islam ◽  
EH Chowdhury
Keyword(s):  
Viral Disease ◽  
Molecular Diagnostic ◽  
N Gene ◽  
Peste Des Petits Ruminants ◽  
Gene Target ◽  
Field Samples ◽  
Successful Control ◽  
Primer Sets ◽  
Molecular Diagnostic Test ◽  
Np Gene

Peste des petits ruminants (PPR) are an acute viral disease of sheep and goats. Rapid and accurate diagnosis is essential for successful control. Reverse transcriptase polymerase chain reaction (RT-PCR), a molecular diagnostic test based on amplification of the gene target is more sensitive than other tests. The study was to find an efficient primer set and structural gene, which would be more specific and sensitive for detecting PPR virus (PPRV) in field samples. Six primer sets for six structural genes of PPR were used. Primer against NP gene (np3/np4) was specific and sensitive. To ensure efficient amplification and detection of viruses in field samples, more than one set of primers should be used and F and N gene specific primers were the most suitable. DOI: http://dx.doi.org/10.3329/bvet.v29i2.14343 Bangl. vet. 2012. Vol. 29, No. 2, 56-62

scholarly journals Comparison of nucleotide sequences of recent and previous lineages of peste-des-petits-ruminants viruses of sheep and goats in Nigeria

2016 ◽  
Vol 83 (1) ◽  
Author(s):  
Samuel Mantip ◽  
Melvyn Quan ◽  
David Shamaki ◽  
Moritz Van Vuuren
Keyword(s):  
Phylogenetic Analysis ◽  
Small Ruminants ◽  
Viral Disease ◽  
N Gene ◽  
Peste Des Petits Ruminants ◽  
East African ◽  
Tissue Samples ◽  
Sheep And Goats ◽  
Ecological Zones ◽  
Agro Ecological Zones

Peste-des-petits-ruminants virus (PPRV) is a highly contagious, fatal and economically important viral disease of small ruminants that is still endemic and militates against the production of sheep and goats in endemic areas of the world. The aim of this study was to describe the viral strains within the country. This was carried out by collecting tissue and swab samples from sheep and goats in various agro-ecological zones of Nigeria. The phylogeny of archived PPRV strains or isolates and those circulating and causing recent outbreaks was determined by sequencing of the nucleoprotein (N)-gene. Twenty tissue and swab samples from apparently healthy and sick sheep and goats were collected randomly from 18 states, namely 3 states in each of the 6 agro-ecological zones visited. A total of 360 samples were collected. A total of 35 samples of 360 (9.7%) tested positive by reverse transcriptase–polymerase chain reaction, of which 25 were from oculo-nasal swabs and 10 were from tissue samples. Neighbour-joining phylogenetic analysis using Phylogenetic Analysis Using Parsimony (PAUP) identified four different lineages, that is, lineages I, II, III and IV. Interestingly, the Nigerian strains described in this study grouped in two separate major lineages, that is, lineages II and IV. Strains from Sokoto, Oyo, Plateau and Ondo states grouped according to the historical distribution of PPRV together with the Nigerian 75/1 strain of lineage II, while other strains from Sokoto, Oyo, Plateau, Akwa-Ibom, Adamawa, Kaduna, Lagos, Bauchi, Niger and Kano states grouped together with the East African and Asian strains of lineage IV. This finding confirms that both lineage II and IV strains of PPRV are circulating in Nigeria. Previously, only strains of lineage II were found to be present in the country.

scholarly journals Clinical Performance of the Luminex NxTAG CoV Extended Panel for SARS-CoV-2 Detection in Nasopharyngeal Specimens from COVID-19 Patients in Hong Kong

2020 ◽  
Vol 58 (8) ◽  
Author(s):  
Jonathan Hon-Kwan Chen ◽  
Cyril Chik-Yan Yip ◽  
Jasper Fuk-Woo Chan ◽  
Rosana Wing-Shan Poon ◽  
Kelvin Kai-Wang To ◽  
...  
Keyword(s):  
Hong Kong ◽  
High Throughput ◽  
Clinical Performance ◽  
Diagnostic System ◽  
Molecular Diagnostic ◽  
N Gene ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Gene Target ◽  
E Gene

ABSTRACT In December 2019, the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first reported in the Hubei province of China and later spread all over the world. There was an urgent need of a high-throughput molecular test for screening the COVID-19 patients in the community. The Luminex NxTAG CoV extended panel is a high-throughput FDA emergency use-authorized molecular diagnostic assay for SARS-CoV-2 detection. This system targets three genes (ORF1ab, N, and E genes) of SARS-CoV-2, the ORF1ab region of SARS-CoV, and the ORF5 region of MERS-CoV. In this study, we evaluated the diagnostic performance of this system with nasopharyngeal swab specimens of 214 suspected COVID-19 patients in Hong Kong. The results were compared with our routine COVID-19 reverse transcription-PCR (RT-PCR) protocol with a LightMix SarbecoV E-gene kit and an in-house RdRp/Hel RT-PCR assay. The NxTAG CoV extended panel demonstrated 97.8% sensitivity and 100% specificity to SARS-CoV-2 in nasopharyngeal specimens. On low-viral load specimens, the sensitivity of the NxTAG panel could still maintain at 85.71%. Strong agreement was observed between the NxTAG panel and the routine COVID-19 RT-PCR protocol (kappa value = 0.98). Overall, the E gene target of the NxTAG panel demonstrated the highest sensitivity among the three SARS-CoV-2 targets, while the N gene targets demonstrated the least. In conclusion, the NxTAG CoV extended panel is simple to use, and it has high diagnostic sensitivity and specificity to SARS-CoV-2 in nasopharyngeal specimens. We recommend this diagnostic system for high-throughput COVID-19 screening in the community.

Optimizing SARS-CoV-2 Molecular Diagnostic Using N Gene Target

2020 ◽  
Author(s):  
Raphael Contelli Klein ◽  
Mary Hellen Fabres-Klein ◽  
Larissa Gomes Barbosa ◽  
Lívia Vasconcelos Gonzaga Knnup ◽  
Larissa Paola Rodrigues Venâncio ◽  
...  
Keyword(s):  
Molecular Diagnostic ◽  
N Gene ◽  
Gene Target

scholarly journals Optimizing SARS-CoV-2 molecular diagnostic using N gene target: insights about reinfection

2020 ◽  
Author(s):  
Raphael Contelli Klein ◽  
Mary Hellen Fabres Klein ◽  
Larissa Gomes Barbosa ◽  
Lívia Vasconcelos Gonzaga Knnup ◽  
Larissa Paola Rodrigues Venâncio ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Molecular Diagnostic ◽  
N Gene ◽  
Molecular Test ◽  
Gene Target ◽  
Infected People ◽  
Remote Locations ◽  
The World ◽  
The Cost ◽  
Huge Challenge

AbstractIntroductionMolecular diagnosis of SARS-CoV-2 is a huge challenge to many countries around the world. The cost of tests to check infected people is inaccessible since specialized teams and equipment are not disposable in remote locations. Herein, we compared the fitness of two primers sets to the SARS-CoV-2 N gene in the molecular diagnosis of COVID-19.Materials and MethodsThe 1029 patient samples were tested to presense/abscence molecular test using in house US CDC protocol. We compared the fitness of two primers sets to two different regions of N gene targets.ResultsBoth targets, N1 and N2 displayed similar fitness during testing with no differences between Ct or measurable viral genome copies. In addition, we verified security ranges Cts related to positive diagnostic with Ct above 35 value failuring in 66,6% after retesting of samples.Main conclusionOur data suggest that it is secure to use just one primer set to the N gene to identify SARS-CoV-2 in samples and the labs should be careful to set positive samples in high Ct values using high cutoffs.

scholarly journals Peste des Petits Ruminants Virus Infection at the Wildlife–Livestock Interface in the Greater Serengeti Ecosystem, 2015–2019

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 838
Author(s):  
Bryony A. Jones ◽  
Mana Mahapatra ◽  
Daniel Mdetele ◽  
Julius Keyyu ◽  
Francis Gakuya ◽  
...  
Keyword(s):  
Small Ruminants ◽  
Viral Disease ◽  
Global Strategy ◽  
Enzyme Linked Immunosorbent Assay ◽  
Weighted Estimate ◽  
Peste Des Petits Ruminants ◽  
African Buffalo ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Serengeti Ecosystem

Peste des petits ruminants (PPR) is a viral disease of goats and sheep that occurs in Africa, the Middle East and Asia with a severe impact on livelihoods and livestock trade. Many wild artiodactyls are susceptible to PPR virus (PPRV) infection, and some outbreaks have threatened endangered wild populations. The role of wild species in PPRV epidemiology is unclear, which is a knowledge gap for the Global Strategy for the Control and Eradication of PPR. These studies aimed to investigate PPRV infection in wild artiodactyls in the Greater Serengeti and Amboseli ecosystems of Kenya and Tanzania. Out of 132 animals purposively sampled in 2015–2016, 19.7% were PPRV seropositive by ID Screen PPR competition enzyme-linked immunosorbent assay (cELISA; IDvet, France) from the following species: African buffalo, wildebeest, topi, kongoni, Grant’s gazelle, impala, Thomson’s gazelle, warthog and gerenuk, while waterbuck and lesser kudu were seronegative. In 2018–2019, a cross-sectional survey of randomly selected African buffalo and Grant’s gazelle herds was conducted. The weighted estimate of PPRV seroprevalence was 12.0% out of 191 African buffalo and 1.1% out of 139 Grant’s gazelles. All ocular and nasal swabs and faeces were negative by PPRV real-time reverse transcription-polymerase chain reaction (RT-qPCR). Investigations of a PPR-like disease in sheep and goats confirmed PPRV circulation in the area by rapid detection test and/or RT-qPCR. These results demonstrated serological evidence of PPRV infection in wild artiodactyl species at the wildlife–livestock interface in this ecosystem where PPRV is endemic in domestic small ruminants. Exposure to PPRV could be via spillover from infected small ruminants or from transmission between wild animals, while the relatively low seroprevalence suggests that sustained transmission is unlikely. Further studies of other major wild artiodactyls in this ecosystem are required, such as impala, Thomson’s gazelle and wildebeest.

scholarly journals Development of Molecular Markers for Detection of Acidovorax citrulli Strains Causing Bacterial Fruit Blotch Disease in Melon

2019 ◽  
Vol 20 (11) ◽  
pp. 2715 ◽  
Author(s):  
Md. Rafiqul Islam ◽  
Mohammad Rashed Hossain ◽  
Hoy-Taek Kim ◽  
Denison Michael Immanuel Jesse ◽  
Md. Abuyusuf ◽  
...  
Keyword(s):  
Infected Leaf ◽  
Bacterial Fruit Blotch ◽  
Early Disease Detection ◽  
Acidovorax Citrulli ◽  
Seed Health ◽  
Field Samples ◽  
Whole Genomes ◽  
Pathogenesis Related ◽  
Primer Sets ◽  
Inoculation Assay

Acidovorax citrulli (A. citrulli) strains cause bacterial fruit blotch (BFB) in cucurbit crops and affect melon significantly. Numerous strains of the bacterium have been isolated from melon hosts globally. Strains that are aggressively virulent towards melon and diagnostic markers for detecting such strains are yet to be identified. Using a cross-inoculation assay, we demonstrated that two Korean strains of A. citrulli, NIHHS15-280 and KACC18782, are highly virulent towards melon but avirulent/mildly virulent to the other cucurbit crops. The whole genomes of three A. citrulli strains isolated from melon and three from watermelon were aligned, allowing the design of three primer sets (AcM13, AcM380, and AcM797) that are specific to melon host strains, from three pathogenesis-related genes. These primers successfully detected the target strain NIHHS15-280 in polymerase chain reaction (PCR) assays from a very low concentration of bacterial gDNA. They were also effective in detecting the target strains from artificially infected leaf, fruit, and seed washing suspensions, without requiring the extraction of bacterial DNA. This is the first report of PCR-based markers that offer reliable, sensitive, and rapid detection of strains of A. citrulli causing BFB in melon. These markers may also be useful in early disease detection in the field samples, in seed health tests, and for international quarantine purposes.

scholarly journals Randomized prospective evaluation of genome sequencing versus standard-of-care as a first molecular diagnostic test

2021 ◽  
Author(s):  
Deanna G. Brockman ◽  
Christina A. Austin-Tse ◽  
Renée C. Pelletier ◽  
Caroline Harley ◽  
Candace Patterson ◽  
...  
Keyword(s):  
Diagnostic Test ◽  
Genome Sequencing ◽  
Standard Of Care ◽  
Molecular Diagnostic ◽  
Prospective Evaluation ◽  
Molecular Diagnostic Test

Development and Application of a New PCR Method for Detection of Blumeria graminis f. sp. tritici

2018 ◽  
Vol 28 (3) ◽  
pp. 137-146 ◽  
Author(s):  
Adam Kuzdraliński ◽  
Hubert Szczerba ◽  
Anna Kot ◽  
Agnieszka Ostrowska ◽  
Michał Nowak ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Puccinia Triticina ◽  
Blumeria Graminis ◽  
Pyrenophora Tritici Repentis ◽  
Field Samples ◽  
Expected Length ◽  
Pcr Assays ◽  
Primer Sets ◽  
Wheat Leaves ◽  
Species Specific

We developed new PCR assays that target beta-tubulin (<i>TUB2</i>) and 14 alpha-demethylase (<i>CYP51</i>) genes and used them for the species-specific detection of <i>Blumeria graminis</i> f. sp. <i>tritici</i> (<i>Bgt</i>). Based on fungi DNA sequences available in the NCBI (National Center for Biotechnology Information) GenBank database we developed simplex and duplex PCR assays. The specificities of the primer sets were evaluated using environmental samples of wheat leaves collected during the 2015/2016 growing season across Poland. Primer sets<i></i> LidBg17/18 and LidBg21/22 strongly amplified fragments of the expected length for all 67 tested samples. Primer specificity was confirmed using field samples of <i>Zymoseptoria tri­tici</i>, <i>Puccinia triticina</i> (syn.<i> P. recondita</i> f. sp.<i> tritici</i>), <i>P. striiformis</i> f. sp.<i> tritici</i>, and <i>Pyrenophora tritici-repentis</i>.

scholarly journals Peste des petits ruminants in Africa: a review of currently available molecular epidemiological data, 2020

2020 ◽  
Vol 165 (10) ◽  
pp. 2147-2163 ◽  
Author(s):  
William G. Dundon ◽  
Adama Diallo ◽  
Giovanni Cattoli
Keyword(s):  
Economic Impact ◽  
International Organizations ◽  
Small Ruminants ◽  
Epidemiological Data ◽  
Viral Disease ◽  
Cash Income ◽  
Small Farmers ◽  
Peste Des Petits Ruminants ◽  
Sheep And Goats ◽  
Global Eradication

Abstract Small ruminants (e.g., sheep and goats) contribute considerably to the cash income and nutrition of small farmers in most countries in Africa and Asia. Their husbandry is threatened by the highly infectious transboundary viral disease peste des petits ruminants (PPR) caused by peste-des-petits-ruminants virus (PPRV). Given its social and economic impact, PPR is presently being targeted by international organizations for global eradication by 2030. Since its first description in Côte d’Ivoire in 1942, and particularly over the last 10 years, a large amount of molecular epidemiological data on the virus have been generated in Africa. This review aims to consolidate these data in order to have a clearer picture of the current PPR situation in Africa, which will, in turn, assist authorities in global eradication attempts.

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