Development of a cost-effective method for capripoxvirus genotyping using snapback primer and dsDNA intercalating dye

Sheep pox virus (SPPV), goat pox virus (GTPV) and lumpy skin disease virus (LSDV) are very closely related viruses of the Capripoxvirus (CaPV) genus of the Poxviridae family. They are responsible for sheep pox, goat pox and lumpy skin disease which affect sheep, goat and cattle, respectively. The epidemiology of capripox diseases is complex, as some CaPVs are not strictly host-specific. Additionally, the three forms of the disease co-exist in many sub-Saharan countries which complicates the identification of the virus responsible for an outbreak. Genotyping of CaPVs using a low-cost, rapid, highly specific, and easy to perform method allows a swift and accurate identification of the causative agent and significantly assists in selecting appropriate control and eradication measures, such as the most suitable vaccine against the virus during the outbreaks. The objective of this paper is to describe the design and analytical performances of a new molecular assay for CaPV genotyping using unlabelled snapback primers in the presence of dsDNA intercalating EvaGreen dye. This assay was able to simultaneously detect and genotype CaPVs in 63 samples with a sensitivity and specificity of 100%. The genotyping was achieved by observing the melting temperature of snapback stems of the hairpins and those of the full-length amplicons, respectively. Fourteen CaPVs were genotyped as SPPVs, 25 as GTPVs and 24 as LSDVs. The method is highly pathogen specific and cross platform compatible. It is also cost effective as it does not use fluorescently labelled probes, nor require high-resolution melting curve analysis software. Thus it can be easily performed in diagnostic and research laboratories with limited resources. This genotyping method will contribute significantly to the early detection and genotyping of CaPV infection and to epidemiological studies. (Résumé d'auteur

One-step multiplex RT-qPCR assay for the detection of Peste des petits ruminants virus, Capripoxvirus, Pasteurella multocida and Mycoplasma capricolum subspecies (ssp.) capripneumoniae

Respiratory infections, although showing common clinical symptoms like pneumonia, are caused by bacterial, viral or parasitic agents. These are often reported in sheep and goats populations and cause huge economic losses to the animal owners in developing countries. Detection of these diseases is routinely done using ELISA or microbiological methods which are being reinforced or replaced by molecular based detection methods including multiplex assays, where detection of different pathogens is carried out in a single reaction. In the present study, a one-step multiplex RT-qPCR assay was developed for simultaneous detection of Capripoxvirus (CaPV), Peste de petits ruminants virus (PPRV), Pasteurella multocida (PM) and Mycoplasma capricolum ssp. capripneumonia (Mccp) in pathological samples collected from small ruminants with respiratory disease symptoms. The test performed efficiently without any cross-amplification. The multiplex PCR efficiency was 98.31%, 95.48%, 102.77% and 91.46% whereas the singleplex efficiency was 93.43%, 98.82%, 102.55% and 92.0% for CaPV, PPRV, PM and Mccp, respectively. The correlation coefficient was greater than 0.99 for all the targets in both multiplex and singleplex. Based on cycle threshold values, intra and inter assay variability, ranged between the limits of 2%–4%, except for lower concentrations of Mccp. The detection limits at 95% confidence interval (CI) were 12, 163, 13 and 23 copies/reaction for CaPV, PPRV, PM and Mccp, respectively. The multiplex assay was able to detect CaPVs from all genotypes, PPRV from the four lineages, PM and Mccp without amplifying the other subspecies of mycoplasmas. The discriminating power of the assay was proven by accurate detection of the targeted pathogen (s) by screening 58 viral and bacterial isolates representing all four targeted pathogens. Furthermore, by screening 81 pathological samples collected from small ruminants showing respiratory disease symptoms, CaPV was detected in 17 samples, PPRV in 45, and PM in six samples. In addition, three samples showed a co-infection of PPRV and PM. Overall, the one-step multiplex RT-qPCR assay developed will be a valuable tool for rapid detection of individual and co-infections of the targeted pathogens with high specificity and sensitivity. (Résumé d'auteur

Polyphenol content and antioxidant activity of fourteen wild edible fruits from Burkina Faso. Molecules 2008

Abstract: A total of fourteen (14) species of wild edible fruits from Burkina Faso were analyzed for their phenolic and flavonoid contents, and their antioxidant activities using the DPPH, FRAP and ABTS methods. The data obtained show that the total phenolic and total flavonoid levels were significantly higher in the acetone than in the methanol extracts. Detarium microcarpum fruit had the highest phenolic and the highest flavonoid content, followed by that of Adansonia digitata, Ziziphus mauritiana, Ximenia americana and Lannea microcarpa. Significant amounts of total phenolics were also detected in the other fruit species in the following order of decreasing levels: Tamarindus indica> Sclerocarya birrea> Dialium guineense> Gardenia erubescens> Diospyros mespiliformis> Parkia biglobosa> Ficus sycomorus> Vitellaria paradoxa. Detarium microcarpum fruit also showed the highest antioxidant activity using the three antioxidant assays. Fruits with high antioxidant activities were also found to possess high phenolic and flavonoid contents. There was a strong correlation between total phenolic and flavonoid levels and antioxidan

Molecular Characterization of the 2020 Outbreak of Lumpy Skin Disease in Nepal

Lumpy skin disease (LSD) is a transboundary viral disease of cattle and buffaloes transmitted by blood-feeding vectors and causes high morbidity and low-to-moderate mortality. Since the first observation of LSD in Zambia in 1929, it has spread in cattle populations across African countries, the Middle East, Europe, and Asia. Following the recent outbreaks of LSD in South Asian countries such as India and Bangladesh, the disease was first reported in cattle farms in Nepal in June 2020. This study investigated the Nepalese LSD outbreak and confirmed that the disease spread rapidly to three neighboring districts in a month, infecting 1300 animals. Both cattle and buffaloes showed common clinical signs of LSD, with the exception that the buffaloes presented small nodular lesions without centered ulcerations. The collected samples were first tested for the presence of LSDV by real-time PCR. We further applied molecular tools, RPO30, GPCR, EEV glycoprotein gene, and B22R, for additional characterization of the LSDV isolates circulating in Nepal. Using a PCR-based Snapback assay, we confirmed that samples collected from cattle and buffaloes were positive of LSDV. Furthermore, sequence analysis (phylogenetic and multiple sequence alignments) of four selected LSDV genes revealed that the Nepal LSDVs resemble the Bangladesh and Indian isolates and the historic isolates from Kenya. We also highlight the importance of a unique B22R gene region harboring single-nucleotide insertions in LSDV Neethling and LSDV KSGPO-240 vaccine strains, enabling us to differentiate them from the Nepalese isolates and other fields isolates. This study demonstrates the importance of disease surveillance and the need to determine the source of the disease introduction, the extent of spread, modes of transmission, and the necessary control measures

Secondary structure of the expected GTPV PCR amplicon.

<p>The Snapback hairpin with a 18-nucleotide stem and a loop of 55 bases is shown. The predictions were done on the Mfold web server <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075971#pone.0075971-Zuker1" target="_blank">[28]</a> using the default parameters of the DNA folding form except for the temperature which was set at 45°C and the salt concentration set at 50 mM.</p

Nucleotides sequence alignment of the RPO30 gene of CaPVs highlighting the snapback tail binding site.

<p>The RPO30 gene sequences of 7 CaPVs representing GTPVs, LSDVs and SPPVs were aligned. A sequence of sixteen nucleotides complementary to the snapback tail in GTPV (100% match), as well as the corresponding positions in SPPV and LSDV are shown in the box. Note the targeted single nucleotide mismatches inside the box: T:A between GTPV and SPPV, and T:G between GTPV and LSDV. Conserved nucleotides are shown as dots.</p

Snapback primer genotyping of CaPVs.

<p>The fluorescence melting curve analysis of the PCR products shows two melting peaks for each of the CaPV three genotypes (GTPV, SPPV and LSDV) corresponding to the snapback stem melting peak at lower temperature and the full-length PCR amplicon melting peak at higher temperature (see arrows).</p