Primer design and in silico PCR test for Ebola virus detection

Detection of Salmonella bacteria based on their virulence genes is among essential steps in the eradication of clinical infection by bacteria. In this study, two pair of primers, PhoPF-PhoPR: 5’- CCGCGCAGGAAAAACTCAAA-3’ and 5’-ATCTGTTCCAGCATCACCGG -3’ as well as PhoQF-PhoQR: 5’-AGAGATGATGCGCGTACTGG-3’ and 5’- CAGACGCCCCATGAGAACAT-3’, had been successfully designed using Primer3Plus to detect the presence of phoP and phoQ genes in Salmonella spp. Using genomic DNA of 44 genomic data of Salmonella spp. as templates, PhoPF-PhoPR could produce 520-bp amplicon, while PhoQF-PhoQR could result in 598-bp amplicon. Results of in silico PCR showed that both pairs of primers PhoPF-PhoPR and PhoQF-PhoQR could detect only Salmonella enterica species, and no Salmonella bongori species could be detected based on phoP and phoQ sequences. Both pairs of PhoPF-PhoPR and PhoQF-PhoQR primers were also able to detect the virulence genes in most of the studied subspecies of Salmonella enterica available in silico database unless Arizona subspecies. As conclusion, based on this in silico study, phoP and phoQ genes appeared to be biomarkers for Salmonella enterica species. Both pairs of primers designed in this study has potential to be used as detection tool to differentiate species Salmonella enterica from Salmonella bongori, and also to distinguish S.enterica subsp. enterica from subsp. Arizonae.Keywords: Gene detection, bacterial virulence, phoP, phoQ, Salmonella spp.

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A comparative computational genomics of Ebola Virus Disease strains: In-silico Insight for Ebola control

Informatics in Medicine Unlocked ◽

10.1016/j.imu.2018.07.004 ◽

2018 ◽

Vol 12 ◽

pp. 106-119

Author(s):

Olugbenga Oluwagbemi ◽

Olaitan Awe

Keyword(s):

In Silico ◽

Ebola Virus ◽

Virus Disease ◽

Computational Genomics ◽

Ebola Virus Disease

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Novel Algorithms for In Silico Peptide Vaccine Design with Reference to Ebola Virus

2020 International Conference on Computer, Electrical & Communication Engineering (ICCECE) ◽

10.1109/iccece48148.2020.9223075 ◽

2020 ◽

Author(s):

Subhamoy Biswas ◽

Tathagata Dey ◽

Shreyans Chatterjee ◽

Smarajit Manna ◽

Ashesh Nandy ◽

...

Keyword(s):

In Silico ◽

Ebola Virus ◽

Peptide Vaccine ◽

Vaccine Design ◽

Novel Algorithms

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Recent Progress in Plasmonic Biosensing Schemes for Virus Detection

Sensors ◽

10.3390/s20174745 ◽

2020 ◽

Vol 20 (17) ◽

pp. 4745 ◽

Cited By ~ 3

Author(s):

Elba Mauriz

Keyword(s):

Global Economy ◽

Recent Progress ◽

Ebola Virus ◽

Hepatitis Virus ◽

Virus Detection ◽

Diagnostic Methods ◽

Effective Control ◽

Plasmonic Nanostructures ◽

Special Focus ◽

Plasmonic Sensing

The global burden of coronavirus disease 2019 (COVID-19) to public health and global economy has stressed the need for rapid and simple diagnostic methods. From this perspective, plasmonic-based biosensing can manage the threat of infectious diseases by providing timely virus monitoring. In recent years, many plasmonics’ platforms have embraced the challenge of offering on-site strategies to complement traditional diagnostic methods relying on the polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). This review compiled recent progress on the development of novel plasmonic sensing schemes for the effective control of virus-related diseases. A special focus was set on the utilization of plasmonic nanostructures in combination with other detection formats involving colorimetric, fluorescence, luminescence, or Raman scattering enhancement. The quantification of different viruses (e.g., hepatitis virus, influenza virus, norovirus, dengue virus, Ebola virus, Zika virus) with particular attention to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was reviewed from the perspective of the biomarker and the biological receptor immobilized on the sensor chip. Technological limitations including selectivity, stability, and monitoring in biological matrices were also reviewed for different plasmonic-sensing approaches.

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