In silico Prediction and Designing of Potential siRNAs to be Used as Antivirals Against SARS-CoV-2

2021 ◽  
Vol 27 ◽  
Author(s):  
Sayed Sartaj Sohrab ◽  
Sherif Aly El-Kafrawy ◽  
Aymn T. Abbas ◽  
Leena H. Bajrai ◽  
Esam Ibraheem Azhar
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Phylogenetic Relationships ◽  
In Silico ◽  
Full Genome ◽  
In Silico Prediction ◽  
High Sequence Identity ◽  
Minor Parent ◽  
Sequence Identity ◽  
The City

Background:: The unusual pneumonia outbreak that originated in the city of Wuhan, China in December 2019 was found to be caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or COVID-19. Methods:: In this work, we have performed an in silico design and prediction of potential siRNAs based on genetic diversity and recombination patterns, targeting various genes of SARS-CoV-2 for antiviral therapeutics. We performed extensive sequence analysis to analyze the genetic diversity and phylogenetic relationships, and to identify the possible source of virus reservoirs and recombination patterns, and the evolution of the virus as well as we designed the siRNAs which can be used as antivirals against SARS-CoV-2. Results:: The sequence analysis and phylogenetic relationships indicated high sequence identity and closed clusters with many types of coronavirus. In our analysis, the full-genome of SARS-CoV-2 showed the highest sequence (nucleotide) identity with SARS-bat-ZC45 (87.7%). The overall sequence identity ranged from 74.3% to 87.7% with selected SARS viruses. The recombination analysis indicated the bat SARS virus is a potential recombinant and serves as a major and minor parent. We have predicted 442 siRNAs and finally selected only 19 functional, and potential siRNAs. Conclusions:: The siRNAs were predicted and selected based on their greater potency and specificity. The predicted siRNAs need to be validated experimentally for their effective binding and antiviral activity.

In silico prediction of influenza vaccine effectiveness by sequence analysis

Vaccine ◽  
2021 ◽  
Vol 39 (7) ◽  
pp. 1030-1034
Author(s):  
Lirong Cao ◽  
Jingzhi Lou ◽  
Shi Zhao ◽  
Renee W.Y. Chan ◽  
Martin Chan ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Influenza Vaccine ◽  
In Silico ◽  
Vaccine Effectiveness ◽  
In Silico Prediction

scholarly journals Genetic diversity of begomoviruses infecting soybean, bean and associated weeds in Northwestern Argentina

2006 ◽  
Vol 31 (4) ◽  
pp. 342-348 ◽  
Author(s):  
Patricia E. Rodríguez-Pardina ◽  
F. Murilo Zerbini ◽  
Daniel A. Ducasse
Keyword(s):  
Genetic Diversity ◽  
Protein Gene ◽  
Weed Species ◽  
Capsid Protein Gene ◽  
High Sequence Identity ◽  
Northwestern Argentina ◽  
Sequence Identity ◽  
High Incidence ◽  
Northwestern Region ◽  
Prevalent Virus

The subtropical Northwestern region of Argentina (provinces of Tucumán, Salta, Jujuy, Santiago del Estero and Catamarca) suffers from a high incidence of the whitefly Bemisia tabaci, and the detection of begomoviruses is also common. The Northwest is the main bean-growing region of the country, and approximately 10% of Argentina's soybean crop is grown in this area. We have used a PCR-based assay to establish the identity and genetic diversity of begomoviruses associated with bean and soybean crops in Northwestern Argentina. Universal begomovirus primers were used to direct the amplification of a fragment encompassing the 5' portion of the capsid protein gene. Amplified fragments were cloned, sequenced and subjected to phylogenetic analysis to determine the sequence identity to known begomoviruses. The data indicated the presence of four distinct begomoviruses, all related to other New World begomoviruses. The prevalent virus, which was present in 94% of bean and soybean samples and also in two weed species, is closely related to Sida mottle virus (SiMoV). A virus with high sequence identity with Bean golden mosaic virus (BGMV) was found in beans. The two remaining viruses displayed less than 89% identity with other known begomoviruses, indicating that they may constitute novel species. One of these putative novel viruses was detected in bean, soybean and tomato samples.

scholarly journals Complete Coding Sequence of a Novel Bluetongue Virus Isolated from a Commercial Sheeppox Vaccine

2020 ◽  
Vol 9 (10) ◽  
Author(s):  
Paulina Rajko-Nenow ◽  
Natalia Golender ◽  
Velizar Bumbarov ◽  
Hannah Brown ◽  
Lorraine Frost ◽  
...  
Keyword(s):  
Bluetongue Virus ◽  
Full Genome ◽  
Genome Sequences ◽  
High Sequence Identity ◽  
Coding Sequence ◽  
Sequence Identity ◽  
Relative Strain

The full genome sequences of two isolates of bluetongue virus (BTV) from a commercial sheeppox vaccine were determined. Strain SPvvvv/02 shows low sequence identity to its closest relative, strain BTV-26 KUW2010/02, indicating the probable detection of a novel BTV genotype, whereas strain SPvvvv/03 shows high sequence identity to strain BTV-28/1537/14.

scholarly journals Analysis of the genetic diversity and phylogenetic relationships of putative human papillomavirus types

2013 ◽  
Vol 94 (11) ◽  
pp. 2480-2488 ◽  
Author(s):  
Diego Chouhy ◽  
Elisa M. Bolatti ◽  
Germán R. Pérez ◽  
Adriana A. Giri
Keyword(s):  
Genetic Diversity ◽  
Human Papillomavirus ◽  
Phylogenetic Relationships ◽  
Systematic Search ◽  
Full Genome ◽  
Genome Characterization ◽  
Putative Species ◽  
The Family ◽  
Hpv Types

More than 170 human papillomavirus (HPV) types have been completely sequenced, curated and divided into five genera: Alphapapillomavirus, Betapapillomavirus, Gammapapillomavirus, Mupapillomavirus and Nupapillomavirus. With the application of PCR methods, hundreds of putative novel HPV types have been identified as PCR amplicons in mucosa and skin. However, at present there are no studies reporting a systematic search of the currently known L1 amplicons and their phylogenetic relationships. This survey revealed the existence of at least 202 different putative HPV types that are pending for full-genome characterization: five alphapapillomaviruses, 37 betapapillomaviruses, 159 gammapapillomaviruses and one mupapillomavirus. All potential viruses of the genera Alphapapillomavirus and Betapapillomavirus were grouped in the defined species, while 59 putative gammapapillomaviruses types were segregated in 21 unidentified putative species. These data highlight the need for progress in the identification of additional taxa of the family Papillomaviridae in order to elucidate the diversity, evolution and medical implications of these viruses.

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