scholarly journals Discrimination of the SARS–CoV-2 strains using of coloured s-LASCA-imaging of GB-speckles, developed for the gene “S” nucleotide sequences

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 503
Author(s):  
Onega Ulianova ◽  
Yury Saltykov ◽  
Sergey Ulyanov ◽  
Sergey Zaytsev ◽  
Alexander Ulyanov ◽  
...  
Keyword(s):  
Speckle Interferometry ◽  
Molecular Target ◽  
Nucleotide Sequences ◽  
Considerable Improvement ◽  
Spike Glycoprotein ◽  
High Effectiveness ◽  
Glycoprotein Gene ◽  
Colour Image ◽  
High Discrimination ◽  
Pathogenic Viruses

Background: A recent bioinformatics technique involves changing nucleotide sequences into 2D speckles. This technique produces speckles called GB-speckles (Gene Based speckles). All classical strategies of speckle-optics, namely speckle-interferometry, subtraction of speckle-images as well as speckle-correlometry have been inferred for processing of GB-speckles. This indicates the considerable improvement in the present tools of bioinformatics.   Methods: Colour s-LASCA imaging of virtual laser GB-speckles, a new method of high discrimination and typing of pathogenic viruses, has been developed. This method has been adapted to the detecting of natural mutations in nucleotide sequences, related to the spike glycoprotein (coding the gene «S») of SARS–CoV-2 gene as the molecular target.    Results: The rate of the colouring images of virtual laser GB-speckles generated by s-LASCA can be described by the specific value of R. If the nucleotide sequences compared utilizing this approach the relevant images are completely identical, then the three components of the resulting colour image will be identical, and therefore the value of R will be equal to zero. However, if there are at least minimal differences in the matched nucleotide sequences, then the value of R will be positive.    Conclusion: The high effectiveness of an application of the colour images of GB-speckles that were generated by s-LASCA- has been demonstrated for discrimination between different variants of the SARS–CoV-2 spike glycoprotein gene.

scholarly journals Discrimination of the SARS–CoV-2 strains using of coloured s-LASCA-imaging of GB-speckles, developed for the gene “S” nucleotide sequences

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 503
Author(s):  
Onega Ulianova ◽  
Yury Saltykov ◽  
Sergey Ulyanov ◽  
Sergey Zaytsev ◽  
Alexander Ulyanov ◽  
...  
Keyword(s):  
Speckle Interferometry ◽  
Molecular Target ◽  
Nucleotide Sequences ◽  
Considerable Improvement ◽  
Spike Glycoprotein ◽  
High Effectiveness ◽  
Glycoprotein Gene ◽  
Colour Image ◽  
High Discrimination ◽  
Pathogenic Viruses

Background: A recent bioinformatics technique involves changing nucleotide sequences into 2D speckles. This technique produces speckles called GB-speckles (Gene Based speckles). All classical strategies of speckle-optics, namely speckle-interferometry, subtraction of speckle-images as well as speckle-correlometry have been inferred for processing of GB-speckles. This indicates the considerable improvement in the present tools of bioinformatics.   Methods: Colour s-LASCA imaging of virtual laser GB-speckles, a new method of high discrimination and typing of pathogenic viruses, has been developed. This method has been adapted to the detecting of natural mutations in nucleotide sequences, related to the spike glycoprotein (coding the gene «S») of SARS–CoV-2 gene as the molecular target.    Results: The rate of the colouring images of virtual laser GB-speckles generated by s-LASCA can be described by the specific value of R. If the nucleotide sequences compared utilizing this approach the relevant images are completely identical, then the three components of the resulting colour image will be identical, and therefore the value of R will be equal to zero. However, if there are at least minimal differences in the matched nucleotide sequences, then the value of R will be positive.    Conclusion: The high effectiveness of an application of the colour images of GB-speckles that were generated by s-LASCA- has been demonstrated for discrimination between different variants of the SARS–CoV-2 spike glycoprotein gene.

scholarly journals Discrimination of the SARS–CoV-2 strains using of coloured s-LASCA-imaging of GB-speckles, developed for the gene “S” nucleotide sequences

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 503
Author(s):  
Onega Ulianova ◽  
Yury Saltykov ◽  
Sergey Ulyanov ◽  
Sergey Zaytsev ◽  
Alexander Ulyanov ◽  
...  
Keyword(s):  
Speckle Interferometry ◽  
Molecular Target ◽  
Nucleotide Sequences ◽  
Considerable Improvement ◽  
Spike Glycoprotein ◽  
High Effectiveness ◽  
Glycoprotein Gene ◽  
Colour Image ◽  
High Discrimination ◽  
Pathogenic Viruses

Background: A recent bioinformatics technique involves changing nucleotide sequences into 2D speckles. This technique produces speckles called GB-speckles (Gene Based speckles). All classical strategies of speckle-optics, namely speckle-interferometry, subtraction of speckle-images as well as speckle-correlometry have been inferred for processing of GB-speckles. This indicates the considerable improvement in the present tools of bioinformatics.   Methods: Colour s-LASCA imaging of virtual laser GB-speckles, a new method of high discrimination and typing of pathogenic viruses, has been developed. This method has been adapted to the detecting of natural mutations in nucleotide sequences, related to the spike glycoprotein (coding the gene «S») of SARS–CoV-2 gene as the molecular target.    Results: The rate of the colouring images of virtual laser GB-speckles generated by s-LASCA can be described by the specific value of R. If the nucleotide sequences compared utilizing this approach the relevant images are completely identical, then the three components of the resulting colour image will be identical, and therefore the value of R will be equal to zero. However, if there are at least minimal differences in the matched nucleotide sequences, then the value of R will be positive.    Conclusion: The high effectiveness of an application of the colour images of GB-speckles that were generated by s-LASCA- has been demonstrated for discrimination between different variants of the SARS–CoV-2 spike glycoprotein gene.

scholarly journals Effective screening of SARS-CoV-2 neutralizing antibodies in patient serum using lentivirus particles pseudotyped with SARS-CoV-2 spike glycoprotein

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ritesh Tandon ◽  
Dipanwita Mitra ◽  
Poonam Sharma ◽  
Martin G. McCandless ◽  
Stephen J. Stray ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Neutralizing Antibodies ◽  
Transduction Efficiency ◽  
Pseudotyped Virus ◽  
Spike Glycoprotein ◽  
Highly Pathogenic ◽  
Mammalian Cell Lines ◽  
Serological Studies ◽  
Pathogenic Viruses ◽  
Vesicular Stomatitis

Abstract Pseuodotyped particles have significant importance and use in virology as tools for studying the biology of highly pathogenic viruses in a lower biosafety environment. The biological, chemical, and serological studies of the recently emerged SARS-CoV-2 will be greatly aided by the development and optimization of a suitable pseudotyping system. Here, we pseudotyped the SARS-CoV-2 Spike glycoprotein (SPG) on a traditional retroviral (MMLV) as well as a third generation lentiviral (pLV) vector and tested the transduction efficiency in several mammalian cell lines expressing SARS-CoV-2 receptor hACE2. While MMLV pseudotyped the vesicular stomatitis virus G glycoprotein (VSV-G) efficiently, it could not pseudotype the full-length SPG. In contrast, pLV pseudotyped both glycoproteins efficiently; however, much higher titers of pLV-G particles were produced. Among all the tested mammalian cells, 293Ts expressing hACE2 were most efficiently transduced using the pLV-S system. The pLV-S particles were efficiently neutralized by diluted serum (>:640) from recently recovered COVID-19 patients who showed high SARS-CoV-2 specific IgM and IgG levels. In summary, pLV-S pseudotyped virus provides a valid screening tool for the presence of anti SARS-CoV-2 specific neutralizing antibodies in convalescent patient serum.

scholarly journals Variations in Spike Glycoprotein Gene of MERS-CoV, South Korea, 2015

2016 ◽  
Vol 22 (1) ◽  
pp. 100-104 ◽  
Author(s):  
Dae-Won Kim ◽  
You-Jin Kim ◽  
Sung Han Park ◽  
Mi-Ran Yun ◽  
Jeong-Sun Yang ◽  
...  
Keyword(s):  
South Korea ◽  
Spike Glycoprotein ◽  
Glycoprotein Gene

scholarly journals Molecular and phylogenetic analysis of bovine coronavirus based on the spike glycoprotein gene

2012 ◽  
Vol 12 (8) ◽  
pp. 1870-1878 ◽  
Author(s):  
Nadia Martínez ◽  
Paulo E. Brandão ◽  
Sibele Pinheiro de Souza ◽  
Maritza Barrera ◽  
Nelson Santana ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Spike Glycoprotein ◽  
Bovine Coronavirus ◽  
Glycoprotein Gene

Sequence analysis of the partial spike glycoprotein gene of porcine epidemic diarrhea viruses isolated in Korea

Virus Genes ◽  
2007 ◽  
Vol 35 (2) ◽  
pp. 321-332 ◽  
Author(s):  
Seong-Jun Park ◽  
Hyoung-Joon Moon ◽  
Jeong-Sun Yang ◽  
Chul-Seung Lee ◽  
Dae-Sub Song ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Spike Glycoprotein ◽  
Glycoprotein Gene ◽  
Porcine Epidemic Diarrhea

scholarly journals The Characteristics of Spike Glycoprotein Gene of Swine Acute Diarrhea Syndrome Coronavirus Strain CH/FJWT/2018 Isolated in China

2021 ◽  
Vol 8 ◽  
Author(s):  
Yan-Yan Guo ◽  
Pei-Hua Wang ◽  
Yuan-Qing Pan ◽  
Rui-Zhu Shi ◽  
Ya-Qian Li ◽  
...  
Keyword(s):  
Acute Diarrhea ◽  
Neutralizing Antibodies ◽  
Watery Diarrhea ◽  
Spike Glycoprotein ◽  
Neonatal Piglets ◽  
Glycoprotein Gene ◽  
The Family ◽  
Viral Host Range ◽  
Gene Similarity ◽  
Diarrhea Syndrome

Swine acute diarrhea syndrome (SADS) is a highly contagious infectious disease characterized by acute vomiting and watery diarrhea in neonatal piglets. The causative agent for SADS is the swine acute diarrhea syndrome coronavirus (SADS-CoV), an alphacoronavirus in the family Coronaviridae. Currently, SADS-CoV was identified only in Guangdong and Fujian provinces of China, not in any other regions or countries in the world. To explore the genetic diversity of SADS-CoV isolates, herein we comparatively analyzed 44 full-length genomes of viruses isolated in Guangdong and Fujian provinces during 2017–2019. The spike glycoprotein gene of SADS-CoV strain CH/FJWT/2018 isolated in Fujian province is distinct from that of other viral isolates in either spike glycoprotein gene-based phylogenetic analysis or whole genome-based gene similarity analysis. Moreover, at least 7 predicted linear B cell epitopes in the spike glycoprotein of CH/FJWT/2018 would be affected by amino acid variations when compared with a representative virus isolated in Guangdong province. The spike glycoprotein of coronaviruses determines viral host range and tissue tropism during virus infection via specific interactions with the cellular receptor and also plays critical roles in eliciting the production of neutralizing antibodies. Since SADS-CoVs have a broad cell tropism, the results in this report further emphasize that the spike glycoprotein gene is a pivotal target in the surveillance of SADS-CoV.

scholarly journals A combination of mutations in the S1 part of the spike glycoprotein gene of coronavirus MHV-A59 abolishes demyelination

2004 ◽  
Vol 10 (1) ◽  
pp. 41-51 ◽  
Author(s):  
Li Fu ◽  
Donna M Gonzales ◽  
Jayasri Das Sarma ◽  
Ehud Lavi
Keyword(s):  
Spike Glycoprotein ◽  
Glycoprotein Gene

scholarly journals Divergent Copies of a Cryptosporidium parvum-Specific Subtelomeric Gene

2019 ◽  
Vol 7 (9) ◽  
pp. 366 ◽  
Author(s):  
Zhang ◽  
Chen ◽  
Li ◽  
Li ◽  
Feng ◽  
...  
Keyword(s):  
Host Range ◽  
Cryptosporidium Parvum ◽  
Genetic Recombination ◽  
Nucleotide Sequences ◽  
Cryptosporidium Species ◽  
Sequence Type ◽  
Broad Host Range ◽  
Previous Conclusion ◽  
Glycoprotein Gene ◽  
Data Support

Subtype families of Cryptosporidium parvum differ in host range, with IIa and IId being found in a broad range of animals, IIc in humans, and IIo and IIp in some rodents. Previous studies indicated that the subtelomeric cgd6_5520-5510 gene in C. parvum is lost in many Cryptosporidium species, and could potentially contribute to the broad host range of the former. In this study, we identified the presence of a second copy of the gene in some C. parvum subtype families with a broad host range, and showed sequence differences among them. The sequence differences in the cgd6_5520-5510 gene were not segregated by the sequence type of the 60 kDa glycoprotein gene. Genetic recombination appeared to have played a role in generating divergent nucleotide sequences between copies and among subtype families. These data support the previous conclusion on the potential involvement of the insulinase-like protease encoded by the subtelomeric cgd6_5520-5510 gene in the broad host range of C. parvum IIa and IId subtypes.

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