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Dr. Sk Sarif Hassan
Pingla Thana Mahavidyalaya

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0 Cellular Automata
0 Dynamical Systems
0 Fractals
0 Quantitative Biology
0 mathematical morphology

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Opinion
Published: 13 July 2021 in Biomolecules
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Two adenovirus-based vaccines, ChAdOx1 nCoV-19 and Ad26.COV2.S, and two mRNA-based vaccines, BNT162b2 and mRNA.1273, have been approved by the European Medicines Agency (EMA), and are invaluable in preventing and reducing the incidence of coronavirus disease-2019 (COVID-19). Recent reports have pointed to thrombosis with associated thrombocytopenia as an adverse effect occurring at a low frequency in some individuals after vaccination. The causes of such events may be related to SARS-CoV-2 spike protein interactions with different C-type lectin receptors, heparan sulfate proteoglycans (HSPGs) and the CD147 receptor, or to different soluble splice variants of the spike protein, adenovirus vector interactions with the CD46 receptor or platelet factor 4 antibodies. Similar findings have been reported for several viral diseases after vaccine administration. In addition, immunological mechanisms elicited by viral vectors related to cellular delivery could play a relevant role in individuals with certain genetic backgrounds. Although rare, the potential COVID-19 vaccine-induced immune thrombotic thrombocytopenia (VITT) requires immediate validation, especially in risk groups, such as the elderly, chronic smokers, and individuals with pre-existing incidences of thrombocytopenia; and if necessary, a reformulation of existing vaccines.

ACS Style

Kenneth Lundstrom; Debmalya Barh; Bruce Uhal; Kazuo Takayama; Alaa Aljabali; Tarek Abd El-Aziz; Amos Lal; ElRashdy Redwan; Parise Adadi; Gaurav Chauhan; Samendra Sherchan; Gajendra Azad; Nima Rezaei; Ángel Serrano-Aroca; Nicolas Bazan; Sk Hassan; Pritam Panda; Pabitra Pal Choudhury; Damiano Pizzol; Ramesh Kandimalla; Wagner Baetas-Da-Cruz; Yogendra Mishra; Giorgio Palu; Adam Brufsky; Murtaza Tambuwala; Vladimir Uversky. COVID-19 Vaccines and Thrombosis—Roadblock or Dead-End Street? Biomolecules 2021, 11, 1020 .

AMA Style

Kenneth Lundstrom, Debmalya Barh, Bruce Uhal, Kazuo Takayama, Alaa Aljabali, Tarek Abd El-Aziz, Amos Lal, ElRashdy Redwan, Parise Adadi, Gaurav Chauhan, Samendra Sherchan, Gajendra Azad, Nima Rezaei, Ángel Serrano-Aroca, Nicolas Bazan, Sk Hassan, Pritam Panda, Pabitra Pal Choudhury, Damiano Pizzol, Ramesh Kandimalla, Wagner Baetas-Da-Cruz, Yogendra Mishra, Giorgio Palu, Adam Brufsky, Murtaza Tambuwala, Vladimir Uversky. COVID-19 Vaccines and Thrombosis—Roadblock or Dead-End Street? Biomolecules. 2021; 11 (7):1020.

Chicago/Turabian Style

Kenneth Lundstrom; Debmalya Barh; Bruce Uhal; Kazuo Takayama; Alaa Aljabali; Tarek Abd El-Aziz; Amos Lal; ElRashdy Redwan; Parise Adadi; Gaurav Chauhan; Samendra Sherchan; Gajendra Azad; Nima Rezaei; Ángel Serrano-Aroca; Nicolas Bazan; Sk Hassan; Pritam Panda; Pabitra Pal Choudhury; Damiano Pizzol; Ramesh Kandimalla; Wagner Baetas-Da-Cruz; Yogendra Mishra; Giorgio Palu; Adam Brufsky; Murtaza Tambuwala; Vladimir Uversky. 2021. "COVID-19 Vaccines and Thrombosis—Roadblock or Dead-End Street?" Biomolecules 11, no. 7: 1020.

Preprint
Published: 18 June 2021
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Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no hypothesis has managed to identify the origin, and the issue has resurfaced. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins across different continents comprising 24 geo-locations. The results showed an evenly uneven distribution of unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across the 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations we have considered. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and to be prepared to meet the challenges of potential future pandemics.

ACS Style

Sk Sarif Hassan; Vaishnavi Kodakandla; Elrashdy M. Redwan; Kenneth Lundstrom; Pabitra Pal Choudhury; Ángel Serrano-Aroca Aroca; Gajendra Kumar Azad; Alaa A.A. Aljabali; Giorgio Palu; Tarek Mohamed Abd El-Aziz; Debmalya Barh; Bruce D. Uhal; Parise Adadi; Kazuo Takayama; Nicolas G. Bazan; Murtaza Tambuwala; Samendra P. Sherchan; Amos Lal; Gaurav Chauhan; Wagner Baetas-Da-Cruz; Vladimir N. Uversky. Non-Uniform Aspects of SARS-CoV-2 Intraspecies Evolution Reopen Questions on Its Origin. 2021, 1 .

AMA Style

Sk Sarif Hassan, Vaishnavi Kodakandla, Elrashdy M. Redwan, Kenneth Lundstrom, Pabitra Pal Choudhury, Ángel Serrano-Aroca Aroca, Gajendra Kumar Azad, Alaa A.A. Aljabali, Giorgio Palu, Tarek Mohamed Abd El-Aziz, Debmalya Barh, Bruce D. Uhal, Parise Adadi, Kazuo Takayama, Nicolas G. Bazan, Murtaza Tambuwala, Samendra P. Sherchan, Amos Lal, Gaurav Chauhan, Wagner Baetas-Da-Cruz, Vladimir N. Uversky. Non-Uniform Aspects of SARS-CoV-2 Intraspecies Evolution Reopen Questions on Its Origin. . 2021; ():1.

Chicago/Turabian Style

Sk Sarif Hassan; Vaishnavi Kodakandla; Elrashdy M. Redwan; Kenneth Lundstrom; Pabitra Pal Choudhury; Ángel Serrano-Aroca Aroca; Gajendra Kumar Azad; Alaa A.A. Aljabali; Giorgio Palu; Tarek Mohamed Abd El-Aziz; Debmalya Barh; Bruce D. Uhal; Parise Adadi; Kazuo Takayama; Nicolas G. Bazan; Murtaza Tambuwala; Samendra P. Sherchan; Amos Lal; Gaurav Chauhan; Wagner Baetas-Da-Cruz; Vladimir N. Uversky. 2021. "Non-Uniform Aspects of SARS-CoV-2 Intraspecies Evolution Reopen Questions on Its Origin." , no. : 1.

Preprint content
Published: 25 May 2021
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Open reading frame 8 (ORF8) protein is one of the most evolving accessory proteins in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits presentation of viral antigens by the major histocompatibility complex class I (MHC-I) and interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 to evade immunity and replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein defines the B.1.1.7 lineage of SARS-CoV-2, which is engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) due to the Q27STOP mutations were identified among 49055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents which includes Africa, Asia, Europe and South America. Based on various quantitative features such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, a collection of nine possible T-ORF8 unique variants were defined. The question of whether T-ORF8 variants work similarly to ORF8 has yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.

ACS Style

Sk. Sarif Hassan; Vaishnavi Kodakandla; Elrashdy M. Redwan; Kenneth Lundstrom; Pabitra Pal Choudhury; Tarek Mohamed Abd El-Aziz; Kazuo Takayama; Ramesh Kandimalla; Amos Lal; Ángel Serrano-Aroca; Gajendra Kumar Azad; Alaa A. A. Aljabali; Giorgio Palu; Gaurav Chauhan; Parise Adadi; Murtaza Tambuwala; Adam M. Brufsky; Wagner Baetas-Da-Cruz; Debmalya Barh; Nicolas G Bazan; Vladimir N. Uversky. An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2. 2021, 1 .

AMA Style

Sk. Sarif Hassan, Vaishnavi Kodakandla, Elrashdy M. Redwan, Kenneth Lundstrom, Pabitra Pal Choudhury, Tarek Mohamed Abd El-Aziz, Kazuo Takayama, Ramesh Kandimalla, Amos Lal, Ángel Serrano-Aroca, Gajendra Kumar Azad, Alaa A. A. Aljabali, Giorgio Palu, Gaurav Chauhan, Parise Adadi, Murtaza Tambuwala, Adam M. Brufsky, Wagner Baetas-Da-Cruz, Debmalya Barh, Nicolas G Bazan, Vladimir N. Uversky. An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2. . 2021; ():1.

Chicago/Turabian Style

Sk. Sarif Hassan; Vaishnavi Kodakandla; Elrashdy M. Redwan; Kenneth Lundstrom; Pabitra Pal Choudhury; Tarek Mohamed Abd El-Aziz; Kazuo Takayama; Ramesh Kandimalla; Amos Lal; Ángel Serrano-Aroca; Gajendra Kumar Azad; Alaa A. A. Aljabali; Giorgio Palu; Gaurav Chauhan; Parise Adadi; Murtaza Tambuwala; Adam M. Brufsky; Wagner Baetas-Da-Cruz; Debmalya Barh; Nicolas G Bazan; Vladimir N. Uversky. 2021. "An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2." , no. : 1.

Preprint content
Published: 18 May 2021
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Spike (S) proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are critical determinants of the infectivity and antigenicity of the virus. Several mutations in the spike protein of SARS-CoV-2 have already been detected, and their effect in immune system evasion and enhanced transmission as a cause of increased morbidity and mortality are being investigated. From pathogenic and epidemiological perspectives, spike proteins are of prime interest to researchers. This study focused on the unique variants of S proteins from six continents Asia, Africa, Europe, Oceania, South America, and North America. In comparison to the other five continents, Africa (29.065%) had the highest percentage of unique S proteins. Notably, only North America had 87% (14046) of the total (16143) specific S proteins available in the NCBI database(across all continents). Based on the amino acid frequency distributions in the S protein variants from all the continents, the phylogenetic relationship implies that unique S proteins from North America were significantly different from those of the other five continents. Overtime, the unique variants originating from North America are most likely to spread to the other geographic locations through international travel or naturally by emerging mutations. Hence it is suggested that restriction of international travel should be considered, and massive vaccination as an utmost measure to combat the spread of COVID-19 pandemic. It is also further suggested that the efficacy of existing vaccines and future vaccine development must be reviewed with careful scrutiny, and if needed, further re-engineered based on requirements dictated by new emerging S protein variants.

ACS Style

Sk. Sarif Hassan; Kenneth Lundstrom; Pabitra Pal Choudhury; Giorgio Palu; Bruce D. Uhal; Ramesh Kandimalla; Murat Seyran; Amos Lal; Samendra P. Sherchan; Gajendra Kumar Azad; Alaa A. A. Aljabali; Adam M. Brufsky; Ángel Serrano-Aroca; Parise Adadi; Tarek Mohamed Abd El-Aziz; Elrashdy M. Redwan; Kazuo Takayama; Debmalya Barh; Nima Rezaei; Murtaza Tambuwala; Vladimir N. Uversky. Implications Derived from S-Protein Variants of SARS-CoV-2 from Six Continents. 2021, 1 .

AMA Style

Sk. Sarif Hassan, Kenneth Lundstrom, Pabitra Pal Choudhury, Giorgio Palu, Bruce D. Uhal, Ramesh Kandimalla, Murat Seyran, Amos Lal, Samendra P. Sherchan, Gajendra Kumar Azad, Alaa A. A. Aljabali, Adam M. Brufsky, Ángel Serrano-Aroca, Parise Adadi, Tarek Mohamed Abd El-Aziz, Elrashdy M. Redwan, Kazuo Takayama, Debmalya Barh, Nima Rezaei, Murtaza Tambuwala, Vladimir N. Uversky. Implications Derived from S-Protein Variants of SARS-CoV-2 from Six Continents. . 2021; ():1.

Chicago/Turabian Style

Sk. Sarif Hassan; Kenneth Lundstrom; Pabitra Pal Choudhury; Giorgio Palu; Bruce D. Uhal; Ramesh Kandimalla; Murat Seyran; Amos Lal; Samendra P. Sherchan; Gajendra Kumar Azad; Alaa A. A. Aljabali; Adam M. Brufsky; Ángel Serrano-Aroca; Parise Adadi; Tarek Mohamed Abd El-Aziz; Elrashdy M. Redwan; Kazuo Takayama; Debmalya Barh; Nima Rezaei; Murtaza Tambuwala; Vladimir N. Uversky. 2021. "Implications Derived from S-Protein Variants of SARS-CoV-2 from Six Continents." , no. : 1.

Journal article
Published: 30 April 2021 in Virus Research
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One of the most important proteins for COVID-19 pathogenesis in SARS-CoV-2 is the ORF3a which is the largest accessory protein among others coded by the SARS-CoV-2 genome. The major roles of the protein include virulence, infectivity, ion channel activity, morphogenesis, and virus release. The coronavirus, SARS-CoV-2 is mutating rapidly, therefore, critical study of mutations in ORF3a is certainly important from the pathogenic perspective. Here, a sum of 175 non-synonymous mutations in the ORF3a of SARS-CoV-2 were identified from 7194 complete genomes of SARS-CoV-2 available from NCBI database. Effects of these mutations on structural stability, and functions of ORF3a were also studied. Broadly, three different classes of mutations, such as neutral, disease, and mixed (neutral and disease) types of mutations were observed. Consecutive phenomena of mutations in ORF3a protein were studied based on the timeline of detection of the mutations. Considering the amino acid compositions of the ORF3a protein, twenty clusters were detected using the K-means clustering method. The present findings on 175 novel mutations of ORF3a proteins will extend our knowledge on ORF3a, a vital accessory protein in SARS-CoV-2, to enlighten the pathogenicity of this life-threatening virus.

ACS Style

Sk. Sarif Hassan; Diksha Attrish; Shinjini Ghosh; Pabitra Pal Choudhury; Bidyut Roy. Pathogenic perspective of missense mutations of ORF3a protein of SARS-CoV-2. Virus Research 2021, 300, 198441 -198441.

AMA Style

Sk. Sarif Hassan, Diksha Attrish, Shinjini Ghosh, Pabitra Pal Choudhury, Bidyut Roy. Pathogenic perspective of missense mutations of ORF3a protein of SARS-CoV-2. Virus Research. 2021; 300 ():198441-198441.

Chicago/Turabian Style

Sk. Sarif Hassan; Diksha Attrish; Shinjini Ghosh; Pabitra Pal Choudhury; Bidyut Roy. 2021. "Pathogenic perspective of missense mutations of ORF3a protein of SARS-CoV-2." Virus Research 300, no. : 198441-198441.

Journal article
Published: 16 April 2021 in International Journal of Biological Macromolecules
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The current Coronavirus Disease 19 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) shows similar pathology to MERS and SARS-CoV, with a current estimated fatality rate of 1.4%. Open reading frame 10 (ORF10) is a unique SARS-CoV-2 accessory protein, which contains eleven cytotoxic T lymphocyte (CTL) epitopes each of nine amino acids in length. Twenty-two unique SARS-CoV-2 ORF10 variants have been identified based on missense mutations found in sequence databases. Some of these mutations are predicted to decrease the stability of ORF10 in silico physicochemical and structural comparative analyses were carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid (aa) homology. Though there is a high degree of ORF10 protein similarity of SARS-CoV-2 and Pangolin-CoV, there are differences of these two ORF10 proteins related to their sub-structure (loop/coil region), solubility, antigenicity and shift from strand to coil at aa position 26 (tyrosine). SARS-CoV-2 ORF10, which is apparently expressed in vivo since reactive T cell clones are found in convalescent patients should be monitored for changes which could correlate with the pathogenesis of COVID-19.

ACS Style

Sk. Sarif Hassan; Diksha Attrish; Shinjini Ghosh; Pabitra Pal Choudhury; Vladimir N. Uversky; Alaa A.A. Aljabali; Kenneth Lundstrom; Bruce D. Uhal; Nima Rezaei; Murat Seyran; Damiano Pizzol; Parise Adadi; Antonio Soares; Tarek Mohamed Abd El-Aziz; Ramesh Kandimalla; Murtaza M. Tambuwala; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Amos Lal; Giorgio Palù; Kazuo Takayama; Ángel Serrano-Aroca; Debmalya Barh; Adam M. Brufsky. Notable sequence homology of the ORF10 protein introspects the architecture of SARS-CoV-2. International Journal of Biological Macromolecules 2021, 181, 801 -809.

AMA Style

Sk. Sarif Hassan, Diksha Attrish, Shinjini Ghosh, Pabitra Pal Choudhury, Vladimir N. Uversky, Alaa A.A. Aljabali, Kenneth Lundstrom, Bruce D. Uhal, Nima Rezaei, Murat Seyran, Damiano Pizzol, Parise Adadi, Antonio Soares, Tarek Mohamed Abd El-Aziz, Ramesh Kandimalla, Murtaza M. Tambuwala, Gajendra Kumar Azad, Samendra P. Sherchan, Wagner Baetas-Da-Cruz, Amos Lal, Giorgio Palù, Kazuo Takayama, Ángel Serrano-Aroca, Debmalya Barh, Adam M. Brufsky. Notable sequence homology of the ORF10 protein introspects the architecture of SARS-CoV-2. International Journal of Biological Macromolecules. 2021; 181 ():801-809.

Chicago/Turabian Style

Sk. Sarif Hassan; Diksha Attrish; Shinjini Ghosh; Pabitra Pal Choudhury; Vladimir N. Uversky; Alaa A.A. Aljabali; Kenneth Lundstrom; Bruce D. Uhal; Nima Rezaei; Murat Seyran; Damiano Pizzol; Parise Adadi; Antonio Soares; Tarek Mohamed Abd El-Aziz; Ramesh Kandimalla; Murtaza M. Tambuwala; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Amos Lal; Giorgio Palù; Kazuo Takayama; Ángel Serrano-Aroca; Debmalya Barh; Adam M. Brufsky. 2021. "Notable sequence homology of the ORF10 protein introspects the architecture of SARS-CoV-2." International Journal of Biological Macromolecules 181, no. : 801-809.

Editorial
Published: 09 March 2021 in Biomolecules
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Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is focused on a single isolate of bat coronaviruses (bat CoVs) which does not adequately represent genetically related coronaviruses (CoVs)

ACS Style

Murat Seyran; Sk. Hassan; Vladimir Uversky; Pabitra Pal Choudhury; Bruce Uhal; Kenneth Lundstrom; Diksha Attrish; Nima Rezaei; Alaa Aljabali; Shinjini Ghosh; Damiano Pizzol; Parise Adadi; Tarek El-Aziz; Ramesh Kandimalla; Murtaza Tambuwala; Amos Lal; Gajendra Azad; Samendra Sherchan; Wagner Baetas-Da-Cruz; Giorgio Palù; Adam Brufsky. Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for Future Outbreaks. Biomolecules 2021, 11, 398 .

AMA Style

Murat Seyran, Sk. Hassan, Vladimir Uversky, Pabitra Pal Choudhury, Bruce Uhal, Kenneth Lundstrom, Diksha Attrish, Nima Rezaei, Alaa Aljabali, Shinjini Ghosh, Damiano Pizzol, Parise Adadi, Tarek El-Aziz, Ramesh Kandimalla, Murtaza Tambuwala, Amos Lal, Gajendra Azad, Samendra Sherchan, Wagner Baetas-Da-Cruz, Giorgio Palù, Adam Brufsky. Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for Future Outbreaks. Biomolecules. 2021; 11 (3):398.

Chicago/Turabian Style

Murat Seyran; Sk. Hassan; Vladimir Uversky; Pabitra Pal Choudhury; Bruce Uhal; Kenneth Lundstrom; Diksha Attrish; Nima Rezaei; Alaa Aljabali; Shinjini Ghosh; Damiano Pizzol; Parise Adadi; Tarek El-Aziz; Ramesh Kandimalla; Murtaza Tambuwala; Amos Lal; Gajendra Azad; Samendra Sherchan; Wagner Baetas-Da-Cruz; Giorgio Palù; Adam Brufsky. 2021. "Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for Future Outbreaks." Biomolecules 11, no. 3: 398.

Short communication
Published: 18 February 2021 in Meta Gene
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A total number of 3080 SARS-CoV-2 genomes from all continents are considered from the NCBI database. Every accessory protein ORF6, ORF7b, and ORF10 of SARS-CoV-2 possess a single missense mutation in less than 1.5% of the 3080 genomes. It has now been observed that different non-synonymous mutations occurred in these three accessory proteins. Most of these rare mutations are changing the amino acids such as hydrophilic to hydrophobic, acidic or basic to hydrophobic, and vice versa etc. So these highly conserved proteins might play an essential role in virus pathogenicity. This study opens a question whether it carries some messages about the virus rapid replications, and virulence.

ACS Style

Sk. Sarif Hassan; Pabitra Pal Choudhury; Bidyut Roy. Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes. Meta Gene 2021, 28, 100873 -100873.

AMA Style

Sk. Sarif Hassan, Pabitra Pal Choudhury, Bidyut Roy. Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes. Meta Gene. 2021; 28 ():100873-100873.

Chicago/Turabian Style

Sk. Sarif Hassan; Pabitra Pal Choudhury; Bidyut Roy. 2021. "Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes." Meta Gene 28, no. : 100873-100873.

Preprint
Published: 15 January 2021
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Therapeutic options for the highly pathogenic human Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) causing the current pandemic Coronavirus disease (COVID-19) are urgently needed. COVID-19 is associated with viral pneumonia and acute respiratory distress syndrome causing significant morbidity and mortality. The proposed treatments for COVID-19, such as hydroxychloroquine, remdesivir and lopinavir/ritonavir, have shown little or no effect in the clinic. Additionally, bacterial and fungal pathogens contribute to the SARS-CoV-2 mediated pneumonia disease complex. The antibiotic resistance in pneumonia treatment is increasing at an alarming rate. Therefore, carbon-based nanomaterials (CBNs), such as fullerene, carbon dots, graphene, and their derivatives constitute a promising alternative due to their wide-spectrum antimicrobial activity, biocompatibility, biodegradability and capacity to induce tissue regeneration. Furthermore, the antimicrobial mode of action is mainly physical (e.g. membrane distortion), which is characterized by a low risk of antimicrobial resistance. In this review, we evaluated the literature on the antiviral activity and broad-spectrum antimicrobial properties of CBNs. CBNs had antiviral activity against 12 enveloped positive-sense single-stranded RNA viruses similar to SARS-CoV-2. CBNs with low or no toxicity to the humans are promising therapeutics against COVID-19 pneumonia complex with other viruses, bacteria and fungi, including those that are multidrug-resistant.

ACS Style

Ángel Serrano-Aroca; Kazuo Takayama; Alberto Tuñón-Molina; Murat Seyran; Sk. Sarif Hassan; Pabitra Pal Choudhury; Vladimir N. Uversky; Kenneth Lundstrom; Parise Adadi; Giorgio Palù; Alaa A. A. Aljabali; Gaurav Chauhan; Ramesh Kandimalla; Murtaza M. Tambuwala; Amos Lal; Bruce D. Uhal; Adam M. Brufsky. Carbon-Based Nanomaterials: Promising Antiviral Agents to Combat COVID-19 in the Microbial Resistant Era. 2021, 1 .

AMA Style

Ángel Serrano-Aroca, Kazuo Takayama, Alberto Tuñón-Molina, Murat Seyran, Sk. Sarif Hassan, Pabitra Pal Choudhury, Vladimir N. Uversky, Kenneth Lundstrom, Parise Adadi, Giorgio Palù, Alaa A. A. Aljabali, Gaurav Chauhan, Ramesh Kandimalla, Murtaza M. Tambuwala, Amos Lal, Bruce D. Uhal, Adam M. Brufsky. Carbon-Based Nanomaterials: Promising Antiviral Agents to Combat COVID-19 in the Microbial Resistant Era. . 2021; ():1.

Chicago/Turabian Style

Ángel Serrano-Aroca; Kazuo Takayama; Alberto Tuñón-Molina; Murat Seyran; Sk. Sarif Hassan; Pabitra Pal Choudhury; Vladimir N. Uversky; Kenneth Lundstrom; Parise Adadi; Giorgio Palù; Alaa A. A. Aljabali; Gaurav Chauhan; Ramesh Kandimalla; Murtaza M. Tambuwala; Amos Lal; Bruce D. Uhal; Adam M. Brufsky. 2021. "Carbon-Based Nanomaterials: Promising Antiviral Agents to Combat COVID-19 in the Microbial Resistant Era." , no. : 1.

Journal article
Published: 13 December 2020 in Molecules
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Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is engendering the severe coronavirus disease 2019 (COVID-19) pandemic. The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 binds to the three sub-domains viz. amino acids (aa) 22–42, aa 79–84, and aa 330–393 of ACE2 on human cells to initiate entry. It was reported earlier that the receptor utilization capacity of ACE2 proteins from different species, such as cats, chimpanzees, dogs, and cattle, are different. A comprehensive analysis of ACE2 receptors of nineteen species was carried out in this study, and the findings propose a possible SARS-CoV-2 transmission flow across these nineteen species.

ACS Style

Sk. Sarif Hassan; Shinjini Ghosh; Diksha Attrish; Pabitra Pal Choudhury; Alaa A. A. Aljabali; Bruce D. Uhal; Kenneth Lundstrom; Nima Rezaei; Vladimir N. Uversky; Murat Seyran; Damiano Pizzol; Parise Adadi; Antonio Soares; Tarek Mohamed Abd El-Aziz; Ramesh Kandimalla; Murtaza M. Tambuwala; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Kazuo Takayama; Ángel Serrano-Aroca; Gaurav Chauhan; Giorgio Palu; Adam M. Brufsky. Possible Transmission Flow of SARS-CoV-2 Based on ACE2 Features. Molecules 2020, 25, 5906 .

AMA Style

Sk. Sarif Hassan, Shinjini Ghosh, Diksha Attrish, Pabitra Pal Choudhury, Alaa A. A. Aljabali, Bruce D. Uhal, Kenneth Lundstrom, Nima Rezaei, Vladimir N. Uversky, Murat Seyran, Damiano Pizzol, Parise Adadi, Antonio Soares, Tarek Mohamed Abd El-Aziz, Ramesh Kandimalla, Murtaza M. Tambuwala, Gajendra Kumar Azad, Samendra P. Sherchan, Wagner Baetas-Da-Cruz, Kazuo Takayama, Ángel Serrano-Aroca, Gaurav Chauhan, Giorgio Palu, Adam M. Brufsky. Possible Transmission Flow of SARS-CoV-2 Based on ACE2 Features. Molecules. 2020; 25 (24):5906.

Chicago/Turabian Style

Sk. Sarif Hassan; Shinjini Ghosh; Diksha Attrish; Pabitra Pal Choudhury; Alaa A. A. Aljabali; Bruce D. Uhal; Kenneth Lundstrom; Nima Rezaei; Vladimir N. Uversky; Murat Seyran; Damiano Pizzol; Parise Adadi; Antonio Soares; Tarek Mohamed Abd El-Aziz; Ramesh Kandimalla; Murtaza M. Tambuwala; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Kazuo Takayama; Ángel Serrano-Aroca; Gaurav Chauhan; Giorgio Palu; Adam M. Brufsky. 2020. "Possible Transmission Flow of SARS-CoV-2 Based on ACE2 Features." Molecules 25, no. 24: 5906.

Preprint content
Published: 30 November 2020
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Clades are monophyletic groups composed of a common ancestor and all its lineal descendants. As the propensity of virulence of a disease depends upon the type of clade the virus belongs to and it causes different fatality rates of disease in different countries, so the clade-wise analysis of SARS-CoV-2 isolates collected from different countries can illuminate the actual evolutionary relationships between them. In this study, 1566 SARS-CoV-2 genome sequences across ten Asian countries are collected, clustered, and characterized based on the clade they belong to. The isolates are compared to the Wuhan reference sequence (Accession no:MN996528.1) to identify the mutations that occurred at different protein regions. Structural changes in amino acids due to mutations lead to functional instability of the proteins. Detailed clade-wise functional assessments are carried out to quantify the stability and vulnerability of the mutations occurring in SARS-CoV-2 genomes which can shade light on personalized prevention and treatment of the disease and encourage towards the invention of clade-specific vaccines.

ACS Style

Antara Sengupta; Sk. Sarif Hassan; Pabitra Pal Choudhury. Clade GR and Clade GH Isolates in Asia Show Highest Amount of SNPs. 2020, 1 .

AMA Style

Antara Sengupta, Sk. Sarif Hassan, Pabitra Pal Choudhury. Clade GR and Clade GH Isolates in Asia Show Highest Amount of SNPs. . 2020; ():1.

Chicago/Turabian Style

Antara Sengupta; Sk. Sarif Hassan; Pabitra Pal Choudhury. 2020. "Clade GR and Clade GH Isolates in Asia Show Highest Amount of SNPs." , no. : 1.

Preprint content
Published: 08 November 2020
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The coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) which is pandemic with an estimated fatality rate less than 1% is ongoing. SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 with putative functions to manipulate host immune mechanisms such as interferons, immune signaling receptor NLRP3 (NOD-, LRR-, and pyrin domain-containing 3) inflammasome, inflammatory cytokines such as interleukin 1β(IL-1β) are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins of all complete proteomes (available as of October 26, 2020, in the National Center for Biotechnology Information depository) of SARS-CoV-2, were observed across six continents. Across all continents, the decreasing order of percentage of unique variations in the accessory proteins was found to be ORF3a>ORF8>ORF7a>ORF6>ORF10>ORF7b. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. This finding suggests that the wide variations of accessory proteins seem to govern the pathogenicity of SARS-CoV-2, and consequently, certain propositions and recommendations can be made in the public interest.

ACS Style

Sk. Sarif Hassan; Pabitra Pal Choudhury; Vladimir N. Uversky; Guy W. Dayhoff; Alaa A. A. Aljabali; Bruce D. Uhal; Kenneth Lundstrom; Nima Rezaei; Murat Seyran; Damiano Pizzol; Parise Adadi; Amos Lal; Antonio Soares; Tarek Mohamed Abd El-Aziz; Ramesh Kandimalla; Murtaza Tambuwala; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Kazuo Takayama; Ángel Serrano-Aroca; Gaurav Chauhan; Giorgio Palu; Adam M. Brufsky. Variability of Accessory Proteins Rules the SARS-CoV-2 Pathogenicity. 2020, 1 .

AMA Style

Sk. Sarif Hassan, Pabitra Pal Choudhury, Vladimir N. Uversky, Guy W. Dayhoff, Alaa A. A. Aljabali, Bruce D. Uhal, Kenneth Lundstrom, Nima Rezaei, Murat Seyran, Damiano Pizzol, Parise Adadi, Amos Lal, Antonio Soares, Tarek Mohamed Abd El-Aziz, Ramesh Kandimalla, Murtaza Tambuwala, Gajendra Kumar Azad, Samendra P. Sherchan, Wagner Baetas-Da-Cruz, Kazuo Takayama, Ángel Serrano-Aroca, Gaurav Chauhan, Giorgio Palu, Adam M. Brufsky. Variability of Accessory Proteins Rules the SARS-CoV-2 Pathogenicity. . 2020; ():1.

Chicago/Turabian Style

Sk. Sarif Hassan; Pabitra Pal Choudhury; Vladimir N. Uversky; Guy W. Dayhoff; Alaa A. A. Aljabali; Bruce D. Uhal; Kenneth Lundstrom; Nima Rezaei; Murat Seyran; Damiano Pizzol; Parise Adadi; Amos Lal; Antonio Soares; Tarek Mohamed Abd El-Aziz; Ramesh Kandimalla; Murtaza Tambuwala; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Kazuo Takayama; Ángel Serrano-Aroca; Gaurav Chauhan; Giorgio Palu; Adam M. Brufsky. 2020. "Variability of Accessory Proteins Rules the SARS-CoV-2 Pathogenicity." , no. : 1.

Editorial
Published: 22 October 2020 in Viruses
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The origin of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) virus causing the COVID-19 pandemic has not yet been fully determined. Despite the consensus about the SARS-CoV-2 origin from bat CoV RaTG13, discrepancy to host tropism to other human Coronaviruses exist. SARS-CoV-2 also possesses some differences in its S protein receptor-binding domain, glycan-binding N-terminal domain and the surface of the sialic acid-binding domain. Despite similarities based on cryo-EM and biochemical studies, the SARS-CoV-2 shows higher stability and binding affinity to the ACE2 receptor. The SARS-CoV-2 does not appear to present a mutational “hot spot” as only the D614G mutation has been identified from clinical isolates. As laboratory manipulation is highly unlikely for the origin of SARS-CoV-2, the current possibilities comprise either natural selection in animal host before zoonotic transfer or natural selection in humans following zoonotic transfer. In the former case, despite SARS-CoV-2 and bat RaTG13 showing 96% identity some pangolin Coronaviruses exhibit very high similarity to particularly the receptor-binding domain of SARS-CoV-2. In the latter case, it can be hypothesized that the SARS-CoV-2 genome has adapted during human-to-human transmission and based on available data, the isolated SARS-CoV-2 genomes derive from a common origin. Before the origin of SARS-CoV-2 can be confirmed additional research is required

ACS Style

Kenneth Lundstrom; Murat Seyran; Damiano Pizzol; Parise Adadi; Tarek Mohamed Abd El-Aziz; Sk. Sarif Hassan; Antonio Soares; Ramesh Kandimalla; Murtaza M. Tambuwala; Alaa A. A. Aljabali; Gajendra Kumar Azad; Pabitra Pal Choudhury; Vladimir N. Uversky; Samendra P. Sherchan; Bruce D. Uhal; Nima Rezaei; Adam M. Brufsky. The Importance of Research on the Origin of SARS-CoV-2. Viruses 2020, 12, 1203 .

AMA Style

Kenneth Lundstrom, Murat Seyran, Damiano Pizzol, Parise Adadi, Tarek Mohamed Abd El-Aziz, Sk. Sarif Hassan, Antonio Soares, Ramesh Kandimalla, Murtaza M. Tambuwala, Alaa A. A. Aljabali, Gajendra Kumar Azad, Pabitra Pal Choudhury, Vladimir N. Uversky, Samendra P. Sherchan, Bruce D. Uhal, Nima Rezaei, Adam M. Brufsky. The Importance of Research on the Origin of SARS-CoV-2. Viruses. 2020; 12 (11):1203.

Chicago/Turabian Style

Kenneth Lundstrom; Murat Seyran; Damiano Pizzol; Parise Adadi; Tarek Mohamed Abd El-Aziz; Sk. Sarif Hassan; Antonio Soares; Ramesh Kandimalla; Murtaza M. Tambuwala; Alaa A. A. Aljabali; Gajendra Kumar Azad; Pabitra Pal Choudhury; Vladimir N. Uversky; Samendra P. Sherchan; Bruce D. Uhal; Nima Rezaei; Adam M. Brufsky. 2020. "The Importance of Research on the Origin of SARS-CoV-2." Viruses 12, no. 11: 1203.

Preprint content
Published: 09 October 2020
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Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is engendering the severe coronavirus disease 2019 (COVID-19) pandemic. The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 binds to the three sub-domains viz. amino acids (aa) 22-42, aa 79-84, and aa 330-393 of ACE2 on human cells to initiate entry. It was reported earlier that the receptor utilization capacity of ACE2 proteins from different species, such as cats, chimpanzees, dogs, and cattle, are different. A comprehensive analysis of ACE2 receptors of nineteen species was carried out in this study, and the findings propose a possible SARS-CoV-2 transmission flow across these nineteen species.

ACS Style

Sk. Sarif Hassan; Shinjini Ghosh; Diksha Attrish; Pabitra Pal Choudhury; Vladimir N Uversky; Bruce Uhal; Kenneth Lundstrom; Nima Rezaei; Alaa A.A Aljabali; Murat Seyran; Damiano Pizzol; Parise Adadi; Antonio Soares; Tarek Mohamed Abd El-Aziz; Ramesh Kandimalla; Murtaza Tambuwala; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Kazuo Takayama; Angel Serrano-Aroca; Gaurav Chauhan; Giorgio Palu; Adam Brufsky. Possible transmission flow of SARS-CoV-2 based on ACE2 features. 2020, 1 .

AMA Style

Sk. Sarif Hassan, Shinjini Ghosh, Diksha Attrish, Pabitra Pal Choudhury, Vladimir N Uversky, Bruce Uhal, Kenneth Lundstrom, Nima Rezaei, Alaa A.A Aljabali, Murat Seyran, Damiano Pizzol, Parise Adadi, Antonio Soares, Tarek Mohamed Abd El-Aziz, Ramesh Kandimalla, Murtaza Tambuwala, Gajendra Kumar Azad, Samendra P. Sherchan, Wagner Baetas-Da-Cruz, Kazuo Takayama, Angel Serrano-Aroca, Gaurav Chauhan, Giorgio Palu, Adam Brufsky. Possible transmission flow of SARS-CoV-2 based on ACE2 features. . 2020; ():1.

Chicago/Turabian Style

Sk. Sarif Hassan; Shinjini Ghosh; Diksha Attrish; Pabitra Pal Choudhury; Vladimir N Uversky; Bruce Uhal; Kenneth Lundstrom; Nima Rezaei; Alaa A.A Aljabali; Murat Seyran; Damiano Pizzol; Parise Adadi; Antonio Soares; Tarek Mohamed Abd El-Aziz; Ramesh Kandimalla; Murtaza Tambuwala; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Kazuo Takayama; Angel Serrano-Aroca; Gaurav Chauhan; Giorgio Palu; Adam Brufsky. 2020. "Possible transmission flow of SARS-CoV-2 based on ACE2 features." , no. : 1.

Preprint content
Published: 24 September 2020
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Phylogeny is a statistical approach displaying the evolutionary history of a genetically related group of organisms with the fundamental prerequisite of the utilization of a significant sample size that could represent the whole population under investigation. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) phylogeny analyses are based on a single isolate of BatCoVs, which is not a sufficient representation of genetically related CoVs. For instance, the unique Bat-CoV RaTG13 sequence that is genetically associated with SARS-CoV-2 was isolated from Yunnan, China, in 2013. To date, no other RaTG13 sequence has been obtained in a different time (temporal), place (spatial), or other host condition. Data scarcity of Bat-CoVs sequences raises concern on the several fundamental experimental and biostatistical aspects, e.g. repeatability of the sequences and intraspecies variation of critical genes, such as the receptor-binding domain of Spike protein. Sunda pangolin has been proposed as the intermediate host and source of SARS-CoV-2, but no Pangolin-CoV isolates have been isolated in Southeast Asia, where Sunda pangolins inhabit. Most Pangolin-CoVs were isolated from deceased pangolins, that were captured during illegal animal trafficking into China, hence raising questions about the reliability and quality of such isolates. Pangolin-CoV sampling problems are also evident in the deposited sequences that are of sub-standard quality. Therefore, there is urgent need for survey the Bat-CoVs and possible intermediate hosts, such as pangolins and civets in Southeast Asia. These surveys are required to investigate the genomic source of SARS-CoV-2 and assess possible future risks for new outbreaks. The current SARS-CoV-2 phylogeny with unacceptably limited numbers of Bat-CoVs and Pangolin-CoVs sequences not sufficient and technically not appropriate for reliable phylogenic analysis.

ACS Style

Murat Seyran; Sk Sarif Hassan; Vladimir N. Uversky; Pabitra Pal Choudhury; Bruce D. Uhal; Kenneth Lundstrom; Diksha Attrish; Nima Rezaei; Alaa A. A. Aljabali; Shinjini Ghosh; Damiano Pizzol; Parise Adadi; Tarek Mohamed Abd El-Aziz; Ramesh Kandimalla; Murtaza Tambuwala; Amos Lal; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Giorgio Palù; Adam Brufsky. Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for the Future Outbreaks. 2020, 1 .

AMA Style

Murat Seyran, Sk Sarif Hassan, Vladimir N. Uversky, Pabitra Pal Choudhury, Bruce D. Uhal, Kenneth Lundstrom, Diksha Attrish, Nima Rezaei, Alaa A. A. Aljabali, Shinjini Ghosh, Damiano Pizzol, Parise Adadi, Tarek Mohamed Abd El-Aziz, Ramesh Kandimalla, Murtaza Tambuwala, Amos Lal, Gajendra Kumar Azad, Samendra P. Sherchan, Wagner Baetas-Da-Cruz, Giorgio Palù, Adam Brufsky. Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for the Future Outbreaks. . 2020; ():1.

Chicago/Turabian Style

Murat Seyran; Sk Sarif Hassan; Vladimir N. Uversky; Pabitra Pal Choudhury; Bruce D. Uhal; Kenneth Lundstrom; Diksha Attrish; Nima Rezaei; Alaa A. A. Aljabali; Shinjini Ghosh; Damiano Pizzol; Parise Adadi; Tarek Mohamed Abd El-Aziz; Ramesh Kandimalla; Murtaza Tambuwala; Amos Lal; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Giorgio Palù; Adam Brufsky. 2020. "Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for the Future Outbreaks." , no. : 1.

Journal article
Published: 12 September 2020 in Genomics
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Envelope (E) protein is one of the structural viroporins (76–109 amino acids long) present in the coronavirus. Sixteen sequentially different E-proteins were observed from a total of 4917 available complete SARS-CoV-2 genomes as on 18th June 2020 in the NCBI database. The missense mutations over the envelope protein across various coronaviruses of the β-genus were analyzed to know the immediate parental origin of the envelope protein of SARS-CoV-2. The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations.

ACS Style

Sk. Sarif Hassan; Pabitra Pal Choudhury; Bidyut Roy. Molecular phylogeny and missense mutations at envelope proteins across coronaviruses. Genomics 2020, 112, 4993 -5004.

AMA Style

Sk. Sarif Hassan, Pabitra Pal Choudhury, Bidyut Roy. Molecular phylogeny and missense mutations at envelope proteins across coronaviruses. Genomics. 2020; 112 (6):4993-5004.

Chicago/Turabian Style

Sk. Sarif Hassan; Pabitra Pal Choudhury; Bidyut Roy. 2020. "Molecular phylogeny and missense mutations at envelope proteins across coronaviruses." Genomics 112, no. 6: 4993-5004.

Preprint content
Published: 06 September 2020
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The global public health is endangered due to COVID-19 pandemic, which is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Despite having similar pathology to MERS and SARS-CoV, the infection fatality rate of SARS-CoV-2 is likely lower than 1%. SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. Some of these mutations decrease the stability of ORF10, e.g. I4L and V6I were found in the MoRF region of ORF10 which may also possibly contribute to Intrinsic protein disorder. Furthermore, a physicochemical and structural comparative analysis was carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid homology. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Altogether, SARS-CoV-2 ORF10 is a promising pharmaceutical target and a protein which should be monitored for changes which correlate to change pathogenesis and clinical course of COVID-19 infection.

ACS Style

Sk. Sarif Hassan; Diksha Attrish; Shinjini Ghosh; Pabitra Pal Choudhury; Vladimir N. Uversky; Bruce D. Uhal; Kenneth Lundstrom; Nima Rezaei; Alaa A. A. Aljabali; Murat Seyran; Damiano Pizzol; Parise Adadi; Tarek Mohamed Abd El-Aziz; Antonio Soares; Ramesh Kandimalla; Murtaza Tambuwala; Amos Lal; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Giorgio Palù; Adam M. Brufsky. Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2. 2020, 1 .

AMA Style

Sk. Sarif Hassan, Diksha Attrish, Shinjini Ghosh, Pabitra Pal Choudhury, Vladimir N. Uversky, Bruce D. Uhal, Kenneth Lundstrom, Nima Rezaei, Alaa A. A. Aljabali, Murat Seyran, Damiano Pizzol, Parise Adadi, Tarek Mohamed Abd El-Aziz, Antonio Soares, Ramesh Kandimalla, Murtaza Tambuwala, Amos Lal, Gajendra Kumar Azad, Samendra P. Sherchan, Wagner Baetas-Da-Cruz, Giorgio Palù, Adam M. Brufsky. Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2. . 2020; ():1.

Chicago/Turabian Style

Sk. Sarif Hassan; Diksha Attrish; Shinjini Ghosh; Pabitra Pal Choudhury; Vladimir N. Uversky; Bruce D. Uhal; Kenneth Lundstrom; Nima Rezaei; Alaa A. A. Aljabali; Murat Seyran; Damiano Pizzol; Parise Adadi; Tarek Mohamed Abd El-Aziz; Antonio Soares; Ramesh Kandimalla; Murtaza Tambuwala; Amos Lal; Gajendra Kumar Azad; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Giorgio Palù; Adam M. Brufsky. 2020. "Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2." , no. : 1.

Preprint content
Published: 26 August 2020
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Immune evasion is one of the unique characteristics of COVID-19 attributed to the ORF8 protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This protein is involved in modulating the host adaptive immunity through downregulating MHC (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the interferon mediated antiviral response of the host. To understand the immune perspective of the host with respect to the ORF8 protein, a comprehensive study of the ORF8 protein as well as mutations possessed by it, is performed. Chemical and structural properties of ORF8 proteins from different hosts, that is human, bat and pangolin, suggests that the ORF8 of SARS-CoV-2 and Bat RaTG13-CoV are very much closer related than that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 (SARS-CoV-2) are grouped into four classes based on their predicted effects. Based on geolocations and timescale of collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were endorsed upon sequence similarity and amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of rapid evolving SARS-CoV-2 through the ORF8.

ACS Style

Sk. Sarif Hassan; Shinjini Ghosh; Diksha Attrish; Pabirtra Pal Choudhury; Murat Seyran; Damiano Pizzol; Parise Adadi; Tarek Muhammed Abd El Aziz; Antonio Soares; Ramesh Kandimalla; Kenneth Lundstrom; Murtaza Tambuwala; Alaa A. A. Aljabali; Amos Lal; Gajendra Kumar Azad; Vladimir N. Uversky; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Bruce D. Uhal; Nima Rezaei; Adam M. Brufsky. A unique view of SARS-CoV-2 through the lens of ORF8 protein. 2020, 1 .

AMA Style

Sk. Sarif Hassan, Shinjini Ghosh, Diksha Attrish, Pabirtra Pal Choudhury, Murat Seyran, Damiano Pizzol, Parise Adadi, Tarek Muhammed Abd El Aziz, Antonio Soares, Ramesh Kandimalla, Kenneth Lundstrom, Murtaza Tambuwala, Alaa A. A. Aljabali, Amos Lal, Gajendra Kumar Azad, Vladimir N. Uversky, Samendra P. Sherchan, Wagner Baetas-Da-Cruz, Bruce D. Uhal, Nima Rezaei, Adam M. Brufsky. A unique view of SARS-CoV-2 through the lens of ORF8 protein. . 2020; ():1.

Chicago/Turabian Style

Sk. Sarif Hassan; Shinjini Ghosh; Diksha Attrish; Pabirtra Pal Choudhury; Murat Seyran; Damiano Pizzol; Parise Adadi; Tarek Muhammed Abd El Aziz; Antonio Soares; Ramesh Kandimalla; Kenneth Lundstrom; Murtaza Tambuwala; Alaa A. A. Aljabali; Amos Lal; Gajendra Kumar Azad; Vladimir N. Uversky; Samendra P. Sherchan; Wagner Baetas-Da-Cruz; Bruce D. Uhal; Nima Rezaei; Adam M. Brufsky. 2020. "A unique view of SARS-CoV-2 through the lens of ORF8 protein." , no. : 1.

Preprint content
Published: 20 August 2020
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There is a consensus that SARS-CoV-2 originated naturally from BatCoVs. Although based on phylogenetic analysis SARS-CoV-2 seems to be related to BatCoVs RaTG13 or RmYN02, its exact origin of lineage is not clear. In fact, the flat and non-sunken surface of the sialic acid-binding domain of SARS-CoV-2 spike protein conflicts with the general adaptation and survival pattern observed for all other coronaviruses (CoVs). Unlike RaTG13, for SARS-CoV-2 a recombination apparently occured between the S1/S2 domains of spike protein that enabled furin protease utilization. Interestingly, the clinical strains of SARS-CoV-2 do not have any further recombination that would be in conflict with the recombination models of CoVs. Despite millions of SARS-CoV-2 infections, the spike protein receptor-binding domain (RBD) has not accumulated a high-frequency substitution, differentiating SARS-CoV-2 from other CoVs that have positive selection sites on their RBDs, calling into question the sources of the origin of the apparently optimized angiotensin-converting enzyme 2 (ACE2) binding of SARS-CoV-2. The SARS-CoV-2 host tropism pattern has these major discrepancies compared to other CoVs, raising questions concerning the proximal origin of SARS-CoV-2.

ACS Style

Murat Seyran; Damiano Pizzol; Parise Adadi; Tarek Mohamed Abd El-Aziz; Sk Sarif Hassan; Antonio Soares; Ramesh Kandimalla; Kenneth Lundstrom; Murtaza Tambuwala. Unique features concerning the proximal origin of SARS-CoV-2. 2020, 1 .

AMA Style

Murat Seyran, Damiano Pizzol, Parise Adadi, Tarek Mohamed Abd El-Aziz, Sk Sarif Hassan, Antonio Soares, Ramesh Kandimalla, Kenneth Lundstrom, Murtaza Tambuwala. Unique features concerning the proximal origin of SARS-CoV-2. . 2020; ():1.

Chicago/Turabian Style

Murat Seyran; Damiano Pizzol; Parise Adadi; Tarek Mohamed Abd El-Aziz; Sk Sarif Hassan; Antonio Soares; Ramesh Kandimalla; Kenneth Lundstrom; Murtaza Tambuwala. 2020. "Unique features concerning the proximal origin of SARS-CoV-2." , no. : 1.

Short communication
Published: 19 August 2020 in Genomics
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The genetic diversity of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) in several countries sums up to worldwide genetic diversity. In this present study, variations in terms of missense mutations among the SARS-CoV2 genomes from 128 Indian patients, as of May 2020, are accounted and thereby some key findings with some hypotheses were made. These mutations across various genes of these genomes show wide genetic variations in sequence and rapid evolution of SARS-CoV2 virus. The presence of unique mutations in the studied SARS-CoV2 genomes may led to their attenuation. Few Genes such as ORF6, ORF10 are free from any mutations in the Indian context of 339 genomes observed as of 14th July 2020. Further, E protein contains only one mutation. This may suggest that designing a therapeutic approach against ORF6, ORF10 and E genes may have a beneficial effect in controlling COVID-19 pandemic especially in India.

ACS Style

Sk. Sarif Hassan; Pabitra Pal Choudhury; Bidyut Roy; Siddhartha Sankar Jana. Missense mutations in SARS-CoV2 genomes from Indian patients. Genomics 2020, 112, 4622 -4627.

AMA Style

Sk. Sarif Hassan, Pabitra Pal Choudhury, Bidyut Roy, Siddhartha Sankar Jana. Missense mutations in SARS-CoV2 genomes from Indian patients. Genomics. 2020; 112 (6):4622-4627.

Chicago/Turabian Style

Sk. Sarif Hassan; Pabitra Pal Choudhury; Bidyut Roy; Siddhartha Sankar Jana. 2020. "Missense mutations in SARS-CoV2 genomes from Indian patients." Genomics 112, no. 6: 4622-4627.