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Gajendra Kumar Azad
Department of Zoology, Patna University, Patna 800005, Bihar, India

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Preprint
Published: 26 July 2021
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The devastating impact of the ongoing coronavirus disease 2019 (COVID-19) on public health, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has made fighting of the COVID-19 pandemic is a top priority in medical research and pharmaceutical development. Surveillance of SARS-CoV-2 mutations is essential for the comprehension of SARS-CoV-2 variant diversity and their impact on virulence and pathogenicity. The SARS-CoV-2 open reading frame 10 (ORF10) protein interacts with multiple human proteins CUL2, ELOB, ELOC, MAP7D1, PPT1, RBX1, THTPA, TIMM8B, and ZYG11B expressed in the lung tissues. Mutations and co-mutations in the emerging SARS-CoV-2 ORF10 variants are expected to impact the severity of the virus and its associated consequences. In this article, We highlight 128 single mutations and 35 co-mutations in the unique SARS-CoV-2 ORF10 variants in this article. The possible predicted effects of these mutations and co-mutations on the secondary structure of ORF10 variants and host protein interactomes are presented. The findings highlight the possible effects of mutations and co-mutations on the emerging 140 ORF10 unique variants from secondary structure and intrinsic protein disorder perspectives.

ACS Style

Sk. Sarif Hassan; Kenneth Lundstrom; Ángel Serrano-Aroca; Parise Adadi; Alaa Aljabali; ElRashdy Redwan; Amos Lal; Ramesh Kandimalla; Tarek El-Aziz; Pabitra Choudhury; Gajendra Azad; Samendra Sherchan; Murtaza Tambuwala; Gaurav Chauhan; Kazuo Takayama; Debmalya Barh; Giorgio Palù; Pallab Basu; Vladimir N Uversky. Emergence of Unique SARS-CoV-2 ORF10 Variants and Their Impact on Protein Structure and Function. 2021, 1 .

AMA Style

Sk. Sarif Hassan, Kenneth Lundstrom, Ángel Serrano-Aroca, Parise Adadi, Alaa Aljabali, ElRashdy Redwan, Amos Lal, Ramesh Kandimalla, Tarek El-Aziz, Pabitra Choudhury, Gajendra Azad, Samendra Sherchan, Murtaza Tambuwala, Gaurav Chauhan, Kazuo Takayama, Debmalya Barh, Giorgio Palù, Pallab Basu, Vladimir N Uversky. Emergence of Unique SARS-CoV-2 ORF10 Variants and Their Impact on Protein Structure and Function. . 2021; ():1.

Chicago/Turabian Style

Sk. Sarif Hassan; Kenneth Lundstrom; Ángel Serrano-Aroca; Parise Adadi; Alaa Aljabali; ElRashdy Redwan; Amos Lal; Ramesh Kandimalla; Tarek El-Aziz; Pabitra Choudhury; Gajendra Azad; Samendra Sherchan; Murtaza Tambuwala; Gaurav Chauhan; Kazuo Takayama; Debmalya Barh; Giorgio Palù; Pallab Basu; Vladimir N Uversky. 2021. "Emergence of Unique SARS-CoV-2 ORF10 Variants and Their Impact on Protein Structure and Function." , no. : 1.

Correspondence
Published: 16 July 2021 in Autoimmunity Reviews
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ACS Style

Elrashdy M. Redwan; Mohammed F. Alghamdi; Tarek Mohamed Abd El-Aziz; Parise Adadi; Alaa A.A. Aljabali; Diksha Attrish; Gajendra Kumar Azad; Wagner Baetas-Da-Cruz; Debmalya Barh; Nicolas G. Bazan; Adam M. Brufsky; Gaurav Chauhan; S.K. Sarif Hassan; Ramesh Kandimalla; Amos Lal; Kenneth Lundstrom; Yogendra Kumar Mishra; Pabitra Pal Choudhury; Giorgio Palù; Pritam K. Panda; Damiano Pizzol; Nima Rezaei; Ángel Serrano-Aroca; Samendra P. Sherchan; Murat Seyran; Kazuo Takayama; Murtaza M. Tambuwala; Bruce D. Uhal; Vladimir N. Uversky. The mechanism behind flaring/triggering of autoimmunity disorders associated with COVID-19. Autoimmunity Reviews 2021, 20, 102909 -102909.

AMA Style

Elrashdy M. Redwan, Mohammed F. Alghamdi, Tarek Mohamed Abd El-Aziz, Parise Adadi, Alaa A.A. Aljabali, Diksha Attrish, Gajendra Kumar Azad, Wagner Baetas-Da-Cruz, Debmalya Barh, Nicolas G. Bazan, Adam M. Brufsky, Gaurav Chauhan, S.K. Sarif Hassan, Ramesh Kandimalla, Amos Lal, Kenneth Lundstrom, Yogendra Kumar Mishra, Pabitra Pal Choudhury, Giorgio Palù, Pritam K. Panda, Damiano Pizzol, Nima Rezaei, Ángel Serrano-Aroca, Samendra P. Sherchan, Murat Seyran, Kazuo Takayama, Murtaza M. Tambuwala, Bruce D. Uhal, Vladimir N. Uversky. The mechanism behind flaring/triggering of autoimmunity disorders associated with COVID-19. Autoimmunity Reviews. 2021; 20 (10):102909-102909.

Chicago/Turabian Style

Elrashdy M. Redwan; Mohammed F. Alghamdi; Tarek Mohamed Abd El-Aziz; Parise Adadi; Alaa A.A. Aljabali; Diksha Attrish; Gajendra Kumar Azad; Wagner Baetas-Da-Cruz; Debmalya Barh; Nicolas G. Bazan; Adam M. Brufsky; Gaurav Chauhan; S.K. Sarif Hassan; Ramesh Kandimalla; Amos Lal; Kenneth Lundstrom; Yogendra Kumar Mishra; Pabitra Pal Choudhury; Giorgio Palù; Pritam K. Panda; Damiano Pizzol; Nima Rezaei; Ángel Serrano-Aroca; Samendra P. Sherchan; Murat Seyran; Kazuo Takayama; Murtaza M. Tambuwala; Bruce D. Uhal; Vladimir N. Uversky. 2021. "The mechanism behind flaring/triggering of autoimmunity disorders associated with COVID-19." Autoimmunity Reviews 20, no. 10: 102909-102909.

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.

Preprint content
Published: 05 May 2021
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The RNA dependent RNA polymerase (RdRp) plays crucial role in virus life cycle by replicating the viral RNA genome. The SARS-CoV-2 is an RNA virus that rapidly spread worldwide and during this process acquired mutations. This study was carried out to identify mutations in RdRp as the SARS-CoV-2 spread in India. We compared the 668 RdRp sequences reported from India with the first reported RdRp sequence from Wuhan, China. Our data revealed that RdRp have acquired sixty mutations among Indian isolates. Our protein modelling study also revealed that several mutants including D833Y, A699S, Y149C and C464F can potentially alter stability and flexibility of RdRp. We also predicted the potential B cell epitopes contributed by RdRp and identified thirty-six linear continuous and twenty-five discontinuous epitopes. Among sixty RdRp mutants identified in this study, 40% of them localizes in the B cell epitopes region. Altogether, this study highlights the need to identify and characterize the variations in RdRp to understand the impact of these mutations on SARS-CoV-2.

ACS Style

Sushant Kumar; Gajendra Kumar Azad. Emerging genetic diversity of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) alters its B-cell epitopes. 2021, 1 .

AMA Style

Sushant Kumar, Gajendra Kumar Azad. Emerging genetic diversity of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) alters its B-cell epitopes. . 2021; ():1.

Chicago/Turabian Style

Sushant Kumar; Gajendra Kumar Azad. 2021. "Emerging genetic diversity of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) alters its B-cell epitopes." , no. : 1.

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.

Preprint content
Published: 02 April 2021
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The on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2 has infected hundreds of millions of people and killed more than two million people worldwide. Currently, there are no effective drugs available for treating SARS-CoV-2 infections; however, vaccines are now being administered worldwide to control this virus. In this study, we have studied SARS-CoV-2 helicase, Nsp13, which is critical for viral replication. We compared the Nsp13 sequences reported from India with the first reported sequence from Wuhan province, China to identify and characterize the mutations occurring in this protein. To correlate the functional impact of these mutations, we characterised the most prominent B cell and T cell epitopes contributed by Nsp13. Our data revealed twenty-one epitopes, which exhibited high antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were also analysed. Furthermore, several of these Nsp13 epitopes harbour mutations, which were further characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. Altogether, we report the candidate epitopes of Nsp13 that may help the scientific community to understand the evolution of SARS-CoV-2 variants and their probable implications.

ACS Style

Sushant Kumar; Gajendra Kumar Azad. An immunoinformatics approach to study the epitopes contributed by Nsp13 of SARS-CoV-2. 2021, 1 .

AMA Style

Sushant Kumar, Gajendra Kumar Azad. An immunoinformatics approach to study the epitopes contributed by Nsp13 of SARS-CoV-2. . 2021; ():1.

Chicago/Turabian Style

Sushant Kumar; Gajendra Kumar Azad. 2021. "An immunoinformatics approach to study the epitopes contributed by Nsp13 of SARS-CoV-2." , no. : 1.

Journal article
Published: 25 March 2021 in Biochemistry and Biophysics Reports
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The population of catfish, Clarias batrachus has substantially diminished in various countries and studies show that another related species Clarias gariepinus is replacing it. The better adaptability and survivability of C. gariepinus over C. batrachus could be attributed to the metabolic differences between these two species, which is primarily regulated by mitochondrial activities. To understand the reasons behind this phenomenon, we performed in silico analyses to decipher the differences between the proteins encoded by the mitochondrial genome of these two related species. Our analysis revealed that out of thirteen, twelve proteins encoded by the mitochondrial genome of these two species have substantial variations between them. We characterised these variations by analysing their effect on secondary structure, intrinsic disorder predisposition, and functional impact on protein and stability parameters. Our data show that most of the parameters are changing between these two closely related species. Altogether, we demonstrate the molecular insights into the mitochondrial genome-encoded proteins of these two species and predict their effect on protein function and stability that might be helping C. gariepinus to gain survivability better than the C. batrachus.

ACS Style

Gyanendra Bahadur Chand; Sushant Kumar; Gajendra Kumar Azad. Molecular assessment of proteins encoded by the mitochondrial genome of Clarias batrachus and Clarias gariepinus. Biochemistry and Biophysics Reports 2021, 26, 100985 .

AMA Style

Gyanendra Bahadur Chand, Sushant Kumar, Gajendra Kumar Azad. Molecular assessment of proteins encoded by the mitochondrial genome of Clarias batrachus and Clarias gariepinus. Biochemistry and Biophysics Reports. 2021; 26 ():100985.

Chicago/Turabian Style

Gyanendra Bahadur Chand; Sushant Kumar; Gajendra Kumar Azad. 2021. "Molecular assessment of proteins encoded by the mitochondrial genome of Clarias batrachus and Clarias gariepinus." Biochemistry and Biophysics Reports 26, no. : 100985.

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.

Journal article
Published: 01 February 2021 in Heliyon
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Coronavirus disease- 2019 (COVID-19) has rapidly become a major threat to humans due to its high infection rate and deaths caused worldwide. This disease is caused by an RNA virus, Severe Acquired Respiratory Syndrome –Corona Virus-2 (SARS-CoV-2). This class of viruses have a high rate of mutation than DNA viruses that enables them to adapt and also evade host immune system. Here, we compared the first known Nucleocapsid Phosphoprotein (N protein) sequence of SARS-CoV-2 from China with the sequences from Indian COVID-19 patients to understand, if this virus is also mutating, as it is spreading to new locations. Our data revealed twenty mutations present among Indian isolates. Out of these, mutation at six positions led to changes in the secondary structure of N protein. Further, we also show that these mutations are primarily destabilising the protein structure. The candidate mutations identified in this study may help to speed up the understanding of variations occurring in SARS-CoV-2.

ACS Style

Gajendra Kumar Azad. The molecular assessment of SARS-CoV-2 Nucleocapsid Phosphoprotein variants among Indian isolates. Heliyon 2021, 7, e06167 -e06167.

AMA Style

Gajendra Kumar Azad. The molecular assessment of SARS-CoV-2 Nucleocapsid Phosphoprotein variants among Indian isolates. Heliyon. 2021; 7 (2):e06167-e06167.

Chicago/Turabian Style

Gajendra Kumar Azad. 2021. "The molecular assessment of SARS-CoV-2 Nucleocapsid Phosphoprotein variants among Indian isolates." Heliyon 7, no. 2: e06167-e06167.

Journal article
Published: 27 January 2021 in Biochemistry and Biophysics Reports
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Severe acquired respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly spread worldwide and acquired multiple mutations in its genome. Orf3a, an accessory protein encoded by the genome of SARS-CoV-2, plays a significant role in viral infection and pathogenesis. In the present in-silico study, 15,928 sequences of Orf3a reported worldwide were compared to identify variations in this protein. Our analysis revealed the occurrence of mutations at 173 residues of Orf3a protein. Subsequently, protein modelling was performed that revealed twelve mutations which can considerably affect the stability of Orf3a. Among the 12 mutations, three mutations (Y160H, D210Y and S171L) also lead to alterations in secondary structure and protein disorder parameters of the Orf3a protein. Further, we used predictive tools to identify five promising epitopes of B-cells, which resides in the mutated regions of Orf3a. Altogether, our study sheds light on the variations occurring in Orf3a that might contribute to alteration in protein structure and function.

ACS Style

Gajendra Kumar Azad; Parimal Kumar Khan. Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Biochemistry and Biophysics Reports 2021, 26, 100933 .

AMA Style

Gajendra Kumar Azad, Parimal Kumar Khan. Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Biochemistry and Biophysics Reports. 2021; 26 ():100933.

Chicago/Turabian Style

Gajendra Kumar Azad; Parimal Kumar Khan. 2021. "Variations in Orf3a protein of SARS-CoV-2 alter its structure and function." Biochemistry and Biophysics Reports 26, no. : 100933.

Genetics
Published: 04 January 2021 in PeerJ
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SARS-CoV-2 genome encodes four structural proteins that include the spike glycoprotein, membrane protein, envelope protein and nucleocapsid phosphoprotein (N-protein). The N-protein interacts with viral genomic RNA and helps in packaging. As SARS-CoV-2 spread to almost all countries worldwide within 2–3 months, it also acquired mutations in its RNA genome. Therefore, this study was conducted with an aim to identify the variations present in N-protein of SARS-CoV-2. Here, we analysed 4,163 reported sequence of N-protein from United States of America (USA) and compared them with the first reported sequence from Wuhan, China. Our study identified 107 mutations that reside all over the N-protein. Further, we show the high rate of mutations in intrinsically disordered regions (IDRs) of N-protein. Our study show 45% residues of IDR2 harbour mutations. The RNA-binding domain (RBD) and dimerization domain of N-protein also have mutations at key residues. We further measured the effect of these mutations on N-protein stability and dynamicity and our data reveals that multiple mutations can cause considerable alterations. Altogether, our data strongly suggests that N-protein is one of the mutational hotspot proteins of SARS-CoV-2 that is changing rapidly and these mutations can potentially interferes with various aspects of N-protein functions including its interaction with RNA, oligomerization and signalling events.

ACS Style

Gajendra Kumar Azad. Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2. PeerJ 2021, 9, e10666 .

AMA Style

Gajendra Kumar Azad. Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2. PeerJ. 2021; 9 ():e10666.

Chicago/Turabian Style

Gajendra Kumar Azad. 2021. "Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2." PeerJ 9, no. : e10666.

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.

Structural snapshot
Published: 02 December 2020 in The FEBS Journal
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Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) is the causative agent of the pandemic coronavirus disease 2019 (COVID‐19) that exhibits an overwhelming contagious capacity over other Human Coronaviruses (HCoVs). This structural snapshot describes the structural bases underlying the pandemic capacity of SARS‐CoV‐2 and explains its fast motion over respiratory epithelia that allow its rapid cellular entry. Based on notable viral spike (S) protein features, we propose that the flat sialic acid‐binding domain at the N‐terminal domain (NTD) of the S1 subunit leads to more effective first contact and interaction with the sialic acid layer over the epithelium and this, in turn, allows faster viral "surfing" of the epithelium and receptor scanning by SARS‐CoV‐2. Angiotensin‐converting enzyme 2 (ACE‐2) protein on the epithelial surface is the primary entry receptor for SARS‐CoV‐2, and protein‐protein interaction assays demonstrate high‐affinity binding of the S protein to ACE‐2. To date, no high‐frequency mutations were detected at the C‐terminal domain (CTD) of the S1 subunit in the S protein, where the receptor‐binding domain (RBD) is located. Tight binding to ACE‐2 by a conserved viral RBD suggests the ACE2‐RBD interaction is likely optimal. Moreover, the viral S subunit contains a cleavage site for furin and other proteases, which accelerates cell entry by SARS‐CoV‐2. The model proposed here describes a structural basis for the accelerated host cell entry by SARS‐CoV‐2 relative to other HCoVs, and also discusses emerging hypotheses that are likely to contribute to the development of antiviral strategies to combat the pandemic capacity of SARS‐CoV‐2.

ACS Style

Murat Seyran; Kazuo Takayama; Vladimir N. Uversky; Kenneth Lundstrom; Giorgio Palù; Samendra P. Sherchan; Diksha Attrish; Nima Rezaei; Alaa A. A. Aljabali; Shinjini Ghosh; Damiano Pizzol; Gaurav Chauhan; Parise Adadi; Tarek Mohamed Abd El‐Aziz; Antonio G. Soares; Ramesh Kandimalla; Murtaza Tambuwala; Sk. Sarif Hassan; Gajendra Kumar Azad; Pabitra Pal Choudhury; Wagner Baetas‐Da‐Cruz; Ángel Serrano‐Aroca; Adam M. Brufsky; Bruce D. Uhal. The structural basis of accelerated host cell entry by SARS‐CoV‐2†. The FEBS Journal 2020, 1 .

AMA Style

Murat Seyran, Kazuo Takayama, Vladimir N. Uversky, Kenneth Lundstrom, Giorgio Palù, Samendra P. Sherchan, Diksha Attrish, Nima Rezaei, Alaa A. A. Aljabali, Shinjini Ghosh, Damiano Pizzol, Gaurav Chauhan, Parise Adadi, Tarek Mohamed Abd El‐Aziz, Antonio G. Soares, Ramesh Kandimalla, Murtaza Tambuwala, Sk. Sarif Hassan, Gajendra Kumar Azad, Pabitra Pal Choudhury, Wagner Baetas‐Da‐Cruz, Ángel Serrano‐Aroca, Adam M. Brufsky, Bruce D. Uhal. The structural basis of accelerated host cell entry by SARS‐CoV‐2†. The FEBS Journal. 2020; ():1.

Chicago/Turabian Style

Murat Seyran; Kazuo Takayama; Vladimir N. Uversky; Kenneth Lundstrom; Giorgio Palù; Samendra P. Sherchan; Diksha Attrish; Nima Rezaei; Alaa A. A. Aljabali; Shinjini Ghosh; Damiano Pizzol; Gaurav Chauhan; Parise Adadi; Tarek Mohamed Abd El‐Aziz; Antonio G. Soares; Ramesh Kandimalla; Murtaza Tambuwala; Sk. Sarif Hassan; Gajendra Kumar Azad; Pabitra Pal Choudhury; Wagner Baetas‐Da‐Cruz; Ángel Serrano‐Aroca; Adam M. Brufsky; Bruce D. Uhal. 2020. "The structural basis of accelerated host cell entry by SARS‐CoV‐2†." The FEBS Journal , 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.

Journal article
Published: 10 October 2020 in Biochemistry and Biophysics Reports
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A recent outburst of the pandemic caused by a member of the coronaviridae family identified as SARS-CoV-2. The highly contagious nature of the virus allows it to spread rapidly worldwide and caused severe healthcare and economic distress. So far, no proper line of treatment or vaccines has been available against SARS-CoV-2. Since, the infected people rapidly increased, causing the saturation of healthcare systems with coronavirus disease (COVID-19) patients. As the virus spread to new locations it also acquired various mutations. Here, in this study, we focused on identifying mutations in one of the crucial complex of SARS-CoV-2, the Nsp10-Nsp16 2′-O-methyltransferase complex. This complex plays indispensable role in the post-transcriptional modifications of viral RNA by its capping. We analysed 208 sequences of Nsp10-Nsp16 reported from India and compared with first reported sequence from Wuhan, China. Our analysis revealed a single mutation in Nsp10 and five mutations in Nsp16 protein. We also show that these mutations are leading to alteration in the secondary structure of Nsp10-Nsp16. Further, the protein modelling studies revealed that the mutation of both Nsp10-Nsp16 impacts the protein dynamicity and stability. Altogether, this study provides novel insights into the variations observed in the proteins of SARS-CoV-2 that might have functional consequences.

ACS Style

Gajendra Kumar Azad. Identification of novel mutations in the methyltransferase complex (Nsp10-Nsp16) of SARS-CoV-2. Biochemistry and Biophysics Reports 2020, 24, 100833 -100833.

AMA Style

Gajendra Kumar Azad. Identification of novel mutations in the methyltransferase complex (Nsp10-Nsp16) of SARS-CoV-2. Biochemistry and Biophysics Reports. 2020; 24 ():100833-100833.

Chicago/Turabian Style

Gajendra Kumar Azad. 2020. "Identification of novel mutations in the methyltransferase complex (Nsp10-Nsp16) of SARS-CoV-2." Biochemistry and Biophysics Reports 24, no. : 100833-100833.

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.

Short communication
Published: 28 September 2020 in Gene Reports
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SARS-CoV-2, the causative agent of the COVID-19 pandemic, is an RNA virus that has inherent high rate of mutation. Due to the mutations, the virus evolves at a rapid pace that helps them to survive better inside the host. One of the hotspots of pharmacological interventions is to inhibit binding of virus with the host cells, which is mediated by Spike glycoprotein of SARS-CoV-2 and ACE2 receptors present on the human cells. This study was conducted with an aim to identify and characterise the mutation (s) present in the Spike glycoprotein of the SARS-CoV-2. Towards this, an in silico methodology was used, and the mutations on Spike glycoprotein were identified by comparing the Spike glycoprotein of first reported sequence from Wuhan wet seafood market virus with the available sequences of SARS-CoV-2 from Indian isolates. Our analysis revealed the presence of twenty-five mutations in Spike glycoprotein among Indian SARS-CoV-2 isolates. These mutations spread all over the protein and can be clustered at least into four distinct positions. Further, mutations at eleven positions exhibited alterations in the secondary structure of the polypeptide chain. We also investigated the influence of these mutations on overall protein dynamics and have shown that they affect the dynamic stability of the Spike glycoprotein.

ACS Style

Gyanendra Bahadur Chand; Atanu Banerjee; Gajendra Kumar Azad. Identification of twenty-five mutations in surface glycoprotein (Spike) of SARS-CoV-2 among Indian isolates and their impact on protein dynamics. Gene Reports 2020, 21, 100891 -100891.

AMA Style

Gyanendra Bahadur Chand, Atanu Banerjee, Gajendra Kumar Azad. Identification of twenty-five mutations in surface glycoprotein (Spike) of SARS-CoV-2 among Indian isolates and their impact on protein dynamics. Gene Reports. 2020; 21 ():100891-100891.

Chicago/Turabian Style

Gyanendra Bahadur Chand; Atanu Banerjee; Gajendra Kumar Azad. 2020. "Identification of twenty-five mutations in surface glycoprotein (Spike) of SARS-CoV-2 among Indian isolates and their impact on protein dynamics." Gene Reports 21, no. : 100891-100891.