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  1. Article: The molecular assessment of SARS-CoV-2 Nucleocapsid Phosphoprotein variants among Indian isolates.

    Azad, Gajendra Kumar

    Heliyon

    2021  Volume 7, Issue 2, Page(s) e06167

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2021-02-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2021.e06167
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  2. Article: Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2.

    Azad, Gajendra Kumar

    PeerJ

    2021  Volume 9, Page(s) e10666

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2021-01-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.10666
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Identification of novel mutations in the methyltransferase complex (Nsp10-Nsp16) of SARS-CoV-2.

    Azad, Gajendra Kumar

    Biochemistry and biophysics reports

    2020  Volume 24, Page(s) 100833

    Abstract: 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 ... ...

    Abstract 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'-
    Keywords covid19
    Language English
    Publishing date 2020-10-10
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2831046-9
    ISSN 2405-5808 ; 2405-5808
    ISSN (online) 2405-5808
    ISSN 2405-5808
    DOI 10.1016/j.bbrep.2020.100833
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13.

    Kumar, Sushant / Kumari, Khushboo / Azad, Gajendra Kumar

    Vacunas

    2023  

    Abstract: Introduction and objective: Vaccines are administered worldwide to control on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2. Vaccine efficacy is largely contributed by the epitopes present on the viral proteins and their ... ...

    Abstract Introduction and objective: Vaccines are administered worldwide to control on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2. Vaccine efficacy is largely contributed by the epitopes present on the viral proteins and their alteration might help emerging variants to escape host immune surveillance. Therefore, this study was designed to study SARS-CoV-2 Nsp13 protein, its epitopes and evolution.
    Methods: Clustal Omega was used to identify mutations in Nsp13 protein. Secondary structure and disorder score was predicted by CFSSP and PONDR-VSL2 webservers. Protein stability was predicted by DynaMut webserver. B cell epitopes were predicted by IEDB DiscoTope 2.0 tools and their 3D structures were represented by discovery studio. Antigenicity and allergenicity of epitopes were predicted by Vaxijen2.0 and AllergenFPv.1.0. Physiochemical properties of epitopes were predicted by Toxinpred, HLP webserver tool.
    Results: Our data revealed 182 mutations in Nsp13 among Indian SARS-CoV-2 isolates, which were characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. 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 antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were analysed. Furthermore, eighteen mutations reside in these Nsp13 epitopes.
    Conclusions: We report appearance of eighteen mutations in the predicted twenty-one epitopes of Nsp13. Among these, at least seven epitopes closely matches with the functionally validated epitopes. Altogether, our study shows the pattern of evolution of Nsp13 epitopes and their probable implications.
    Language English
    Publishing date 2023-03-02
    Publishing country Spain
    Document type Journal Article
    ISSN 1576-9887
    ISSN 1576-9887
    DOI 10.1016/j.vacun.2023.02.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implications.

    Yasmin, Shahla / Kumar, Sushant / Azad, Gajendra Kumar

    Journal, genetic engineering & biotechnology

    2023  Volume 21, Issue 1, Page(s) 80

    Abstract: Background: The Pavo cristatus population, native to the Indian subcontinent, is thriving well in India. However, the Pavo muticus population, native to the tropical forests of Southeast Asia, has reduced drastically and has been categorised as an ... ...

    Abstract Background: The Pavo cristatus population, native to the Indian subcontinent, is thriving well in India. However, the Pavo muticus population, native to the tropical forests of Southeast Asia, has reduced drastically and has been categorised as an endangered group. To understand the probable genetic factors associated with the decline of P. muticus, we compared the mitogenome-encoded proteins (13 proteins) between these two species.
    Results: Our data revealed that the most frequent variant between these two species was mtND1, which had an alteration in 9.57% residues, followed by mtND5 and mtATP6. We extended our study on the rest of the proteins and observed that cytochrome c oxidase subunits 1, 2, and 3 do not have any change. The 3-dimensional structure of all 13 proteins was modeled using the Phyre2 programme. Our data show that most of the proteins are alpha helical, and the variations observed in P. muticus reside on the surface of the respective proteins. The effect of variation on protein function was also predicted, and our results show that amino acid substitution in mtND1 at 14 sites could be deleterious. Similarly, destabilising changes were observed in mtND1, 2, 3, 4, 5, and 6 and mtATP6-8 due to amino acid substitution in P. muticus. Furthermore, protein disorder scores were considerably altered in mtND1, 2, and 5 of P. muticus.
    Conclusions: The results presented here strongly suggest that variations in mitogenome-encoded proteins of P. cristatus and P. muticus may alter their structure and functions. Subsequently, these variations could alter energy production and may correlate with the decline in the population of P. muticus.
    Language English
    Publishing date 2023-08-07
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2637420-1
    ISSN 2090-5920 ; 1687-157X ; 2090-5920
    ISSN (online) 2090-5920
    ISSN 1687-157X ; 2090-5920
    DOI 10.1186/s43141-023-00534-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The molecular assessment of SARS-CoV-2 Nucleocapsid Phosphoprotein variants among Indian isolates

    Gajendra Kumar Azad

    Heliyon, Vol 7, Iss 2, Pp e06167- (2021)

    2021  

    Abstract: 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 ... ...

    Abstract 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.
    Keywords COVID-19 ; SARS-CoV-2 ; Mutations ; Nucleocapsid Phosphoprotein (N) ; Infectious diseases ; India ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Identification of novel mutations in the methyltransferase complex (Nsp10-Nsp16) of SARS-CoV-2

    Azad, Gajendra Kumar

    Biochemistry and Biophysics Reports

    2020  Volume 24, Page(s) 100833

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2831046-9
    ISSN 2405-5808
    ISSN 2405-5808
    DOI 10.1016/j.bbrep.2020.100833
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Molecular assessment of proteins encoded by the mitochondrial genome of

    Chand, Gyanendra Bahadur / Kumar, Sushant / Azad, Gajendra Kumar

    Biochemistry and biophysics reports

    2021  Volume 26, Page(s) 100985

    Abstract: The population of catfish, ...

    Abstract The population of catfish,
    Language English
    Publishing date 2021-03-25
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2831046-9
    ISSN 2405-5808 ; 2405-5808
    ISSN (online) 2405-5808
    ISSN 2405-5808
    DOI 10.1016/j.bbrep.2021.100985
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Variations in Orf3a protein of SARS-CoV-2 alter its structure and function.

    Azad, Gajendra Kumar / Khan, Parimal Kumar

    Biochemistry and biophysics reports

    2021  Volume 26, Page(s) 100933

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2021-01-27
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2831046-9
    ISSN 2405-5808 ; 2405-5808
    ISSN (online) 2405-5808
    ISSN 2405-5808
    DOI 10.1016/j.bbrep.2021.100933
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Identification of novel mutations in the methyltransferase complex (Nsp10-Nsp16) of SARS-CoV-2

    Gajendra Kumar Azad

    Biochemistry and Biophysics Reports, Vol 24, Iss , Pp 100833- (2020)

    2020  

    Abstract: 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 ... ...

    Abstract 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.
    Keywords COVID-19 ; SARS-CoV-2 ; Mutations ; Nsp10-Nsp16 ; Infectious diseases ; India ; Biology (General) ; QH301-705.5 ; Biochemistry ; QD415-436 ; covid19
    Subject code 570
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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