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  1. Article: An overview of current COVID-19 vaccine platforms.

    Nagy, Abdou / Alhatlani, Bader

    Computational and structural biotechnology journal

    2021  Volume 19, Page(s) 2508–2517

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) pandemic that emerged in December 2019 in Wuhan city, China. An effective vaccine is urgently needed to protect humans and to mitigate ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) pandemic that emerged in December 2019 in Wuhan city, China. An effective vaccine is urgently needed to protect humans and to mitigate the economic and societal impacts of the pandemic. Despite standard vaccine development usually requiring an extensive process and taking several years to complete all clinical phases, there are currently 184 vaccine candidates in pre-clinical testing and another 88 vaccine candidates in clinical phases based on different vaccine platforms as of April 13, 2021. Moreover, three vaccine candidates have recently been granted an Emergency Use Authorization by the United States Food and Drug Administration (for Pfizer/BioNtech, Moderna mRNA vaccines, and Johnson and Johnson viral vector vaccine) and by the UK government (for University of Oxford/AstraZeneca viral vector vaccine). Here we aim to briefly address the current advances in reverse genetics system of SARS-CoV-2 and the use of this in development of SARS-CoV-2 vaccines. Additionally, we cover the essential points concerning the different platforms of current SARS-CoV-2 vaccine candidates and the advantages and drawbacks of these platforms. We also assess recommendations for controlling the COVID-19 pandemic and future pandemics using the benefits of genetic engineering technology to design effective vaccines against emerging and re-emerging viral diseases with zoonotic and/or pandemic potential.
    Language English
    Publishing date 2021-04-27
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2021.04.061
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Engineered CHO cells as a novel AAV production platform for gene therapy delivery.

    Nagy, Abdou / Chakrabarti, Lina / Kurasawa, James / Mulagapati, Sri Hari Raju / Devine, Paul / Therres, Jamy / Chen, Zhongying / Schmelzer, Albert E

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 19210

    Abstract: The Herpes simplex virus (HSV)-based platform for production of recombinant adeno-associated viral vectors (rAAVs) yields higher titers and increased percentage of full capsids when compared to the triple transient transfection (TTT) method. However, ... ...

    Abstract The Herpes simplex virus (HSV)-based platform for production of recombinant adeno-associated viral vectors (rAAVs) yields higher titers and increased percentage of full capsids when compared to the triple transient transfection (TTT) method. However, this platform currently faces two major challenges. The first challenge is the reliance on commercial media, sometimes supplemented with serum, leading to costly manufacturing and a high risk for introduction of adventitious agents. The second challenge is that the production of HSV-1 relies on adherent complementing Vero cells (V27), making it difficult to scale up. We engineered serum-free-adapted CHO cells expressing key HSV-1 entry receptors, HVEM and/or Nectin-1 to address the first challenge. Using high-throughput cloning methods, we successfully selected a HVEM receptor-expressing clone (CHO-HV-C1) that yields 1.62 × 10
    MeSH term(s) Cricetinae ; Animals ; Chlorocebus aethiops ; CHO Cells ; Cricetulus ; Vero Cells ; Tissue Distribution ; Herpesvirus 1, Human/genetics ; Genetic Therapy
    Language English
    Publishing date 2023-11-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-46298-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Engineered CHO cells as a novel AAV production platform for gene therapy delivery

    Abdou Nagy / Lina Chakrabarti / James Kurasawa / Sri Hari Raju Mulagapati / Paul Devine / Jamy Therres / Zhongying Chen / Albert E. Schmelzer

    Scientific Reports, Vol 13, Iss 1, Pp 1-

    2023  Volume 16

    Abstract: Abstract The Herpes simplex virus (HSV)-based platform for production of recombinant adeno-associated viral vectors (rAAVs) yields higher titers and increased percentage of full capsids when compared to the triple transient transfection (TTT) method. ... ...

    Abstract Abstract The Herpes simplex virus (HSV)-based platform for production of recombinant adeno-associated viral vectors (rAAVs) yields higher titers and increased percentage of full capsids when compared to the triple transient transfection (TTT) method. However, this platform currently faces two major challenges. The first challenge is the reliance on commercial media, sometimes supplemented with serum, leading to costly manufacturing and a high risk for introduction of adventitious agents. The second challenge is that the production of HSV-1 relies on adherent complementing Vero cells (V27), making it difficult to scale up. We engineered serum-free-adapted CHO cells expressing key HSV-1 entry receptors, HVEM and/or Nectin-1 to address the first challenge. Using high-throughput cloning methods, we successfully selected a HVEM receptor-expressing clone (CHO–HV–C1) that yields 1.62 × 109, 2.51 × 109, and 4.07 × 109 viral genome copies/mL with rAAV6.2-GFP, rAAV8-GFP, and rAAV9-GFP vectors respectively, within 24 h post rHSV-1 co-infection. Moreover, CHO–HV–C1-derived rAAVs had comparable in vitro transduction, infectivity, and biodistribution titers to those produced by TTT. The second challenge was addressed via engineering CHO–HV–C1 cells to express HSV-1 CP27. These cells successfully produced rHSV-1 vectors, but with significantly lower titers than V27 cells. Taken together, the CHO/HSV system provides a novel, scalable, reduced cost, serum-free AAV manufacturing platform.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals.

    Nagy, Abdou / Basiouni, Shereen / Parvin, Rokshana / Hafez, Hafez M / Shehata, Awad A

    Archives of virology

    2021  Volume 166, Issue 9, Page(s) 2541–2549

    Abstract: The SARS-CoV-2 spike protein Q677P/H mutation and furin cleavage site (FCS) have been shown to affect cell tropism and virus transmissibility. Here, we analyzed the frequency of Q677P/H and FCS point mutations in 1,144,793 human and 1042 animal spike ... ...

    Abstract The SARS-CoV-2 spike protein Q677P/H mutation and furin cleavage site (FCS) have been shown to affect cell tropism and virus transmissibility. Here, we analyzed the frequency of Q677P/H and FCS point mutations in 1,144,793 human and 1042 animal spike protein sequences and from those of the emergent variants B.1.1.7, B.1.351, P.1, B.1.429 + B.1.427, and B.1.525, which were deposited in the database of the GISAID Initiative. Different genetic polymorphisms, particularly P681H and A688V, were detected in the FCS, mainly in human isolates, and otherwise, only pangolin and bat sequences had these mutations. Multiple FCS amino acid deletions such as Δ
    MeSH term(s) Amino Acid Sequence ; Animals ; Binding Sites ; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Chiroptera/virology ; Epidemiological Monitoring ; Eutheria/virology ; Evolution, Molecular ; Furin/chemistry ; Furin/metabolism ; Gene Expression ; Humans ; Models, Molecular ; Polymorphism, Genetic ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Proteolysis ; SARS-CoV-2/chemistry ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Furin (EC 3.4.21.75)
    Language English
    Publishing date 2021-07-13
    Publishing country Austria
    Document type Journal Article
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-021-05166-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals

    Nagy, Abdou / Basiouni, Shereen / Parvin, Rokshana / Hafez, Hafez M. / Shehata, Awad A.

    Archives of virology. 2021 Sept., v. 166, no. 9

    2021  

    Abstract: The SARS-CoV-2 spike protein Q677P/H mutation and furin cleavage site (FCS) have been shown to affect cell tropism and virus transmissibility. Here, we analyzed the frequency of Q677P/H and FCS point mutations in 1,144,793 human and 1042 animal spike ... ...

    Abstract The SARS-CoV-2 spike protein Q677P/H mutation and furin cleavage site (FCS) have been shown to affect cell tropism and virus transmissibility. Here, we analyzed the frequency of Q677P/H and FCS point mutations in 1,144,793 human and 1042 animal spike protein sequences and from those of the emergent variants B.1.1.7, B.1.351, P.1, B.1.429 + B.1.427, and B.1.525, which were deposited in the database of the GISAID Initiative. Different genetic polymorphisms, particularly P681H and A688V, were detected in the FCS, mainly in human isolates, and otherwise, only pangolin and bat sequences had these mutations. Multiple FCS amino acid deletions such as Δ⁶⁸⁰SPRRA⁶⁸⁴ and Δ⁶⁸⁵RSVA⁶⁸⁸ were only detected in eight and four human isolates, respectively. Surprisingly, deletion of the entire FCS motif as Δ⁶⁸⁰SPRRARSVA⁶⁸⁸ and Δ⁶⁸⁰SPRRARSVAS⁶⁸⁹ was detected only in three human isolates. On the other hand, analysis of FCS from emergent variants showed no deletions in the FCS except for spike P681del, which was detected in seven B.1.1.7 isolates from the USA. Spike Q677P was detected only once in variant, B.1.1.7, whereas Q677H was detected in all variants, i.e., B.1.1.7 (n = 1938), B.1.351 (n = 28), P.1 (n = 9), B.1.429 + B.1.427 (n = 132), and B.1.525 (n = 1584). Structural modeling predicted that mutations or deletions at or near the FCS significantly alter the cleavage loop structure and would presumably affect furin binding. Taken together, our results show that Q677H and FCS point mutations are prevalent and may have various biological effects on the circulating variants. Therefore, we recommend urgent monitoring and surveillance of the investigated mutations, as well as laboratory assessment of their pathogenicity and transmissibility.
    Keywords Chiroptera ; Severe acute respiratory syndrome coronavirus 2 ; amino acids ; databases ; humans ; monitoring ; pathogenicity ; virology ; viruses
    Language English
    Dates of publication 2021-09
    Size p. 2541-2549.
    Publishing place Springer Vienna
    Document type Article
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-021-05166-z
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Characterization and genetic analysis of recent and emergent virulent newcastle disease viruses in Egypt.

    Nagy, Abdou / Ali, Ahmed / Zain El-Abideen, Mohamed A / Kilany, Walid / Elsayed, Magdy

    Transboundary and emerging diseases

    2020  Volume 67, Issue 5, Page(s) 2000–2012

    Abstract: Extensive vaccination against Newcastle disease virus (NDV) induced more selective immune pressure from hosts that enhanced the evolutionary process of NDV. Herein, we characterized 13 recently isolated NDV isolates from vaccinated chicken flocks during ... ...

    Abstract Extensive vaccination against Newcastle disease virus (NDV) induced more selective immune pressure from hosts that enhanced the evolutionary process of NDV. Herein, we characterized 13 recently isolated NDV isolates from vaccinated chicken flocks during 2014-2017. Sequence analysis of F gene showed the presence of
    Language English
    Publishing date 2020-04-07
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2414822-2
    ISSN 1865-1682 ; 1865-1674
    ISSN (online) 1865-1682
    ISSN 1865-1674
    DOI 10.1111/tbed.13543
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Genetic characterization of upper respiratory tract virome from nonvaccinated Egyptian cow-calf operations.

    Nagy, Abdou / Abdallah, Fatma / El Damaty, Hend M / Tariq, Ahmed / Merwad, Abdallah M A / Alhatlani, Bader Y / Elsohaby, Ibrahim

    PloS one

    2022  Volume 17, Issue 5, Page(s) e0267036

    Abstract: Bovine respiratory disease (BRD) is the costliest complex disease affecting the cattle industry worldwide, with significant economic losses. BRD pathogenesis involves several interactions between microorganisms, such as bacteria and viruses, and ... ...

    Abstract Bovine respiratory disease (BRD) is the costliest complex disease affecting the cattle industry worldwide, with significant economic losses. BRD pathogenesis involves several interactions between microorganisms, such as bacteria and viruses, and management factors. The present study aimed to characterize the nasal virome from 43 pooled nasal swab samples collected from Egyptian nonvaccinated cow-calf operations with acute BRD from January to February 2020 using metagenomic sequencing. Bovine herpesvirus-1 (BHV-1), first detection of bovine herpesvirus-5 (BHV-5), and first detection of bovine parvovirus-3 (BPV-3) were the most commonly identified in Egyptian cattle. Moreover, phylogenetic analysis of glycoprotein B revealed that the BHV-1 isolate is closely related to the Cooper reference strain (genotype 1.1), whereas the BHV-5 isolate is closely related to the reference virus GenBank NP_954920.1. In addition, the whole-genome sequence of BPV-3 showed 93.02% nucleotide identity with the reference virus GenBank AF406967.1. In this study, several DNA viruses, such as BHV-1 and first detection BHV-5, and BPV-3, were detected and may have an association with the BRD in Egyptian cattle. Therefore, further research, including investigating more samples from different locations to determine the prevalence of detected viruses and their contributions to BRD in cattle in Egypt, is needed.
    MeSH term(s) Animals ; Cattle ; Cattle Diseases/epidemiology ; Female ; Herpesvirus 1, Bovine/genetics ; Herpesvirus 5, Bovine ; Phylogeny ; Respiratory Tract Diseases ; Virome ; Viruses/genetics
    Language English
    Publishing date 2022-05-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0267036
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Genetic characterization of upper respiratory tract virome from nonvaccinated Egyptian cow-calf operations.

    Abdou Nagy / Fatma Abdallah / Hend M El Damaty / Ahmed Tariq / Abdallah M A Merwad / Bader Y Alhatlani / Ibrahim Elsohaby

    PLoS ONE, Vol 17, Iss 5, p e

    2022  Volume 0267036

    Abstract: Bovine respiratory disease (BRD) is the costliest complex disease affecting the cattle industry worldwide, with significant economic losses. BRD pathogenesis involves several interactions between microorganisms, such as bacteria and viruses, and ... ...

    Abstract Bovine respiratory disease (BRD) is the costliest complex disease affecting the cattle industry worldwide, with significant economic losses. BRD pathogenesis involves several interactions between microorganisms, such as bacteria and viruses, and management factors. The present study aimed to characterize the nasal virome from 43 pooled nasal swab samples collected from Egyptian nonvaccinated cow-calf operations with acute BRD from January to February 2020 using metagenomic sequencing. Bovine herpesvirus-1 (BHV-1), first detection of bovine herpesvirus-5 (BHV-5), and first detection of bovine parvovirus-3 (BPV-3) were the most commonly identified in Egyptian cattle. Moreover, phylogenetic analysis of glycoprotein B revealed that the BHV-1 isolate is closely related to the Cooper reference strain (genotype 1.1), whereas the BHV-5 isolate is closely related to the reference virus GenBank NP_954920.1. In addition, the whole-genome sequence of BPV-3 showed 93.02% nucleotide identity with the reference virus GenBank AF406967.1. In this study, several DNA viruses, such as BHV-1 and first detection BHV-5, and BPV-3, were detected and may have an association with the BRD in Egyptian cattle. Therefore, further research, including investigating more samples from different locations to determine the prevalence of detected viruses and their contributions to BRD in cattle in Egypt, is needed.
    Keywords Medicine ; R ; Science ; Q
    Subject code 630
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Nanoparticles as a novel and promising antiviral platform in veterinary medicine.

    Fawzy, Mohamed / Khairy, Gasser M / Hesham, Ahmed / Rabaan, Ali A / El-Shamy, Ahmed G / Nagy, Abdou

    Archives of virology

    2021  Volume 166, Issue 10, Page(s) 2673–2682

    Abstract: Traditional veterinary virus vaccines, such as inactivated and live-attenuated vaccines, have achieved tremendous success in controlling many viral diseases of livestock and chickens worldwide. However, many recent viral outbreaks caused by different ... ...

    Abstract Traditional veterinary virus vaccines, such as inactivated and live-attenuated vaccines, have achieved tremendous success in controlling many viral diseases of livestock and chickens worldwide. However, many recent viral outbreaks caused by different emerging and re-emerging viruses continue to be reported annually worldwide. It is therefore necessary to develop new control regimens. Nanoparticle research has received considerable attention in the last two decades as a promising platform with significant success in veterinary medicine, replacing traditional viral vector vaccines. However, the field of nanoparticle applications is still in its initial phase of growth. Here, we discuss various preparation methods, characteristics, physical properties, antiviral effects, and pharmacokinetics of well-developed nanoparticles and the potential of nanoparticles or nano-vaccines as a promising antiviral platform for veterinary medicine.
    MeSH term(s) Animals ; Antiviral Agents/chemistry ; Antiviral Agents/classification ; Antiviral Agents/therapeutic use ; Chickens ; Livestock ; Nanoparticles/chemistry ; Nanoparticles/classification ; Nanoparticles/therapeutic use ; Pharmaceutical Preparations ; Veterinary Medicine ; Viral Vaccines/chemistry ; Viral Vaccines/classification ; Viral Vaccines/therapeutic use ; Virus Diseases/drug therapy ; Virus Diseases/prevention & control ; Virus Diseases/veterinary ; Viruses/drug effects ; Viruses/immunology
    Chemical Substances Antiviral Agents ; Pharmaceutical Preparations ; Viral Vaccines
    Language English
    Publishing date 2021-07-23
    Publishing country Austria
    Document type Journal Article ; Review
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-021-05177-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Nanoparticles as a novel and promising antiviral platform in veterinary medicine

    Fawzy, Mohamed / Khairy, Gasser M. / Hesham, Ahmed / Rabaan, Ali A. / El-Shamy, Ahmed G. / Nagy, Abdou

    Archives of virology. 2021 Oct., v. 166, no. 10

    2021  

    Abstract: Traditional veterinary virus vaccines, such as inactivated and live-attenuated vaccines, have achieved tremendous success in controlling many viral diseases of livestock and chickens worldwide. However, many recent viral outbreaks caused by different ... ...

    Abstract Traditional veterinary virus vaccines, such as inactivated and live-attenuated vaccines, have achieved tremendous success in controlling many viral diseases of livestock and chickens worldwide. However, many recent viral outbreaks caused by different emerging and re-emerging viruses continue to be reported annually worldwide. It is therefore necessary to develop new control regimens. Nanoparticle research has received considerable attention in the last two decades as a promising platform with significant success in veterinary medicine, replacing traditional viral vector vaccines. However, the field of nanoparticle applications is still in its initial phase of growth. Here, we discuss various preparation methods, characteristics, physical properties, antiviral effects, and pharmacokinetics of well-developed nanoparticles and the potential of nanoparticles or nano-vaccines as a promising antiviral platform for veterinary medicine.
    Keywords live vaccines ; pharmacokinetics ; veterinary medicine ; virology ; viruses
    Language English
    Dates of publication 2021-10
    Size p. 2673-2682.
    Publishing place Springer Vienna
    Document type Article
    Note Review
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-021-05177-w
    Database NAL-Catalogue (AGRICOLA)

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