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  1. Article: Viral Prefusion Targeting Using Entry Inhibitor Peptides: The Case of SARS-CoV-2 and Influenza A virus.

    Behzadipour, Yasaman / Hemmati, Shiva

    International journal of peptide research and therapeutics

    2022  Volume 28, Issue 1, Page(s) 42

    Abstract: In this study, peptide entry inhibitors against the fusion processes of severe acute respiratory syndrome coronavirus-2 (SCV2) and influenza A virus (IAV) were designed and evaluated. Fusion inhibitor peptides targeting the conformational shift of the ... ...

    Abstract In this study, peptide entry inhibitors against the fusion processes of severe acute respiratory syndrome coronavirus-2 (SCV2) and influenza A virus (IAV) were designed and evaluated. Fusion inhibitor peptides targeting the conformational shift of the viral fusion protein were designed based on the relatively conserved sequence of HR2 from SCV2 spike protein and the conserved fusion peptide from hemagglutinin (HA) of IAV. Helical HR2 peptides bind more efficiently to HR1 trimer, while helical amphipathic anti-IAV peptides have higher cell penetration and endosomal uptake. The initial sequences were mutated by increasing the amphipathicity, using helix favoring residues, and residues likely to form salt- and disulfide-bridges. After docking against their targets, all anti-SCV2 designed peptides bonded with the HR1 3-helical bundle's hydrophobic crevice, while AntiSCV2P1, AntiSCV2P3, AntiSCV2P7, and AntiSCV2P8 expected to form coiled coils with at least one of the HR1 strands. Four of the designed anti-IAV peptides were cell-penetrating (AntiIAVP2, AntiIAVP3, AntiIAVP4, AntiIAVP7). All of them interacted with the fusion peptide of HA and some of the residues in the conserved hydrophobic pocket of HA2 in H1N1, H3N1, and H5N1 subtypes of IAV. AntiIAVP3 and AntiIAVP4 peptides had the best binding to HA2 conserved hydrophobic pocket, while, AntiIAVP2 and AntiIAVP6 showed the best binding to the fusion peptide region. According to analyses for in-vivo administration, AntiSCV2P1, AntiSCV2P7, AntiIAVP2, and AntiIAVP7 were the best candidates. AntiSCV2 and AntiIAV peptides were also conjugated using an in vivo cleavable linker sensitive to TMPRSS2 applicable as a single therapeutic in coinfections or uncertain diagnosis.
    Supplementary information: The online version contains supplementary material available at 10.1007/s10989-021-10357-y.
    Language English
    Publishing date 2022-01-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2192632-3
    ISSN 1573-3904 ; 1573-3149
    ISSN (online) 1573-3904
    ISSN 1573-3149
    DOI 10.1007/s10989-021-10357-y
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  2. Article ; Online: Considerations on the Rational Design of Covalently Conjugated Cell-Penetrating Peptides (CPPs) for Intracellular Delivery of Proteins: A Guide to CPP Selection Using Glucarpidase as the Model Cargo Molecule.

    Behzadipour, Yasaman / Hemmati, Shiva

    Molecules (Basel, Switzerland)

    2019  Volume 24, Issue 23

    Abstract: Access of proteins to their intracellular targets is limited by a hydrophobic barrier called the cellular membrane. Conjugation with cell-penetrating peptides (CPPs) has been shown to improve protein transduction into the cells. This conjugation can be ... ...

    Abstract Access of proteins to their intracellular targets is limited by a hydrophobic barrier called the cellular membrane. Conjugation with cell-penetrating peptides (CPPs) has been shown to improve protein transduction into the cells. This conjugation can be either covalent or non-covalent, each with its unique pros and cons. The CPP-protein covalent conjugation may result in undesirable structural and functional alterations in the target protein. Therefore, we propose a systematic approach to evaluate different CPPs for covalent conjugations. This guide is presented using the carboxypeptidase G2 (CPG2) enzyme as the target protein. Seventy CPPs -out of 1155- with the highest probability of uptake efficiency were selected. These peptides were then conjugated to the
    MeSH term(s) Base Sequence ; Cell Membrane/metabolism ; Cell-Penetrating Peptides/metabolism ; Humans ; Protein Transport/physiology ; Recombinant Proteins/metabolism ; gamma-Glutamyl Hydrolase/metabolism
    Chemical Substances Cell-Penetrating Peptides ; Recombinant Proteins ; glucarpidase (2GFP9BJD79) ; gamma-Glutamyl Hydrolase (EC 3.4.19.9)
    Language English
    Publishing date 2019-11-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules24234318
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  3. Article: Decoding the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for cell-penetrating peptides involved in pathogenesis or applicable as drug delivery vectors

    Hemmati, Shiva / Behzadipour, Yasaman / Haddad, Mahdi

    Infection, genetics, and evolution. 2020 Nov., v. 85

    2020  

    Abstract: Synthetic or natural derived cell-penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are intracellular obligate parasites, viral originated CPPs have been considered ... ...

    Abstract Synthetic or natural derived cell-penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are intracellular obligate parasites, viral originated CPPs have been considered as suitable intracellular shuttling vectors for cargo transportation. A total of 310 CPPs were identified in the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Screening the proteome of the cause of COVID-19 reveals that SARS-CoV-2 CPPs (SCV2-CPPs) span the regions involved in replication, protein-nucleotide and protein-protein interaction, protein-metal ion interaction, and stabilization of homo/hetero-oligomers. However, to find the most appropriate peptides as drug delivery vectors, one might face several hurdles. Computational analyses showed that 94.3% of the identified SCV2-CPPs are non-toxins, and 38% are neither antigenic nor allergenic. Interestingly, 36.70% of SCV2-CPPs were resistant to all four groups of protease families. Nearly 1/3 of SCV2-CPPs had sufficient inherent or induced helix and sheet conformation leading to increased uptake efficiency. Heliquest lipid-binding discrimination factor revealed that 44.30% of the helical SCV2-CPPs are lipid-binding helices. Although Cys-rich derived CPPs of helicase (NSP13) can potentially fold into a cyclic conformation in endosomes with a higher rate of endosomal release, the most optimal SCV2-CPP candidates as vectors for drug delivery were SCV2-CPP118, SCV2-CPP119, SCV2-CPP122, and SCV2-CPP129 of NSP12 (RdRp). Ten experimentally validated viral-derived CPPs were also used as the positive control to check the scalability and reliability of our protocol in SCV2-CPP retrieval. Some peptides with a cell-penetration ability known as bioactive peptides are adopted as biotherapeutics themselves. Therefore, 59.60%, 29.63%, and 32.32% of SCV2-CPPs were identified as potential antibacterial, antiviral, and antifungals, respectively. While 63.64% of SCV2-CPPs had immuno-modulatory properties, 21.89% were recognized as anti-cancers. Conclusively, the workflow of this study provides a platform for profound screening of viral proteomes as a rich source of biotherapeutics or drug delivery carriers.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; allergenicity ; antifungal agents ; endosomes ; evolution ; genetics ; infection ; pathogenesis ; peptides ; protein-protein interactions ; proteinases ; proteome ; transportation
    Language English
    Dates of publication 2020-11
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2037068-4
    ISSN 1567-1348
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2020.104474
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5645: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Decoding the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for cell-penetrating peptides involved in pathogenesis or applicable as drug delivery vectors.

    Hemmati, Shiva / Behzadipour, Yasaman / Haddad, Mahdi

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

    2020  Volume 85, Page(s) 104474

    Abstract: Synthetic or natural derived cell-penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are intracellular obligate parasites, viral originated CPPs have been considered ... ...

    Abstract Synthetic or natural derived cell-penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are intracellular obligate parasites, viral originated CPPs have been considered as suitable intracellular shuttling vectors for cargo transportation. A total of 310 CPPs were identified in the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Screening the proteome of the cause of COVID-19 reveals that SARS-CoV-2 CPPs (SCV2-CPPs) span the regions involved in replication, protein-nucleotide and protein-protein interaction, protein-metal ion interaction, and stabilization of homo/hetero-oligomers. However, to find the most appropriate peptides as drug delivery vectors, one might face several hurdles. Computational analyses showed that 94.3% of the identified SCV2-CPPs are non-toxins, and 38% are neither antigenic nor allergenic. Interestingly, 36.70% of SCV2-CPPs were resistant to all four groups of protease families. Nearly 1/3 of SCV2-CPPs had sufficient inherent or induced helix and sheet conformation leading to increased uptake efficiency. Heliquest lipid-binding discrimination factor revealed that 44.30% of the helical SCV2-CPPs are lipid-binding helices. Although Cys-rich derived CPPs of helicase (NSP13) can potentially fold into a cyclic conformation in endosomes with a higher rate of endosomal release, the most optimal SCV2-CPP candidates as vectors for drug delivery were SCV2-CPP118, SCV2-CPP119, SCV2-CPP122, and SCV2-CPP129 of NSP12 (RdRp). Ten experimentally validated viral-derived CPPs were also used as the positive control to check the scalability and reliability of our protocol in SCV2-CPP retrieval. Some peptides with a cell-penetration ability known as bioactive peptides are adopted as biotherapeutics themselves. Therefore, 59.60%, 29.63%, and 32.32% of SCV2-CPPs were identified as potential antibacterial, antiviral, and antifungals, respectively. While 63.64% of SCV2-CPPs had immuno-modulatory properties, 21.89% were recognized as anti-cancers. Conclusively, the workflow of this study provides a platform for profound screening of viral proteomes as a rich source of biotherapeutics or drug delivery carriers.
    MeSH term(s) Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Cell-Penetrating Peptides/chemistry ; Cell-Penetrating Peptides/metabolism ; Computational Biology/methods ; Drug Evaluation, Preclinical ; Humans ; Protein Folding ; Protein Structure, Secondary ; Proteome/drug effects ; SARS-CoV-2/drug effects ; SARS-CoV-2/metabolism ; SARS-CoV-2/pathogenicity ; Support Vector Machine ; Viral Proteins/chemistry ; Viral Proteins/metabolism ; Virus Replication
    Chemical Substances Antiviral Agents ; Cell-Penetrating Peptides ; Proteome ; Viral Proteins
    Keywords covid19
    Language English
    Publishing date 2020-07-24
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2037068-4
    ISSN 1567-7257 ; 1567-1348
    ISSN (online) 1567-7257
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2020.104474
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5645: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Introducing a delivery system for melanogenesis inhibition in melanoma B16F10 cells mediated by the conjugation of tyrosine ammonia-lyase and a TAT-penetrating peptide.

    Behzadipour, Yasaman / Sadeghian, Issa / Ghaffarian Bahraman, Ali / Hemmati, Shiva

    Biotechnology progress

    2020  Volume 37, Issue 1, Page(s) e3071

    Abstract: Hyperpigmentation disorders negatively influence an individual's quality of life and may cause emotional distress. Over the years, various melanogenesis inhibitors (mainly tyrosinase inhibitors) have been developed, most of which with low efficacy or ... ...

    Abstract Hyperpigmentation disorders negatively influence an individual's quality of life and may cause emotional distress. Over the years, various melanogenesis inhibitors (mainly tyrosinase inhibitors) have been developed, most of which with low efficacy or high toxicity. Although metabolic engineering by deviation in the flux of substrate is of considerable interest, trials to develop a melanogenesis inhibitor based on L-tyrosine (L-Tyr) restriction are missing. We propose a novel proteinaceous melanogenesis inhibitor called tyrosine ammonia-lyase (TAL), an enzyme that catalyzes the conversion of L-Tyr to p-coumaric acid and ammonia. Since the cell membrane can act as a barrier for intracellular protein delivery, we have covalently conjugated a recombinant TAL enzyme from Rhodobacter sphaeroides (RsTAL) to a trans-activator of transcription (TAT) cell-penetrating peptide (CPP) to afford the intracellular delivery. The heterologously expressed TAT-RsTAL fusion protein was delivered successfully into B16F10 melanocytes as confirmed by the direct fluorescence microscopy with increased intensity from 30 to 180 min. TAT-RsTAL showed sufficient intracellular activity of about 0.83 ± 0.04 and 0.34 ± 0.03 nmol•mg
    MeSH term(s) Ammonia-Lyases/metabolism ; Animals ; Cell Survival/drug effects ; Cell-Penetrating Peptides/chemistry ; Cell-Penetrating Peptides/pharmacology ; Drug Delivery Systems ; Gene Products, tat/chemistry ; Gene Products, tat/metabolism ; Melanins/metabolism ; Melanocytes/drug effects ; Melanocytes/metabolism ; Melanocytes/pathology ; Melanoma, Experimental/drug therapy ; Melanoma, Experimental/metabolism ; Melanoma, Experimental/pathology ; Mice ; Rhodobacter sphaeroides/enzymology ; Tyrosine/metabolism
    Chemical Substances Cell-Penetrating Peptides ; Gene Products, tat ; Melanins ; Tyrosine (42HK56048U) ; Ammonia-Lyases (EC 4.3.1.-) ; L-tyrosine ammonia-lyase (EC 4.3.1.-)
    Language English
    Publishing date 2020-09-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 165657-0
    ISSN 1520-6033 ; 8756-7938
    ISSN (online) 1520-6033
    ISSN 8756-7938
    DOI 10.1002/btpr.3071
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    Zs.A 4253: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article: Viral 3CL

    Behzadipour, Yasaman / Gholampour, Maryam / Pirhadi, Somayeh / Seradj, Hassan / Khoshneviszadeh, Mehdi / Hemmati, Shiva

    International journal of peptide research and therapeutics

    2021  Volume 27, Issue 4, Page(s) 2703–2716

    Abstract: Viruses of the picornavirus-like supercluster mainly achieve cleavage of polyproteins into mature proteins through viral 3-chymotrypsin proteases (3C: Supplementary information: The online version contains supplementary material available at 10.1007/ ... ...

    Abstract Viruses of the picornavirus-like supercluster mainly achieve cleavage of polyproteins into mature proteins through viral 3-chymotrypsin proteases (3C
    Supplementary information: The online version contains supplementary material available at 10.1007/s10989-021-10284-y.
    Language English
    Publishing date 2021-09-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2192632-3
    ISSN 1573-3904 ; 1573-3149
    ISSN (online) 1573-3904
    ISSN 1573-3149
    DOI 10.1007/s10989-021-10284-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Decoding the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for cell-penetrating peptides involved in pathogenesis or applicable as drug delivery vectors

    Hemmati, Shiva / Behzadipour, Yasaman / Haddad, Mahdi

    Infect Genet Evol

    Abstract: Synthetic or natural derived cell-penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are intracellular obligate parasites, viral originated CPPs have been considered ... ...

    Abstract Synthetic or natural derived cell-penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are intracellular obligate parasites, viral originated CPPs have been considered as suitable intracellular shuttling vectors for cargo transportation. A total of 310 CPPs were identified in the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Screening the proteome of the cause of COVID-19 reveals that SARS-CoV-2 CPPs (SCV2-CPPs) span the regions involved in replication, protein-nucleotide and protein-protein interaction, protein-metal ion interaction, and stabilization of homo/hetero-oligomers. However, to find the most appropriate peptides as drug delivery vectors, one might face several hurdles. Computational analyses showed that 94.3% of the identified SCV2-CPPs are non-toxins, and 38% are neither antigenic nor allergenic. Interestingly, 36.70% of SCV2-CPPs were resistant to all four groups of protease families. Nearly 1/3 of SCV2-CPPs had sufficient inherent or induced helix and sheet conformation leading to increased uptake efficiency. Heliquest lipid-binding discrimination factor revealed that 44.30% of the helical SCV2-CPPs are lipid-binding helices. Although Cys-rich derived CPPs of helicase (NSP13) can potentially fold into a cyclic conformation in endosomes with a higher rate of endosomal release, the most optimal SCV2-CPP candidates as vectors for drug delivery were SCV2-CPP118, SCV2-CPP119, SCV2-CPP122, and SCV2-CPP129 of NSP12 (RdRp). Ten experimentally validated viral-derived CPPs were also used as the positive control to check the scalability and reliability of our protocol in SCV2-CPP retrieval. Some peptides with a cell-penetration ability known as bioactive peptides are adopted as biotherapeutics themselves. Therefore, 59.60%, 29.63%, and 32.32% of SCV2-CPPs were identified as potential antibacterial, antiviral, and antifungals, respectively. While 63.64% of SCV2-CPPs had immuno-modulatory properties, 21.89% were recognized as anti-cancers. Conclusively, the workflow of this study provides a platform for profound screening of viral proteomes as a rich source of biotherapeutics or drug delivery carriers.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #663917
    Database COVID19

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  8. Book ; Online: Decoding the Proteome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for Cell-Penetrating Peptides Involved in Pathogenesis or Applicable as Drug Delivery Vectors

    Hemmati, Shiva / Behzadipour, Yasaman / Haddad, Mahdi

    2020  

    Abstract: Synthetic or natural-derived cell penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are obligate intracellular parasites, viral originated CPPs have been considered ... ...

    Abstract Synthetic or natural-derived cell penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are obligate intracellular parasites, viral originated CPPs have been considered as suitable shuttling vectors for cargo transportation. A total of 310 CPPs were identified in the proteome of SARS-CoV-2. SCV2-CPPs span the regions involved in replication, protein-nucleotide and protein-protein interaction, protein-metal ion interaction, and stabilization of homo/hetero-oligomers. Computational analyses showed that the most optimal SCV2-CPP candidates as vectors for drug delivery are SCV2-CPP118, SCV2-CPP119, SCV2-CPP122, and SCV2-CPP129 of NSP12. Conclusively, the workflow of this study provides a platform for profound screening of viral proteomes as a rich source of bio-therapeutics or drug delivery carriers.

    Keywords covid19
    Publisher American Chemical Society (ACS)
    Publishing country us
    Document type Book ; Online
    DOI 10.26434/chemrxiv.12401306.v1
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Book ; Online: Decoding the Proteome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for Cell-Penetrating Peptides Involved in Pathogenesis or Applicable as Drug Delivery Vectors

    Hemmati, Shiva / Behzadipour, Yasaman / Haddad, Mahdi

    2020  

    Abstract: Synthetic or natural-derived cell penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are obligate intracellular parasites, viral originated CPPs have been considered ... ...

    Abstract Synthetic or natural-derived cell penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are obligate intracellular parasites, viral originated CPPs have been considered as suitable shuttling vectors for cargo transportation. A total of 310 CPPs were identified in the proteome of SARS-CoV-2. SCV2-CPPs span the regions involved in replication, protein-nucleotide and protein-protein interaction, protein-metal ion interaction, and stabilization of homo/hetero-oligomers. Computational analyses showed that the most optimal SCV2-CPP candidates as vectors for drug delivery are SCV2-CPP118, SCV2-CPP119, SCV2-CPP122, and SCV2-CPP129 of NSP12. Conclusively, the workflow of this study provides a platform for profound screening of viral proteomes as a rich source of bio-therapeutics or drug delivery carriers.

    Keywords covid19
    Publisher American Chemical Society (ACS)
    Publishing country us
    Document type Book ; Online
    DOI 10.26434/chemrxiv.12401306
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Decoding the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for cell-penetrating peptides involved in pathogenesis or applicable as drug delivery vectors

    Hemmati, Shiva / Behzadipour, Yasaman / Haddad, Mahdi

    Infection, Genetics and Evolution

    2020  Volume 85, Page(s) 104474

    Keywords Microbiology (medical) ; Genetics ; Ecology, Evolution, Behavior and Systematics ; Molecular Biology ; Microbiology ; Infectious Diseases ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2037068-4
    ISSN 1567-1348
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2020.104474
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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