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  1. Article ; Online: Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins.

    Prandi, Ingrid Guarnetti / Mavian, Carla / Giombini, Emanuela / Gruber, Cesare E M / Pietrucci, Daniele / Borocci, Stefano / Abid, Nabil / Beccari, Andrea R / Talarico, Carmine / Chillemi, Giovanni

    International journal of molecular sciences

    2022  Volume 23, Issue 15

    Abstract: The vast amount of epidemiologic and genomic data that were gathered as a global response to the COVID-19 pandemic that was caused by SARS-CoV-2 offer a unique opportunity to shed light on the structural evolution of coronaviruses and in particular on ... ...

    Abstract The vast amount of epidemiologic and genomic data that were gathered as a global response to the COVID-19 pandemic that was caused by SARS-CoV-2 offer a unique opportunity to shed light on the structural evolution of coronaviruses and in particular on the spike (S) glycoprotein, which mediates virus entry into the host cell by binding to the human ACE2 receptor. Herein, we carry out an investigation into the dynamic properties of the S glycoprotein, focusing on the much more transmissible Delta and Omicron variants. Notwithstanding the great number of mutations that have accumulated, particularly in the Omicron S glycoprotein, our data clearly showed the conservation of some structural and dynamic elements, such as the global motion of the receptor binding domain (RBD). However, our studies also revealed structural and dynamic alterations that were concentrated in the aa 627-635 region, on a small region of the receptor binding motif (aa 483-485), and the so-called "fusion-peptide proximal region". In particular, these last two S regions are known to be involved in the human receptor ACE2 recognition and membrane fusion. Our structural evidence, therefore, is likely involved in the observed different transmissibility of these S mutants. Finally, we highlighted the role of glycans in the increased RBD flexibility of the monomer in the up conformation of Omicron.
    MeSH term(s) Angiotensin-Converting Enzyme 2/genetics ; COVID-19/genetics ; Glycoproteins ; Humans ; Mutation ; Pandemics ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/metabolism
    Chemical Substances Glycoproteins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Language English
    Publishing date 2022-08-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23158680
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: ESCA pipeline: Easy-to-use SARS-CoV-2 genome Assembler

    Rueca, Martina / Giombini, Emanuela / Messina, Francesco / Bartolini, Barbara / Di Caro, Antonino / Capobianchi, Maria R. / Gruber, Cesare E.M.

    bioRxiv

    Abstract: Early sequencing and quick analysis of SARS-CoV-2 genome are contributing to un-derstand the dynamics of COVID19 epidemics and to countermeasures design at global level. Amplicon-based NGS methods are widely used to sequence the SARS-CoV-2 genome and to ... ...

    Abstract Early sequencing and quick analysis of SARS-CoV-2 genome are contributing to un-derstand the dynamics of COVID19 epidemics and to countermeasures design at global level. Amplicon-based NGS methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession, harboring multiple deletions and amino acid changing mutations. To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here we propose an easy-to-use SARS-CoV-2 genome Assembler: the ESCA pipeline. Results showed that ESCA can perform high quality genome assembly from IonTor-rent and Illumina raw data, and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility to compare assembled genomes of multi sample runs through an easy table format.
    Keywords covid19
    Language English
    Publishing date 2021-05-21
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.05.21.445156
    Database COVID19

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  3. Article: Late Relapse and Reinfection in HCV Patients Treated with Direct-Acting Antiviral (DAA) Drugs

    Minosse, Claudia / Gruber, Cesare E. M. / Rueca, Martina / Taibi, Chiara / Zaccarelli, Mauro / Grilli, Elisabetta / Montalbano, Marzia / Capobianchi, Maria R. / Antinori, Andrea / D’Offizi, Gianpiero / McPhee, Fiona / Garbuglia, Anna Rosa

    Viruses. 2021 June 16, v. 13, no. 6

    2021  

    Abstract: The risk of hepatitis C virus (HCV) recurrence after direct-acting antiviral (DAA) treatment is <0.5%. However, the distinction between HCV RNA late relapse and reinfection still represents a challenge in virological diagnostics. The aim of this study ... ...

    Abstract The risk of hepatitis C virus (HCV) recurrence after direct-acting antiviral (DAA) treatment is <0.5%. However, the distinction between HCV RNA late relapse and reinfection still represents a challenge in virological diagnostics. The aim of this study was to employ next-generation sequencing (NGS) to investigate HCV RNA recurrence in patients achieving a sustained virologic response (SVR) at least six months post-treatment. NGS was performed on plasma samples from six HCV-positive patients (Pt1–6) treated with DAA. NGS of HCV NS5B was analyzed before treatment (T0), after HCV RNA rebound (T1), and, for Pt3, after a second rebound (T2). Reinfection was confirmed for Pt5, and for the first rebound observed in Pt3. Conversely, viral relapse was observed when comparing T0 and T1 for Pt6 and T1 and T2 for Pt3. Z-scores were calculated and used to predict whether HCV-positive patient samples at different time points belonged to the same quasispecies population. A low Z-score of <2.58 confirmed that viral quasispecies detected at T0 and T1 were closely related for both Pt1 and Pt2, while the Z-score for Pt4 was suggestive of possible reinfection. NGS data analyses indicate that the Z-score may be a useful parameter for distinguishing late relapse from reinfection.
    Keywords Hepatitis C virus ; RNA ; diagnostic techniques ; patients ; relapse ; risk
    Language English
    Dates of publication 2021-0616
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13061151
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Late Relapse and Reinfection in HCV Patients Treated with Direct-Acting Antiviral (DAA) Drugs.

    Minosse, Claudia / Gruber, Cesare E M / Rueca, Martina / Taibi, Chiara / Zaccarelli, Mauro / Grilli, Elisabetta / Montalbano, Marzia / Capobianchi, Maria R / Antinori, Andrea / D'Offizi, Gianpiero / McPhee, Fiona / Garbuglia, Anna Rosa

    Viruses

    2021  Volume 13, Issue 6

    Abstract: The risk of hepatitis C virus (HCV) recurrence after direct-acting antiviral (DAA) treatment is <0.5%. However, the distinction between HCV RNA late relapse and reinfection still represents a challenge in virological diagnostics. The aim of this study ... ...

    Abstract The risk of hepatitis C virus (HCV) recurrence after direct-acting antiviral (DAA) treatment is <0.5%. However, the distinction between HCV RNA late relapse and reinfection still represents a challenge in virological diagnostics. The aim of this study was to employ next-generation sequencing (NGS) to investigate HCV RNA recurrence in patients achieving a sustained virologic response (SVR) at least six months post-treatment. NGS was performed on plasma samples from six HCV-positive patients (Pt1-6) treated with DAA. NGS of HCV NS5B was analyzed before treatment (T0), after HCV RNA rebound (T1), and, for Pt3, after a second rebound (T2). Reinfection was confirmed for Pt5, and for the first rebound observed in Pt3. Conversely, viral relapse was observed when comparing T0 and T1 for Pt6 and T1 and T2 for Pt3. Z-scores were calculated and used to predict whether HCV-positive patient samples at different time points belonged to the same quasispecies population. A low
    MeSH term(s) Amino Acid Sequence ; Antiviral Agents/therapeutic use ; Base Sequence ; Female ; Genotype ; Hepacivirus/classification ; Hepacivirus/drug effects ; Hepacivirus/genetics ; Hepatitis C/diagnosis ; Hepatitis C/drug therapy ; Hepatitis C/virology ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Phenotype ; Phylogeny ; RNA, Viral ; Recurrence ; Reinfection ; Treatment Outcome
    Chemical Substances Antiviral Agents ; RNA, Viral
    Language English
    Publishing date 2021-06-16
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13061151
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Impact of ART on dynamics of growth factors and cytokines in primary HIV infection.

    Bordoni, Veronica / Sacchi, Alessandra / Casetti, Rita / Cimini, Eleonora / Tartaglia, Eleonora / Pinnetti, Carmela / Mondi, Annalisa / Gruber, Cesare E M / Antinori, Andrea / Agrati, Chiara

    Cytokine

    2019  Volume 125, Page(s) 154839

    Abstract: Antiretroviral treatment (ART) of Primary HIV Infection (PHI) has demonstrated virological and immunological benefits. The effect of early ART during PHI on the level of growth factors and chemokines modulating immune cell functions remains to be ... ...

    Abstract Antiretroviral treatment (ART) of Primary HIV Infection (PHI) has demonstrated virological and immunological benefits. The effect of early ART during PHI on the level of growth factors and chemokines modulating immune cell functions remains to be established. The aim of our work was to analyze the dynamics of 27 cytokines, chemokines and growth/regulation factors in plasma of HIV infected patients treated during PHI. Patients with PHI (n = 43) were enrolled before, 24 and 48 weeks after therapy initiation. Quantification of soluble immune mediators was performed in plasma from HIV infected patients and healthy donors (HD, n = 7) by Luminex technology. The cytokines profile was strongly perturbed in primary HIV infected patients when compared to healthy donors (HD). After 48 weeks of ART, some of these factors were restored to HD level (IL-2, IL-5, IL-7, IL-9, IL12p70, TNFα) while others persisted higher than HD (IL-6, IL-10, IL-13). Interestingly, a subset of chemokines, such as IL-8, MCP-1, RANTES and CCL27, and growth factors such as HGF, SCF and GM-CSF, increased during ART, reaching values significantly higher than HD after 48 weeks. Moreover, the G-CSF and MIP-1β soluble mediators were persistently altered and showed an inverse correlation with the CD4/CD8 T cell ratio. The increase of chemokines with antiviral activity and of growth factors with hematopoietic and immunomodulatory properties may have beneficial effects. Other studies are mandatory to evaluate the effects of long lasting levels of these factors to clarify their possible role in the context of protection/pathogenesis.
    MeSH term(s) Anti-Retroviral Agents/therapeutic use ; Antiretroviral Therapy, Highly Active ; CD4-Positive T-Lymphocytes/cytology ; CD4-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/cytology ; CD8-Positive T-Lymphocytes/immunology ; Chemokine CCL2/blood ; Chemokine CCL27/blood ; Chemokine CCL5/blood ; Chemokines/blood ; Cytokines/blood ; Down-Regulation ; Granulocyte Colony-Stimulating Factor/blood ; Granulocyte-Macrophage Colony-Stimulating Factor/blood ; HIV Infections/blood ; HIV Infections/drug therapy ; Hepatocyte Growth Factor/blood ; Humans ; Intercellular Signaling Peptides and Proteins/metabolism ; Interleukin-10/blood ; Interleukin-12/blood ; Interleukin-13/blood ; Interleukin-2/blood ; Interleukin-5/blood ; Interleukin-7/blood ; Interleukin-8/blood ; Principal Component Analysis ; Stem Cell Factor/blood ; Tumor Necrosis Factor-alpha/blood
    Chemical Substances Anti-Retroviral Agents ; CCL2 protein, human ; CCL27 protein, human ; CCL5 protein, human ; CSF2 protein, human ; CXCL8 protein, human ; Chemokine CCL2 ; Chemokine CCL27 ; Chemokine CCL5 ; Chemokines ; Cytokines ; HGF protein, human ; IL2 protein, human ; IL5 protein, human ; IL7 protein, human ; Intercellular Signaling Peptides and Proteins ; Interleukin-13 ; Interleukin-2 ; Interleukin-5 ; Interleukin-7 ; Interleukin-8 ; KITLG protein, human ; Stem Cell Factor ; Tumor Necrosis Factor-alpha ; Interleukin-10 (130068-27-8) ; Granulocyte Colony-Stimulating Factor (143011-72-7) ; Interleukin-12 (187348-17-0) ; Hepatocyte Growth Factor (67256-21-7) ; Granulocyte-Macrophage Colony-Stimulating Factor (83869-56-1)
    Language English
    Publishing date 2019-09-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1018055-2
    ISSN 1096-0023 ; 1043-4666
    ISSN (online) 1096-0023
    ISSN 1043-4666
    DOI 10.1016/j.cyto.2019.154839
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Geographical Variability Affects CCHFV Detection by RT-PCR: A Tool for In-Silico Evaluation of Molecular Assays.

    Gruber, Cesare E M / Bartolini, Barbara / Castilletti, Concetta / Mirazimi, Ali / Hewson, Roger / Christova, Iva / Avšič, Tatjana / Grunow, Roland / Papa, Anna / Sánchez-Seco, María P / Kopmans, Marion / Ippolito, Giuseppe / Capobianchi, Maria R / Reusken, Chantal B E M / Di Caro, Antonino

    Viruses

    2019  Volume 11, Issue 10

    Abstract: The Crimean-Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high ...

    Abstract The Crimean-Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high genetic variability of CCHFV often hampers the efficacy of available molecular tests and can affect their diagnostic potential. Recently, increasing numbers of complete CCHFV genomic sequences have become available, allowing a better appreciation of the genomic evolution of this virus. We summarized the current knowledge on molecular methods and developed a new bioinformatics tool to evaluate the existing assays for CCHFV detection, with a special focus on strains circulating in different geographical areas. Twenty-two molecular methods and 181 sequences of CCHFV were collected, respectively, from PubMed and GenBank databases. Up to 28 mismatches between primers and probes of each assay and CCHFV strains were detected through in-silico PCR analysis. Combinations of up to three molecular methods markedly decreased the number of mismatches within most geographic areas. These results supported the good practice of CCHFV detection of performing more than one assay, aimed for different sequence targets. The choice of the most appropriate tests must take into account patient's travel history and geographic distribution of the different CCHFV strains.
    MeSH term(s) Computational Biology ; Computer Simulation ; Genetic Variation ; Geography ; Hemorrhagic Fever Virus, Crimean-Congo/isolation & purification ; Hemorrhagic Fever, Crimean/diagnosis ; Humans ; Molecular Diagnostic Techniques/methods ; Molecular Diagnostic Techniques/standards ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sensitivity and Specificity ; Software
    Language English
    Publishing date 2019-10-16
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v11100953
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Geographical Variability Affects CCHFV Detection by RT–PCR: A Tool for In-Silico Evaluation of Molecular Assays

    Gruber, Cesare E. M / Bartolini, Barbara / Castilletti, Concetta / Mirazimi, Ali / Hewson, Roger / Christova, Iva / Avšič, Tatjana / Grunow, Roland / Papa, Anna / Sánchez-Seco, María P / Koopmans, Marion / Ippolito, Giuseppe / Capobianchi, Maria R / Reusken, Chantal B. E. M / Di Caro, Antonino

    Viruses. 2019 Oct. 16, v. 11, no. 10

    2019  

    Abstract: The Crimean–Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high ...

    Abstract The Crimean–Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high genetic variability of CCHFV often hampers the efficacy of available molecular tests and can affect their diagnostic potential. Recently, increasing numbers of complete CCHFV genomic sequences have become available, allowing a better appreciation of the genomic evolution of this virus. We summarized the current knowledge on molecular methods and developed a new bioinformatics tool to evaluate the existing assays for CCHFV detection, with a special focus on strains circulating in different geographical areas. Twenty-two molecular methods and 181 sequences of CCHFV were collected, respectively, from PubMed and GenBank databases. Up to 28 mismatches between primers and probes of each assay and CCHFV strains were detected through in-silico PCR analysis. Combinations of up to three molecular methods markedly decreased the number of mismatches within most geographic areas. These results supported the good practice of CCHFV detection of performing more than one assay, aimed for different sequence targets. The choice of the most appropriate tests must take into account patient’s travel history and geographic distribution of the different CCHFV strains.
    Keywords bioinformatics ; computer simulation ; evolution ; fever ; genetic databases ; genetic variation ; genomics ; geographical distribution ; geographical variation ; nucleotide sequences ; reverse transcriptase polymerase chain reaction ; travel ; viruses
    Language English
    Dates of publication 2019-1016
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v11100953
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Whole Genome Characterization of

    Gruber, Cesare E M / Giombini, Emanuela / Selleri, Marina / Tausch, Simon H / Andrusch, Andreas / Tyshaieva, Alona / Cardeti, Giusy / Lorenzetti, Raniero / De Marco, Lorenzo / Carletti, Fabrizio / Nitsche, Andreas / Capobianchi, Maria R / Ippolito, Giuseppe / Autorino, Gian Luca / Castilletti, Concetta

    Viruses

    2018  Volume 10, Issue 10

    Abstract: ... ...

    Abstract Orthopoxviruses
    MeSH term(s) Animals ; Cercopithecidae/virology ; DNA, Viral/genetics ; Genes, Viral/genetics ; Genome, Viral/genetics ; Orthopoxvirus/classification ; Orthopoxvirus/genetics ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid
    Chemical Substances DNA, Viral
    Language English
    Publishing date 2018-10-06
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v10100546
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Microarray gene expression profiling of neural tissues in bovine spastic paresis.

    Pariset, Lorraine / Bongiorni, Silvia / Bueno, Susana / Gruber, Cesare E M / Prosperini, Gianluca / Chillemi, Giovanni / Bicorgna, Silvia / Gentile, Arcangelo / Valentini, Alessio

    BMC veterinary research

    2013  Volume 9, Page(s) 122

    Abstract: Background: Bovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both limbs and is associated with a ... ...

    Abstract Background: Bovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both limbs and is associated with a scarce increase in body weight. This disease seems to be caused by an autosomal and recessive gene, with incomplete penetration, although no genes clearly involved with its onset have been so far identified. We employed cDNA microarrays to identify metabolic pathways affected by BSP in Romagnola cattle breed. Investigation of those pathways at the genome level can help to understand this disease.
    Results: Microarray analysis of control and affected individuals resulted in 268 differentially expressed genes. These genes were subjected to KEGG pathway functional clustering analysis, revealing that they are predominantly involved in Cell Communication, Signalling Molecules and Interaction and Signal Transduction, Diseases and Nervous System classes. Significantly enriched KEGG pathway's classes for the differentially expressed genes were calculated; interestingly, all those significantly under-expressed in the affected samples are included in Neurodegenerative Diseases. To identify genome locations possibly harbouring gene(s) involved in the disease, the chromosome distribution of the differentially expressed genes was also investigated.
    Conclusions: The cDNA microarray we used in this study contains a brain library and, even if carrying an incomplete transcriptome representation, it has proven to be a valuable tool allowing us to add useful and new information to a poorly studied disease. By using this tool, we examined nearly 15000 transcripts and analysed gene pathways affected by the disease. Particularly, our data suggest also a defective glycinergic synaptic transmission in the development of the disease and an alteration of calcium signalling proteins. We provide data to acquire knowledge of a genetic disease for which literature still presents poor results and that could be further and specifically analysed in the next future. Moreover this study, performed in livestock, may also harbour molecular information useful for understanding human diseases.
    MeSH term(s) Animals ; Cattle ; Cattle Diseases/genetics ; Cattle Diseases/metabolism ; Female ; Gene Expression/genetics ; Gene Expression Profiling/veterinary ; Male ; Nervous System/metabolism ; Oligonucleotide Array Sequence Analysis/veterinary ; Paraparesis, Spastic/genetics ; Paraparesis, Spastic/metabolism ; Paraparesis, Spastic/veterinary ; Real-Time Polymerase Chain Reaction/veterinary ; Sarcoplasmic Reticulum Calcium-Transporting ATPases/genetics
    Chemical Substances Sarcoplasmic Reticulum Calcium-Transporting ATPases (EC 3.6.3.8)
    Language English
    Publishing date 2013-06-19
    Publishing country England
    Document type Journal Article
    ISSN 1746-6148
    ISSN (online) 1746-6148
    DOI 10.1186/1746-6148-9-122
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Geographical Variability Affects CCHFV Detection by RT–PCR

    Gruber, Cesare E. M. / Bartolini, Barbara / Castilletti, Concetta / Mirazimi, Ali / Hewson, Roger / Christova, Iva / Avšič, Tatjana / Grunow, Roland / Papa, Anna / Sánchez-Seco, Maria P. / Koopmans, Marion / Ippolito, Giuseppe / Capobianchi, Maria R. / Reusken, Chantal B. E. M. / Antonino, Di Caro

    A Tool for In-Silico Evaluation of Molecular Assays

    2019  

    Abstract: The Crimean–Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high ...

    Abstract The Crimean–Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high genetic variability of CCHFV often hampers the efficacy of available molecular tests and can affect their diagnostic potential. Recently, increasing numbers of complete CCHFV genomic sequences have become available, allowing a better appreciation of the genomic evolution of this virus. We summarized the current knowledge on molecular methods and developed a new bioinformatics tool to evaluate the existing assays for CCHFV detection, with a special focus on strains circulating in different geographical areas. Twenty-two molecular methods and 181 sequences of CCHFV were collected, respectively, from PubMed and GenBank databases. Up to 28 mismatches between primers and probes of each assay and CCHFV strains were detected through in-silico PCR analysis. Combinations of up to three molecular methods markedly decreased the number of mismatches within most geographic areas. These results supported the good practice of CCHFV detection of performing more than one assay, aimed for different sequence targets. The choice of the most appropriate tests must take into account patient’s travel history and geographic distribution of the different CCHFV strains.

    Peer Reviewed
    Keywords CCHFV ; molecular detection ; Crimean–Congo hemorrhagic fever virus ; arthropod-borne virus ; laboratory preparedness ; emerging diseases ; 610 Medizin und Gesundheit ; ddc:610
    Subject code 500
    Language English
    Publishing date 2019-10-16
    Publisher Robert Koch-Institut
    Publishing country de
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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