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  1. Article ; Online: Biological and Clinical Significance of Adaptive Evolution of Coronaviruses

    Apostolos Beloukas / Theodoros Rampias

    Life, Vol 11, Iss 1129, p

    2021  Volume 1129

    Abstract: RNA viral genomes are generally small genomes that rarely exceed 10 kb in size [.] ...

    Abstract RNA viral genomes are generally small genomes that rarely exceed 10 kb in size [.]
    Keywords n/a ; Science ; Q
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Population Genomics Insights into the First Wave of COVID-19

    Maria Vasilarou / Nikolaos Alachiotis / Joanna Garefalaki / Apostolos Beloukas / Pavlos Pavlidis

    Life, Vol 11, Iss 2, p

    2021  Volume 129

    Abstract: Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to ... ...

    Abstract Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to infer the mutation rate and plausible recombination events between the Betacoronavirus genomes in nonhuman hosts that may have contributed to the evolution of SARS-CoV-2. Furthermore, we localized the targets of recent and strong, positive selection during the first pandemic wave. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from nonhuman hosts took place. Our results suggest that the pangolin coronavirus genome may have contributed to the SARS-CoV-2 genome by recombination with the bat coronavirus genome. However, we find evidence for additional recombination events that involve coronavirus genomes from other hosts, i.e., hedgehogs and sparrows. We further infer that recombination may have recently occurred within human hosts. Finally, we estimate the parameters of a demographic scenario involving an exponential growth of the size of the SARS-CoV-2 populations that have infected European, Asian, and Northern American cohorts, and we demonstrate that a rapid exponential growth in population size from the first wave can support the observed polymorphism patterns in SARS-CoV-2 genomes.
    Keywords SARS-CoV-2 ; population genetics ; recombination ; mutation rate ; selective sweeps ; demographic inference ; Science ; Q
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Assessing the Presence of IgG Antibodies against Influenza Viruses in Neonates after Maternal Vaccination and Factors That May Affect the Transplacental Transfer

    Chrysoula Taskou / Antigoni Sarantaki / Vasiliki Ε. Georgakopoulou / Gerasimos A. Spyratos / Panagiotis V. Drossos / Georgios Daskalakis / Apostolos Beloukas / Aikaterini Lykeridou

    Diseases, Vol 11, Iss 4, p

    2023  Volume 166

    Abstract: Special populations, particularly pregnant women, are uniquely susceptible to infectious diseases due to alterations in their immunological, respiratory, and cardiovascular systems during gestation. Influenza infections during the perinatal period have ... ...

    Abstract Special populations, particularly pregnant women, are uniquely susceptible to infectious diseases due to alterations in their immunological, respiratory, and cardiovascular systems during gestation. Influenza infections during the perinatal period have been associated with more severe maternal and perinatal outcomes, underscoring the critical importance of vaccination data for pregnant women. According to the World Health Organization (WHO), all pregnant women and those of childbearing age should receive the inactivated influenza vaccine, irrespective of their pregnancy stage. This study aimed to elucidate factors influencing neonatal antibody presence following maternal influenza vaccination. Conducted through convenience sampling in Athens, Greece, this study involved 78 pregnant women who received flu vaccinations. The participants completed questionnaires covering demographics, obstetric history, attitudes toward influenza vaccination, and knowledge about the influenza virus and pregnancy vaccination. Blood samples were collected from 83 neonates to assess IgG antibody presence. Five of the surveyed women had twin pregnancies. The statistical analysis employed IBM SPSS-Statistics version 26.0. This study revealed the presence of positive influenza A and B antibodies in neonates following maternal immunization. Furthermore, it identified factors such as the gestational week and timing of vaccination during pregnancy that influenced the transfer of antibodies from mother to fetus. These findings offer valuable insights for healthcare professionals to provide informed recommendations on influenza vaccination during pregnancy and empower expectant mothers to make informed decisions about the benefits of immunization.
    Keywords maternal vaccination ; influenza vaccines ; influenza antibodies ; IgG transplacental transfer ; Medicine ; R
    Subject code 610
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Molecular Characterization and Prevalence of Antimicrobial-Resistant Escherichia coli Isolates Derived from Clinical Specimens and Environmental Habitats

    Chrysoula Dioli / Olga Pappa / Eirini Siatravani / Spyridoula Bratakou / Apostolos Tatsiopoulos / Panagiota Giakkoupi / Vivi Miriagou / Apostolos Beloukas

    Microorganisms, Vol 11, Iss 1399, p

    2023  Volume 1399

    Abstract: Antibiotic-resistant bacteria (ARB) are present in wastewaters as their elimination during treatment in wastewater treatment plants (WWTPs) is often impossible. Water plays an important role in the spread of these microorganisms among humans, animals and ...

    Abstract Antibiotic-resistant bacteria (ARB) are present in wastewaters as their elimination during treatment in wastewater treatment plants (WWTPs) is often impossible. Water plays an important role in the spread of these microorganisms among humans, animals and the environment. This study aimed to assess the antimicrobial resistance patterns, resistance genes and molecular genotypes by means of phylogenetic groups of E. coli isolates in aquatic habitats, including sewage and receiving water bodies, as well as clinical settings in the Boeotia regional district of Greece. The highest resistance rates among both environmental and clinical isolates were observed to be for penicillins, ampicillin and piperacillin. Resistance patterns related to extended spectrum β-lactamases (ESBL) production and ESBL genes were also detected in both environmental and clinical isolates. Phylogenetic group B2 was predominant in clinical settings and the second most frequent among wastewaters, whereas group A was dominant in all environmental isolates. In conclusion, the studied river water and wastewaters may serve as reservoirs of resistant E. coli isolates that pose potential threats to both human and animal health.
    Keywords E. coli ; environment ; antibiotic resistance ; antibiotic resistance genes ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Screening, Diagnostic and Prognostic Tests for COVID-19

    Mariana Ulinici / Serghei Covantev / James Wingfield-Digby / Apostolos Beloukas / Alexander G. Mathioudakis / Alexandru Corlateanu

    Life, Vol 11, Iss 561, p

    A Comprehensive Review

    2021  Volume 561

    Abstract: While molecular testing with real-time polymerase chain reaction (RT-PCR) remains the gold-standard test for COVID-19 diagnosis and screening, more rapid or affordable molecular and antigen testing options have been developed. More affordable, point-of- ... ...

    Abstract While molecular testing with real-time polymerase chain reaction (RT-PCR) remains the gold-standard test for COVID-19 diagnosis and screening, more rapid or affordable molecular and antigen testing options have been developed. More affordable, point-of-care antigen testing, despite being less sensitive compared to molecular assays, might be preferable for wider screening initiatives. Simple laboratory, imaging and clinical parameters could facilitate prognostication and triage. This comprehensive review summarises current evidence on the diagnostic, screening and prognostic tests for COVID-19.
    Keywords SARS-CoV2 ; COVID-19 ; coronavirus ; diagnosis ; screening ; prognosis ; Science ; Q
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: The Role of Coronavirus RNA-Processing Enzymes in Innate Immune Evasion

    Georgia Mandilara / Marianna A. Koutsi / Marios Agelopoulos / Georgios Sourvinos / Apostolos Beloukas / Theodoros Rampias

    Life, Vol 11, Iss 571, p

    2021  Volume 571

    Abstract: Viral RNA sensing triggers innate antiviral responses in humans by stimulating signaling pathways that include crucial antiviral genes such as interferon. RNA viruses have evolved strategies to inhibit or escape these mechanisms. Coronaviruses use ... ...

    Abstract Viral RNA sensing triggers innate antiviral responses in humans by stimulating signaling pathways that include crucial antiviral genes such as interferon. RNA viruses have evolved strategies to inhibit or escape these mechanisms. Coronaviruses use multiple enzymes to synthesize, modify, and process their genomic RNA and sub-genomic RNAs. These include Nsp15 and Nsp16, whose respective roles in RNA capping and dsRNA degradation play a crucial role in coronavirus escape from immune surveillance. Evolutionary studies on coronaviruses demonstrate that genome expansion in Nidoviruses was promoted by the emergence of Nsp14-ExoN activity and led to the acquisition of Nsp15- and Nsp16-RNA-processing activities. In this review, we discuss the main RNA-sensing mechanisms in humans as well as recent structural, functional, and evolutionary insights into coronavirus Nsp15 and Nsp16 with a view to potential antiviral strategies.
    Keywords viral RNA sensing ; coronavirus ; innate immunity ; immune evasion ; SARS-CoV-2 ; Science ; Q
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Animal Coronaviruses Induced Apoptosis

    Katerina Gioti / Christine Kottaridi / Chrysa Voyiatzaki / Dimitrios Chaniotis / Theodoros Rampias / Apostolos Beloukas

    Life, Vol 11, Iss 3, p

    2021  Volume 185

    Abstract: Apoptosis is a form of programmed death that has also been observed in cells infected by several viruses. It is considered one of the most critical innate immune mechanisms that limits pathogen proliferation and propagation before the initiation of the ... ...

    Abstract Apoptosis is a form of programmed death that has also been observed in cells infected by several viruses. It is considered one of the most critical innate immune mechanisms that limits pathogen proliferation and propagation before the initiation of the adaptive immune response. Recent studies investigating the cellular responses to SARS-CoV and SARS-CoV-2 infection have revealed that coronaviruses can alter cellular homeostasis and promote cell death, providing evidence that the modulation of apoptotic pathways is important for viral replication and propagation. Despite the genetic diversity among different coronavirus clades and the infection of different cell types and several hosts, research studies in animal coronaviruses indicate that apoptosis in host cells is induced by common molecular mechanisms and apoptotic pathways. We summarize and critically review current knowledge on the molecular aspects of cell-death regulation during animal coronaviruses infection and the viral–host interactions to this process. Future research is expected to lead to a better understanding of the regulation of cell death during coronavirus infection. Moreover, investigating the role of viral proteins in this process will help us to identify novel antiviral targets related to apoptotic signaling pathways.
    Keywords animal coronaviruses ; apoptosis ; apoptotic pathways ; Science ; Q
    Subject code 570
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Epidemiological data for hepatitis D in Africa – Authors' reply

    Alexander J Stockdale / Apostolos Beloukas / Anna Maria Gerretti

    The Lancet Global Health, Vol 6, Iss 1, p e

    2018  Volume 34

    Keywords Public aspects of medicine ; RA1-1270
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Large‐scale screening for factor V Leiden (G1691A), prothrombin (G20210A), and MTHFR (C677T) mutations in Greek population

    Alkistis Raptopoulou / Vassiliki Michou / Niki Mourtzi / Efstathia G. Papageorgiou / Chrysa Voyiatzaki / Vassilis Tsilivakos / Apostolos Beloukas / Thaleia A. Bei

    Health Science Reports, Vol 5, Iss 4, Pp n/a-n/a (2022)

    2022  

    Abstract: Abstract Background and aims To provide a fair estimate of the prevalence of factor V Leiden (FVL) (G1691A), prothrombin (G20210A), and MTHFR (C677T) mutations in the Greek population. Methods We genotyped a representative sample of 974 apparently ... ...

    Abstract Abstract Background and aims To provide a fair estimate of the prevalence of factor V Leiden (FVL) (G1691A), prothrombin (G20210A), and MTHFR (C677T) mutations in the Greek population. Methods We genotyped a representative sample of 974 apparently healthy Greek adults by the method of real‐time PCR and we calculated the allele frequencies of factor V Leiden (FVL) (G1691A), prothrombin (G20210A), and MTHFR (C677T) mutations. In addition, we determined the frequency of co‐occurrence of FVL (1691A) and prothrombin (20210A), FVL (1691A) and MTHFR (677T), prothrombin (20210A) and MTHFR (677T) mutations. Results Τhe career frequencies of FVL (1691A), prothrombin (20210A), and MTHFR (677T) alleles were 7.5%, 4.5%, and 49.3% while the allele frequencies were 4%, 2.25%, and 39.5%, respectively. The coexistence of the allele frequencies combinations of two, FVL (1691A) and Prothrombin (20210A), FVL (1691A) and MTHFR (677T), prothrombin (20210A) and MTHFR (677T) was found in 1 (0.9%), 29 (3.5%), and 22 (3%) samples, respectively. Triple heterozygous carriers were not found. Conclusion Allele frequencies of the two (FVL and MTHFR) mutations are higher compared with published data. The large sample size of our study enhances the validity of our results and suggests a biological affinity of Greek population with Southern Italian populations.
    Keywords FVL ; Greece ; MTHFR ; prothrombin ; thrombophilia ; Medicine ; R
    Subject code 306
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Prevalence and clinical implications of respiratory viruses in asthma during stable disease state and acute attacks

    Gioulinta S Alimani / Sachin Ananth / Cristina Boccabella / Ekaterina Khaleva / Graham Roberts / Nikolaos G Papadopoulos / Chris Kosmidis / Jørgen Vestbo / Effie Papageorgiou / Apostolos Beloukas / Alexander G Mathioudakis

    PLoS ONE, Vol 18, Iss 11, p e

    Protocol for a meta-analysis.

    2023  Volume 0294416

    Abstract: Introduction Viruses are detected in over 50% of acute asthma attacks and in a notable proportion of patients with asthma during stable disease state They are associated with worse outcomes. We will conduct a series of systematic reviews and meta- ... ...

    Abstract Introduction Viruses are detected in over 50% of acute asthma attacks and in a notable proportion of patients with asthma during stable disease state They are associated with worse outcomes. We will conduct a series of systematic reviews and meta-analyses to quantify the prevalence and clinical burden of various respiratory viruses in stable asthma and acute asthma attacks. In addition, we will assess the viral loads of respiratory viruses during stable and acute asthma, to explore whether viral load could differentiate attacks triggered by viruses versus those where viruses are present as "innocent bystanders". Materials and methods Based on a prospectively registered protocol (PROSPERO, ID: CRD42023375108) and following standard methodology recommended by Cochrane, we will systematically search Medline/PubMed, EMBASE, the Cochrane Library and relevant conference proceedings for studies assessing the prevalence or clinical burden of respiratory viruses in asthma. Methodological rigour of the included studies will be appraised using a tool specific for prevalence studies and the Newcastle-Ottawa Scale respectively. In anticipation of significant clinical and methodological heterogeneity, we will conduct random effect meta-analyses. For evaluating the prevalence of viruses, we will perform meta-analyses of proportions using the inverse variance method, and the Freeman-Tukey transformation. We will conduct meta-regression analyses for exploring heterogeneity. Conclusion We envisage that these systematic reviews and meta-analyses will quantify the prevalence and burden of respiratory viruses in stable and acute asthma and will drive future research and clinical practice.
    Keywords Medicine ; R ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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