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  1. Article: Recommendations for the nomenclature of enteroviruses and rhinoviruses [Erratum: Jun. 2020, v.165(6), p.1515]

    Simmonds, P / Gorbalenya, A. E / Harvala, H / Hovi, T / Knowles, N. J / Lindberg, A. M / Oberste, M. S / Palmenberg, A. C / Reuter, G / Skern, T / Tapparel, C / Wolthers, K. C / Woo, P. C. Y / Zell, R

    Archives of virology. 2020 Mar., v. 165, no. 3

    2020  

    Abstract: Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and ... ...

    Abstract Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and control of emerging pathogenic EV types worldwide. EVs and RVs are highly diverse in their antigenic properties, tissue tropism, disease associations and evolutionary relationships, but the latter often conflict with previously developed biologically defined terms, such as “coxsackieviruses”, “polioviruses” and “echoviruses”, which were used before their genetic interrelationships were understood. This has created widespread formatting problems and inconsistencies in the nomenclature for EV and RV types and species in the literature and public databases. As members of the International Committee for Taxonomy of Viruses (ICTV) Picornaviridae Study Group, we describe the correct use of taxon names for these viruses and have produced a series of recommendations for the nomenclature of EV and RV types and their abbreviations. We believe their adoption will promote greater clarity and consistency in the terminology used in the scientific and medical literature. The recommendations will additionally provide a useful reference guide for journals, other publications and public databases seeking to use standardised terms for the growing multitude of enteroviruses and rhinoviruses described worldwide.
    Keywords public health ; taxonomy ; terminology ; tissue tropism ; virology
    Language English
    Dates of publication 2020-03
    Size p. 793-797.
    Publishing place Springer Vienna
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-019-04520-6
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Psychological Distress and Quality of Life in Participants Undergoing Genetic Testing for Arrhythmogenic Right Ventricular Cardiomyopathy Caused by TMEM43 p.S358L: Is It Time to Offer Population-Based Genetic Screening?

    Brothers, Cassidy / Etchegary, Holly / Curtis, Fiona / Simmonds, Charlene / Houston, Jim / Young, Terry-Lynn / Pullman, Daryl / Mariathas, Hensley H / Connors, Sean / Hodgkinson, Kathleen

    Public health genomics

    2021  Volume 24, Issue 5-6, Page(s) 253–260

    Abstract: ... TMEM43 p.S358L responsible for 1 form of arrhythmogenic right ventricular cardiomyopathy. Current ... explored the acceptability among subjects to TMEM43 p.S358L population-based genetic screening (PBGS ... health-related quality of life (QOL) in unselected individuals who underwent genetic screening for the TMEM43 p ...

    Abstract Purpose: We have identified 27 families in Newfoundland and Labrador (NL) with the founder variant TMEM43 p.S358L responsible for 1 form of arrhythmogenic right ventricular cardiomyopathy. Current screening guidelines rely solely on cascade genetic screening, which may result in unrecognized, high-risk carriers who would benefit from preemptive implantable cardioverter-defibrillator therapy. This pilot study explored the acceptability among subjects to TMEM43 p.S358L population-based genetic screening (PBGS) in this Canadian province.
    Methods: A prospective cohort study assessed attitudes, psychological distress, and health-related quality of life (QOL) in unselected individuals who underwent genetic screening for the TMEM43 p.S358L variant. Participants (n = 73) were recruited via advertisements and completed 2 surveys at baseline, 6 months, and 1 year which measured health-related QOL (SF-36v2) and psychological distress (Impact of Events Scale).
    Results: No variant-positive carriers were identified. Of those screened through a telephone questionnaire, >95% felt positive about population-genetic screening for TMEM43 p.S358L, though 68% reported some degree of anxiety after seeing the advertisement. There were no significant changes in health-related QOL or psychological distress scores over the study period.
    Conclusion: Despite some initial anxiety, we show support for PBGS among research subjects who screened negative for the TMEM43 p.S358L variant in NL. These findings have implications for future PBGS programs in the province.
    MeSH term(s) Arrhythmogenic Right Ventricular Dysplasia/diagnosis ; Arrhythmogenic Right Ventricular Dysplasia/genetics ; Canada ; Genetic Testing ; Humans ; Membrane Proteins/genetics ; Pilot Projects ; Prospective Studies ; Psychological Distress ; Quality of Life
    Chemical Substances Membrane Proteins ; TMEM43 protein, human
    Language English
    Publishing date 2021-09-09
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2457023-0
    ISSN 1662-8063 ; 1662-4246
    ISSN (online) 1662-8063
    ISSN 1662-4246
    DOI 10.1159/000517265
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories.

    Simmonds, P

    mSphere

    2020  Volume 5, Issue 3

    Abstract: The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a data set ...

    Abstract The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a data set of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean of 5.5 to 9.5 nucleotide differences from each other, consistent with a midrange coronavirus substitution rate of 3 × 10
    MeSH term(s) APOBEC Deaminases ; Base Composition/genetics ; Base Sequence/genetics ; Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/pathology ; Cytidine Deaminase/genetics ; Cytosine/analysis ; Genome, Viral/genetics ; Humans ; Middle East Respiratory Syndrome Coronavirus/genetics ; Pandemics ; Pneumonia, Viral/pathology ; Polymorphism, Single Nucleotide/genetics ; Severe acute respiratory syndrome-related coronavirus/genetics ; SARS-CoV-2 ; Uracil/analysis
    Chemical Substances Uracil (56HH86ZVCT) ; Cytosine (8J337D1HZY) ; APOBEC Deaminases (EC 3.5.4.5) ; APOBEC3 proteins, human (EC 3.5.4.5) ; Cytidine Deaminase (EC 3.5.4.5)
    Keywords covid19
    Language English
    Publishing date 2020-06-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2379-5042
    ISSN (online) 2379-5042
    DOI 10.1128/mSphere.00408-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Pervasive RNA Secondary Structure in the Genomes of SARS-CoV-2 and Other Coronaviruses.

    Simmonds, P

    mBio

    2020  Volume 11, Issue 6

    Abstract: The ultimate outcome of the coronavirus disease 2019 (COVID-19) pandemic is unknown and is dependent on a complex interplay of its pathogenicity, transmissibility, and population immunity. In the current study, severe acute respiratory syndrome ... ...

    Abstract The ultimate outcome of the coronavirus disease 2019 (COVID-19) pandemic is unknown and is dependent on a complex interplay of its pathogenicity, transmissibility, and population immunity. In the current study, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated for the presence of large-scale internal RNA base pairing in its genome. This property, termed genome-scale ordered RNA structure (GORS) has been previously associated with host persistence in other positive-strand RNA viruses, potentially through its shielding effect on viral RNA recognition in the cell. Genomes of SARS-CoV-2 were remarkably structured, with minimum folding energy differences (MFEDs) of 15%, substantially greater than previously examined viruses such as hepatitis C virus (HCV) (MFED of 7 to 9%). High MFED values were shared with all coronavirus genomes analyzed and created by several hundred consecutive energetically favored stem-loops throughout the genome. In contrast to replication-associated RNA structure, GORS was poorly conserved in the positions and identities of base pairing with other sarbecoviruses-even similarly positioned stem-loops in SARS-CoV-2 and SARS-CoV rarely shared homologous pairings, indicative of more rapid evolutionary change in RNA structure than in the underlying coding sequences. Sites predicted to be base paired in SARS-CoV-2 showed less sequence diversity than unpaired sites, suggesting that disruption of RNA structure by mutation imposes a fitness cost on the virus that is potentially restrictive to its longer evolution. Although functionally uncharacterized, GORS in SARS-CoV-2 and other coronaviruses represents important elements in their cellular interactions that may contribute to their persistence and transmissibility.
    MeSH term(s) Animals ; Base Sequence ; Betacoronavirus/genetics ; COVID-19 ; Coronavirus/genetics ; Coronavirus Infections/virology ; Evolution, Molecular ; Genome, Viral ; Humans ; Nucleic Acid Conformation ; Pandemics ; Pneumonia, Viral/virology ; RNA, Viral/chemistry ; RNA, Viral/genetics ; SARS-CoV-2 ; Sequence Alignment
    Chemical Substances RNA, Viral
    Keywords covid19
    Language English
    Publishing date 2020-10-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mBio.01661-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online: People - Marine Mammal Interactions

    Butterworth, Andrew / Simmonds, Mark P.

    2017  

    Abstract: Our relationships with marine mammals are complex. We have used them as resources, and in some places this remains the case; viewed them as competitors and culled them (again ongoing in some localities); been so captivated and intrigued by them that we ... ...

    Abstract Our relationships with marine mammals are complex. We have used them as resources, and in some places this remains the case; viewed them as competitors and culled them (again ongoing in some localities); been so captivated and intrigued by them that we have taken them into captivity for our entertainment; and developed a lucrative eco-tourism activity focused on them in many nations. When we first envisaged this special topic, we had two overarching aims: Firstly, we hoped to generate critical evaluation of some of our relationships with these animals. Secondly, we hoped to attract knowledgeable commentators and experts who might not traditionally publish in the peer-reviewed literature. We were also asking ourselves a question about what responsibility mankind might have to marine mammals, on our rapidly changing planet? The answer to the question; can, or should, humans have responsibility for the lives of marine mammals when they are affected by our activities? - is, in our opinion, 'yes' - and the logical progression from this question is to direct research and effort to understand and optimise the actions, reactions and responses that mankind may be able to take. We hope that the papers in this special issue bring some illumination to a small selection of topics under this much wider topic area, and prove to be informative and stimulating
    Keywords Oceanography ; Science (General)
    Size 1 electronic resource (109 p.)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020095935
    ISBN 9782889452316 ; 288945231X
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  6. Article ; Online: Xenon tracers for cost effective laser induced fluorescence of alternative propellant Hall thrusters.

    Simmonds, J B / Byrne, M P / Chaplin, V H

    The Review of scientific instruments

    2024  Volume 95, Issue 2

    Abstract: One of the limiting factors to developing plasma thrusters on alternative propellants is the cost associated with changing the diagnostic tools, which are often propellant-dependent. For laser induced fluorescence (LIF), which is typically used for ion ... ...

    Abstract One of the limiting factors to developing plasma thrusters on alternative propellants is the cost associated with changing the diagnostic tools, which are often propellant-dependent. For laser induced fluorescence (LIF), which is typically used for ion velocity distribution measurements to determine ion trajectories and potential profiles, either new lasers need to be bought, which are tuned to the wavelength of the new element's excitation level, or a costly tunable laser is required. A method to use existing LIF setups designed for xenon on any propellant has been demonstrated on a Hall thruster operating on krypton. In the demonstration test, a small amount of xenon (0.01%-4%) was mixed with the main krypton propellant for use as a diagnostic tracer, and xenon ion velocities were measured while also monitoring changes in the mean discharge current and oscillations. High signal-to-noise ratios in LIF data acquired along the channel centerline were obtained with tracer gas fractions ≤1% that negligibly affected the thruster operation. These results and comparison of the emission spectra of xenon and other common propellants suggest that the tracer LIF method should be broadly applicable to LIF measurements in Hall thrusters operating on alternative propellants.
    Language English
    Publishing date 2024-02-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209865-9
    ISSN 1089-7623 ; 0034-6748
    ISSN (online) 1089-7623
    ISSN 0034-6748
    DOI 10.1063/5.0179938
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: New oligonucleotide primers for P-typing of rotavirus strains: Strategies for typing previously untypeable strains.

    Simmonds, Mirjam Kühne / Armah, George / Asmah, Richard / Banerjee, Indrani / Damanka, Susan / Esona, Mathew / Gentsch, Jon R / Gray, Jim J / Kirkwood, Carl / Page, Nicola / Iturriza-Gómara, Miren

    Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

    2008  Volume 42, Issue 4, Page(s) 368–373

    Abstract: ... the UK.: Results: The new primer pair allowed P-typing of rotavirus strains and provided increased ... sensitivity, allowing typing of a significant number of strains that previously could not be P-typed ...

    Abstract Background: The use of molecular methods for rotavirus characterisation provides increased sensitivity for typing, and allows the identification of putative reassortant strains. However, due to the constant accumulation of point mutations through genetic drift; and to the emergence of novel genotypes; and possibly zoonotic transmission and subsequent reassortment, the reagents and methods used for genotyping require close monitoring and updating.
    Objectives: To design and evaluate a new VP4 consensus oligonucleotide primer pair that provides increased sensitivity and allows typing of strains that were untypeable using available methods.
    Study design: A total of 489 rotavirus-positive faecal specimens from studies conducted between 1996 and 2006 were used for the evaluation of the new VP4 primers which was performed in the WHO Rotavirus Collaborating and Reference centres in the US, Australia, South Africa and the UK.
    Results: The new primer pair allowed P-typing of rotavirus strains and provided increased sensitivity, allowing typing of a significant number of strains that previously could not be P-typed.
    Conclusions: This study highlights the importance of a constant reconsideration of primer sequences employed for the molecular typing of rotaviruses.
    MeSH term(s) Australia ; Capsid Proteins/genetics ; DNA Primers/genetics ; Feces/virology ; Humans ; RNA, Viral/genetics ; Rotavirus/classification ; Rotavirus/genetics ; Rotavirus/isolation & purification ; Rotavirus Infections/virology ; Sensitivity and Specificity ; South Africa ; United Kingdom ; United States
    Chemical Substances Capsid Proteins ; DNA Primers ; RNA, Viral ; VP4 protein, Rotavirus
    Language English
    Publishing date 2008-08
    Publishing country Netherlands
    Document type Evaluation Studies ; Journal Article
    ZDB-ID 1446080-4
    ISSN 1873-5967 ; 1386-6532
    ISSN (online) 1873-5967
    ISSN 1386-6532
    DOI 10.1016/j.jcv.2008.02.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: The roles of nucleic acid editing in adaptation of zoonotic viruses to humans.

    Ratcliff, Jeremy / Simmonds, Peter

    Current opinion in virology

    2023  Volume 60, Page(s) 101326

    Abstract: Following spillover, viruses must adapt to new selection pressures exerted by antiviral responses in their new hosts. In mammals, cellular defense mechanisms often include viral nucleic acid editing pathways mediated through protein families ... ...

    Abstract Following spillover, viruses must adapt to new selection pressures exerted by antiviral responses in their new hosts. In mammals, cellular defense mechanisms often include viral nucleic acid editing pathways mediated through protein families apolipoprotein-B mRNA-editing complex (APOBEC) and Adenosine Deaminase Acting on ribonucleic acid (ADAR). APOBECs induce C→U transitions in viral genomes; the APOBEC locus is highly polymorphic with variable numbers of APOBEC3 paralogs and target preferences in humans and other mammals. APOBEC3 paralogs have shaped the evolutionary history of human immunodeficiency virus, with compelling bioinformatic evidence also for its mutagenic impact on monkeypox virus and severe acute respiratory syndrome coronavirus 2. ADAR-1 induces adenose-to-inosine (A→I) substitutions in double-stranded ribonucleic acid (RNA); its role in virus adaptation is less clear, as are epigenetic modifications to viral genomes, such as methylation. Nucleic acid editing restricts evolutionary space in which viruses can explore and may restrict viral-host range.
    MeSH term(s) Animals ; Humans ; Nucleic Acids ; COVID-19 ; Viruses/genetics ; Mammals ; RNA
    Chemical Substances Nucleic Acids ; RNA (63231-63-0)
    Language English
    Publishing date 2023-04-07
    Publishing country Netherlands
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2611378-8
    ISSN 1879-6265 ; 1879-6257
    ISSN (online) 1879-6265
    ISSN 1879-6257
    DOI 10.1016/j.coviro.2023.101326
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses

    P. Simmonds

    mSphere, Vol 5, Iss 3, p e00408-

    Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories

    2020  Volume 20

    Abstract: The wealth of accurately curated sequence data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), its long genome, and its low substitution rate provides a relatively blank canvas with which to investigate effects of mutational and editing ...

    Abstract The wealth of accurately curated sequence data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), its long genome, and its low substitution rate provides a relatively blank canvas with which to investigate effects of mutational and editing processes imposed by the host cell. The finding that a large proportion of sequence change in SARS-CoV-2 in the initial months of the pandemic comprised C→U mutations in a host APOBEC-like context provides evidence for a potent host-driven antiviral editing mechanism against coronaviruses more often associated with antiretroviral defense. In evolutionary terms, the contribution of biased, convergent, and context-dependent mutations to sequence change in SARS-CoV-2 is substantial, and these processes are not incorporated by standard models used in molecular epidemiology investigations. The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a data set of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean of 5.5 to 9.5 nucleotide differences from each other, consistent with a midrange coronavirus substitution rate of 3 × 10−4 substitutions/site/year. Almost one-half of sequence changes were C→U transitions, with an 8-fold base frequency normalized directional asymmetry between C→U and U→C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARS-CoV, Middle East respiratory syndrome [MERS]-CoV), and decreasing ratios were observed in other human coronaviruses (HCoV-NL63, -OC43, -229E, and -HKU1) proportionate to their increasing divergence. C→U transitions underpinned almost one-half of the amino acid differences between SARS-CoV-2 variants and occurred preferentially in both 5′ U/A and 3′ U/A flanking sequence contexts comparable to favored motifs of human APOBEC3 proteins. Marked base asymmetries observed in nonpandemic human coronaviruses (U ≫ A > G ≫ C) and low G+C contents may represent long-term effects of prolonged C→U hypermutation in their hosts. The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short- and long-term evolution. Repeated cycles of mutation and reversion in favored mutational hot spots and the widespread occurrence of amino acid changes with no adaptive value for the virus represent a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks and are not incorporated by standard models used in molecular epidemiology investigations.
    Keywords apobec ; covid-19 ; sars ; sars coronavirus 2 ; coronavirus ; hypermutation ; sars-cov-2 ; Microbiology ; QR1-502 ; covid19
    Subject code 572
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher American Society for Microbiology
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories

    Simmonds, P.

    bioRxiv

    Abstract: The pandemic of SARS coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 ... ...

    Abstract The pandemic of SARS coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean 5.5-9.5 nucleotide differences from each other, commensurate with a mid-range coronavirus substitution rate of 3×10−4 substitutions/site/year. Almost half of sequence changes were C->U transitions with an 8-fold base frequency normalised directional asymmetry between C->U and U->C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARS-CoV and MERS-CoV) and to a decreasing degree in other human coronaviruses (HCoV-NL63, -OC43, -229E and -HKU1) proportionate to their increasing divergence. C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5’U/A and 3’U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Marked base asymmetries observed in non-pandemic human coronaviruses (U>>A>G>>C) and low G+C contents may represent long term effects of prolonged C->U hypermutation in their hosts. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. Repeated cycles of mutation and reversion in favoured mutational hotspots and the widespread occurrence of amino acid changes with no adaptive value for the virus represents a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks that are typically used in molecular epidemiology investigations.
    Keywords covid19
    Publisher BioRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.05.01.072330
    Database COVID19

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