COVID-19 and SARS-CoV-2: Mechanisms and Impacts
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What is the role of the TMPRSS2 protein in the entry of SARS-CoV-2 into a cell?

  • TMPRSS2 helps the virus to release its genomic material into the cytoplasm.
  • TMPRSS2 binds to the ACE2 receptor on the cell surface, allowing the virus to enter.
  • TMPRSS2 cleaves the spike protein, separating the S1 and S2 subunits. (correct)
  • TMPRSS2 is responsible for fusing the membranes of the virus and the cell.
  • Why is the receptor binding domain (RBD) of the spike protein a target for the immune system and a common site of mutations?

  • The RBD is the only part of the spike protein that interacts with the ACE2 receptor.
  • The RBD is the most variable part of the spike protein, making it difficult for antibodies to bind. (correct)
  • Antibodies that target the RBD are unable to prevent the virus from entering the cell.
  • Mutations in the RBD are always associated with increased infectivity and lower mortality.
  • How does the D614G mutation affect the infectivity and mortality of SARS-CoV-2?

  • The D614G mutation does not significantly affect either infectivity or mortality.
  • The D614G mutation is associated with increased infectivity, but does not significantly affect mortality. (correct)
  • The D614G mutation is associated with decreased infectivity, but does not significantly affect mortality.
  • The D614G mutation is associated with decreased infectivity and increased mortality.
  • What is the significance of targeting non-mutating regions of the spike protein for vaccine development?

    <p>Targeting non-mutating regions of the spike protein can increase the effectiveness of vaccines, as these regions are less likely to be affected by mutations. (A)</p> Signup and view all the answers

    What is the typical timeframe for becoming infectious with SARS-CoV-2 after exposure?

    <p>You become infectious 4-5 days before symptoms appear. (D)</p> Signup and view all the answers

    What was the total number of COVID-19 cases reported in January 2024?

    <p>773 million (B)</p> Signup and view all the answers

    Which of the following human coronaviruses was first described in 1968?

    <p>HCoV-OC43 (D)</p> Signup and view all the answers

    What type of genetic material do coronaviruses possess?

    <p>Single-stranded positive sense RNA (C)</p> Signup and view all the answers

    What is the diameter of coronavirus particles as mentioned?

    <p>125 nm (A)</p> Signup and view all the answers

    Which protein is not a structural protein of coronaviruses?

    <p>Replication protein (R) (C)</p> Signup and view all the answers

    Which factor is NOT related to the virulence of a virus?

    <p>Social status of the infected individual (A)</p> Signup and view all the answers

    What is a characteristic symptom of COVID-19 that appears after 4-10 days post-infection?

    <p>High fever and sore throat (A)</p> Signup and view all the answers

    What is the main outcome of programmed ribosomal frameshifting in coronaviruses?

    <p>It leads to the synthesis of multiple non-structural proteins. (C)</p> Signup and view all the answers

    What is the primary function of the proteases derived from non-structural proteins like nsp3 and nsp5?

    <p>They play a role in the proteolytic processing of replicase polyproteins. (D)</p> Signup and view all the answers

    Which condition is NOT considered a co-morbidity affecting the immune response to infections?

    <p>Age younger than 18 (C)</p> Signup and view all the answers

    Which of the following statements about COVID-19 is accurate?

    <p>Long COVID can results in symptoms such as brain fog and joint pain. (D)</p> Signup and view all the answers

    Which of the following non-structural proteins function in cytoplasmic vesicle biogenesis?

    <p>nsp3, nsp4, nsp6 (A)</p> Signup and view all the answers

    What process involves the inflammatory cell death triggered by COVID-19?

    <p>Pyroptosis (B)</p> Signup and view all the answers

    What mechanism leads to the simultaneous −1 shift of tRNAs during programmed ribosomal frameshifting?

    <p>Regulatory RNA elements. (A)</p> Signup and view all the answers

    How many unique proteins are generated from the cleavage of the polyproteins produced during coronavirus replication?

    <p>16 (C)</p> Signup and view all the answers

    What is the primary role of sub-genomic mRNAs in relation to proteins?

    <p>They encode structural and accessory proteins. (B)</p> Signup and view all the answers

    Which proteins are synthesized from the sub-genomic mRNAs?

    <p>Spike, nucleoprotein, envelope, and matrix proteins. (B)</p> Signup and view all the answers

    How many structural and accessory proteins are translated from sub-genomic mRNAs?

    <p>4 structural and 9 accessory proteins. (B)</p> Signup and view all the answers

    Which component is considered a major part of the pore embedded in double-membrane vesicles?

    <p>Nsp3 protein. (B)</p> Signup and view all the answers

    What type of vesicles do coronaviruses generate during replication?

    <p>Double-membrane vesicles. (D)</p> Signup and view all the answers

    Which protein functions as an RNA-binding protein during viral replication?

    <p>Nsp9. (C)</p> Signup and view all the answers

    What are the components of the RTC core involved in replication?

    <p>Nsp7, nsp8, and nsp12. (C)</p> Signup and view all the answers

    What role does nsp14 play in the viral replication process?

    <p>It acts as a co-factor for other proteins. (B)</p> Signup and view all the answers

    Which accessory protein functions as a 2ʹ-O-methyltransferase?

    <p>Nsp16. (D)</p> Signup and view all the answers

    Why are the numerous enzymatic activities of these proteins significant?

    <p>They provide potential therapeutic targets. (A)</p> Signup and view all the answers

    What was the first indication of a mysterious pneumonia outbreak associated with a specific location?

    <p>A mysterious pneumonia outbreak was first linked to the Wuhan wet market on December 8th. (D)</p> Signup and view all the answers

    According to the timeline, what date marks the official declaration of the outbreak as a pandemic?

    <p>March 11th (B)</p> Signup and view all the answers

    In the timeline, what action was taken on January 1st?

    <p>The Wuhan wet market was closed. (B)</p> Signup and view all the answers

    What was the reported cause of death on February 23rd in Italy?

    <p>COVID-19 (B)</p> Signup and view all the answers

    What was the reported action taken on March 8th in the US?

    <p>A state of emergency was declared in 8 states. (A)</p> Signup and view all the answers

    What event happened around the same time the UK PM announced a lockdown?

    <p>The UK reported around 422 deaths. (D)</p> Signup and view all the answers

    The initial SARS-CoV-2 outbreaks were associated with which location?

    <p>Wuhan wet market (A)</p> Signup and view all the answers

    What is the name of the protein that is present on the envelope of some, but not all viruses?

    <p>Spike/HA (D)</p> Signup and view all the answers

    What are the two main proteins that are generated through programmed ribosomal frameshifting?

    <p>Polyprotein 1 and Polyprotein 2 (C)</p> Signup and view all the answers

    What is the primary function of the proteins nsp3 and nsp5?

    <p>Proteolytic processing of replicase polyproteins (A)</p> Signup and view all the answers

    What is the primary function of nsp7-nsp10 and nsp12-nsp16, among other proteins?

    <p>Genome transcription and replication (A)</p> Signup and view all the answers

    What do nsp3, nsp4, and nsp6 function in?

    <p>Cytoplasmic vesicle biogenesis (D)</p> Signup and view all the answers

    Which of the following groups of proteins function primarily in genome transcription and replication?

    <p>nsp7-nsp10, nsp12-nsp16 (D)</p> Signup and view all the answers

    According to the information provided, which of these human coronaviruses was first described in 1968?

    <p>HCoV-229E (C)</p> Signup and view all the answers

    Which of these proteins is not a structural protein of coronaviruses?

    <p>Angiotensin-converting enzyme 2 (ACE2) (D)</p> Signup and view all the answers

    What is the approximate diameter of coronavirus particles, as mentioned in the text?

    <p>125 nm (A)</p> Signup and view all the answers

    Based on the content, what is the main outcome of the process of programmed ribosomal frameshifting in coronaviruses?

    <p>Production of non-structural proteins (D)</p> Signup and view all the answers

    What is the primary role of the envelope in the structure of a virus?

    <p>It helps the virus attach to and enter host cells. (D)</p> Signup and view all the answers

    What is the significance of the discovery that the SARS-CoV-2 genome sequence was similar to that of a bat coronavirus?

    <p>All of the above. (D)</p> Signup and view all the answers

    According to the timeline, in what month was the first death associated with COVID-19 announced?

    <p>January (A)</p> Signup and view all the answers

    What action was taken on January 23rd in China in response to the growing number of COVID-19 cases?

    <p>The virus's genome was sequenced. (A)</p> Signup and view all the answers

    Which of the following is NOT a common characteristic of viruses?

    <p>Viruses have a metabolic system of their own. (B)</p> Signup and view all the answers

    Which of the following are translated from sub-genomic mRNAs in SARS-CoV-2?

    <p>Structural proteins (A), Accessory proteins (B)</p> Signup and view all the answers

    Which of the following proteins is NOT translated from sub-genomic mRNAs?

    <p>RNA polymerase (D)</p> Signup and view all the answers

    What is the primary function of the replication-transcription complex (RTC) core?

    <p>To generate sub-genomic mRNAs for the production of structural and accessory proteins (B)</p> Signup and view all the answers

    Which of the following proteins is directly involved in the production of new viral RNA?

    <p>nsp12 (B)</p> Signup and view all the answers

    What is the significance of the various enzymatic activities associated with the SARS-CoV-2 proteins?

    <p>They make these proteins potential drug targets for antiviral therapeutics (C)</p> Signup and view all the answers

    Flashcards

    Programmed Ribosomal Frameshifting

    A process that alters the reading frame of the ribosome to produce two distinct polyproteins from a single RNA genome.

    Coronavirus Replicase Polyproteins

    Large proteins coded by the coronavirus genome that are cleaved into multiple active proteins involved in replication.

    Non-structural Proteins (nsp)

    Proteins derived from the coronavirus replicase polyproteins that do not form the virus's structure but are essential for its lifecycle.

    Proteolytic Processing

    The cleavage of polyproteins into smaller, active proteins necessary for viral replication and transcription.

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    Integral Membrane Replicase Proteins

    Non-structural proteins (nsp3, nsp4, nsp6) involved in the formation of vesicles in the cells during virus replication.

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    Sub-genomic mRNAs

    mRNAs generated from the RNA genome that encode proteins.

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    Structural proteins

    Proteins that provide shape and structure to viruses, such as Spike, Envelope, and Membrane.

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    Spike protein (S)

    A structural protein on the virus surface that helps in attachment to host cells.

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    Nucleocapsid protein (N)

    Protein that encapsulates viral RNA, aiding in genome protection.

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    Double-membrane vesicles (DMV)

    Cellular structures formed by the virus that facilitate replication.

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    RNA polymerase

    Enzyme that synthesizes RNA from a DNA template during replication.

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    Accessary proteins

    Proteins that assist in various functions during viral replication.

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    Nsp (non-structural proteins)

    Proteins expressed from the viral genome that are not part of the virus structure but have other roles.

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    RTC core

    A complex composed of various proteins essential for RNA synthesis in viruses.

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    N7-methyltransferase

    An enzyme involved in adding a methyl group to RNA, enhancing stability and function.

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    COVID-19 cases in 2024

    The estimated number of COVID-19 cases in January 2024 is 773 million.

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    COVID-19 vaccines administered

    As of January 2024, 13.6 billion COVID-19 vaccine doses have been administered globally.

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    Structure of coronaviruses

    Coronaviruses have an envelope and contain spike (S), membrane (M), nucleocapsid (N), and envelope (E) proteins.

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    Key human coronaviruses

    Important human coronaviruses include SARS-CoV, MERS, and SARS-CoV-2.

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    Coronavirus replication cycle

    The coronavirus genome is (+) RNA and is capped and polyadenylated for direct translation.

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    Spike Protein

    A viral component that allows entry into host cells by binding to receptors.

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    ACE2

    A receptor on host cells that the virus spike protein binds to initiate infection.

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    TMPRSS2

    An enzyme that cleaves the spike protein, facilitating membrane fusion.

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    Mutation Hot-spot

    Areas on the virus where mutations frequently occur, affecting vaccine efficacy.

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    Infectious Period

    The timeframe when an infected individual can spread the virus, starting about 4 days before symptoms.

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    Virus Virulence

    The ability of a virus to cause disease, influenced by viral and host factors.

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    COVID-19 Symptoms

    Common symptoms of COVID-19 include fever, sore throat, cough, and loss of taste/smell.

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    Long COVID

    Persistent symptoms after initial COVID-19 infection, such as fatigue and shortness of breath.

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    Cytokine Storm

    An overreaction of the immune system causing excessive inflammation and damage to organs.

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    Immune Response Factors

    Factors like age, immune status, and co-morbidities that affect how a body responds to a virus.

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    SARS-CoV-2

    The virus responsible for COVID-19, part of the coronavirus family.

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    Viral structure

    Viruses consist of a genetic core, protein coat (capsid), and may have an envelope.

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    Genetic core

    The part of the virus containing DNA or RNA, never both.

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    Protein coat (capsid)

    A protective layer made up of proteins called capsomeres surrounding the genetic core.

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    Viral envelope

    A lipid layer surrounding some viruses, often containing surface proteins like spikes.

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    COVID-19 pathogenesis

    The process by which the COVID-19 disease develops after infection with SARS-CoV-2.

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    Timeline of COVID-19

    Key dates marking the outbreak and spread of COVID-19 starting from December 2019.

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    First cases of COVID-19

    Initial reports of mysterious pneumonia with links to Wuhan wet market in December 2019.

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    Viruses

    Infectious agents not considered cells, lacking metabolism and reliant on host cells.

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    Capsid

    The protective protein coat surrounding a virus's genetic material, made of capsomeres.

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    COVID-19 deaths in 2024

    As of January 2024, the number of deaths due to COVID-19 is 6.99 million.

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    Coronaviruses classification

    Coronaviruses belong to a family of viruses categorized by their single-stranded positive sense RNA.

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    Important human coronaviruses

    Key human coronaviruses include HCoV-NL63, HCoV-OC43, SARS-CoV, and SARS-CoV-2.

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    Programmed Ribosomal Frameshifting Mechanism

    A process causing tRNAs to shift frames, producing two polyproteins from one RNA genome.

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    Polyproteins Cleavage

    The process where polyproteins are cut into 16 unique proteins necessary for viral functions.

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    Nsp Proteases Functions

    Proteins nsp3 and nsp5 act as proteases for processing replicase polyproteins.

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    Integral Membrane Proteins Roles

    Nsp3, nsp4, nsp6 create cytoplasmic vesicles for the virus's replication cycle.

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    Replicase Protein Functions

    Proteins nsp7-nsp10 and nsp12-nsp16 are vital for genome transcription and replication.

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    Structural and Accessory Proteins

    Proteins translated from sub-genomic mRNAs vital for viral structure and function.

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    Nsp Proteins

    Non-structural proteins performing various functions during viral replication.

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    Study Notes

    COVID-19 Virology and Pathology

    • Presentation covers SARS-CoV-2 virology and pathology
    • Presentation outlines topics: SARS-CoV-2, viral replication, virus entry/evolution, and COVID-19 pathogenesis
    • A virus has three basic components: genetic core (DNA or RNA, never both), protein coat/capsid (capsomeres), and envelope (not all viruses have)

    Virus Structure

    • Viruses are not considered cells; they lack metabolism and rely on the host cell's machinery
    • Viruses infect a wide range of organisms, including plants, animals, protists, archaea, and bacteria
    • Viruses exhibit diverse morphologies, with various shapes and sizes.

    Timeline of Initial SARS-CoV-2 Outbreak

    • December 2019: First case of mysterious pneumonia linked to Wuhan wet market.
    • January 2020: Official announcement of the outbreak, deaths reported in China, cases outside Hubei province.
    • January/February 2020: Identified as a novel coronavirus, global emergency declared, spread across continents. Subsequent months saw a surge in cases globally

    COVID-19 Cases and Deaths (Jan 2023)

    • Globally: 655,689,115 confirmed cases, 6,671,624 deaths
    • Global data reported to WHO as of January 4, 2023. 13,073,712,554 COVID-19 vaccine doses administered by December 22, 2022

    COVID-19 Cases and Deaths (Jan 2024)

    • 773,119,173 confirmed cases globally reported to WHO as of December 24, 2023
    • Global cases and deaths continued to rise, with reported figures provided as of December 2023.

    Classification of Viruses

    • Classification grouped by genetic material (DNA or RNA, single or double stranded)

    Classification of Coronaviruses

    • Coronaviruses are single-stranded positive-sense RNA viruses
    • Virus classified into different taxonomic groupings: order (Nidovirales), family (Coronaviridae), sub-family (Coronavirinae), genera (Alpha-, Beta-, Gamma-, Delta-CoV),

    Important Human Coronaviruses

    • Alphacoronavirus: include Human coronavirus NL63 and 229E.
    • Betacoronavirus: SARS-CoV and MERS-CoV, and SARS-CoV-2.
    • Gammacoronavirus: Gammacoronavirus
    • Deltacoronavirus: Deltacoronavirus

    Coronavirus Replication Cycle

    • Attachment: Virus engages with ACE2 receptors on host cells, assisted by TMPRSS2
    • Entry: Spike protein mediates membrane fusion, releasing viral genome into the cytoplasm
    • Replication and Transcription: Viral RNA genome is translated to produce non-structural proteins that replicate the genome, and additional proteins are created
    • Assembly and Budding: New viral particles assemble and exit the host cell.

    Coronavirus Genome Structure

    • (+) sense RNA genome (~ 29.8 kb)
    • Two polyproteins (ppla, pp1ab)
    • 16 proteins cleaved from polyproteins
    • Genome is capped and polyadenylated for direct translation

    Programmed Ribosomal Frameshifting

    • Ribosomes shift reading frame to create two polyproteins
    • Generates non-structural proteins essential for viral RNA replication

    Protein Products of Coronavirus Replicase Gene

    • Identification of proteins produced from the replicase gene, detailing their roles. Includes nsp proteins and their functions.

    Structural and Accessory Proteins

    • Translated from subgenomic mRNAs
    • Include structural proteins (spike(S), envelope(E), membrane (M), nucleocapsid(N)) and accessory proteins.

    Coronavirus Remodeled ER

    • Coronaviruses remodel ER to create replication organelles (DMVs and DMS), NSP3 functions in creating virus pores in these vesicles.

    RTC Core

    • Composed of three subunits, performing RNA replication.

    Accessory Proteins

    • Many proteins are involved in replication process, including their specific functions.

    COVID-19 Pathology

    • SARS-CoV-2 spreads via aerosols and droplets (sizes and distances specified)
    • Masks reduce transmission

    Transmissibility

    • Infectious ~4 days prior to symptoms appearing

    Virus Virulence

    • Depends on viral dose and route of infection, and host factors such as age, co-morbidities, immune status, and genetics

    COVID-19 Characteristics

    • Symptoms include fever, cough, exhaustion, anosmia, ageusia, myalgia, shortness of breath, nausea, diarrhea.
    • Other symptoms like pneumonia, organ failure, blood clots, and low lymphocytes, and additional symptoms are listed.

    COVID-19 Effects on Body Systems

    • COVID-19 can damage multiple systems causing vasculopathy and vasculitis leading to symptoms like stroke, hemorrhage, myocarditis, and acute kidney injury; including inflammation with symptoms in the lungs, circulatory systems, etc..

    COVID-19 Clearance

    • Pyroptosis, immune cell recruitment, cytokine release and elimination of infected cells are key events in clearance.

    Progression to Severe COVID-19

    • Cytokine storm and immune response dysregulation can lead to severe disease, involving multiple organ dysfunction, coagulation, or possibly death. This is influenced by IFN response (type I/III) speed and intensity

    Personal Genetics and COVID-19 Response

    • Personal genetics, specifically inborn errors of type I IFN immunity or APOE protein variants, modify viral response, influencing disease outcomes
    • Some personal variants associated with higher risk of severe COVID-19

    SARS-CoV-2 Persistence

    • SARS-CoV-2 can persist in various tissues, including the brain, for months following infection, potentially contributing to long COVID, including in the gut. This includes the existence of "viral ghosts."

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    Description

    This quiz explores various aspects of SARS-CoV-2, including the role of proteins in viral entry, key mutations, immune responses, and vaccine development. Test your knowledge on COVID-19 transmission, character traits of coronaviruses, and significant findings related to infection and immunity. A must for anyone looking to deepen their understanding of the virus.

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