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Questions and Answers
What is the role of the TMPRSS2 protein in the entry of SARS-CoV-2 into a cell?
What is the role of the TMPRSS2 protein in the entry of SARS-CoV-2 into a cell?
Why is the receptor binding domain (RBD) of the spike protein a target for the immune system and a common site of mutations?
Why is the receptor binding domain (RBD) of the spike protein a target for the immune system and a common site of mutations?
How does the D614G mutation affect the infectivity and mortality of SARS-CoV-2?
How does the D614G mutation affect the infectivity and mortality of SARS-CoV-2?
What is the significance of targeting non-mutating regions of the spike protein for vaccine development?
What is the significance of targeting non-mutating regions of the spike protein for vaccine development?
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What is the typical timeframe for becoming infectious with SARS-CoV-2 after exposure?
What is the typical timeframe for becoming infectious with SARS-CoV-2 after exposure?
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What was the total number of COVID-19 cases reported in January 2024?
What was the total number of COVID-19 cases reported in January 2024?
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Which of the following human coronaviruses was first described in 1968?
Which of the following human coronaviruses was first described in 1968?
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What type of genetic material do coronaviruses possess?
What type of genetic material do coronaviruses possess?
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What is the diameter of coronavirus particles as mentioned?
What is the diameter of coronavirus particles as mentioned?
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Which protein is not a structural protein of coronaviruses?
Which protein is not a structural protein of coronaviruses?
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Which factor is NOT related to the virulence of a virus?
Which factor is NOT related to the virulence of a virus?
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What is a characteristic symptom of COVID-19 that appears after 4-10 days post-infection?
What is a characteristic symptom of COVID-19 that appears after 4-10 days post-infection?
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What is the main outcome of programmed ribosomal frameshifting in coronaviruses?
What is the main outcome of programmed ribosomal frameshifting in coronaviruses?
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What is the primary function of the proteases derived from non-structural proteins like nsp3 and nsp5?
What is the primary function of the proteases derived from non-structural proteins like nsp3 and nsp5?
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Which condition is NOT considered a co-morbidity affecting the immune response to infections?
Which condition is NOT considered a co-morbidity affecting the immune response to infections?
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Which of the following statements about COVID-19 is accurate?
Which of the following statements about COVID-19 is accurate?
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Which of the following non-structural proteins function in cytoplasmic vesicle biogenesis?
Which of the following non-structural proteins function in cytoplasmic vesicle biogenesis?
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What process involves the inflammatory cell death triggered by COVID-19?
What process involves the inflammatory cell death triggered by COVID-19?
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What mechanism leads to the simultaneous −1 shift of tRNAs during programmed ribosomal frameshifting?
What mechanism leads to the simultaneous −1 shift of tRNAs during programmed ribosomal frameshifting?
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How many unique proteins are generated from the cleavage of the polyproteins produced during coronavirus replication?
How many unique proteins are generated from the cleavage of the polyproteins produced during coronavirus replication?
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What is the primary role of sub-genomic mRNAs in relation to proteins?
What is the primary role of sub-genomic mRNAs in relation to proteins?
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Which proteins are synthesized from the sub-genomic mRNAs?
Which proteins are synthesized from the sub-genomic mRNAs?
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How many structural and accessory proteins are translated from sub-genomic mRNAs?
How many structural and accessory proteins are translated from sub-genomic mRNAs?
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Which component is considered a major part of the pore embedded in double-membrane vesicles?
Which component is considered a major part of the pore embedded in double-membrane vesicles?
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What type of vesicles do coronaviruses generate during replication?
What type of vesicles do coronaviruses generate during replication?
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Which protein functions as an RNA-binding protein during viral replication?
Which protein functions as an RNA-binding protein during viral replication?
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What are the components of the RTC core involved in replication?
What are the components of the RTC core involved in replication?
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What role does nsp14 play in the viral replication process?
What role does nsp14 play in the viral replication process?
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Which accessory protein functions as a 2ʹ-O-methyltransferase?
Which accessory protein functions as a 2ʹ-O-methyltransferase?
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Why are the numerous enzymatic activities of these proteins significant?
Why are the numerous enzymatic activities of these proteins significant?
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What was the first indication of a mysterious pneumonia outbreak associated with a specific location?
What was the first indication of a mysterious pneumonia outbreak associated with a specific location?
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According to the timeline, what date marks the official declaration of the outbreak as a pandemic?
According to the timeline, what date marks the official declaration of the outbreak as a pandemic?
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In the timeline, what action was taken on January 1st?
In the timeline, what action was taken on January 1st?
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What was the reported cause of death on February 23rd in Italy?
What was the reported cause of death on February 23rd in Italy?
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What was the reported action taken on March 8th in the US?
What was the reported action taken on March 8th in the US?
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What event happened around the same time the UK PM announced a lockdown?
What event happened around the same time the UK PM announced a lockdown?
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The initial SARS-CoV-2 outbreaks were associated with which location?
The initial SARS-CoV-2 outbreaks were associated with which location?
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What is the name of the protein that is present on the envelope of some, but not all viruses?
What is the name of the protein that is present on the envelope of some, but not all viruses?
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What are the two main proteins that are generated through programmed ribosomal frameshifting?
What are the two main proteins that are generated through programmed ribosomal frameshifting?
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What is the primary function of the proteins nsp3 and nsp5?
What is the primary function of the proteins nsp3 and nsp5?
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What is the primary function of nsp7-nsp10 and nsp12-nsp16, among other proteins?
What is the primary function of nsp7-nsp10 and nsp12-nsp16, among other proteins?
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What do nsp3, nsp4, and nsp6 function in?
What do nsp3, nsp4, and nsp6 function in?
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Which of the following groups of proteins function primarily in genome transcription and replication?
Which of the following groups of proteins function primarily in genome transcription and replication?
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According to the information provided, which of these human coronaviruses was first described in 1968?
According to the information provided, which of these human coronaviruses was first described in 1968?
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Which of these proteins is not a structural protein of coronaviruses?
Which of these proteins is not a structural protein of coronaviruses?
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What is the approximate diameter of coronavirus particles, as mentioned in the text?
What is the approximate diameter of coronavirus particles, as mentioned in the text?
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Based on the content, what is the main outcome of the process of programmed ribosomal frameshifting in coronaviruses?
Based on the content, what is the main outcome of the process of programmed ribosomal frameshifting in coronaviruses?
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What is the primary role of the envelope in the structure of a virus?
What is the primary role of the envelope in the structure of a virus?
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What is the significance of the discovery that the SARS-CoV-2 genome sequence was similar to that of a bat coronavirus?
What is the significance of the discovery that the SARS-CoV-2 genome sequence was similar to that of a bat coronavirus?
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According to the timeline, in what month was the first death associated with COVID-19 announced?
According to the timeline, in what month was the first death associated with COVID-19 announced?
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What action was taken on January 23rd in China in response to the growing number of COVID-19 cases?
What action was taken on January 23rd in China in response to the growing number of COVID-19 cases?
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Which of the following is NOT a common characteristic of viruses?
Which of the following is NOT a common characteristic of viruses?
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Which of the following are translated from sub-genomic mRNAs in SARS-CoV-2?
Which of the following are translated from sub-genomic mRNAs in SARS-CoV-2?
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Which of the following proteins is NOT translated from sub-genomic mRNAs?
Which of the following proteins is NOT translated from sub-genomic mRNAs?
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What is the primary function of the replication-transcription complex (RTC) core?
What is the primary function of the replication-transcription complex (RTC) core?
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Which of the following proteins is directly involved in the production of new viral RNA?
Which of the following proteins is directly involved in the production of new viral RNA?
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What is the significance of the various enzymatic activities associated with the SARS-CoV-2 proteins?
What is the significance of the various enzymatic activities associated with the SARS-CoV-2 proteins?
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Flashcards
Programmed Ribosomal Frameshifting
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
Coronavirus Replicase Polyproteins
Large proteins coded by the coronavirus genome that are cleaved into multiple active proteins involved in replication.
Non-structural Proteins (nsp)
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
Proteolytic Processing
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Integral Membrane Replicase Proteins
Integral Membrane Replicase Proteins
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Sub-genomic mRNAs
Sub-genomic mRNAs
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Structural proteins
Structural proteins
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Spike protein (S)
Spike protein (S)
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Nucleocapsid protein (N)
Nucleocapsid protein (N)
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Double-membrane vesicles (DMV)
Double-membrane vesicles (DMV)
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RNA polymerase
RNA polymerase
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Accessary proteins
Accessary proteins
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Nsp (non-structural proteins)
Nsp (non-structural proteins)
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RTC core
RTC core
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N7-methyltransferase
N7-methyltransferase
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COVID-19 cases in 2024
COVID-19 cases in 2024
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COVID-19 vaccines administered
COVID-19 vaccines administered
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Structure of coronaviruses
Structure of coronaviruses
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Key human coronaviruses
Key human coronaviruses
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Coronavirus replication cycle
Coronavirus replication cycle
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Spike Protein
Spike Protein
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ACE2
ACE2
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TMPRSS2
TMPRSS2
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Mutation Hot-spot
Mutation Hot-spot
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Infectious Period
Infectious Period
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Virus Virulence
Virus Virulence
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COVID-19 Symptoms
COVID-19 Symptoms
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Long COVID
Long COVID
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Cytokine Storm
Cytokine Storm
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Immune Response Factors
Immune Response Factors
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SARS-CoV-2
SARS-CoV-2
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Viral structure
Viral structure
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Genetic core
Genetic core
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Protein coat (capsid)
Protein coat (capsid)
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Viral envelope
Viral envelope
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COVID-19 pathogenesis
COVID-19 pathogenesis
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Timeline of COVID-19
Timeline of COVID-19
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First cases of COVID-19
First cases of COVID-19
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Viruses
Viruses
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Capsid
Capsid
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COVID-19 deaths in 2024
COVID-19 deaths in 2024
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Coronaviruses classification
Coronaviruses classification
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Important human coronaviruses
Important human coronaviruses
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Programmed Ribosomal Frameshifting Mechanism
Programmed Ribosomal Frameshifting Mechanism
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Polyproteins Cleavage
Polyproteins Cleavage
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Nsp Proteases Functions
Nsp Proteases Functions
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Integral Membrane Proteins Roles
Integral Membrane Proteins Roles
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Replicase Protein Functions
Replicase Protein Functions
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Structural and Accessory Proteins
Structural and Accessory Proteins
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Nsp Proteins
Nsp Proteins
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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.