Virology Exam 4

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Hong Kong as of March 28, 2003. Patient zero of the SARS pandemic stayed at the Metropole Hotel.
Eventually spread to about 20 countries
Main reservoir is birds, mosquitos pick up WN from feeding birds and give it to humans and horses, who are dead-end hosts (cannot transmit due to low viremia)
Mosquito bites by Aedes spp. and vertical transmission
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Bats can also contaminate fruit leading to human and pig infection
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Mosquito incidentally feeds on a virus infected host to acquire viruses circulating in the host blood
Viruses infect epithelial cells in the mosquito gut and then spread into the mosquito 
10^4 plaque-forming units (PFU) of viruses are required to achieve productive mosquito infection
Tissues in the mosquito such as haemolymph, salivary glands, and fat body are highly permissive to arboviral propagation 
Viruses subsequently disseminate into salivary glands, thus enabling viral transmission by the infected mosquito to naïve hosts through blood feeding
-Very large +RNA genome (cat IV)
- Nonseg
an Rdrp that has exonuclease activity (some proofreading ability)
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More transmissible, less pathogenic
R0 is defined as the average number of secondary transmissions from one infected person; when R0 is greater than 1, the epidemic is growing
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Sars binding to ACEII  causes activation of angiotensin II  (regulates bp, etc), when SARS inhibits this it leads to inflammation, lung injury and leaky vessels
CoV-2’s RBD hides more frequently instead of remaining standing up most of the time as CoV’s does. This allows for less immunological evasion and CoV-2 has an enhanced entry mechanism as well as being pre-activated by furin given more enhanced entry.
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loss of vascular integrity (1), activation of the coagulation pathway (2) and inflammation (3)
covid infects lower lungs
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This is where the ORFs are. 
Programmed ribosomal frameshifting generates 2 polyproteins encoding the replicase proteins.
-        Slippery heptanucleotide make ribosome read thru past stop codon
-        Pseudoknot can cause ribosome to pause and frameshift (moves back the reading frame by one and then continues reading, bypasses one stop codon)
When the spike protein of SARS-CoV-2 binds to the receptor of the host cell, the virus enters the cell, and then the envelope is peeled off, which lets genomic RNA be present in the cytoplasm. The ORF1a and ORF1b RNAs are made by genomic RNA, and then translated into pp1a and pp1ab proteins, respectively. Protein pp1a and ppa1b are cleaved by protease to make a total of 16 nonstructural proteins. Some nonstructural proteins form a replication/transcription complex (RNA-dependent RNA polymerase, RdRp), which use the (+) strand genomic RNA as a template. The (+) strand genomic RNA produced through the replication process becomes the genome of the new virus particle. Subgenomic RNAs produced through the transcription are translated into structural proteins (S: spike protein, E: envelope protein, M: membrane protein, and N: nucleocapsid protein), which form a viral particle. Spike, envelope, and membrane proteins enter the endoplasmic reticulum, and the nucleocapsid protein is combined with the (+) strand genomic RNA to become a nucleoprotein complex. They merge into the complete virus particle in the endoplasmic reticulum-Golgi apparatus compartment and are excreted to extracellular region through the Golgi apparatus and the vesicle.
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SARS-CoV2 is very efficient at blocking immune response. NSP13 blunts intracellular signaling such as rig1 or the nucleocapsid itself. Other proteins are involved in blocking various downstream signals in the immune system which inhibits the immune system from recognizing SARS-CoV-2.
it is a nucleoside analog
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(1) Once the genome of a pathogen has been sequenced, a sequence for the target antigen is designed and inserted into a plasmid DNA construct. (2) Plasmid DNA is transcribed into mRNA by bacteriophage polymerases in vitro and (3) mRNA transcripts are purified by high performance liquid chromatography (HPLC) to remove contaminants and reactants. (4) Purified mRNA is mixed with lipids in a microfluidic mixer to form lipid nanoparticles. Rapid mixing causes the lipids to encapsulate mRNA instantaneously and precipitate as self-assembled nanoparticles. (5) The nanoparticle solution is dialysed or filtered to remove non-aqueous solvents and any unencapsulated mRNA and (6) the filtered mRNA vaccine solution is stored in sterilized vials.
(1) Injected mRNA vaccines are endocytosed by antigen-presenting cells. (2) After escaping the endosome and entering the cytosol, mRNA is translated into protein by the ribosome. The translated antigenic protein can stimulate the immune system in several ways. (3) Intracellular antigen is broken down into smaller fragments by the proteasome complex, and the fragments are displayed on the cell surface to cytotoxic T cells by major histocompatibility complex (MHC) class I proteins. (4) Activated cytotoxic T cells kill infected cells by secreting cytolytic molecules, such as perforin and granzyme. (5) Additionally, secreted antigens can be taken up by cells, degraded inside endosomes and presented on the cell surface to helper T cells by MHC class II proteins. (6) Helper T cells facilitate the clearance of circulating pathogens by stimulating B cells to produce neutralizing antibodies, and by activating phagocytes, such as macrophages, through inflammatory cytokines. BCR, B cell receptor; ER, endoplasmic reticulum; TCR, T cell receptor.
Human adenovirus (harmless) has spike protein
•IgG1 mAbs with unmodified Fc regions. 
•These two mAbs were chosen from a pool of more than 200 neutralizing mAbs present in the initial isolation of thousands of antibodies and were derived from parallel efforts using humanized mice and the sera of patients recovering from COVID-19.
•Bind two distinct and non-overlapping sites on the RBD
•The rationale for this antibody combination is that it is unlikely that a mutation in the S protein of SAR-CoV-2 will simultaneously render both antibodies ineffective.
Monoclonal antibodies can directly interfere with viral pathogenesis in multiple ways. First, binding of a neutralizing antibody to the virion can prevent target cell binding and/or fusion. Furthermore, antibody binding opsonizes the virions or infected cells for phagocytic uptake. If viral proteins are intercalated into target cell membranes during viral egress, monoclonal antibodies can facilitate target cell death via complement fixation and membrane attack complex (MAC) activation or antibody-dependent cytotoxicity. These mechanisms may result in apoptosis or necrosis of the infected cell.
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•E7 binds to a region of the Rb protein
•Rb is to bind E2F-family transcription factors 
•Rb is cell-cycle regulatory protein/prevent entry into S phase/cell-cycle arrest
•E2F is a cell cycle transcription factor
•E7 disrupts the interaction between Rb and E2F
•Resulting in the release of E2F factors in their transcriptionally active forms
-One available
-Virus-like particles (no genome) empty capsids
-Made from yeast
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Could be NS5a as oncogene
- proliferation
- apoptosis (surpression of apoptosis)
- promotion of angiogenesis
- promoting epithelial mesinchymal transition (helps create metastatic tumors)
- increase in bad oxygen species
•DNA of BL tumors contain genetic aberrations of chromosomes 8 and either 14, 22, or 2
•c-myc (transcription factor promoting cell division) gene moves near the immunoglobulin heavy chain or light chain gene
–Abnormal expression of the c-myc gene and increased tumorigenicity of the cells
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•Model implicates Tax in tumor initiation, and HBZ in maintenance.
•Tax promotes viral expression directly and indirectly.
• The HTLV-I trans-activator (Tax) is a 40-kDa protein containing 353 amino acid residues located within the U3 region of the LTR. 
•Interactions with these factors are responsible for HTLV-I LTR-trans-activation, as well as the activation of certain mitogenic genes during cellular transformation.
•HBZ (for HTLV-I bZIP factor), contains nuclear localizing motifs (127), and a N-terminal transcriptional activation domain and a leucine zipper motif in its C terminus 
•HBZ is the only viral gene that is constitutively expressed in ATL cases
•HBZ prevents apoptosis
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