Coronavirus and COVID-19

SARS-Cov-2 genome organisation and structure

29 kb positive/sense ssRNA genome. ssRNA genome codes for structural proteins several non structural proteins, one of which is RNA-dependent RNA Polymerase Genome has 5' and 3' end untranslated regions

Epidemic

A sudden increase in the number of cases of a disease, above what is typically expected in a particular area

Pandemic

An epidemic that has spread over several countries or continents, impacting many people. Pandemics typically happen when a new virus spreads easily among people. COVID-19 was declared a pandemic by The Who in March, 2020

Multi-organ injury in COVID-19

COVID doesn't just cause severe lung damage, it also targets: Brain (endema, degeneration of neurons) Liver (cholangiocytes damage) Pancreas (Inflammation, focal inflammation, islets damage) Blood vessels (permeability increase, coagulation activation, microcirculation disturbance) Heart (Endema, atrophy of myocardial fibers, inflammatory infiltrates) Muscles (myofiber necrosis, atrophy)

Taxonomy of coronavirus

Genus: Alphacoronavirus, Alphacorona 1, HCoV-229E*, HCoV-NL63*) Genus: Betacoronaviruses Lineage A- Murine coronavirus, HCoV-OC43* HCOV-HKU1* Lineage B- SARS-CoV*, SARS-CoV (2)* Lineage C- MERS-CoV*, BtCoV-HKU4, BtCoV-HKU5, Lineage D- BtCoV-HKu9) Genus: Gammacoronavirus Avian Coronavirus Genus: Deltacoronavirus BuCoV-HKU11 6 species of human coronaviruses, span lineages A, B, and C (*)

M (membrane proteins)

Main structural protein of the viral envelope that provides its overall shape; crucial in the life cycle of the virus

E (envelope) protein

Minor structural protein (~20 per virus); responsible for virion assembly, intracellular trafficking and morphogenesis (budding)

S (spike) protein

Most distinguishing feature of the coronavirus (~70 per virus), responsible for the corona-like surface; binds host cell receptor protein

History of Pandemics and death toll

Plague of Justinian (541-542): 30-50M dead Black Death (1347-1351): 200M dead Small pox (1520): 56M dead The Third Plague (1855): 12M dead Spanish flu (1918-1919): 40-50M dead HIV/AIDS (1981-present): 25-35M dead COVID-19 only has 1M deaths, by far not the biggest/worst pandemic we've ever seen as a species! Definitely not when the Black Death wiped out 30-50% of Europe's population

Naming

The Disease: COVID-19- Coronavirus Disease 2019 The Virus: SARS-CoV-2: Severe Acute Respiratory Syndrome Coronavirus-2 (Also called 2019-nCOV: 2019 novel coronavirus)

How does COVID enter the human body?

Virus enters through the respiratory tract and then replicates itself in the mucus membrane. The respiratory tract swells as a result and becomes inflamed. Then, the virus enters the lungs and bloodstream which is when symptoms are shown. ACE 2 is a cell receptor that recognizes viral spike proteins (viral spike proteins mimic shape of ACE 2 protein) and receptors take the entire virus into human cells via membrane fusion. Then there is a release of viral RNA, and the virus grows and reproduces within the cell (If we can block ACE2 receptors, could we block the virus from entering the cell?)

N (nucleocapsid) protein

bound to the RNA genome in a continuous beads-on-a string type conformation

HE (hemagglutinin esterase) protein

shorter spike-like surface protein that helps in attachment to and detachment from the host cell

Oligonucleotide-based therapeutics for COVID

siRNA: ds siRNA cocktails targeting conserved regions of COVID-19 mRNAs can be injected into cells in order to pair with RISC and cleave/degrade complementary viral RNA ASO (anti-sense oligonucleotide): ASO (ssDNA) cocktail targeting conserved regions of COVID-19 mRNAs is injected into cells and is used as a template by RNAse H to cleave/degrade viral RNA

Lines of Stack: experimental treatment strategies attempt to interfere with different steps in the coronavirus life cycle So far, experimental drugs have:

-Attacked an essential state, the attachment of virus to cell (rACE 2, antibodies inhibit viral/host interaction by attaching to spike proteins in place of virus, effective) -Inhibited endocytic membrane transport proteins so that cells can't take in viruses through membrane fusion (hydroxychloroquine, but this doesn't work) -Created protein inhibiters for protease so that virus can't chop up translated viral proteins, complete life cycle (lopinavir, danoprevir, don't work) -Inhibited RNA genome replication by interfering with viral RNA-dependent RNA polymerase (Remdesivir, effective? Or not)

History of Coronavirus

1920a- Earliest reporting of a respiratory infection in animals (domestic chickens) 1930s- Isolation of the virus (then called infectious bronchitis virus, IBV) 1940s- Discovery of IBV-related viruses in mice 1960s- Discovery of novel human common cold viruses distinct from other known respiratory viruses (the name coronavirus was coined in 1968) 2003- Identification of a newly emerged human coronavirus (SARS-CoV) that caused SARS (Severe Acute Respiratory Syndrome) 2004&5- Discovery of coronaviruses (NL63 and HKU1) in pneumonia patients 2012- Identification of a new coronavirus (MERS-CoV) from pneumonia patients 2020- Identification of coronavirus (SARS-CoV2) that causes COVID-19

Mutation in spike protein of COVID

A mutation arose in the SARS-CoV-2 virus: the spike protein amino acid 614 D (aspartic acid) changed to G (glycine, D614G) There are now more G614 viruses circulating globally than original D614 viruses, the mutation in the virus may have contributed to the pandemic really starting. Patients infected with G614 shed more viral RNAs. G viruses show a significantly higher infectivity than D. G614 mutation emerged in Italy in mid February, D614 virus first emerged in Asia New York City is the center of pandemic in our country, and most COVID cases there came from Europe (G614 mutation was quickly brought to the US)

Outbreak

An epidemic in a more limited geographic area.

Adaptive Immune Defense of Human Body

Cell mediated immunity (antigens within cells): cytotoxic T cells, helper T cells (cytokines make helper T cells into cytotoxic T cells), these cells produce memory T cells and initiate phagocytosis or apoptosis of infected cells when antigen is detected within cells. Antibody mediated immunity (antigens outside of cells): B cells, produce memory B cells. Cytokines can also function in antibody-mediated immunity. Cells produce plasma cells and antibodies to defend against outside threat. Antibodies (immunoglobulins) involved in COVID: IgM, IgG

Nucleoside analogues

Class of antiviral agents that fall into three general classes: MUTAGENIC NUCLEOSIDES cause mutations in viral genome when incorporated into it and inhibit viral function or cause lethal mutagenesis, but are not effective against COVID because RdRP has proofreading activity OBLIGATE CHAIN TERMINATORS lack the reactive 3' OH group and directly prevent additional RNA synthesis after their incorporation into a growing RNA molecule DELAYED CHAIN TERMINATORS like Remdesivir block transcription despite still possessing the 3' OH group and can still form a phosphodiester bond with the next incorporated nucleotide, then terminate replication after 3 more nucleotides are added to the chain

Nonstructural proteins (nsps) of coronavirus and their functions

Codes for ~18 non-structural proteins with ~12 distinct functions, most important for virus' infectivity and survival is nsp12: replication enzyme (RNA-dependent RNA polymerase, makes complementary strands to ssRNA genome)

Animal origins of human coronavirus

HCoV-NL63: Bat —> unknown—> human, mild disease HCoV-229E: Bat —> llama —> human, mild disease HCoV-OC43: mouse —> cow —> human, mild disease HCoV-HKU1: mouse—>unknown—> human, mild disease *SARS-CoV: bat —> civet —> human, MILD OR SEVERE SARS *MERS-CoV: Bat —> camel —> human, MILD OR SEVERE MERS *SARS-CoV-2- Bat —> unknown —> human, MILD OR SEVERE COVID-19

Immune response to SARS-CoV-2

IgG presence in cells increases from week 0 of infection, plateaus at high levels at week 2 (after virus has infected cells) IgM presence increases till week 1 (most infectious/severe period of virus) then curves down like a bell curve until its levels are low post-infection

Contagiousness and mortality

Not as contagious as chickenpox and measles and lower mortality than SARS, ebola, and smallpox. Estimated contagiousness (reproductive rate) between common cold and polio, estimated mortality between seasonal flu and Spanish flu (0.1-7.0% mortality)

Testing of COVID-19

Nucleic Acid Test: Nasal swab extracts viral cells, then RNA is extracted from virus cells using reverse transcription and PCR amplification of viral cDNA. Fluorescents and real-time PCR using specially created viral DNA primers will show whether viral RNA was present and has been amplified. Antibody Test: Detects the presence of IgG and IgM versus a control in a blood sample. High IgM levels mean they're probably currently infected, high IgG levels mean that they were infected at one point

RNAi to defend the cells against viral infection

RNAi can defend against viral infection, as siRNAs can be formed by dicer when viral RNA replication by RdRP results in dsRNA. This dsRNA is chopped up and separated into ss siRNAs. These join with the RISC complex and can and pair with additional viral mRNA to cause its degradation. siRNAs can also be amplified by RdRP when viral RNA targeted by RISC is purposefully replicated in order to create more siRNA.

T cell COVID study

T cell responses are focused not only on the spike protein that cell receptors recognize, but also on M N and memory proteins Why: Study launched to understand human adaptive immunity to SARS-CoV2 How: Examined if T-cells in COVID-19 patients responded to/recognized SARS-CoV2 proteins What: Found that T cells responded to M, spike, and N proteins of the virus robustly, and to other viral proteins less robustly So what: measuring and understanding human T cell responses to COVID infection will facilitate COVID-19 vaccine development and interpretation of COVID-19 pathogenesis Study extracted CD4 and T cells from 10 COVID patients and exposed them to manufactured SARS-CoV-2 proteins to test for T-cell binding. Surprisingly, even in uninfected people, there was some T-cell binding, probably from their body's adaptive immunity to cold and flu.

COVID-19 Symptoms

Takes 2-14 days after exposure (incubation period) to show symptoms, hence 14-day quarantine Common symptoms: fever, cough, tiredness Some Other Symptoms: shortness of breath, sore throat, muscle aches, runny nose, headache, chest pain, pink eye, loss of taste/smell, nausea, chills, increased sputum production

Endemic

The baseline, or expected level of the disease in the community-meaning it always exists, like the common cold and flu, which are usually at low, predictable rates

Structure

The coronavirus is a large, spherical particle with unique surface projections, giving it its distinct appearance. The lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus outside the host.

Remdesivir

The only FDA-approved drug that can be used to treat COVID. Nucleotide analogue prodrug that inhibits coronavirus replication by incorporating itself into new copies of viral RNA and terminating RNA chains after the addition of 3 more nucleotides

Lifecycle of virus

The virus travels through the blood vessels, and enters organs with high ACE 2 expression. The spike protein is recognized by cell ACE 2 receptors, the virus enters the cell body through membrane fusion and releases its viral RNA A first round of translation using the host cell's ribosomes makes polyproteins, one of which is RNA-dependent RNA polymerase. RdRp makes complementary copies of viral RNA through RNA replication (these other polyproteins are purposefully broken down by viral protease to complete the viral life cycle) Viral RNA copies within the cell are no longer recognized by the cell's defense mechanisms as foreign, so they can be translated to assemble new viral particles. Polypeptides are assembled and packaged by the host cells and new virions (virus particles) pass through the cell membrane to infect other cells.