01 - COVID-19

Positive-sense ssRNA virus (group IV)

• Positive-sense ssRNA virus (Group IV): genome directly utilized (like mRNA) to translate proteins

  • Easier to make lots of copies

negative sense RNA viruses (e.g. flu)

first ned to change to positive sense ssRNA

SArS-CoV-2

• Member of coronavirus family (positive-sense RNA viruses)

• Seasonal coronaviruses  common colds

• Longer genome vs. other RNA viruses (30K vs.10-15K BPs)

  • More base pairs → can change 

  • (can recombine w/ itself to change → variants)

• Can mutate (+/-) & recombine with each others

• Other examples: SARS & MERS

• SARS-CoV-2 = virus, COVID-19 = disease

SARS-CoV-2 Virus Replication

1. (+)RNA enter cells via endocytosis

2. (+)RNA genome released into cytoplasm

• Takes off coating → release +RNA

3. translated by host ribosomes

4. viral replication proteins (+)RNA to subcellular membrane compartments → functional viral replication complexes (VRCs)

• Assemble along the membrane 

5. small amount of (−)RNA synthesized → template to synthesize large number of (+)RNA progeny

• Immediately reproduce because positive-sense ssRNA virus (doesn’t need to be converted)

• Negative strand retained → used as template for replication

6. new (+)RNAs are released from the VRCs, (−)RNA is retained

7. Encapsidated (packaged) (+)RNAs → exit the cell to start new cycles of translation & replication

• → repeat process

Infectivity (R0)

• Virulence (R0): ability to infect others

  • Influences vaccination and death 

Immune Response of COVID-19

• Innate immune response: immediate

  • Body senses threat → general immune response (inflammation, fever, cough, flu-like symptoms)

  • Rapid (occurs soon after exposure)

  • No memory! 

• Increase in viral load as virus hijacks ribosomes and makes copies 

• Adaptive immune response: two weeks later

  • Occurs after exposure (including vaccines)

  • Slower onset 

  • Memory to specific pathogens 

    • Specific COVID-19 effects

COVID-19 pathophysiology overview

• spike subdomain → angiotensin-converting enzyme 2 (ACE2) receptors in the lungs

• ACE2 also highly expressed in small intestine, heart, vascular endothelium & kidneys

• ACE2 inducing a vasodilatory response (via degrading angiotensin II [kidney lecture]

• by opposing the pressor response (pressor = ↑BP) of angiotensin II

• COVID → systemic oxidative stress, RAAS inhibition, cytokine storm, microvascular damage

COVID-19 Pathophysiology: Oxidative Stress

• Severe acute respiratory syndromes → hypoxemia (low O2) → oxidative stress (free radicals (unpaired electrons)/reactive oxygen species > antioxidants) → damaging tissues 

• hypoxemia damages cardiomyocytes → intracellular acidosis &

• mitochondrial damage → damage heart muscle 

COVID-19 Pathophysiology: RAAS (Inhibition)

ACE2 receptors (also located in CV) system dysregulate the renin-angiotensin-aldosterone (RAAS) system → ↓ BP → ↑ ventricular (cardiac) demand → further cardiomyocyte damage

RAAS System

Renin (juxtaglomerular cells): baroreceptors → sympathetic (β1 adrenergic) & macula densa (DCT) → Na+ chemoreceptors

COVID-19 Pathophysiology: Cytokine Storm

• System inflammatory response → cytokine storm 

• Immune response triggered by: 

  • Pathogen-associated molecular patterns (PAMPs)

    • Pathogen not recognized as “self” (e.g. bacteria)

    • Triggers innate immune response

  • Damage-associated molecular patterns (DAMPs)

    • Damage to tissues (e.g. infection, cut)

• Cytokines = chemical messengers

  • Pro-inflammatory: immune-stimulating (beginning of infection)

  • Anti-inflammatory: immune-suppressing (end of infection)

Cytokine Storm: Immune Dysregulation

• Cytokine storm is a life-threatening systemic inflammatory syndrome (systemic inflammation & multiorgan failure)

• Involves ↑ circulating cytokines (IL-6, CRP) & immune-cell hyperactivation (C-reactive protein [CRP] correlates with severity)

• Immune dysregulation: Inappropriate triggering/danger sensing → immune hyperactivation

  • Iatrogenic, pathogen (sepsis/virus), autoimmune, cancer

  • Regulatory cells:

    • Proinflam. (IL1RA)

    • Anti-inflam. (IL-10)

    • Antagonize inflammatory-cell & prevent hyperactivity

  • Failed negative feedback loop → hyperinflammation → inflammatory cytokines overproduction → (“collateral damage”) → multiorgan failure ( → damage)

3 criteria for cytokine storm

1. ↑ cytokine levels (CRP [inflammation], D-dimer [clotting]) AND

2. acute systemic inflammatory symptoms (viral shift, eosinophilia) AND

3. either 2° dysfunction (renal, hepatic, pulmonary) R/T pathogen or any cytokine-driven organ dysfunction

COVID-19 Pathophysiology: microvascular

• Local + systemic effects → microvascular damage → poor perfusion

• COVID-19: increased IL-6 levels are associated with increased mortality 

  • Alveolar macrophages: help detect pathogens 

    • Once they sense pathogens → release chemical messengers

  • Chemical messengers: recruit other immune cells (e.g. eosinophils) to area → vasodilation

    • RBCs can escape through junctions (which open when immune cells travel) → alveoli

      • When they lyse → release iron (toxic!)

    • Fluid can also escape the vasculature → fill up alveoli → impair gas exchange and surfactant production ( → crackles in lungs)

COVID risk factors

• Older age

• Chronic obstructive pulmonary disease

• Cardiovascular disease (e.g. heart failure, CAD, cardiomyopathy) 

• Type 2 diabetes mellitus

• Obesity (BMI > 30)

• Sickle cell disease

• Chronic kidney disease

• Immunocompromised state from solid-organ transplantation 

• Cancer 

• (all these risk factors → weakened immune system)

Cytokine Storm: Sequelae

• Constitutional symptoms: cytokines  FEVER, fatigue, anorexia, HA, rash, diarrhea, arthralgia/myalgia, neuropsych findings

• Progression: disseminated intravascular coagulation (DIC) & vascular occlusion or catastrophic hemorrhages, dyspnea, hypoxemia, hypotension, hemostatic imbalance, vasodilatory shock, and death.

• Respiratory symptoms: (cough & tachypnea) that progress to acute respiratory distress syndrome (ARDS) & hypoxemia

• Blood abnormalities: hypertriglyceridemia, leukocytosis (↑ WBCs), leukopenia (↓ WBCs), anemia, thrombocytopenia (↓ platelets), ↑ ferritin (from lysing of RBC), ↑ D-dimer levels [i.e. clotting marker]

autoimmune disease + viruses

• Viruses can trigger chronic inflammation and autoimmune disease (failure to differentiate “self”)

  • Epstein-Barr-virus (EBV)

    • Associated with: multiple sclerosis, hepatitis, gastric and nasopharyngeal cancers 

  • Cytomegalovirus (CMV)

  • Herpes-6

  • parvovirus B19

  • Hepatitis A&C

  • Rubella

autoimmune disease: immune thrombocytopenia purpura (ITP)

• autoantibodies vs. glycoproteins on platelet surface (↓ platelet count).

• clinical course: acute, life-threatening (especially in children)

autoimmune diseaser: Guillain-Barre Syndrome (GBS)

• Progressive (days-weeks) ascending, symmetrical flaccid limbs paralysis & hyporeflexia ± CN (cranial nerve) involvement

• triggered by respiratory/intestinal infections or vaccinations 

  • known triggers = influenza; Chlamydia; CMV; varicella; mumps; rubella; HIV; Polio; Hepatitis E; Borrelia; M. pneumonia & Campilobacter jejuni

autoimmune disease: miller fisher syndrome (MFS)

• rare, acquired mild variant of GBS (∼ 5% of GBS)

• triad of ataxia, hypo- / a-reflexia, & opthalmoplegia

• Also: mild limb weakness, ptosis, facial palsy, or bulbar palsy (i.e., lower CN: IX, X, XI, XII). Occasionally respiratory failure

autoimmune disease: antiphospholipid antibodies (thrombosis)

deep vein thrombosis, pulmonary embolism and stroke (mostly elderly)

autoimmune disease: Kawasaki-like disease

• systemic vasculitis (usually affects children <5 yo)

• usually self-limiting, but coronary artery aneurysm in many cases

autoimmune disease: subacute thyroiditis

• i.e. De Quervain’s, granulomatous thyroiditis or giant cell thyroiditis

• Inflammation of thyroid causing overactivity  S&S of hyperthyroidism

• Thyrotoxicosis  thyroid storm (dangerous ↑ HR, ↑ BP & ↑temp)

importance of vitamin D in COVID-19

• Inhibits cytokines (e.g. IL-6)

• Inhibits dendritic cell maturation

  • Dendritic cells: antigen-presenting cells help program adaptive immune response 

  • Suppress adaptive immune response 

• “calms” the immune system

• receptor expressed on

• immune cells:

  • B cells: CD4 (+), CD19 (-)

  • T-helper cells (+)

  • antigen presenting cells (-)

• can modulate innate & adaptive immune responses

• deficiency → ↑ autoimmunity, ↑ susceptibility to infection

COVID-19 MSISC

• MSISC = Multi-System Inflammatory Syndrome in Children

6 criteria of MSISC

1. serious illness leading to hospitalization

2. age < 21 yrs.

3. fever lasting ≥ 24 hrs.

4. laboratory evidence of inflammation (e.g. increase CRP)

5. multisystem organ involvement

6. evidence of COVID-19 with severe acute respiratory syndrome

“Long COVID”

• “Signs, symptoms, & conditions that continue/develop after initial infection.

• (present for ≥ 4 wks s/p initial infection)

• May be:

  • Multisystemic

  • Relapsing–remitting

  • progressive or worsening

  • possibly severe/life-threatening

• NOT just one condition!

  • Represents MANY overlapping entities

  • different biological causes (likely)

  • different risk factors & outcomes

effects of long COVID

• Cardiovascular: MI, HF, arrhythmias, dysautonomia (postural orthostatic hypotension → heart failure)

• Atherosclerosis 

• Neurologic: 

  • Central nervous system: increased sympathetic function → anxiety, palpitations, hot flashes, low GI mobility 

  • Peripheral nervous system: decreased sympathetic function → chronic fatigue, brain fog, orthostatic intolerance 

• all systems may be affected! 

“Long COVID” = PASC

Post Acute Sequelae of SARS-CoV-2

S/S of PASC at 6 months

• Fatigue

• Anxiety

• Amnesia

• Insomnia

• Cognitive dysfunction

S/S of PASC at 12 months

• (neurocognitive effects)

  • Amnesia

  • Insomnia 

  • Anxiety

  • Fatigue

  • Arthralgias 

S/S of PASC at 24 months

• Fatigue

• Amnesia

• Insomnia

• Decreased concentration

• Depression & anxiety 

PASC mechanism: dysbiosis

• Infection in gut → leaky gut → chronic inflammation → brain fog

• Increased deaths at lower microbial diversity

Long COVID (PASC) & vaccine status (adults and children)

• Adults & vaccines: dose-response relationship

  • 1x → 21% lower risk

  • 2x → 59%

  • 3+ → 73%

• Children & vaccines

  • 35% effectiveness vs. PASC symptoms @ 1 yr.

  • 42% effectiveness vs. PASC diagnosis @ 1 yr.

  • protection wanes over time (immunity not forever)

• (I think just know that vaccines are effective against PASC)

COVID testing: Antigen test

• (diagnostic)

  • What: mucosal swab

  • How: Detects proteins from the virus (infectious)

  • When: within minutes

  • Pros: rapid

  • Cons: false negative results (↓ viral load)

COVID testing: antibody testing

• (serology)

  •  What: blood sample

  • How: Detects antibodies against SARS-CoV-2 (adaptive immune response – i.e., one has been infected)

  • When: within hours

  • Pros: reveals presence of protective antibodies

  • Cons: can’t confirm a current infection (disease vs. vaccine?)

COVID testing: molecular (PCR)

• (diagnostic)

  • What: mucosal swab

  • How: Detects SARS-CoV-2 by DNA analysis (virus is present)

  • When: hours-day

  • Pros: highly sensitive, can detect variants

  • Cons: possible false negative results with low viral load

COVID vaccine types: “Classic”

• Live-attenuated virus OR whole-inactivated virus 

• Inactivate virus (so you can’t get sick) → exposure programs adaptive immune response

COVID vaccine types: “Conventional”

• Protein subunit

  • Deliver s-protein (spike) to sensitize the body’s adaptive immune response to “recognize” the protein

• Virus-like particle

  • Uses a weakened virus

  • Replaces part of the viral DNA with a sequence encoding the antigen (S-protein)

1. Replication defective : virus cannot replicate

2. Replication competent : virus replicates in the cell (e.g. technology used by Merck to make the Ebola vaccine)

COVID vaccine types": “Next Generation”

• Viral vector vaccines: packaged into glycoprotein coat

• Genetic vaccines: (mRNA vaccines)