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COVID-19 science


  • Covid-19 is a viral pandemic caused by the pathogen SARS-CoV-2 which belongs to the coronaviridae / corona viruses (CoV)
  • It originated in Wuhan in China with 1st cases recognized in Dec 2019
  • it is thought to have evolved from a coronavirus in bats
  • it shares 96.2% identity at the nucleotide level with the coronavirus RaTG13, which was detected in horseshoe bats (Rhinolophus spp) in Yunnan province in 2013 1)
  • this virus appears to be unique amongst primary respiratory viruses in that it is a respiratory virus that can infect vascular enothelial cells throughout the body

The SARS-CoV-2 virus

  • it is a spherical enveloped RNA virus of around 0.1 micron in diameter and being enveloped, this means it does not require host cell lysis to spread but it could replicate within the host cell and be secreted through usual cell processes and thus this could allow infectivity in the pre-syptomatic phase.2)
  • the virus surface has spike proteins which allow the virus to bind to ACE2 proteins on host cells and activate a cellular mechanism to enter the cell where it can replicate
  • viral replication
    • as it is a virus it cannot replicate without being inside a host cell
    • CoVs employ a multi-subunit replication/transcription machinery.
      • A set of non-structural proteins (nsp) produced as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription.
      • A key component, the RNA-dependent RNA polymerase (RdRp, also known as nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of COVID-19 virus, possibly with the assistance of nsp7 and nsp8 as co-factors3)
  • disruption of host cell protein synthesis and the innate immune response:
    • one end of the Nsp1 protein produced by SARS-CoV-2 interacts with the 40S subunit in such a way that it prevents binding of the mRNA and inhibits the formation of functional ribosomes and can also interact with specific configurational states of the fully assembled ribosome. The shutdown of protein synthesis leads to an almost complete collapse of the innate immune response by inhibiting a vital signaling cascade.4)

Major variants of concern

  • C.1.2
    • first identified in the Gauteng and Mpumalanga provinces in Sth Africa May 2021;
    • main issue is the speed of mutations and number of mutations but it is yet to be seen if it becomes a variant of concern to out-compete with Delta
  • Mu variant
    • B.1.621 originated in Sth America and was placed as variant of concern by WHO on 30/8/21
    • appears to effectively compete with Delta accounting for 39% of Colombia's cases during the Delta surge but global prevalence is decreasing
  • Lambda S strain
    • belongs to the C.37 VOI lineage and emerged in July 2020
    • by July 2021 it was predominantly spreading in South American countries where it seems to be evading vaccination immunity
    • the spike protein of the Lambda variant is more infectious and it is attributed to the T76I and L452Q mutations; insertion of RSYLTPGD246- 253N mutation in the NTD of the Lambda Spike protein is associated with the increased virulence and is responsible for evasion from neutralizing antibodies 5)
  • Kappa strain (B.1.167.1)
    • “Indian strain” from Oct 2020
    • said to be 50% more infectious than UK variant and R0 > 6 while transmission period seems to be as short as 24hrs from infection instead of previous 4-7 days
    • community spread in Victoria, Australia in April 2021
  • Eta strain (B.1.525)
    • multiple countries from Dec 2020
  • Iota strain (B.1.256)
    • USA from Nov 2020
  • Theta strain (P3 Philippines)
    • Philippines from Jan 2021
  • Zeta strain (P2 Brazilian)
    • Brazil from Apr 2020
  • Epsilon strain (B.1.427/B.1.429)
    • USA from Mar 2020
  • Delta strain (B.1.167.2)
    • from India Oct 2020
    • said to be 50% more infectious than UK variant and R0 > 6 while transmission period seems to be as short as 24hrs from infection instead of previous 4-7 days
    • NB. an R0 of 6 suggests that herd immunity would occur once more than 84% of entire population (including children) are vaccinated or infected and now immune
  • Gamma strain (P.1 Brazilian strain)
    • first identified in Japan among travelers from Brazil in January 2021 but documented earliest from Brazil in Oct 2020
    • a branch off the B.1.1.28 lineage
    • 17 unique mutations, including three in the receptor binding domain of the spike protein.
    • has the N501Y mutation as with UK strain
    • has the E484K mutation as with Sth African strain
    • seems to have a much higher rate of infection and severe illness in young adults
    • 1.4–2.2 times more transmissible and was shown to be capable of evading 25–61% of inherited immunity from previous coronavirus diseases, leading to the possibility of reinfection.
    • can be 10–80% more lethal
  • Beta strain (B.1.351 South African strain)
    • first reported in South Africa in December 2020 but found from May 2020 onwards
    • shares some mutations with B.1.1.7 but does not contain the deletion at 69/70
    • has multiple mutations in the spike protein, including K417N, E484K, N501Y
    • 50% more transmissible than pre-existing variants
    • seems to reduce the efficacy of the AstraZeneca vaccine against mild to moderate illness
      • neutralisation titres significantly reduced to Pfizer and AstraZeneca vaccines6)
  • Alpha strain (B.1.1.7 UK strain)
    • first reported in the United Kingdom in December 2020 but found from Sept 2020 onwards
    • more transmissible than pre-existing “wild” variants


75% of droplets observed are moving at velocities less than 0.5 m/s and the motion is equally distributed in all the directions, which implies that they do not settle rapidly and may follow the ambient airflow pattern. These results points toward high aerosol generation, as the behaviour of these droplets is like airborne particles source: Clinical Infectious Diseases Sept 2020. Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs

Viral stability outside of host cells

  • virus can survive at least 3 days on most surfaces and is more stable on plastic and stainless steel (median half life of 6.8hrs and 5.6hrs respectively), than on copper and cardboard8)
  • viral load in the air and on domestic surfaces in the homes of infected persons appears to be minimal, however, a possibly more significant reservoir of viral particles may be in wash basins, showers and toilets and in the waste water.9)
  • Viable virus has been isolated from air samples collected 2 to 4.8m away from patients suggesting aerosol spread in hospitals especially if poorly ventilated10)
  • an Australian study suggests for each 1% drop in relative humidity, there was about a 7% increase in the pooled estimate of daily counts of COVID‐19 cases in the NSW 1st wave of community transmission. There was no correlation with outdoor temperatures. 11)
  • another Australian study in Oct 202012) showed the virus, in the absence of UV light, can:
    • survive up to 28 days on some surfaces at 20degC, 50% RH and in the dark on glass, stainless steel, vinyl and banknotes
    • can survive over a week at 30degC
    • but survives only up to 24 hours at 40degC on some surfaces

Host cell mechanisms

  • the virus binds to the cell's neuropilin-1 receptor and, if present, the ACE2 protein on host cells but requires these cells to also express TMPRSS2 (or perhaps an alternate protein). Two proteins, PIKFyve kinase and CD147 have also been shown to bind Spike protein and facilitate viral entry 13)
  • SARS-CoV-2 has a 10-20-fold higher affinity of ACE2 compared to SARS virus14)
  • binding of the coronavirus S (spike) protein to ACE2 triggers a conformational change in the S protein of the coronavirus, allowing for proteolytic digestion by host cell proteases (TMPRSS2)
    • TMPRSS2 expression and cell fusion pathway appears to overcome the antiviral effect of hydroxychloroquine which blocks the alternate Cathepsin L pathway to fusion with cells, providing a mechanistic explanation for hydroxychloroquine's poor therapeutic efficacy against SARS-CoV-2 – despite somewhat encouraging cell culture results15)
  • the intracellular enzyme furin plays an important role in this viral life cycle of SARS-CoV-2 and this is distinctly different than SARS-CoV.16)
  • The furin cleavage site in the SARS-CoV-2S protein may provide a priming mechanism, and Alveolar type II cells were strongly positive for furin while transient secretory cells had an intermediate level of expression
  • nasal epithelial cells appear to be the primary target for infection as these are more susceptible than lower airway cells to infection, however, the same types of nasal epithelial cells from various human donors vary markedly in their vulnerability to infection plus the virus does not seem to infect other nasal cells such as club cells despite them also expressing both ACE2 and TMPRSS2 which suggests there are other yet to be discovered factors which permit infection17)
  • After cellular detection of viral entry into a host cell, interferon (IFN) induction of interferon-stimulated genes (ISGs) is essential for host antiviral defense. IFNα also drives up-regulation of ACE2. SARS-CoV-2 could exploit species-specific interferon-driven up-regulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection 18)
  • a lung organoid model19) seems to show that when exposed to the virus:
    • the virus begins to replicate rapidly, reaching full cellular infection just six hours after infection.
    • cells begin to produce interferons – signals to neighbouring cells, telling them to activate their antiviral defences
    • after 48 hours, the interferons triggered the innate immune response and the cells started fighting back against infection
    • 60 hours after infection, a subset of alveolar cells began to disintegrate, leading to cell death and damage to the lung tissue.

Host cell ACE2 expression

which cells express both ACE2 and TMPRSS2

up-regulation on ACE2 expression

  • many believe that those who have higher expression of ACE2 or perhaps certain polymorphisms of ACE2 on their cells are at higher risk of severe illness and death although recent studies have failed to demonstrate a significant association with ACE inhibitors or angiotensin II receptor blockers (ARBs) with infection rates or severity of Covid-1923)24)
  • ACE2 receptor is not expressed on fetal or placental cells, and is minimally expression in children
  • factors which are known to increase ACE2 expression on cells include:
    • age
    • diabetes
      • both of which reduce the effect of Ang II on the AT1R which acts to reduce ACE2 expression via lysosomal internalization of ACE2
      • ARBs increase ACE2 receptor numbers by 3-5x
    • perhaps with genetic polymorphisms of ACE2
    • human influenza infection induces broader expression of ACE2 in upper airway epithelial cells
    • Covid-19 activated interferon alpha 25)

potential other protein interactions

  • co-evolved proteins with ACE2
    • ACE2 may have novel protein interactions that are disrupted during SARS-CoV-2 infection26) such as:
      • ACE2 has clear connections to coagulation pathway proteins, such as Coagulation Factor V and fibrinogen components FGA, FGB, and FGG, the latter possibly mediated through ACE2 connections to Clusterin (which clears misfolded extracellular proteins) and GPR141 (whose functions are relatively unknown)
      • ACE2 also connects to proteins involved in cytokine signaling and immune response (e.g. XCR1, IFNAR2 and TLR8), and to Androgen Receptor (AR)

transmission to other species including pets

  • it has been shown that the virus can be transmitted to pets which may then become vectors and reservoirs for the virus, especially ferrets and young cats, while dogs have only low susceptibility, and pigs, chickens, and ducks are not susceptible to SARS-CoV-2 27)
  • ferrets and cats have only two amino acid differences in the SARS-CoV-2 spike-contacting regions of ACE2
  • ACE2 is mainly expressed in type II pneumocytes and serous epithelial cells of tracheo-bronchial submucosal glands in ferrets but seems to only be replicated in upper airways and not affect the lungs of ferrets

Risk factors for severe disease


  • male
  • Blood group O have lower risk (OR 0.65) and blood group A, higher risk (OR 1.45) for severe disease28)
  • 5 genes (IFNAR2, TYK2, OAS1, DPP9 and CCR2) appear to be correlated with severe disease according to UK study of 2700 ICU patients
  • rare X chromosomal genes producing loss-of-function Toll-like receptor 7 (TLR7) resulting in impaired immune response and reduced type I and type II interferon production appears to markedly increase severity in young men. The highly specific defect in host defense against SARS-CoV-2 and potentially other coronaviruses in these individuals with TLR7 deficiency has similarities with the specific susceptibility to herpes encephalitis in patients with defects in the TLR3 recognition pathway 29)
  • rare type I IFN immunodeficiencies such as the AR form of IFNAR1 deficiency30)


  • elderly
  • cardiovascular disease

other factors

  • low levels of mumps antibody titres may be a factor as MMRII vaccine may be protective31)
  • chronic use or high dose use of use of opioids especially Tramadol32)
  • low educational attainment33)


Immune response and immunity

  • SARS-CoV-2 generates robust antibody responses, including specific IgG, IgA, and IgM.
  • seroconversion in infected individuals occurs within 20 days after symptom onset
  • it appears that early production of secretory IgA plays an important role and appear to occur prior to specific IgG production and to decline rapidly after a month34)
  • the TLR7 pathway is instrumental in the production of type I IFNs in airway epithelial cells
    • the SARS-CoV-2 genome contains more ssRNA motifs that could interact with TLR7 than the SARS-CoV genome, indicating that TLR7 signaling might be even more relevant in the pathogenesis of COVID-19 disease
    • in comparison with other respiratory viruses, SARS-CoV-2 induces a lower antiviral transcriptional response marked by low type I IFN levels and elevated chemokine expression
    • patients with severe COVID-19 exhibit an impaired type I IFN response and a lower viral clearance


  • vaccination appears to produce two main immune responses:
    • vaccine-induced humoral response
      • provides rapid protection against symptomatic infection by controlling viral replication but this tends to wane over time and may warrant boosters to reduce mild breakthrough infections as it wanes
      • vaccinated persons appear to have 5x lower risk of catching Covid-19 35)
    • memory immune cells (B cells and T cells)
      • take a relatively longer time to be expressed after vaccination play the central role in providing long-term protection against severe disease 36)
      • vaccinated persons appear to have 10x lower risk of catching Covid-19 requiring hospitalisation37)


  • breakthrough infections are possible as humoral immunity wanes but is generally mild although new variant infections may result in severe infections

Pathogenesis of illness

asymptomatic nasal carriage

  • the virus enters the nasal goblet and ciliated cells and is secreted along with nasal secretions which can then be spread to others primarily by droplet transmission
  • the high rates of transmission from asymptomatic infected persons makes control much more difficult and requires testing of all people especially in high risk environments such as aged care facilities 38)

mild URTI/LRTI illness +/- diarrhoea

  • infection of nasal cells may result in rhinorrhoea and spread down bronchi to the lung alveolar cells
  • this may result in cough, fever and SOB
  • even in this mild illness stage a ground glass radiologic appearance of the lungs is often evident suggesting the presence of alveolar fluid
  • some will develop silent hypoxia with mild symptoms and this is most likely due to the development of a V/Q shunt whereby pulmonary blood is still provided to alveolar regions with poor oxygen diffusion capacity
  • viral particles from the nose will also be ingested and presumably will be taken up by upper oesophageal cells as well as ileal and colonic enterocytes
    • this may cause diarrhoea (usually mild), nausea and abdominal pains in some patients
    • this may also be a mechanism for fecal-oral transmission

endothelial cell infection and cardiovascular complications

  • the ACE2 receptor is also widely expressed on endothelial cells which form an active paracrine, endocrine, and autocrine organ that is indispensable for the regulation of vascular tone and the maintenance of vascular homoeostasis
  • induction of apoptosis and pyroptosis might have an important role in endothelial cell injury in patients with COVID-19
  • COVID-19-endotheliitis could explain the systemic impaired microcirculatory function in different vascular beds and their clinical sequelae in patients with COVID-1939)

severe disease and CRS

  • up to 20% develop severe disease, and 5% become criticall ill most notably with severe pneumonitis / ARDS-like syndrome
  • this is thought to occur due to the development of cytokine release syndrome (CRS) and secondary hemophagocytic lymphohistiocytosis (sHLH)
  • The efficacy of IL-6–IL-6R antagonists for the treatment of CRS as well as sHLH underscores the central role of IL-6 signaling in the pathophysiology of cytokine-driven hyperinflammatory syndromes
  • ARDS results in severe hypoxia due to damage of the alveolar epithelial and endothelial capillary barriers, leading to fluid accumulation, alveolar collapse and reduced gas exchange
    • recovery partly relies upon fluid reabsorption and surfactant production which involve metabolic processes performed by the alveolar epithelial cells

cytokine release syndrome (CRS)

  • CRS was found to be the major cause of morbidity in patients infected with SARS virus and MERS
  • SARS-CoV efficiently infects primary human monocytes and dendritic cells, whereas MERS-CoV infects monocytes and T cells via dipeptidyl peptidase 4 (DPP4)
  • it is thought SARS-CoV-2 may function similarly to SARS-CoV in this regard
  • betacoronavirus infection of monocytes, macrophages, and dendritic cells results in40):
    • dendritic cell dysfunction is thought to lead to defective activation of T cells and resultant T cell apoptosis and exhaustion and lymphopenia.
    • their activation and secretion of IL-6 and other inflammatory cytokines
      • elevated serum IL-6 increases C reactive protein (CRP) and correlates with respiratory failure, ARDS, and adverse clinical outcomes
      • IL-6 can signal through three main pathways:
        • classic cis signaling:
          • IL-6 binds to membrane-bound IL-6 receptor (mIL-6R) in a complex with gp130;
          • downstream signal transduction is mediated by JAKs (Janus kinases) and STAT3 (signal transducer and activator of transcription 3).
          • Membrane-bound gp130 is ubiquitously expressed, whereas mIL-6R expression is restricted largely to immune cells.
          • Activation of cis signaling results in pleiotropic effects on the acquired immune system (B and T cells) as well as the innate immune system (neutrophils, macrophages, and natural killer (NK) cells), which can contribute to CRS
        • trans signaling:
          • high circulating concentrations of IL-6 bind to the soluble form of IL-6R (sIL-6R), forming a complex with a gp130 dimer on potentially all cell surfaces.
          • The resultant IL-6–sIL-6R–JAK-STAT3 signaling is then activated in cells that do not express mIL-6R, such as endothelial cells.
          • This results in a systemic “cytokine storm” involving secretion of vascular endothelial growth factor (VEGF), monocyte chemoattractant protein–1 (MCP-1), IL-8, and additional IL-6, as well as reduced E-cadherin expression on endothelial cells.
          • VEGF and reduced E-cadherin expression contribute to vascular permeability and leakage, which participate in the pathophysiology of hypotension and pulmonary dysfunction in ARDS.
        • trans presentation
          • IL-6 binding to mIL-6R expressed on an immune cell, which forms a complex with gp130 on T helper 17 (TH17) cells, leading to downstream T cell signaling that may be involved in ARDS
          • this can be blocked by IL‐6R inhibitors but not by IL‐6 inhibitors which can only suppress only cis and trans signaling

secondary hemophagocytic lymphohistiocytosis (sHLH)

  • sHLH is a hyperinflammatory syndrome (aka macrophage activation syndrome) characterized by:
    • CRS with elevated serum cytokines
    • cytopenias (low blood cell counts)
    • high concentrations of ferritin thought to be due to activation of CD163-expressing macrophages which have a role in reticuloendothelial iron signaling
    • multiorgan failure

cell death and apotosis induced by the virus


  • fortunately it does not seem to have a dramatic impact on pregnant women compared to non-pregnant women with Covid infection, nor to their babies
  • in this systematic review of the literature published in July 2020 in The Lancet41):
    • ICU admission rate 7% (higher in those with co-morbidities or aged over 35yrs)
    • intubation rate 3.4%
    • maternal mortality 1%
    • pre-term delivery before 37 wks was 22% but mainly medically indicated


  • anticoagulants
    • anticoagulants reduce Covid clotting complications and ICU admits and death
    • individuals using anticoagulation therapy who developed COVID-19 had a 43% lower risk of hospital admission 42)
  • Dexamethasone
    • the Recovery Trial published in June 2020 showed that 6mg dexamethasone daily for 10 days reduced deaths by 1/3rd for ventilated patients and by 20% for those on oxygen but without need for ventilator care43)
  • Metadichol®, a nano lipid formulation of long chain alcohols:
    • it apparently is a safe, non-toxic product
    • inhibits TMPRSS2 (EC50 of 96 ng/ml). It is 270 times more potent than another another well known inhibitor Camostat mesylate, which has EC50 of (26000 ng/ml)
    • is also a moderate inhibitor of ACE2 with an EC50 of 31 µg/ml. Moderate inhibition of ACE2 allows it to perform its key functions in the body, yet fend off SARS-COV-2 entry to the cell
    • by binding to the Vitamin D receptor (VDR), acts on proteases like Furin and Adam-17, which activate the S-protein spikes for viral spread and pathogenesis in the infected hosts.
    • in small studies appears to rapidly clear the virus from infected patients44)
  • ultra-high dose vitamin C
    • produced a radical improvement in a Melbourne patient in severe sepsis with Covid-19 and seems to have support in animal models
    • initial dose of 30 grams of IV sodium ascorbate (vitamin C) over 30 minutes, then a maintenance dose of 30 grams over six and a half hours
  • molnupiravir
    • Merck say early results (Oct 2021) in their trials appears to show giving 5 day course of this oral medication within five days of onset of COVID-19 symptoms had about half the rate of hospitalisation and death compared to placebo hence trial was stopped early. Merck say they can make 10 million doses by end of year and US have committed to buying 1.7 million doses if authorised by FDA.
Jeonghwan Youk et al. Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2. Cell Stem Cell; 21 Oct 2020; DOI: 10.1016/j.stem.2020.10.004
covid19_science.txt · Last modified: 2021/10/04 08:54 by gary1