COVID 19 Virology

What type of viruses does COVID-19 belong to?

A broad spectrum of highly transmissible animal and human coronaviruses.

What is the structure of a COVID-19 virion?

Spherical or pleiomorphic with an envelope, surrounded by a fringe of embedded glycoproteins (spikes).

What is the length of the positive ssRNA genome of COVID-19?

25.5kb to 32kb.

What significant coronavirus emerged in 2003?

SARS-CoV-1, which caused acute respiratory syndrome with a 10% mortality rate.

What coronavirus emerged in 2012 and what did it cause?

MERS-CoV, which caused severe pneumonia.

What is the zoonotic potential of SARS?

SARS has a zoonotic potential, meaning it can be transmitted from animals to humans.

What are the two types of cells SARS-CoV-2 binds to?

Epithelial cells in the nasopharynx and cells expressing ACE-2.

What is the first step in the SARS-CoV-2 life cycle?

Virus entry into the host via aerosol transmission.

What happens after SARS-CoV-2 binds to ACE-2?

A conformational change in the spike protein occurs, leading to viral membrane and cell membrane fusion.

What are the outcomes of SARS-CoV-2 infection?

Pauci-symptomatic, mild, severe, 'long haulers', and Long COVID-19.

What factors contribute to asymptomatic or pauci-syndromic COVID-19?

Low viral loads and a strong innate immune response that resolves the infection.

What symptoms manifest in mild COVID-19 cases?

Fever, malaise, and dry cough.

What characterizes severe COVID-19 cases?

Maladaptive inflammatory response leading to acute respiratory distress and lung injury.

What are common risk factors for severe COVID-19 outcomes?

Older age, males, diabetes, malignancy, hypertension, cardiovascular disease, COPD, and obesity.

What complications can arise from COVID-19?

Acute ARDS, respiratory failure, sepsis, coagulopathies, and organ injuries.

What antiviral inhibits the 3C-like protease in hospitalized SARS-CoV-2 patients?

Nirmatrelvir, often used with Ritonavir.

What is the function of Remdesivir?

It inhibits RNA-dependent RNA polymerase.

What is the role of Dexamethasone in COVID-19 treatment?

It is a glucocorticoid anti-inflammatory used to reduce lung inflammation.

What is the mechanism of action of Tocilizumab?

It inhibits the pro-inflammatory cytokine IL-6.

What type of protein does the S gene of SARS-CoV-2 encode?

Spike surface glycoprotein, which has fusion protein S1/S2 subunits.

What is the function of the N protein in SARS-CoV-2?

It protects the ssRNA genome.

Inactivated vaccines

Whole dead virus vaccines such as Sinovac, Sinopharm, Bharat Biotech.

Adenovirus vector vaccines

Vaccines that use a harmless virus to deliver spike protein instructions, including Sputnik-V and ChAdOx1.

mRNA vaccines

Vaccines that provide genetic instructions for cells to make spike protein, such as BNT162b2 (Pfizer) and mRNA-1273 (Moderna).

Subunit vaccines

Vaccines that consist only of spike protein pieces, like Novavax.

Severe COVID lung damage

Includes tracheal inflammation, patchy grey-white consolidation, blood clots, diffuse lung consolidation, and progressive X-ray changes.

ARDS (Acute Respiratory Distress Syndrome)

Features macrophage hyperinflammation, AT2 cell damage, endothelial activation leading to clots, fibrin deposition, and neutrophil infiltration.

Cytokine storm

A severe immune response characterized by excess IL-1, IL-2, IL-6, IL-7, IL-10, TNF, and GCSF.

Neutrophils and Lymphocytes

In severe COVID, there is an increase in neutrophils and a decrease in lymphocytes (lymphopenia).

Spike protein

A key protein in SARS-CoV-2 that binds to the ACE2 receptor.

ACE2 receptor

The receptor that SARS-CoV-2 binds to very tightly for cell entry.

SARS-CoV-2 size

The virus measures 110-150 nm.

Group IV ssRNA+ virus

SARS-CoV-2 is classified as a Group IV single-stranded RNA virus.

SARS-CoV-2 genome length

The genome is approximately 29,800-29,900 bases long.

Life cycle of SARS-CoV-2

Involves ACE2 binding, entry, genome release, translation, replication, assembly, and release.

Variants of SARS-CoV-2

Includes Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron subvariants (BA.1, BA.2, BA.5, BQ.1).

R₀ of SARS-CoV-2

The basic reproduction number (R₀) is approximately 3.

CFR of SARS-CoV-2

The case fatality rate (CFR) is less than 1%.

Global COVID-19 statistics

As of the time of data collection, there were over 704 million cases and over 7 million deaths globally.

UK COVID-19 statistics

In the UK, there were 24.9 million cases and 232,112 deaths.

SARS-CoV-2 relatives

Closest known relative is bat coronavirus BANAL-52 with 96.8% identity.

Origins timeline of coronaviruses

Includes the discovery of common cold CoVs in the 1960s-1980s, SARS-CoV from civets in 2002-2003, and MERS-CoV from camels in 2012.

Common cold coronaviruses

Share 65-68% identity with SARS-CoV-2.