Coronaviruses

Coronaviruses with a Focus on Sars-CoV-2

Topics on Coronaviruses helpful to understand the infections they cause.

major (re)work in progress, April 2021

Description

Coronaviruses with a focus on SARS-CoV-2: features, life cycle, tropism, habitats and evolution.

Systematics of Coronaviruses

Nidovirales

Coronaviruses belong to the order of Nidovirales. Nidovirales are positive single-stranded, non-segmented and enveloped RNA viruses. This means that their genetic material is encoded as a single positive strand of RNA - the same way as messenger RNA pieces of the cell. Enveloped means they have a membrane. Nido is latin for nest and describes two distinguishing features:

Coronaviruses

The membrane is spherical and consists of structural proteins which are coated in a lipid bilayer membrane acquired from the host cell. This membrane is called envelope.

Coronaviruses Species

[in work]

SARS-CoV-1

Betacoronavirus identified causing Sars in 2003/2004.

SARS-CoV-2

Betacoronavirus identified causing the current Covid-19 pandemics. A focus of this page and many sections contain special notes about features of Sars-CoV-2.

MERS-CoV

Betacoronavirus identified causing MERS.

Bovine Coronaviruses

Abbreviated BCoV. Betacoronavirus causing diarrhea and respiratory infections in cattle.

Coronavirus Life Cycle

As mentioned in Introduction to Viruses viruses have a multiphase life cycle. Coronaviruses have a two phase life cycle:

Virion Phase

Travel and Wait for Activation. Virions have behave similar as seeds of plants: Travel and wait for the right conditions to unleash their energy (spring loaded proteins for viruses and starch for seeds) to start the active phase.

Virion Travel

Once released from a cell virions are moved by external forces (movement-of-virions) until they are activated to start the cell infection process. A virion needs to reach possibly a host, the location of the target cells (e.g. an organ), a specific cell and then it needs to be matched to a receptor on the cell membrane in the order of nanometers. All this without being able to move on its own and thus relying on external movements. The virion-target match can happen because the virion is moved to the target, the target is moved to the virion or a combination.

The infectable cell can be:

Virion Priming

Coronaviruses virions usually need to be primed before they bind to cell or initiate cell fusion. Since:

Coronavirus virions interact with the environment mainly though the spikes, so the spike need to be primed. There can be several priming steps ahead or during the cell entry process.

Plant Seeds to Virions

Plant seeds evolved first to travel and then to be activated under favorable conditions for growth, at least as far as the seeds are able to check the conditions. Similarly virions need to be primed to initiate cell entry and thereby start the metabolic phase. Plants mainly need and check the right physical and chemical conditions to growth. Correspondingly seeds are primed by their physical environmental factors such as temperature, humidity, light and minerals dissolved in the surrounding water to start their metabolism. Viruses need the right biological conditions inside the cells. Coronaviruses evolved to check biological conditions: receptors on cell membranes and proteases available in the environment around the cell.

Cell Entry

  1. The virus gets attached to a matching receptor on the target cell mostly via the spike protein
    • The virions may slide along the cell surface or travel with the cell.
    • The virions may enter directly via fusion with the outer cell membrane or the virions may first be taken up into a cell internal vesicle and fuse with the surrounding internal membrane.
  2. Fusion of the viral envelope with host cell membrane once primed:
    1. binding to a receptor on the cell membrane -> cleavage sites are exposed
    2. cleavage through proteases at specific cleavage sites enable a conformation change
    3. the conformation change push the fusion-peptides of the spike protein into the cell membrane
    4. with the fusion peptides anchored in the cell membrane a further conformation change of the spike protein presses the viral and cell membrane together which can result in membrane fusion.
  3. Release and unpacking of genome and the structural proteins
  4. Start the metabolism

Metabolic Phase

The viral metabolism starts once the genetic material of a virion is processed by a cell and thus the virus changes the cells metabolism. This happens in a foreign cell and cells have mechanism in place to prevent its metabolism being changed i.e. keeping the metabolism immune. For that reason, each of the following steps has a noteworthy probability of failing.

Metabolism Phase 1: Build the Factory Hall and incorporate Host Machines (Ribosomes)

in work

Build double membrane shielded replication complexes.

Metabolism Phase 2: Build the Machines = Build the RdRP Protein

[in work] The goal of the first phase in the metabolism is to produce RdRP (RNA dependent RNA Polymerase protein). Additionally let the ribosomes produce some proteins that diminish the cells immune mechanisms such that the cell doesn’t ring the bells. Steps:

  1. Release RNA – let the host ribosomes translate two ORFs of the viral genome with frame-shifting—> two large proteins
  2. –cleave–> pieces of proteins
  3. –like magnets these pieces self arrange to structures–>
    • proteins providing the right setting for the phase 2 metabolism e.g. prevent the cells protection mechanisms working
    • polymerase protein (protein capable of transcription of RNA to RNA)

Metabolism Phase 3: Produce Self Copies = Replicate

The metabolism can produce new virions that are released from the cell. The properties and and the environment of the cell influence the properties of the virions produced. This phase is initiated by the transcription of the (+) strand RNA to a (-) strand RNA template mediated by the polymerase protein:

  1. (+) RNA –transcription–> (-) RNA template
  2. (-) RNA template – transcription–>
    • pieces of subgenomic mRNAs which get translated to mostly structural proteins (N, S, M, E, HE)
    • (+) RNA genomes to get packed together with the N proteins to form the nucleocapsids of new virions and thus building up new virions.

Molecular Biology

in work

Coronavirus Proteins

RNA viruses have small but highly optimized genomes. Each protein is often - like a swiss army knife - capable and used for different functions.

Virion Proteins

in work and incomplete June 2021

Virion proteins = structural proteins: since they are used to give newly built viruses structure. These are the membrane proteins (E, S, M, [HE]) and the internal protein N. Besides their function in virions these proteins usually have functions in the metabolic phase as well.

N Protein

N stand for Nucleocapsid protein

M Protein

M stand for Membrane protein

E Protein

E stand for Envelop protein

S Protein

S stand for Spike protein. The spike proteins point spike-like out of the spherical virions. This gives coronaviruses virions a corona (from latin corona=crown or from solar corona) like appearance under the electron microscope. Functions:

Metabolic Phase only Proteins

Capabilities

[in work]

Capabilities in the Virion Phase

Capabilities in the Metabolic Phase

in work and >95% incomplete

Behaviors of Coronaviruses

Introduction to the Behavior of Coronaviruses

Viruses optimized to their environment usually infect cells beneficial to the survival of the virus strain:

Cell Specific Behavior of Coronaviruses

In Vitro Experiments

Coronaviruses often have a preference for the apical side of polarized epithelial cells:

Cell Entry Mechanisms:

    • Attachment Receptor: Cell membrane expression of ACE2 or an other adhesion receptor.
    • Get Taken Up by the Cell: Some cells (e.g. macrophages, dendritic cells) phagocyte coronaviruses (antibodies can mark virions for phagocytosis). Once phagocytosed the coronaviruses usually find themselves within intracellular vehicles.

      Antibody induced phagocytosis is both relevant upon reinfection and for the design of vaccines. Antibodies against the outer membrane proteins (e.g. the spike) can be a two-sided sword. The risk is much greater for spike-only vaccines since the immune response induced is very narrow.

  2. Once attached on the outside or within intracellular vehicles, coronaviruses need to pass the membranes. They do this by using their spikes. The spikes attached to the cell surface undergo a conformation change which brings the cell membrane and virus membrane together and fuses them.

The spikes can be imagined like spring under tension: Upon activation this energy is released to fuse the membranes.

Cell Specific Behavior of Sars-Cov-2

[in work]

Tropisms of Coronaviruses

Tropism for viruses denotes the cells and tissues they preferable populate (defined on the Viruses Page). The tropism is determined by the cell behavior and how the viruses are moved.

Respiratory Tract Tropism

Coronaviruses are initially deposited and replicate well on the surface of the respiratory tract, thus they have a tropism for epithelial cells in the respiratory tract:

Human coronaviruses usually don’t use the respiratory tract as passway to enter tissues but keep restricted to the surface of the respiratory tract. Coronaviruses are thus typical respiratory viruses.

Coronaviruses can cause persistent infections of other tissues, their clinical significance is unclear as of November 2021.

Evolution

[in work]

Coronaviruses can adapt fast to changed or new environments if given time and opportunity 15.11.21: coronaviruses don’t need much space and time to evolve. The adaption over multiple generations occurs through genetic evolution i.e. mutation of RNA genome. Measured in mutations per time unit coronaviruses are among the fastest evolving life forms on earth. More in the Evolution Chapter.

Conquering to New Hosts

Interspecies Infections of Coronaviruses

Observed Interspecies Jumps

References

RNA Viruses

Environmental Factors on Betacoronaviruses

References Cell Entry

Summary Jia 2005

Hong Peng Jia, Dwight C. Look, Lei Shi, Melissa Hickey, Lecia Pewe, Jason Netland, Michael Farzan, Christine Wohlford-Lenane, Stanley Perlman, Paul B. McCray ACE2 Receptor Expression and Severe Acute Respiratory Syndrome Coronavirus Infection Depend on Differentiation of Human Airway Epithelia
Jr Journal of Virology Nov 2005, 79 (23) 14614-14621; https://doi.org/10.1128/JVI.79.23.14614-14621.2005

Methods

“We studied host-pathogen interactions using native lung tissue and a model of well-differentiated cultures of primary human airway epithelia.”

Findings