COVID-19 is a disease resulting from infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Viruses, including SARS-CoV-2, cannot reproduce independently. These microscopic agents must invade living host cells to multiply. Once inside a host cell, the virus commandeers the cell’s machinery to produce new viral components. This process of viral replication allows the virus to spread throughout the body, leading to disease symptoms.
The SARS-CoV-2 Virus
SARS-CoV-2 is an enveloped virus, characterized by an outer lipid membrane derived from the host cell during its formation. Embedded within this lipid envelope are three types of structural proteins: the Spike (S) protein, the Envelope (E) protein, and the Membrane (M) protein. The virus is classified as a coronavirus because its surface, when viewed under an electron microscope, is adorned with these large, club-shaped Spike proteins, creating a crown-like appearance.
Inside this protective envelope, the virus contains its genetic material, a single strand of positive-sense RNA. This RNA genome is protected by the Nucleocapsid (N) protein, which binds to the RNA. The Spike protein on the viral surface plays a direct role in initiating infection by recognizing and binding to specific receptors on human host cells.
Entering a Host Cell
The infection process begins when the SARS-CoV-2 virus attaches to a human cell. The Spike (S) protein on the viral surface binds to a protein on the host cell called Angiotensin-converting enzyme 2 (ACE2). This interaction determines which cells the virus can infect.
Following attachment, host cellular proteases prepare the Spike protein for entry into the cell. One host protease is Transmembrane Protease Serine 2 (TMPRSS2), found on the surface of many human cells, including those in the respiratory tract. TMPRSS2 cleaves the Spike protein at specific sites, which is necessary for the virus to fuse with the host cell membrane. This cleavage exposes regions of the Spike protein involved in mediating the fusion of the viral envelope with the host cell membrane.
Viral entry can occur through two main pathways. In cells expressing TMPRSS2, the virus can directly fuse its lipid envelope with the host cell’s outer membrane at the cell surface, allowing the viral genetic material to immediately enter the cytoplasm. Alternatively, the virus can enter the cell via endocytosis, where the entire virus particle is engulfed by the cell in a vesicle. In this endosomal pathway, fusion of the viral envelope with the endosomal membrane occurs later, often requiring the acidic environment within the endosome to activate the Spike protein.
Taking Over the Cell’s Machinery
Once the virus has entered the host cell, the viral RNA genome is released into the cell’s cytoplasm. Since SARS-CoV-2 has a positive-sense RNA genome, it directly functions as messenger RNA (mRNA) and can be immediately translated by the host cell’s ribosomes. These ribosomes translate the viral RNA into large precursor proteins called polyproteins.
These large polyproteins are not functional in their initial form; they must be cut into smaller, active proteins. This cleavage is performed by viral proteases encoded within the polyproteins themselves. These proteases cut the polyproteins into non-structural proteins (nsps). Among these non-structural proteins is RNA-dependent RNA polymerase (RdRp).
RdRp is a protein unique to viruses and is absent in human cells, making it a target for antiviral therapies. This enzyme works with other non-structural proteins to replicate the viral genome and transcribe viral genes. RdRp uses the original positive-sense RNA genome as a template to synthesize complementary negative-sense RNA strands.
These negative-sense strands then serve as templates for two processes: the synthesis of new positive-sense RNA genomes for packaging into new virions, and the production of smaller subgenomic mRNAs. These subgenomic mRNAs encode the structural proteins (Spike, Envelope, Membrane, Nucleocapsid) of the virus. The entire process of RNA replication and transcription occurs within structures derived from the host cell’s endoplasmic reticulum (ER).
Building and Releasing New Viruses
After the viral structural proteins (Spike, Envelope, and Membrane) are synthesized from the subgenomic mRNAs, they are inserted into the membranes of the host cell’s endoplasmic reticulum (ER) and subsequently traffic to the Golgi apparatus. Meanwhile, the newly replicated positive-sense RNA genomes are bound by the Nucleocapsid (N) proteins to form new ribonucleocapsid complexes. The N protein plays a role in packaging the RNA genome into these structures.
The assembly of new viral particles takes place in the ER-Golgi intermediate compartment (ERGIC). Here, the ribonucleocapsids containing the viral RNA and N proteins associate with the ERGIC membrane, which contains the newly synthesized Spike, Envelope, and Membrane proteins. The budding process occurs as the nucleocapsid acquires its lipid envelope, embedded with the structural proteins, by budding into the lumen of the ERGIC.
Once assembled, these new viral particles, or virions, are enclosed within vesicles. These vesicles then transport the virions through the cell’s secretory pathway towards the cell surface. Finally, the new SARS-CoV-2 particles are released from the host cell into the extracellular space through exocytosis, where the virus-containing vesicles fuse with the cell’s outer membrane. This release mechanism allows the virions to spread and infect other neighboring cells, perpetuating the viral life cycle.