Coronaviruses are a large family of viruses, characterized by their large RNA genomes and a distinctive crown-like appearance under an electron microscope. These enveloped viruses, including SARS-CoV-2 (which causes COVID-19), are obligate intracellular parasites. They cannot multiply on their own; instead, they must invade and take over the machinery of a living host cell to produce new viral particles.
Entering the Host Cell
The initial step in the coronavirus replication cycle involves the virus gaining entry into a susceptible host cell. This process is orchestrated by the Spike (S) protein, a prominent glycoprotein on the virus surface. The S protein acts as a molecular key, binding to specific receptors on human cells. For SARS-CoV-2, the main receptor is Angiotensin-converting enzyme 2 (ACE2), abundant on type II alveolar cells in the lungs.
The S protein is composed of two subunits, S1 and S2. The S1 subunit contains the receptor-binding domain (RBD) which directly interacts with the ACE2 receptor. This binding triggers conformational changes in the S protein, preparing the virus for membrane fusion. Host cell proteases, such as TMPRSS2, often cleave the S protein, further activating it for entry.
Following receptor binding and S protein priming, the virus can enter the host cell through two primary mechanisms. One method involves direct fusion of the viral envelope with the host cell’s plasma membrane, releasing the viral genetic material directly into the cytoplasm. Alternatively, the virus can enter through endocytosis, where the cell membrane engulfs the virus-receptor complex, forming an endosome. Inside this acidic endosomal compartment, the viral and endosomal membranes fuse, releasing the viral RNA genome into the cytoplasm.
Replicating the Genome and Producing Viral Proteins
Once the viral RNA genome is released into the host cell’s cytoplasm, it begins to hijack the cellular machinery. The coronavirus genome is a positive-sense single-stranded RNA, meaning it can directly serve as a messenger RNA (mRNA) and be translated by the host cell’s ribosomes. This initial translation produces two large polyproteins, pp1a and pp1ab, from open reading frames (ORFs) 1a and 1b.
These polyproteins are then cleaved by viral proteases, such as papain-like proteases (PLpro) and the main protease (Mpro), into 16 individual non-structural proteins (nsps). Many of these nsps, including the RNA-dependent RNA polymerase (RdRp), assemble to form a replicase-transcriptase complex (RTC). This RTC synthesizes new viral RNA, both full-length genomic RNA and shorter subgenomic RNAs.
The RdRp uses the original positive-sense genomic RNA as a template to create a full-length negative-sense RNA strand. This negative-sense strand then serves as a template for producing new positive-sense genomic RNA copies for new virus particles. The RTC also performs discontinuous transcription, synthesizing a nested set of subgenomic RNAs. These subgenomic RNAs each contain a common leader sequence and serve as mRNAs for the translation of the viral structural proteins (Spike, Envelope, Membrane, and Nucleocapsid) and other accessory proteins.
Assembling and Releasing New Viruses
The final stages of the coronavirus replication cycle involve the assembly of new viral particles and their release from the infected cell. Following genome replication and structural protein production, these components gather. The newly synthesized Spike (S), Envelope (E), and Membrane (M) proteins are inserted into the endoplasmic reticulum (ER) and then trafficked to the ER-Golgi intermediate compartment (ERGIC).
Within the ERGIC, the replicated positive-sense genomic RNA associates with the Nucleocapsid (N) protein to form the ribonucleoprotein complex. This complex then buds into the membranes of the ERGIC, which are studded with the S, E, and M structural proteins. The M protein plays a role in directing these protein-protein interactions necessary for the assembly of new virions.
Once assembled within the ERGIC, the virions are enclosed within vesicles. These virus-containing vesicles then transport the mature virions through the cell’s secretory pathway. Viruses are released from the infected cell through exocytosis, a process where the vesicles fuse with the cell’s plasma membrane, expelling new infectious particles into the extracellular space. This allows the viruses to spread and infect other neighboring cells.