Coronavirus Structure, Genome, Replication, Symptoms, Pathogenesis, and Prevention

Structure of Coronavirus

Coronaviruses (enveloped RNA viruses) fall in the virus family Coronaviridae, order Nidovirales.
They are enveloped, 120–160 nm particles containing an unsegmented genome of single-stranded positive-sense RNA (27–32 kb).
The large plus-stranded RNA genome associates with the N protein (nucleocapsid protein) to form a helical nucleocapsid, 9–11 nm in diameter.
Spike projections: 20 nm long, club- or petal-shaped, widely spaced on the envelope, giving a “solar corona” appearance.
Viral structural proteins:

Nucleocapsid (N) protein (50–60 kDa, phosphorylated)
Membrane (M) glycoprotein (20–35 kDa, matrix protein, interacts with nucleocapsid)
Spike (S) glycoprotein (180–220 kDa, forms petal-shaped peplomers)
Some viruses (e.g., HCoV-OC43) also have HE glycoprotein (65 kDa) causing hemagglutination (clumping of red blood cells) and possessing acetylesterase activity.

Coronavirus genomes are monopartite, single-stranded, positive-sense, polyadenylated, and capped RNAs of 27–32 kb.
The 5′ end (~20–22 kb) carries the replicase gene, encoding multiple enzymatic activities.
Replicase gene products: encoded within ORFs 1a and 1b (open reading frames).
Order of structural genes: Pol-S-E-M-N (Polymerase, Spike, Envelope, Membrane, Nucleocapsid).
Additional ORFs encode 2–4 nonstructural proteins of unknown function.
Intergenic sequence (IS): ~7 bases at the 5′ end of each gene, essential for subgenomic RNA formation.
Infected cells contain overlapping subgenomic, capped, and polyadenylated mRNAs.
Each subgenomic mRNA and genomic RNA is translated to produce only the protein encoded by the 5′ gene.

Natural outbreaks of coronavirus-caused colds occur mostly in winter.
Coronaviruses cause 15–30% of all colds.
HCoV 229E, OC43, NL63 are found worldwide.
Contribution of each HCoV varies yearly: e.g., 229E can account for 1%–35% of acute respiratory infections.
Incidence fluctuates: one 3-year study showed 1%–35% infection rates.

Human infection occurs via respiratory secretions.
Attachment: mediated by S glycoproteins binding to host cell receptors.
Entry: fusion of viral envelope with host membrane or receptor-mediated endocytosis.

Fusion: mediated by S2 portion of spike protein (class 1 fusion protein).
Translation of genomic RNA → large polyprotein → processed into RNA-dependent RNA polymerase (RdRp).
RdRp synthesizes a negative-strand RNA, template for nested set of subgenomic mRNAs.
Translation of subgenomic mRNAs → structural proteins.
N protein + genomic RNA → helical nucleocapsids.
Membrane glycoprotein M: inserted into ER, anchored in Golgi apparatus.
Nucleocapsid + M protein assemble at budding compartment (ERGIC).
E and M proteins trigger virion budding, enclosing nucleocapsid.

Primary route of transmission: via the respiratory tract, spread by aerosols and large droplets (e.g., sneezes).
Infection with common-cold coronaviruses causes ciliostasis (loss of ciliary action) and degenerative changes in respiratory epithelial cilia.
Infection is usually localized to the upper respiratory tract because the optimum viral growth temperature is 33–35°C, though it may extend to the lower respiratory tract in some cases.
HCoV-OC43 generally causes mild upper respiratory infections, but may exhibit neuroinvasive properties.

HCoVs in the 229E- and OC43-related serogroups cause upper respiratory symptoms in adults and children, varying in frequency and severity.
Respiratory infections include bronchiolitis and pneumonia; gastroenteritis and neurological disorders can also occur.
In adults, HCoVs usually cause “common colds”, often afebrile.
Symptoms: nasal discharge, malaise, rhinorrhea, headache, chills, sore throat, cough.
Incubation period: 2–5 days.
Duration of symptoms: mean of 7 days (range 3–18 days).
Immune response: rise in neutralizing and complement fixation antibodies, which wane over months.
Lower respiratory tract involvement is rare, but pneumonia may occur.
Asthmatic children may experience wheezing, and adults with chronic pulmonary disease may have worsened respiratory symptoms.
HCoV-OC43 can infect neurons, potentially causing encephalitis.

Molecular detection: RT-PCR for viral RNA.
Electron microscopy (EM): detection in negatively stained stool for enteric coronaviruses.
Serology: complement fixation, ELISA, immunofluorescence, or virus neutralization tests.
Passive hemagglutination test: detects antibodies to strain 229E.
Hemagglutination and acetyl esterase assays: detect HCoV-OC43 virions expressing HE glycoprotein.

Frequent handwashing with soap and water.
Avoid touching eyes, nose, or mouth with unwashed hands.
Avoid close contact with sick individuals.
Cover mouth and nose with a tissue when coughing or sneezing; dispose of the tissue properly and wash hands afterward.