MICROBIOLOGY LECTURE 10: CORONAVIRUSES
A. THE CORONAVIRUSES
General Properties
Coronaviruses are large, enveloped RNA viruses.
Known to cause common colds and may lead to lower respiratory tract infections (e.g., pneumonia) and gastrointestinal infections in infants.
Highest mortality rates observed during the Delta variant due to severe pneumonia caused by these viruses.
Can present with diarrhea, particularly in infants; adults may experience diarrhea during infection, notably during the COVID-19 pandemic.
A novel coronavirus was identified as the cause of a worldwide outbreak of severe acute respiratory syndrome (SARS) in 2003.
Human coronaviruses are difficult to culture, resulting in poorer characterization.
Nucleocapsid: contains RNA and polymerase enzyme.
Figure 1: Structure of SARS-CoV-2
B. GENERAL PROPERTIES
Characteristic: Description
Virion: Spherical, 120-160 nm in diameter with a helical nucleocapsid.
Genome: Single-stranded RNA, linear, non-segmented, positive sense, 27-32 kb, capped, and polyadenylated, infectious.
Proteins: Two glycoproteins and one phosphoprotein; some coronaviruses also contain a third glycoprotein known as hemagglutinin esterase.
Envelope: Contains large, widely spaced, club- or petal-shaped spikes.
Replication: Occurs in the cytoplasm; particles mature by budding into the endoplasmic reticulum and Golgi apparatus.
Outstanding Characteristics:
Causes colds, SARS, and MERS.
Displays a high frequency of recombination (e.g., spike protein changes or mutations).
Difficult to grow in cell culture.
C. CLASSIFICATION
Coronaviridae is one of two families within the order Nidovirales, alongside Arteriviridae.
Classification Characteristics:
Particle morphology
Unique RNA replication strategy
Genome organization
Nucleotide sequence homology
Subfamilies:
Coronavirinae
Torovirinae
Genera in Coronaviridae:
Five genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, Bafinivirus, and Torovirus.
The Alphacoronavirus, Betacoronavirus, and Torovirus primarily include viruses that infect humans.
Toroviruses are widespread in ungulates and are associated with diarrhea.
Figure 2: Characterization and replication cycle of coronaviruses.
Attachment is primarily to the ACE-2 receptor through the glycoprotein.
Following attachment, RNA is released, leading to replication and maturation.
D. TRANSCRIPTION
Unique Biochemical Mechanisms:
Ribosome frameshifting during genome translation.
Synthesis of both genomic and multiple subgenomic RNA species.
The hallmark is the production of subgenomic mRNAs (HE, S, E, M, N, plus non-structural proteins).
These mRNAs are generated from the original RNA genome and contain sequences from both ends.
Mechanism:
Binds to ACE2 receptor Conformational changes occur, altering the plasma membrane, facilitating receptor-mediated endocytosis, pulling the virus into the cytoplasm, resulting in uncoating the genomic RNA (+) remains and is utilized to create RNA-dependent RNA polymerase.
The (+) strand is replicated into (-) strand RNA.
E. REPLICATION
Occurs in the cytoplasm:
Progeny virions are produced via the secretory rough endoplasmic reticulum (RER), Golgi apparatus, and subsequently released through exocytosis.
The host cell machinery, primarily the ribosome, translates the RNA strand into several open reading frames (ORFs).
Figure 3: Coronavirus replication cycle.
Attachment: Virions bind to specific receptor glycoproteins/glycans through the spike protein.
Penetration and uncoating occur via S protein-mediated fusion between the viral envelope and either the plasma membrane or endosomal membranes.
Gene 1 from the viral genomic RNA is translated into a polyprotein, which is then processed to yield the transcriptase-replicase complex.
The genomic RNA serves as a template to create negative-stranded RNAs, which further synthesize both full-length genomic RNA and subgenomic mRNAs.
Each mRNA is translated to produce only the proteins encoded by the 5’ end of the mRNA, including nonstructural proteins (NSPs).
The N protein and newly synthesized genomic RNA assemble to form helical nucleocapsids.
The membrane glycoprotein M is integrated into the endoplasmic reticulum and anchored in the Golgi apparatus.
The nucleocapsid, consisting of the N protein and genomic RNA, binds to the M protein at the budding compartment (ERGIC).
E and M proteins interact to induce the budding of virions, encapsulating the nucleocapsid.
Spike (S) and hemagglutinin esterase (HE) glycoproteins are glycosylated, trimerized, associated with M protein, and incorporated into maturing virus particles.
Release: Virions are released via exocytosis-like fusion of vesicles with the plasma membrane, although some virions may remain attached to the plasma membranes of infected cells.
The entire replication cycle occurs within the cytoplasm.
F. CORONAVIRUS INFECTION IN HUMANS
Pathogenesis:
Coronaviruses demonstrate a tropism for epithelial cells within the respiratory system (RES) and the gastrointestinal tract (GIT).
The SARS coronavirus can also infect epithelial cells lining the salivary gland ducts.
The 2003 SARS outbreak was characterized by significant respiratory illness, including pneumonia and progressive respiratory failure.
The virus has been detected in various organs, including the kidney, liver, small intestine, and stool.
The SARS virus likely originated from a nonhuman host (possibly bats), went through an amplification stage in palm civets, and was transmitted to humans, notably in live animal markets.
Chinese horseshoe bats are known as natural reservoirs for SARS-like coronaviruses.
Figure 5: COVID-19 symptoms.
Clinical Findings:
Common symptoms associated with Coronavirus (COVID-19/SARS-CoV-2) include:
Cough
Shortness of breath or difficulty breathing
Fever or chills
Muscle or body aches
Vomiting or diarrhea
New loss of taste or smell
The incubation period ranges from 2 to 5 days, with symptoms typically lasting about 1 week.
Disease Severity (in patients with confirmed COVID-19):
Non-Severe: Absence of signs of severe or critical disease.
Severe: Oxygen saturation <90% on room air; signs of pneumonia; severe respiratory distress.
Critical: Requires life-sustaining treatment; may involve acute respiratory distress syndrome, sepsis, or septic shock.
Immunity:
The immune response against the surface projection antigen is crucial for protection against infection.
Resistance to reinfection may last for several years; however, reinfections with similar strains are common.
More than 95% of patients with SARS developed an antibody response against viral antigens, detectable using fluorescent antibody tests or enzyme-linked immunoassays (ELISAs).
Laboratory Diagnosis:
Antigen and Nucleic Acid Detection:
COVID-19 antigens can be identified in respiratory secretions via ELISA tests if quality antiserum is available.
Enteric coronaviruses may be detected through stool sample examinations facilitated by electron microscopy.
PCR assays play a significant role in detecting coronavirus nucleic acid in both respiratory and stool samples.
SARS virus RNA was notably detectable in plasma via PCR, especially between days 4 and 8 post-infection.
Isolation and Identification of Virus:
Isolation of human coronaviruses in cell culture remains challenging, but the SARS virus was successfully isolated from oropharyngeal specimens using Vero monkey kidney cells.
Serology:
ELISA, indirect immunofluorescent antibody assays, and hemagglutination tests aid in serological evaluations.
Due to the difficulty of isolating the virus, serodiagnoses using acute and convalescent sera are recognized as practical methods for confirming coronavirus infections.
Serologic identification of strain 229E infections is feasible through passive hemagglutination tests where red blood cells coated with coronavirus antigen agglutinate in the presence of antibody-containing sera.
Figure 6: COVID-19 (SARS-CoV-2) serologic testing process.
The test begins by placing the patient’s blood sample at one end of a test strip (1). The strip contains pads that absorb the blood sample, allowing it to flow via capillary action.
At the initial end, the conjugate pad contains SARS-CoV2 “S” protein attached to colored probes.
If the blood sample holds SARS-CoV2 antibodies, they will tag onto the “S” protein color probes.
As the sample advances along the strip, the colored “S” protein attached to any SARS-CoV2 antibodies will pass a detection line designed for IgM antibodies, with visible color lines appearing in this region if IgM is present (2).
The sample continues towards a detection line for IgG antibodies, operating similarly (3).
A control line confirms that the test functions properly and verifies operational accuracy.
References
Zara, R. (2026). Coronaviruses [PPT].
Riedel, S. et al (2019). Jawetz, Melnick, & Adelberg's Medical Microbiology (28th ed.). New York: Mc Graw Hill.
Ackerman, S. (2020). Research America. Explained: How a COVID-19 Serology Test Works And Obstacles to its Use.