Coronaviruses are named for the solar corona–like appearance (the surface projections) of their virions when viewed with an electron microscope (Fig. 1). Coronaviruses are the second most prevalent cause of the common cold (rhinoviruses are the first) (Fig. 2). Coronaviruses are zoo noses which transitioned to become human viruses. SARS (severe acute respiratory syndrome coronavirus (SARS-CoV, SARS), SARS-CoV-2 and MERS (Middle East respiratory syndrome coronavirus [MERS-CoV]) made the jump more recently to humans to cause outbreaks and serious disease especially in adults. SARS and SARS-CoV-2 originated in China and MERS in the Middle East. In 2019, SARS-CoV-2 became a worldwide pandemic with great potential to cause serious coronavirus disease (COVID-19). SARS and SARS CoV-2 are members of the Betacoronavirus genus and are called sarbecoviruses. Both viruses were endemic in bats before adapting to man. Electron microscopic findings have also linked coronaviruses to gastroenteritis in children and adults (Fig. 3).
Fig1. Electron micrograph of the human respiratory coronavirus (magnification 90,000×) and models of a coronavirus. The viral nucleocapsid is a long, flexible helix composed of the positive-strand genomic RNA and many molecules of the phosphorylated nucleocapsid protein N. The viral envelope includes two or three viral glycoproteins (Spike [S1, S2]), E, possibly hemagglutinin-esterase [HE]), and a matrix protein (M). The S proteins create the appearance of a corona surrounding the virion, when viewed electron microscopically. (Courtesy Centers for Disease Control and Prevention, Atlanta, Georgia. Modified from Fields, B.F., Knipe, D.M., 1985. Virology. Raven, New York, NY.)
Fig2. Human Coronaviruses (blue boxes) include the more human adapted common cold coronaviruses and the more zoonotic and serious disease causing SARS, SARS-CoV-2 and MERS viruses. HCoV, human coronavirus; HKU1, Hong Kong University 1; MERS, Middle Eastern respiratory syn drome; SARS, severe acute respiratory syndrome coronavirus. (Adapted from Cui, J., Li, F., Shi, Z.L., 2019. Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 17(3), 181–192. doi: 10.1038/s41579-018-0118-9. PMID: 30531947; PMCID: PMC7097006.)
Fig3. The SARS-CoV-2 genome and proteins. The infecting (+) RNA genome is initially translated into proteins from two open reading frames (ORF1a, ORF1b) due to a translation frameshift of one nucleotide by the ribosome. Late transcripts are generated from the (-) RNA template used for replication and include individual shorter ORFs for additional proteins. Nsp, non-structural protein; PLpro, protease; 3CL-pro, protease; RdRp, RNA dependent RNA polymerase; Virion proteins: S, spike glycoprotein; E, envelope protein; M, membrane protein, N, nucleocapsid protein. Other (accessory) proteins facilitate replication and escape from innate and immune responses. More in depth descriptions can be obtained in Table 46.1 and the source of this figure. (Modified from Islam, J., Islam, N.N., Alom, S., Kabir, M., Halim, M.A. 2023. A review on structural, non-structural, and accessory proteins of SARS-CoV-2: Highlighting drug target sites. Immunobiology 228 (1) https://doi.org/10.1016/j.imbio.2022.152302.)
STRUCTURE AND REPLICATION
Coronaviruses are enveloped virions with the longest positive (+) ribonucleic acid (RNA) genome (27,000 32,0000 bases). Virions measure 120 nm in diameter. For SARS-CoV-2, the genome encodes 16 non structural proteins (nsp1-16) that provide replicative and accessory functions, four structural proteins (S, E, M, and N) and nine accessory proteins which facilitate replication and immune escape (Table 1 Fig.3). The large plus stranded RNA genome associates with the N protein to form a helical nucleocapsid which is encased in an envelope. Virions contain a trimer of the spike glycoprotein (S), a core nucleoprotein (N), the hydrophobic E protein, a pore forming protein, and the M glycoprotein in addition to the RNA genome. For infection, each S protein of the trimer must be cleaved at the target cell surface into two subunits: S1 viral attachment protein and S2 fusion protein. A modified S protein is included or expressed by SARS-CoV-2 vaccines and elicits neutralizing antibodies. The glycoproteins on the surface of the envelope appear as club-shaped projections and generate a halo (corona) around the virus. The E and M proteins are within the envelope. Unlike most enveloped viruses, the “corona” formed by the glycoproteins allows the virus to endure the conditions in the gastrointestinal tract and be spread by the fecal-oral route.
Table1. SARS-CoV-2 Proteins and Their Functions a,b
Replication of the SARS-COV-2 virus will be described as an example with reference to the other coronaviruses (See (Figs. 3 and 4). The glycoprotein spike (S) protein intiates infection by binding to its receptor. The major receptor is the angiotensin-converting enzyme 2 (ACE-2) receptor expressed on ciliated bronchial epithelial cells, type II pneumocytes, mucoepithelial cells of the GI tract and also vascular epithelium, neurons, lymphocytes, and other cell types allowing the virus to infect many different cells and tissues. Other SARS-CoV-2 receptors facilitate binding and entry to these and other cells. The MERS-CoV uses dipeptidyl peptidase 4 (DPP4; also known as CD26) as receptor, which is also on these cells. The common cold coronaviruses use different receptors. After binding, the S protein must be cleaved by cell surface or endosomal proteases into S1 and S2 to promote fusion of the envelope with cell membranes and release of its genome into the cytoplasm. SARS-CoV-2 binds tighter to its receptor and its S protein is cleaved more readily than for SARS or MERS which enhances its infectivity and ability to infect the upper respiratory tract.
Fig4. Genome and replication cycle for SARS-C0V-2. The glycoprotein spike (S1) protein binds to the angiotensin-converting enzyme 2 (ACE-2) receptor. The S protein is then cleaved by cell surface proteases (transmembrane serine protease 2 [TMPRSS2]) to promote fusion of the envelope with the endosomal membrane to release the genome into the cytoplasm. Translation of the genomic RNA produces two polyproteins (ORF1a, ORF1b) which yield proteases (scissors), the polymerase (RdRp) and other enzymes. These proteins create membrane vesicles associated with the endoplasmic reticulum where sequestered replication and transcription of the RNA take place. A (-)RNA replicative intermediate is generated to replicate the (+) RNA genome (which is also mRNA) and a (-) RNA subgenomic template is also generated for individual mRNAs for late protein structural and accessory pro teins. N protein binds to new genomes, which associate with S, E, and M containing membranes and the virion assembles and buds into endoplasmic reticulum-golgi complex membranes, and then is released from the cell by vesicular endocytic transport. (From Philip V’kovski et.al., Coronavirus biology and replication: implications for SARS-CoV-2, Nature Reviews Microbiology. 19:55–170. https://www.nature.com/articles/s41579-020-00468-6.)
Protein synthesis occurs in two phases, similar to that of the togaviruses. Initially, the infecting (+)RNA genome is translated to produce two polyproteins (open reading frame (ORF)1a, ORF1b) which include two proteases, to cleave the polyprotein into functional proteins; the RNA-dependent RNA polymerase (RdRp); enzymes to apply 5’ methyl guanosine caps to the mRNA; and other accessory enzyme functions. A 3’poly adenosine sequence is also attached to each RNA. Subsequent transcription and replication of the genome occurs within membrane vesicles extended from the endoplasmic reticulum that is created by viral proteins. The polymerase produces and then uses a full length negative-sense (-) template RNA to replicate new positive-sense genomes (which are also mRNA). A shorter template (-)RNA is also generated to produce 10 individual messenger RNAs (mRNAs) for the late structural and accessory proteins. New genomes are encased in the N protein to generate the nucleocapsid and the virion assembles and buds into endoplasmic reticulum-golgi complex (ERG IC) membranes containing the envelope proteins, and then is exocytosed from the cell.
SARS-COV-2, SARS-COV AND MERS-COV
SARS-CoV-2, SARS-CoV, and MERS-CoV are zoonoses. The outbreaks of these viral diseases occurred when the virus in the animal reservoir came in contact with man. These viruses are cytolytic viruses that can replicate at body temperatures in epithelial and other cells. Serious disease results from a combination of viral pathogenesis and immunopathogenesis causing pneumonia and serious multisystem disorder disease.
PATHOGENESIS
Unlike SARS and MERS, SARS-CoV-2 efficiently infects the upper respiratory tract before progressing to the lung and hence requires less viral inoculum and is more readily acquired from aerosols. The greater ability of SARS-CoV-2 than SARS-CoV or MERS-CoV to evade the initiation of types I and III interferon allows the virus to infect and spread to surrounding cells quicker and with less of the initial flu-like symptoms than influenza or other respiratory viruses. The deficit also limits interferon steering of the response towards antiviral immune mechanisms. As a result, individuals may harbor the virus for up to 14 days before serious disease occurs. Individuals with compromised interferon responses are at risk for more extensive disease.
During serious disease, infection and cytolysis of lung epithelium triggers damage associated molecular signals that activate acute phase responses from macrophages. Due to the insufficient initial interferon response, the timing and development of antiviral immunity is delayed and disrupted, including the very important antiviral NK cell and CD8 T cell antiviral responses. This allows the development of a hyper inflammatory cytokine response that recruits and activates neutrophils to the lung to cause pathogenic inflammation and acute respiratory distress syndrome (ARDS) (Fig. 5). The presentation resembles an antibacterial rather than an antiviral response and pneumonia. The hyperinflammatory cytokine response can become systemic and affect multiple organs and systems and initiate life-threatening inflammation. In addition, these inappropriate responses also can induce COVID-19-associated coagulopathy (CAC) leading to endothelial damage, thrombosis and multiorgan failure.
Fig5. Progression of COVID-19 disease with symptomatology. ARDS, Acute respiratory distress syndrome; CRP, C-reactive protein; LDH, lactate dehydrogenase; NT-proBNP, N-terminal pro B-type naturietic peptide, SIRS, systemic inflammatory response syndrome. (Modified from Siddiqi, H.K., Mehra, M.R., 2020. COVID-19 illness in native and immunosuppressed states: A clinical-therapeutic staging proposal. J. Heart Lung Transplant. 39(5), 405–407. DOI: https://doi.org/10.1016/j.healun.2020.03.012)
Peak shedding of infectious virus occurs between 5 and 12 days postinfection, approximately 1 to 2 days before onset of symptoms and continues until 5 to 7 days post-onset. The highest concentration of virus is in nasal secretions followed by sputum in patients who develop pneumonia. Antibody and cell-mediated immunity are detectable approximately 12 days after infection coinciding with the recovery period of a normal infection.
As an RNA virus, SARS-CoV-2 continues to mutate and produce variants of the virus, especially in the S protein. The variants have been selected by herd immunity to evade the antibody elicited in the population to the S protein following infection or vaccination for prior strains. Other changes in replication and disease severity generate variants of differing virulence.
EPIDEMIOLOGY
The SARS outbreak started in November 2002 in South China’s Guangdong Province, was brought to Hong Kong by a physician working within the original outbreak, and then was brought to Vietnam, Toronto, and other places by travelers. The virus was shown to be a coronavirus by its electron microscopic morphology and by RT-PCR. The virus is a bat virus that apparently jumped to man from animals (masked-palm civets, raccoon dogs, and Chinese ferret badgers) raised for food or as pets. A World Health Organization (WHO) global alert prompted containment measures to control the spread of the virus and limited the outbreak to 8000 known diseased individuals, but there were at least 784 deaths. Travel restrictions and public concern resulted in loss of hundreds of millions of dollars in travel and other business.
The SARS-CoV-2 pandemic also originated in China in a similar manner as SARS, but unlike SARS, it spreads more efficiently by aerosols, is spread by individuals who are asymptomatic or have symptoms resembling other respiratory infections, and public health measures were not initiated early enough to restrict its worldwide dissemination. Since 2019, WHO and CDC statistics indicate that there have been 776 million confirmed cases and 7 million deaths (September 7, 2023) worldwide and over 103 million cases and 1.2 million deaths in the United States due to SARS-CoV-2.
SARS-CoV-2 spreads quickly in respiratory droplets, upon exhalation and speaking, and can also be spread on fomites. Its distribution is facilitated by the imperviousness of the coronavirus envelope, which is stable to drying, detergents, and acids. In addition, the virus is spread by asymptomatic individuals making it difficult to limit the dissemination of the disease.
As the adult human population becomes immunized by vaccine or infection, new variants of differing disease severity are being selected, emerging, and spreading through the population. Children are seronegative to previous variants, are susceptible, usually have milder presentations than adults, and maintain the different variants in the population. Due to the stability of the virus in stool, the presence of the virus in inhabitants of a dormitory or a city can be monitored by assaying for viral RNA in sewage.
The highest rates of morbidity and mortality are in people aged 65 years and older. Risk factors other than advanced age include cancer, chronic kidney disease, COPD (chronic obstructive pulmonary disease), immunocompromised state (weakened immune system), obesity (body mass index [BMI] of 30 or higher), hypertension, serious lung or heart conditions, sickle cell disease and type 2 diabetes mellitus. In addition, individuals with ongoing inflammatory processes, indicated by elevated neutrophil to lymphocyte ratios, are also at higher risk to serious disease. The pandemic has identified a significant population that have autoantibodies to type I and III interferons or have defects in the interferon pathways and are at great risk for serious disease.
CLINICAL SYNDROMES
Infection with SARS-CoV-2 is asymptomatic in as many as 40% of individuals or cause symptoms similar to a common cold coronavirus. Initial disease signs of more serious COVID-19 disease include fever, chills, cough, shortness of breath or difficulty breathing, fatigue, muscle or body aches, headache, new loss of taste or smell, sore throat, congestion or runny nose, or gastrointestinal symptoms of nausea, vomiting or diarrhea within 2 to 14 days of exposure. Recovery may occur within a week, as for a common cold, or require several weeks before resolution of the respiratory and fatigue symptoms. Disease can progress through mild respiratory distress to pneumonia, acute respiratory distress syndrome (ARDS), septic shock and multisystem organ failure (especially kidney and heart), coagulopathy, neurological, vascular, and renal complications, and multisystem inflammatory syndrome in adults (MIS-A) or children (MIS-C). Even with mild COVID-19, many patients complain of cognitive dysfunction (brain fog) during and after the disease. The hyperinflammatory disease caused by infection requires both antiviral and anti inflammatory treatments.
Reinfection occurs in many individuals due to either an insufficient IgA or other ineffective antigen-specific response, or exposure to a new variant of SARS-CoV-2. Oftentimes, the symptoms are milder upon reinfection.
A significant number of infected individuals develop “Long-COVID” or Post Acute sequelae of SARS-CoV-2 (PASC) even after mild initial disease. Long-COVID can last for months or years. Symptoms may be an extension of the acute disease or include additional multiorgan problems due to an inability to resolve the virus infection or resultant inflammation and include neurologic, cardiopulmonary and digestive symptoms, such as diarrhea, rash, memory loss, brain fog, headache, or resemble chronic fatigue syn drome. Loss of normal taste and smell sensation may also last for an extended period. People who experienced more severe COVID-19 disease and those who did not get vaccinated are at higher risk for Long-COVID.
The classical form of atypical pneumonia caused by SARS is similar to SARS-CoV-2 and characterized by high fever, chills, rigors, headache, dizziness, malaise, myalgia, cough, or breathing difficulty, leading to acute respiratory distress syndrome. Mortality was at least 10% of symptomatic people. Although SARS is most likely transmitted in respiratory droplets, it is also present in sweat, urine, and feces.
MERS-CoV also causes acute respiratory distress syn drome, with 50% mortality of those identified as infected with MERS. Most of the cases of MERS have occurred in the Arabian Peninsula. Bats are the natural reservoirs and camels are the intermediate host of MERS-CoV.
LABORATORY DIAGNOSIS
For SARS-CoV-2, RT-PCR is the method of choice for detection and strain designation of the viral RNA genome in nasal swabs, saliva, respiratory secretions, and stool samples. Viral antigen is detected in rapid SARS-CoV-2 tests and laboratory ELISA assays. The rapid antigen tests use a lateral flow assay similar in concept to a pregnancy test and can be done at home. Positive RT-PCR results can persist for many weeks beyond detection of virus. Antibody can be detected after the first week and generally peaks 3 to 4 weeks after onset of disease. Care should be used in handling specimens to minimize production of aerosols and contact with contaminated materials. Virus isolation is not routinely performed and should be conducted in a BSL-3 laboratory using BSL-3 practices.
TREATMENT
Treatment of serious COVID-19 disease requires supportive care to ensure breathing and to limit inflammatory disease. Antiviral drugs are available for prophylaxis and mild dis ease but for serious disease, anti-inflammatory treatments as well as antiviral drugs are necessary. Immunosuppressive therapies are directed at limiting the cytokine storm and inflammatory responses that drive ARDS and multisystem organ failure.
Antiviral drugs are available but should be administered as early as possible in the disease course to be effective. Nirmatrelvir co-administered with ritonavir (Paxlovid) combines a viral protease inhibitor with ritonavir to slow metabolism of nirmatrelvir and extend its activity. Remdesivir (Veklury) is a broad-spectrum antiviral drug that targets the viral RNA-dependent RNA polymerase. As an adenosine nucleoside triphosphate analog, the drug is incorporated into the growing RNA chain and then causes termination and decrease in viral RNA production. Molnupiravir is a cytidine nucleoside analogue.
Monoclonal antibodies directed at the viral spike protein (S) are also available to prevent and treat COVID-19. They include Sotrovimab, Bamlanivimab plus etesevimab and Casirivimab plus imdevimab (known as REGEN-COV). These treatments may not be effective against newer SARS CoV-2 variants due to changes in the antigenic epitopes of the S protein and have limited usage.
PREVENTION AND CONTROL
Limiting respiratory dissemination and exposure restricts the transmission of SARS-CoV-2. During the height of the pandemic and prior to extensive vaccine usage, recommendations were for social distancing, avoidance of large gatherings of people and to wear masks in public. Masks, especially N95 or KN95 masks, restrict the spread and acquisition of SARS-CoV-2 and other respiratory viruses.
Home and laboratory antigen screening tests for SARS CoV-2 are available. Laboratory nucleic acid amplification tests are more sensitive and more likely to detect virus earlier and more dependably. Untreated wastewater from dormitories, hospitals, prisons, other buildings and cities can be screened for the presence and type of virus.
The CDC recommends that individuals who test positive for COVID-19 or have symptoms should undergo an isolation period lasting at least 5 days beyond the symptoms. Individuals who have been exposed to an individual who then tests positive for COVID-19 should wear a mask for up to 10 days and be tested after 5 days.
Vaccinated individuals are less likely to be infected or have serious disease. Several different types of vaccines are available to prevent infection and serious COVID-19 disease. mRNA vaccines incorporate a modified genomic sequence of the S protein to produce the protein locked in its pre fusion conformation and also use N-methylpseudouridine (like in transfer RNAs) instead of uridine to stabilize the RNA and limit interferon activation and undesirable side effects. The RNA is administered in a cationic lipid vesicle which also acts as an adjuvant. These vaccines initiate the synthesis of the glycoprotein in cells, elicit T cell and antibody responses, and are very effective. Also approved are the adjuvanted, modified S protein trimer containing particles. Hybrid adenoviruses incorporating the sequence modified gene for S protein and inactivated SARS-CoV-2 virion vaccines are also administered, worldwide. Vaccines are updated to incorporate the S protein gene or protein of the most recent virus variant and are suggested as booster immunizations to protect against infection with previous and latest variants.
The virus is disrupted by ethanol (>70% ) hand cleaners, rigorous hand washing and bleach.
COMMON COLD CORONAVIRUSES
The most common cold coronavirus is HCoV-229E. The common cold coronaviruses have an optimum temperature for viral growth of 33°C to 35°C; therefore infection remains localized to the upper respiratory tract. They cause cytolytic infections and infect and disrupt the function of ciliated epithelial cells.
The virus is spread by aerosols and cause an upper respiratory tract infection, accounting for approximately 10% to 15% of upper respiratory tract infections in humans. The disease is similar to the common cold caused by rhinoviruses but with a longer incubation period (average, 2–5 days) and disease lasting from 2 to 18 days. Symptoms include malaise, headache, sneezing, rhinorrhea, and sore throat and possibly fever and cough. The infection may exacerbate a preexisting chronic pulmonary disease, such as asthma or bronchitis, and on rare occasions may cause pneumonia.
Infections occur mainly in infants and children but reinfection can occur later in life. Coronavirus disease appears either sporadically or in outbreaks in the winter and spring. Usually, one strain predominates in an outbreak. Antibodies to coronaviruses are uniformly present by adulthood and ameliorate disease.
Coronavirus-like particles have also been seen in electron micrographs of stool specimens obtained from adults and children with diarrhea and gastroenteritis and in infants with neonatal necrotizing enterocolitis.
Laboratory tests are not routinely performed to diagnose common cold coronavirus infections.
