Severe Acute Respiratory Syndrome Coronavirus 2: Manifestations of Disease and Approaches to Treatment and Prevention in Humans

Abstract

The coronavirus disease 2019 (COVID-19) pandemic was caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus has challenged civilization and modern science in ways that few infectious diseases and natural disasters have previously, causing globally significant human morbidity and mortality and triggering economic downturns across financial markets that will be dealt with for generations. Despite this, the pandemic has also brought an opportunity for humanity to come together and participate in a shared scientific investigation. Clinically, SARS-CoV-2 is associated with lower mortality rates than other recently emerged coronaviruses, such as SARS-CoV and the Middle East respiratory syndrome coronavirus (MERS-CoV). However, SARS-CoV-2 exhibits efficient human-to-human spread, with transmission often occurring before symptom recognition; this feature averts containment strategies that had worked previously for SARS-CoV and MERS-CoV. Severe COVID-19 disease is characterized by dysregulated inflammatory responses associated with pulmonary congestion and intravascular coagulopathy leading to pneumonia, vascular insults, and multiorgan disease. Approaches to treatment have combined supportive care with antivirals, such as remdesivir, with immunomodulatory medications, including corticosteroids and cytokine-blocking antibody therapies; these treatments have advanced rapidly through clinical trials. Innovative approaches to vaccine development have facilitated rapid advances in design, testing, and distribution. Much remains to be learned about SARS-CoV-2 and COVID-19, and further biomedical research is necessary, including comparative medicine studies in animal models. This overview of COVID-19 in humans will highlight important aspects of disease, relevant pathophysiology, underlying immunology, and therapeutics that have been developed to date.

In December 2019, a cluster of cases of pneumonia without a clear etiology occurred in Wuhan, China. With remarkable speed and efficiency, the etiology of this illness was soon identified as a novel coronavirus; the complete viral genome was sequenced and published on January 10, 2020.¹⁸² These events introduced the world to coronavirus disease 2019 (COVID-19). The disease, now known to be caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has developed into the most significant pandemic of recent times. In less than a year since the virus was first recognized, multiple candidate vaccines were developed worldwide, and some of them rapidly progressed to clinical trials and widespread administration. As the pandemic continues, a number of sequence variants of the virus have emerged around the world. This continued viral evolution highlights the need for continued biomedical research to facilitate understanding of the pathogenesis of COVID-19, seeking innovative therapeutic and preventative strategies for the current and possibly future pandemics. This article will review aspects of SARS-CoV-2 infection of humans and COVID-19, focusing on important aspects of clinical disease, pathophysiology, immunology, and the development of therapeutic and preventative measures to provide context for discussion of the animal models used to study SARS-CoV-2 and COVID-19.

Clinical Aspects of COVID-19

Essential Virology.

COVID-19 is caused by the novel coronavirus, SARS-CoV-2.¹⁸² Coronaviruses belong to the family Coronaviridae (subfamily Coronavirinae), which are large, enveloped, single-stranded, positive-sense RNA viruses that infect a broad range of host species. SARS-CoV-2 is one of 7 recognized human coronaviruses (HCoV), including human coronavirus 229E (HCoV-229E), HCoV-NL63, HCoV-OC43, HCoV-HKU1, severe acute respiratory syndrome coronavirus (SARS-CoV), and Middle East respiratory syndrome coronavirus (MERS-CoV). Most of the coronaviruses are associated with relatively mild upper respiratory tract infections similar to the common cold. SARS-CoV and MERS-CoV are notable exceptions, with previous outbreaks resulting in high rates of human mortality in 2002 and 2012, respectively. SARS-CoV-2 is genetically distinct from SARS-CoV and MERS-CoV, with approximately 80% and 50% similarity, respectively.⁹⁴ Evidence suggests a likely phylogenetic origin from bat coronaviruses, and a possible zoonotic transfer to humans through intermediate hosts, including the Malayan pangolin.^94,186

Viral Transmission.

As the COVID-19 epidemic evolved, it became evident that SARS-CoV-2 was capable of efficient human-to-human transmission, a key feature distinguishing it from SARS-CoV and MERS-CoV. Both SARS-CoV and MERS-CoV were limited to relatively regional outbreaks, perhaps due to their transmissibility peaking after symptom onset, when most patients were already isolated in hospital settings.²⁰⁰ In contrast, SARS-CoV-2 spread beyond the regional outbreaks achieved by SARS-CoV and MERS-CoV and caused a global pandemic, in part because it can be transmitted before symptoms develop.⁵⁶ A study of familial clusters found an incubation period is 2 to 11 d, with a mean incubation period of 6.4 d.⁷ The viral load peaks in the respiratory tract around the time of symptom onset, and viral RNA can be detected in the upper respiratory tract for a mean of 17 d and for up to 12 wk after the onset of symptoms.²⁵ Transmission of virions from epithelial shedding may begin 2 to 3 d before the symptoms, contributing to spread from presymptomatic carriers (asymptomatic individuals who later develop symptomatic disease).^56,170,195 Viral transmission leading to infection seems to be relatively short-lived. Viable SARS-CoV-2 is generally no longer detectable by viral culture 9 d after the onset of symptoms despite PCR-positivity, and transmission to others seems to last no longer than about 5 d after symptom onset in an index case.^30,178 Presymptomatic carriers who transmit the virus are believed to have contributed significantly to early outbreaks in China and elsewhere, as individuals were infectious before their illness had become clinically apparent.¹⁷⁰ However, debate remains about the role of viral transmission by asymptomatic individuals. While asymptomatic individuals have been reported to transmit SARS-CoV-2, transmission is less efficient from asymptomatic carriers than from symptomatic cases.^42,88 Even with lower transmission efficiency, a modeling study suggests that individuals without symptoms cause over half of new SARS-CoV-2 infections,⁶⁸ suggesting the need for additional investigation into the mechanisms of viral transmission by using relevant animal models.

SARS-CoV-2 is primarily transmitted from person to person by respiratory droplets that are discharged during talking, coughing and sneezing and by direct contact with nasal, conjunctival, or oral mucosa.¹⁵⁰ Prolonged exposure, defined as being within 6 feet of an infected individual for at least 15 min, has been associated with higher rates of SARS-CoV-2 transmission from respiratory droplers.³³ Indoor exposure through household contacts or gatherings of family and friends substantially is associated with higher transmission efficiency as compared with outdoor exposure.²⁴ Transmission via smaller droplets that remain suspended in the air (often called droplet nuclei) is referred to as airborne transmission. Airborne transmission has been demonstrated in controlled environments, but current data are not insufficient to determine the importance of airborne transmission in SARS-CoV-2 transmission.^4,84 The potential for fomite transmission from an inanimate surface also exists, as SARS-CoV-2 remains viable for many days on contaminated surfaces such as glass, stainless steel, and plastic. However, the importance of this route of transmission is thought to be minimal.^31,157 Finally, vertical transmission from pregnant women to the developing fetus in utero seems uncommon and has not been associated with significant clinical effects on the fetus.^37,77,192

Viral Attachment and Tissue Tropism.

The SARS-CoV-2 spike (S) protein, specifically the S₁ subunit, contains the receptor binding domain (RBD) that binds to the peptidase-domain of the angiotensin-converting enzyme 2 (ACE2) receptor.^58,189 The S protein is cleaved by the host cell type 2 transmembrane serine protease (TMPRSS2), and is then primed for infection.⁵⁸ The distribution of ACE2 and TMPRSS2 partially dictates the tissue tropism of the virus. The expression of both proteins is particularly abundant in respiratory, conjunctival, and gut epithelial cells.¹⁵⁰ Among the respiratory epithelial cells, nasal goblet cells and ciliated cells in the airway show exceptionally high surface ACE2 expression levels, possibly contributing to viral transmission by respiratory droplets.¹⁵⁰ However, although these studies suggest cellular susceptible to infection (that is, these cells have the receptors needed for entry), the permissiveness of different cell types to viral replication is another crucial factor in determining cellular tropism and requires further research.

COVID-19 Pathogenesis and Inflammation.

SARS-CoV-2 infects pulmonary capillary endothelial cells throughout the respiratory epithelium.¹⁸⁸ Circulating monocytes, pulmonary neutrophils, and alveolar macrophages respond by releasing proinflammatory cytokines, recruiting additional immune cells and promoting congestion. Activation of the bradykinin cascade further promotes inflammatory infiltrates and lung angioedema.^156,188 As the inflammatory response increases, pulmonary edema develops in alveolar spaces and form hyaline membranes, impairing oxygen exchange across the alveolar wall and the capillary and causing the development of acute respiratory distress syndrome (ARDS). Pathology specimens from lung biopsy and autopsy examinations demonstrate diffuse alveolar damage, thickening of the alveolar wall, cellular fibromyxoid exudate, hyaline membranes, and desquamation of pneumocytes.¹⁸⁸ Altogether, disruption of the endothelial barrier and impaired oxygen diffusion across the alveoli into the bloodstream is the hallmark feature of severe COVID-19 pathology.

The hyperinflammatory response generates systemic consequences, with proinflammatory cytokine mediators enhancing the expression of endothelial cell adhesion molecules.^72,141 This, in turn, promotes more inflammatory cell infiltration and vascular congestion, leading to endothelial cell damage and microthrombi formation. This hypercoagulable condition contributes to the high number of COVID-19 cases with deep venous thrombosis, pulmonary embolism, and arterial thromboses, which in turn precipitate myocardial and cerebrovascular ischemia.^76,152 Disseminated intravascular coagulation and end-organ injury follow. Multiorgan failure and the development of sepsis are the most severe manifestations of COVID-19.

Clinical Disease.

Infection with SARS-CoV-2 and the ensuing COVID-19 can present with multiple signs and symptoms (Table 1). The signature and major manifestation of COVID-19 is pneumonia with multiorgan disease. However, SARS-CoV-2 infection may be asymptomatic or may present with relatively mild upper respiratory tract infection. Initial symptoms of COVID-19 can include fever, dry cough, shortness of breath, fatigue, myalgias, nausea/vomiting/diarrhea, headache, and weakness.^44,75,122 Loss of smell (anosmia) and taste (ageusia) may be the only presenting symptoms in a minority of infected individuals.¹⁴²

Table 1.

Clinical spectrum of COVID-19 human infection

Clinical spectrum	Description
Asymptomatic or presymptomatic	Absence of clinical symptoms, but some may have objective radiographic findings on chest imaging consistent with COVID-19 infection
Mild	Dry cough, myalgias, headache, nausea, diarrhea, sore throat, abnormalities of smell or taste, fever
Moderate	As above, plus shortness of breath and mild tachypnea, fever, may have evidence of pneumonia on chest imaging
Severe	As above, plus respiratory distress with dyspnea, tachypnea, and significant hypoxia requiring supplemental oxygen
Critically ill	As above, plus respiratory failure, cardiac dysfunction, exaggerated inflammatory response, exacerbation of underlying comorbidities, sepsis and shock with multi-organ dysfunction (e.g., cardiac, hepatic, renal, CNS, or thrombotic disease)

Patients with severe COVID-19 that requires hospitalization often have significant comorbidities, such as hypertension, diabetes mellitus, cardiovascular disease, chronic pulmonary disease, chronic kidney disease, malignancy, and chronic liver disease.^49,122 Complications of severe COVID-19 among hospitalized patients may include pneumonia, ARDS, acute liver injury, myocardial injury, coagulopathy and thrombotic complications, neurologic manifestations, and multiorgan failure with shock.¹⁷⁵ Myocarditis, cardiomyopathy, and arrhythmias can also occur and can result in long-lasting effects on hemodynamic stability.⁹² Neurologic manifestations may include aseptic meningitis, encephalitis, and cerebrovascular disease.⁹⁹

Children and adolescents have consistently accounted for a minority of laboratory-confirmed cases of COVID-19 for reasons that are not entirely clear. At least early in the pandemic, less than 5% of confirmed cases occurred in individuals younger than 18 y of age.⁷⁵ In general, children have fewer and milder symptoms than adults, have fewer complications, and are less likely to be hospitalized with severe COVID-19. One possible theory accounting for this difference is that children have fewer ACE2 viral receptors to permit SARS-CoV-2 infection. Gene expression of ACE2 in the nasal epithelium varies with age, with the lowest gene expression being found in younger children and rising significantly in older children and on into adulthood.¹⁸ Other potential explanations for relatively mild disease severity as compared with adults may be that children are less likely to have a robust proinflammatory cytokine response, may have partial immunity provided from other coronavirus infections, and overall have less exposure to SARS-CoV-2 outside of the home.⁷⁵ Most pediatric cases are mild, but a small percentage of children (<7%) develop severe infection requiring hospitalization and mechanical ventilation.⁴⁸

Laboratory and Radiographic Abnormalities.

Measurement of blood cell counts and inflammatory markers in patients with COVID-19 may be informative regarding the severity of infection, with the degree of laboratory abnormality correlating with the severity of the disease.^44,75 During acute infection, patients may have leukocytosis or, more commonly, leukopenia with lymphopenia. Mild thrombocytopenia is common, and in association with prolonged prothrombin time and elevated D-dimer, it suggests active coagulopathy. Laboratory markers of inflammation such as serum C-reactive protein and erythrocyte sedimentation rate are typically elevated. Serum albumin levels are frequently low, while levels of LDH, AST, and ALT are often elevated.¹²⁷

Over half of patients hospitalized with severe respiratory disease have chest X-ray results demonstrating bilateral lung infiltrates that are consistent with pneumonia.¹²⁷ Chest CT typically reveals characteristic diffuse, ground-glass opacities in the peripheral chest, air bronchograms, interlobular or septal thickening, and thickening of the adjacent pleura.¹³⁸ Radiographic findings in the chest can be nonspecific yet in some cases be completely normal early in the course of illness. Negative findings can potentially contribute to a false sense of normalcy, but chest radiography can rapidly change as clinical status deteriorates during the first 2 wk of illness.¹⁴

Post-Infectious Sequelae.

Some COVID-19 survivors continue to exhibit a variety of symptoms for extended periods after recovery from their acute illness. A post-COVID-19 illness, or “long COVID Syndrome,” has been reported in which patients continue to have fatigue, headaches, cognitive impairment or “brain fog,” intermittent fevers, myalgias, and joint pains for many weeks to months after acute illness resolves.^{10,11,21,60,139} Symptoms can be relapsing and remitting over time. The mechanism(s) underlying these postinfectious sequelae are not well understood, but they may relate to the hyperinflammatory response and immune dysregulation triggered by infection.¹¹ In addition, a multisystem inflammatory syndrome in children (MIS-C) has been described in a small number of children several weeks after infection with SARS-CoV-2.^83,159 Children with MIS-C have prolonged fevers and at least 2 additional symptoms, including rash, conjunctivitis, mucocutaneous inflammation, hypotension, cardiac disease, coagulopathy, or acute gastrointestinal symptoms.^83,191 Children undergoing evaluation for MIS-C are rarely PCR-positive for SARS-CoV-2, but frequently have detectable SARS-CoV-2-specific IgG, suggesting that infection in the preceding weeks may have triggered an aberrant hyperinflammatory response.^129,191 Treatment for MIS-C is focused on decreasing systemic inflammation by using modalities that include intravenous immune globulin (IVIG), corticosteroids, and other immunomodulatory therapies targeting proinflammatory cytokines (for example, inhibitors of TNF, IL1, or IL6).^83,159

Effects of SARS-CoV-2 Genetic Variants on Transmission and Disease.

Multiple SARS-CoV-2 variants with S protein mutations have been identified, such as the B.1.1.7 (501Y.V1) variant first detected in the United Kingdom and the B.1.351 (501Y.V2) variant first reported in South Africa, and more are likely to emerge in the future.^74,153 Information regarding the effects of these and other mutations on transmission and disease continues to accumulate as variants are identified and tracked across the world. Existing data suggest that variants such as B.1.1.7 promote transmissibility, potentially due to alterations in interactions between the S protein and ACE2.^38,53,59,144 Some data suggest that variants such as B.1.1.7 may be more likely to cause severe disease, although others have not found such an effect.³⁸ Additional information is clearly needed to better define how potential mutations will influence the severity of disease pathology.

Host Immune Responses to SARS-CoV-2 Infection

Appropriate innate and adaptive immune responses are essential for controlling acute viral infection and for protection against future challenges with the same, or related, pathogens. However, dysregulated host inflammatory responses are also likely to contribute to disease. A disruption of the careful balance between these protective and harmful factors likely contributes to many clinical manifestations of severe COVID-19. Targeting general aspects of inflammation or specific inflammatory mediators may be clinically beneficial. Information about inflammatory and immune responses to SARS-CoV-2 has accumulated at a rapid pace; Key host responses to SARS-CoV-2 infection include type I interferons (IFNs), multiple proinflammatory cytokines, and components of the adaptive immune response such as T cells and antibody production.

Cytokine Responses to SARS-CoV-2.

IFNs ↑ and ↓ (type I IFNs) are critical components of the innate immune response and can inhibit the replication of a wide variety of viruses, including in vitro SARS-CoV-2 replication.^16,91 However, minimal and delayed type I IFN production has been detected after infection of cultured cells with SARS-CoV-2 in vitro and in patients with COVID-19.^16,101 As a group, coronaviruses have evolved multiple ways to modulate and evade IFN production, signaling, and effector function (reviewed in¹¹³). The use of similar evasive mechanisms by SARS-CoV-2 is an important aspect of COVID-19 pathogenesis; type I IFN responses are likely to be important for controlling viral infection and limiting immunopathology during SARS-CoV-2 infection. Inadequate type I IFN responses in patients with severe COVID-19 are associated with persistent SARS-CoV-2, enhanced inflammation.⁵⁵ Mutations in IFN signaling pathways are more common in patients with severe COVID-19 as compared with patients who develop less severe disease or asymptomatic infection.¹⁹⁴ Studies such as these suggest that an impaired type I IFN response may allow increased viral replication and an ensuing exaggerated inflammatory response.

Multiple reports document vigorous inflammatory responses in patients with COVID-19. characterized by upregulation of multiple proinflammatory cytokines, chemokines, and other mediators – similar to the “cytokine storm” described in other conditions such as ARDS and sepsis.¹⁷³ High levels of circulating IL-6, IFN-↖, and TNF are common findings in patients with COVID-19, as is the upregulation of a wide variety of other cytokines (for example, IL1↓, IL1RA, IL2, IL2R, IL7, IL10, IL12p70) and chemokines (for example, CCL2, CCL3, CCL7, CCL8, CXCL2, CXCL8, CXCL9, CXCL10, CXCL16).^{16,27,78,93,107,141,176} The degree of cytokine induction correlates with COVID-19 severity.^{61,93,118,163} The mediators are produced by multiple types of structural and immune cells and are likely to contribute to host pathology. They also recruit other types of immune cells such as neutrophils, monocytes, NK cells, and T lymphocytes, which further contribute to immune-mediated protection and/or disease.

T Cell Responses to SARS-CoV-2.

Lymphopenia is a characteristic finding in COVID-19, with decreased numbers of total T cells and CD4 and CD8 T cells during acute disease and convalescence.^{20,26,27,61,110,118,135,173,193} The magnitude of the lymphopenia correlates with disease severity.^110,118,187 Virus-specific CD4 and CD8 T cells can be identified in hospitalized patients during acute COVID-19¹⁷³ and are present in the vast majority of convalescent patients after the resolution of symptoms.^52,114 T cell responses are directed against a wide array of structural proteins, including the S protein and nonstructural viral proteins, with some data suggesting an increased breadth of T cell responses in individuals with severe disease.^{52,114,135,173} Patients with COVID-19 also develop activation of unconventional T cells, including mucosa-associated invariant T, ↖↗T, and invariant NKT (iNKT) cells.⁶⁹ T cell activation during COVID-19 is greater in women than in men¹⁵¹ but is lower in children as compared with adults.¹¹⁵ Memory CD4 and CD8 T cells that recognize SARS-CoV-2 can be detected in many individuals for at least 6 mo after infection.³⁶

T cells are likely to be important in developing protective immune responses to SARS-CoV-2 infection, but they may also contribute to immune-mediated manifestations of disease. A substantial amount of work is still needed to fully characterize the contribution of T cells to the pathogenesis of SARS-CoV-2 infection and COVID-19 in humans and to define the importance of T cell function for the development of vaccines. Virus-specific T cells are crucial to the clearance of other HCoV such as SARS-CoV and MERS-CoV,^197,198 and some research has already begun to document protective roles of T cells in SARS-CoV-2 infection. For example, T cells are necessary for SARS-CoV-2 clearance in a mouse model,¹⁴⁹ and CD8 T cell depletion impairs protective immunity after rechallenge of convalescent rhesus macaques.¹⁰⁴ SARS-CoV-2-reactive T cells have been detected in healthy humans without a history of SARS-CoV-2 infection,^17,52,81,173 suggesting cross-reactivity with endemic human coronaviruses can to modify susceptibility to SARS-CoV-2 infection or alter the course of COVID-19. However, those possibilities have not yet been proven.

Antibody Responses to SARS-CoV-2.

SARS-CoV-2-specific antibodies are detected within the first 1 to 2 wk after symptom onset in most infected individuals. IgG, IgM, and IgA specific to the full-length SARS-CoV-2 S protein and to the S protein’s RBD can be detected, as can antibodies recognizing other SARS-CoV-2 proteins such as the nucleocapsid protein.^129,172 A high proportion of anti-RBD antibody blocks interactions with ACE2,¹⁹ and neutralizing antibody is detected in most COVID-19 patients.^{27,110,118,124,164,172} Levels of virus-specific antibodies tend to correlate with both proinflammatory cytokine levels¹⁶⁴ and disease severity.^{27,93,96,118,119,148} The duration of antibody-mediated protection has not yet been fully defined. Some reports suggest a relatively rapid decline of antibody titers, particularly after mild disease,^63,136 in a manner consistent with short-lasting protective immunity to seasonal coronaviruses.⁴⁰ Other data indicate that IgG responses, neutralizing antibody titers, and S-specific memory B cells persist for 5 mo or more after symptom onset,^36,64,65,161 and the presence of anti-S and antinucleocapsid antibodies reduces the risk of SARS-CoV-2 reinfection.⁹⁵ Virus-specific antibody production has been detected in children, although the breadth of antibody response and neutralizing antibody activity is lower in children than in adults.^129,172 Levels of virus-specific antibody are higher in children with MIS-C than in children with acute infection and COVID-19.¹²⁹ The reason for that difference remains unclear, but it may relate to the presumed delayed timing of MIS-C after acute SARS-CoV-2 infection.

Therapy and Prevention

Patients with mild COVID-19 are primarily managed by supportive care. However, as the pandemic evolves and adverse outcomes are increasingly reported, a number of therapeutic agents with a wide range of reported efficacy have been proposed and used. Antiviral agents and antiviral antibodies (for example, monoclonal antibodies, convalescent plasma) acting directly against SARS-CoV-2 may be intuitive and attractive as therapeutic/preventive modalities, whereas immunomodulatory agents have drawn attention as the role of a hyperactive host immune response in COVID-19 pathogenesis of COVID-19 becomes more apparent.

While treatment of SARS-CoV-2 patients is important, prevention of infection is crucial for controlling the pandemic, given substantial mortality and morbidity associated with COVID-19 even after treatment. Nonpharmaceutical interventions can range from personal-level measures such as physical distancing, wearing masks, and adherence to hygienic principles to community-level measures, including the closure of businesses, schools, and public services, which curtail the spread of the virus. However, a resurgence of outbreaks has been widely observed, even in areas that appeared to have controlled the epidemic. Thus, population immunity via immunization is desired for controlling the pandemic, and vaccines based on various platforms have been developed.

Therapeutic Interventions.

Directly Acting Antiviral Agents.

Remdesivir Remdesivir (GS-5734) is a monophosphate prodrug of an adenosine analog (GS-441524) that inhibits viral RNA-dependent RNA polymerase. GS-441524 was known to exhibit broad-spectrum in vitro antiviral activity against viruses including hepatitis C virus, yellow fever virus, dengue virus serotype-2, influenza A virus, parainfluenza 3 virus, and SARS-CoV.³² The prodrug version (GS-5734, or remdesivir) generates high intracellular levels of GS-441524-triphosphate, and also has in vitro activity against viruses including Ebola virus, RSV,¹⁶⁹ Nipah henipavirus,⁸⁹ and a wide range of epidemic and zoonotic coronaviruses.¹³⁷ A randomized controlled trial conducted between 2018 and 2019 during an Ebola virus outbreak provided human safety data, although efficacy was less robust than that of monoclonal antibodies.¹⁰⁶

Remdesivir’s ability to inhibit SARS-CoV-2 replication in cell culture (Vero E6 cells) was reported within several months of the identification of the virus.¹⁶⁵ Observational studies suggested some promise of the therapeutic use of remdesivir,⁵⁰ but larger randomized controlled trials provided more definitive data on its efficacy,^13,143 indicating that remdesivir shortens the time to recovery in adults with COVID-19 and lower respiratory tract infections.^13,143 In one of these studies, recovery time was 10 d in the remdesivir arm and 15 d in the placebo arm,¹³ and in the other study, those in the remdesivir arm (5 d of therapy) had higher odds of a better clinical status.¹⁴³ Effects on mortality did not reach statistical significance in either of these studies; the point estimate was slightly lower in the remdesivir arm in one study,¹³ and was essentially the same in each arm in the other study.¹⁴³ No statistically significant differences in clinical status were found between those receiving 10 d of remdesivir compared with standard care.¹⁴³ Thus, remdesivir may have some clinical efficacy in the treatment of COVID-19, theoretically more so in the early phase of the disease, but does not have a robust effect, despite the enthusiasm driven by its strong antiviral effects observed in vitro. Nonetheless, the medication has been incorporated into various treatment guidelines based on these data, primarily in those with severe disease requiring oxygen support.^{109,125,152,177} Another randomized trial that compared remdesivir plus baricitinib (a Janus kinase inhibitor) to remdesivir alone showed that the combination had a superior effect on time to recovery, with no clear mortality benefit.⁷¹ The World Health Organization (WHO) SOLIDARITY trial reported little or no effect on mortality, initiation of ventilation, or length of stay associated with remdesivir,¹⁷⁴ and the WHO has made a conditional recommendation against using remdesivir in clinical settings.¹⁸⁰

Other Agents with Potential Antiviral Activity.

Hydroxychloroquine and chloroquine have been used as antimalarial and antiinflammatory agents. Early in the pandemic, these agents were found to have in vitro activity against SARS-CoV-2.¹⁶⁵ These agents, particularly hydroxychloroquine, had been used in clinical settings (although the patient populations and indications were quite different), and it rapidly gained popularity as a treatment modality. A number of observational studies on these agents were conducted, and one reported viral load reduction based on a cohort of 36 patients.⁴⁵ The study also reported that the addition of the antibiotic azithromycin might further promote viral load reduction. A larger observational study even suggested mortality benefit.⁶ However, subsequent randomized controlled studies found no benefit of hydroxychloroquine, with or without azithromycin.^22,174 The case of hydroxychloroquine underscores the importance of randomized clinical trials in seeking therapeutic agents against novel pathogens.

Immunomodulatory Agents.

Corticosteroids

The use of corticosteroids in the setting of infection may be counterintuitive given its immunosuppressive effects. However, this class of medications has been used as part of treatment for various infectious diseases,¹⁰³ attempting to control the excessively upregulated inflammatory responses triggered by infections. Corticosteroids were often used during the SARS and MERS epidemics, but their clinical benefit was never proven.^5,145 Given this lack of definitive proof of efficacy, corticosteroid therapy was not favored at the beginning of the SARS-CoV-2 pandemic.¹³⁰ However, in a randomized, open-label controlled trial, dexamethasone was subsequently shown to reduce deaths in patients requiring respiratory support.¹²⁰ The mortality benefit was more substantial among those with severe disease requiring mechanical ventilation. Conversely, individuals not receiving respiratory support showed no benefit, as statistical significance was not achieved. These results suggest that excessive inflammatory responses may drive COVID-19 morbidity and mortality, whereas virus replication itself may be less important in the disease process. Mitigation of the host response is therefore likely to be crucial in improving outcomes. Most clinical guidelines currently recommend the use of corticosteroid in treating severe COVID-19.^15,109,180

Tocilizumab

Several early studies from China reported higher IL6 levels among those with severe disease or fatal outcomes.^181,199 Another study found that levels of IL6 correlated inversely with the cytotoxic potential of natural killer cells in humans,¹⁰² and the IL6 signaling may contribute to endothelial dysfunction.⁷² Tocilizumab, a humanized monoclonal antibody against the IL6 receptor, became the subject of widespread empirical use and investigational studies. Tocilizumab had been used for treatment of various autoimmune disorders,^98,147,190 but had not been used to treat inflammation caused by infections. Case reports and observational studies suggested its efficacy in the treatment of COVID-19.^{54,100,108,117,126,154} Initial randomized trials showed no mortality benefit, although an effect on progression of the disease in the early phase of the infection could not be excluded.^{57,133,134,146} A trial enrolling critically ill patients who required respiratory or cardiovascular organ support and were receiving dexamethasone treatment demonstrated increased survival at 90 d with IL6 inhibition (tocilizumab and sarilumab).¹²¹ Thus, treatment guidelines include the use of tocilizumab in combination with corticosteroids for treating critically ill COVID-19 patients.^15,109

Other Immunomodulatory Agents

Anakinra, which is an IL1 receptor antagonist, has been evaluated in observational studies for possible beneficial effects on clinical outcomes, but a randomized trial comparing its effect to usual care did not show improved outcomes.^23,34,62 Fluvoxamine, which is a selective serotonin reuptake inhibitor that is widely used as an antidepressant, was associated with a lower likelihood of clinical deterioration in a double-blind, randomized placebo controlled trial that enrolled 152 nonhospitalized SARS-CoV-2 infected participants.⁸² Fluvoxamine has high affinity for the signa-1 receptor, an endoplasmic reticulum chaperone protein with various cellular functions including regulation of cytokine production and modulation of the inflammatory response.¹²⁸ Determining the usefulness of this class of agent in COVID-19 treatment will require additional research.

Passive Immunotherapy.

Convalescent plasma

Providing passive immunity to patients by treating them with plasma of patients who have recovered from the same diseases has been used to treat patients for more than 100 y, and has been evaluated and used for treatment of various infectious diseases such as influenza,¹² and Ebola virus.¹⁵⁸ Convalescent plasma was used extensively for patients with COVID-19, even before substantial evidence of clinical benefit became available. Subsequent randomized trials have not shown benefit in time to clinical improvement or mortality rates in patients with severe COVID-19,^93,140 although plasma with higher antibody titers may be more effective than lower titer plasma.⁷⁰ Conflicting results have been reported with regard to its effect on disease progression in SARS-CoV-2 infected individuals. One trial enrolling older adults with mild COVID-19 (within 3 d of symptom onset) showed reduced progression of disease after receiving convalescent plasma,⁸⁵ but another study enrolling adults with moderate COVID-19 did not prevent disease progression.² Existing clinical guidelines have not definitively recommended treatment with convalescent plasma.^15,109,180

Antiviral monoclonal antibodies

When patients with mild to moderate COVID-19 early in the course of infection (within 3 days of positive SARS-CoV-2 test) were treated with bamlanivimab (formerly known as LY-CoV555 or LY3819253), a monoclonal neutralizing antibody that binds to the SARS-CoV-2 S protein RBD, the decline in SARS-CoV-2 viral load was significantly faster as compared with patients receiving placebo; however, a substantial decline in viral load occurred in both treatment and control arms.²⁸ The use of bamlanivimab was not associated with a better outcome when used for treatment of severe infection requiring hospitalization.¹ A cocktail of the monoclonal antibodies casirivimab and imdevimab did not significantly reduce hospitalizations and emergency room visits as compared with placebo.¹⁷¹ When used as monotherapy, bamlanivimab had no clinical benefit as compared with placebo in a subsequent randomized trial.⁴⁷ However, in the same trial, the combination of bamlanivimab with etesevimab, another anti-S neutralizing monoclonal antibody, was associated with significant improvements as compared with placebo in mean total symptom scores and COVID-related hospitalizations or emergency department visits.These results suggest that targeting multiple epitopes with a cocktail of neutralizing monoclonal antibodies may be beneficial in treating mild COVID-19. However, emerging SARS-CoV-2 variants with mutations in the S receptor binding protein may be less susceptible to the neutralizing activity of these anti-S monoclonal antibodies.²⁹

SARS-CoV-2 Vaccines.

Since the beginning of the COVID-19 pandemic, the development of vaccines capable of preventing infection, disease, and transmission of the virus has been a major goal. The global scientific effort rapidly resulted in a large number of vaccine candidates. Approaches have included nucleic acid vaccines, nonreplicating or replicating viral vector vaccines, inactivated vaccines, virus like particle vaccines, and protein subunit vaccines.⁶¹ Overall efficacy of SARS-CoV-2 vaccines in phase 3 clinical trials has ranged from 66% to 95%, with protection from severe disease reaching 100% in the vast majority of trials (reviewed further in ⁴⁶).

Nucleic Acid (mRNA and DNA) Vaccines.

After intramuscular injection in animals, DNA and mRNA expression vectors can be taken up by local muscle cells, which can express the protein encoded by the gene.¹⁷⁹ While mRNA can be easily degraded by ubiquitous extracellular ribonucleases, advances in carrier complexation has permitted its use as a vaccine. When used for viral infection by injecting plasmid DNA encoding influenza A nucleoprotein, this approach elicited protective immune responses in mice.¹⁵⁵ mRNA vaccines may elicit higher titers of neutralizing antibody than do DNA vaccines.^{39,80,111,123} Theoretically, injected DNA could be integrated into the genome, potentially resulting in oncogenicity, or injected DNA could precipitate or worsen autoimmune disease secondary to elicitation of anti-DNA antibodies. However, clear evidence of such phenomena has not been reported.⁸⁶ mRNA has the potential for rapid and scalable manufacturing due to the high yields of in vitro transcription reactions.¹¹² Nucleic acid vaccines have been investigated in humans for other microorganisms including rabies virus,⁵ influenza,⁹ and HIV1,⁶⁷ and they may be useful for cancer immunotherapy.⁷⁹ However, nucleic acid vaccines have not been licensed for these pathogens.

A number of SARS-CoV-2 vaccine candidates using both mRNA and DNA approaches have been evaluated in clinical trials. The phase 1 trial of mRNA-1273, a vaccine encoding a pre-fusion stabilized form of the S protein (consisting of the SARS-CoV-2 glycoprotein with a transmembrane anchor and an intact S1-S2 cleavage site) showed induction of virus-specific antibody (including neutralizing antibody) and T cell (primarily Th1) responses.⁶⁶ The subsequent phase 3 trial using this vaccine enrolled over 30,000 participants and reached its primary endpoint at the interim analysis, showing substantial vaccine efficacy (94% against COVID-19 and 100% against severe disease).⁸ Similarly, a phase 3 trial of another mRNA vaccine (BNT162b2)¹⁶² that enrolled over 43,000 participants showed 95% vaccine efficacy.¹¹⁶ Those vaccines became publicly available in December 2020, and widespread vaccination efforts began thereafter. The rapid development of these vaccines was a remarkable achievement, as they became available within a year of identifying the virus.

Viral Vector Vaccines.

Viral vector vaccines use recombinant DNA techniques to create a vector that expresses a vaccine target antigen. Adenovirus vectors have been the most commonly used platform in the context of COVID-19 vaccine development. One such vaccine (ChAdOx1 nCoV19), which is based on a nonreplicating chimpanzee adenovirus vector, elicited both humoral and cellular immune responses in a phase 2 trial.⁴³ The vaccine efficacy in the phase 3 trial, which enrolled over 11,000 participants, was 90% when using a prime-boost regimen consisting of a half dose followed by a full dose, as opposed to 62% when 2 full doses were given.¹⁶⁰ The cause of the lower vaccine efficacy in the 2 full-dose regimen is unknown. Other groups have used nonreplicating human adenovirus-based vectors as platforms for SARS-CoV-2 vaccines, and some have gained emergency authorization for human use.^90,132 Infrequent but serious thrombotic complications have been associated with ChAdOx1 nCoV19.⁵¹ This complication may be related to an immunologic phenotype similar to that of heparin-induced thrombocytopenia, with detection of antibodies against platelet factor 4-heparin, even though none of the patients had received heparin.⁵¹ The complication was fatal in some cases, and thrombosis often occurred in cerebral vasculature. Similar adverse events have been observed with a human adenovirus type 26-based vaccine (Ad26.COV2.S).¹⁰⁵

Other Vaccine Candidates.

Candidate vaccines have been developed by inactivating SARS-CoV-2, often from viruses isolated locally early in pandemic.^184,185,196 Those vaccines elicited humoral responses, as evidenced by neutralizing antibodies, but it is uncertain that they elicited adequate T cell responses. Protein subunit vaccines based on the SARS-CoV-2 S protein or S protein RBD have also been developed. One such vaccine, composed of trimeric full-length S protein, induced neutralizing antibody and virus-specific T cell responses in a phase 1 to 2 trial.⁷³ Virus-like particle vaccines are also under development.¹⁶⁸

Effects of SARS-CoV-2 Genetic Variants on Vaccine Efficacy.

Mutations in the SARS-CoV-2 genome resulting in amino acid changes that alter protein structure can affect binding of vaccine-induced antibodies to their antigenic target. In vitro neutralizing activity of sera from recipients of mRNA vaccines is modestly decreased against the B.1.1.7 variant and decreased to a greater extent against the B.1.351 variant.^{87,166,167,183} Limited data address vaccine efficacy against specific SARS-CoV-2 variants in vivo. However, the BNT162b2 mRNA vaccine had greater than 90% efficacy in preventing infection in Israel, a setting in which the majority of SARS-CoV-2 isolates were the B.1.1.7 variant.³⁵ ChAdOx1 nCoV19 also retained reasonably high clinical efficacy against the B.1.1.7 variant, but did not protect against mild or moderate COVID-19 caused by the B.1.351 variant that was prevalent in South Africa.^41,97 Ad26.COV2.S maintained 64% overall efficacy in preventing mild-moderate infection and 82% efficacy in preventing severe-critical disease in South Africa, where the B.1.351 variant was the dominant isolate.¹³¹ Continued surveillance of emerging SARS-CoV-2 variants is crucial for informing ongoing vaccine strategies, as the virus is expected to continue mutating under immunologic pressure.

Conclusions

An unprecedented amount of information has been obtained about SARS-CoV-2 and COVID-19 in a relatively short period of time. The efforts of clinicians, public health officials, and scientists worldwide have provided significant insight into this novel virus and its various disease manifestations. Identification of specific pathways involved in the immune response to SARS-CoV-2 has facilitated the understanding of links between dysregulated inflammatory responses and COVID-19. Innovative therapies and vaccines have been developed in an effort to combat this pandemic. However, much remains to be learned about SARS-CoV-2 pathogenesis in order to optimize those approaches. Issues such as the potential impacts of ongoing genetic evolution of SARS-CoV-2 over time, and the identification of new manifestations of disease linked to SARS-CoV-2, such as MIS-C, highlight the need for ongoing research on SARS-CoV-2 and COVID-19. Those efforts may also help to identify novel antiviral pathways and mechanisms relevant to other human diseases related to dysregulated immune function and inflammatory responses (for example, Kawasaki disease, macrophage activation syndrome, and hemophagocytic lymphohistiocytosis).