COVID-19 and lung involvement

Abstract

In late December 2019, a novel coronavirus emerged and had a rapid and worldwide spread, resulting in an ongoing pandemic. This virus, designated SARS-CoV-2, causes a respiratory disease named COVID-19 which can range in severity, depending not only on the viral infection but also conditioned by the immune system and the host's response. COVID-19 is often associated with aggressive and uncontrolled inflammation that may lead to acute respiratory distress syndrome (ARDS), multiorgan damage and failure, and death. In this chapter, we review the general characteristics of SARS-CoV-2 infection, its interaction with target cells and the resulting immune response, as well as current and potential therapeutic interventions.

Introduction

Coronaviruses are group of viruses capable of infecting many different animals, including humans, resulting mainly in respiratory diseases that can range from mild to severe [[1], [2], [3], [4]]. Given their high prevalence and wide distribution, large genetic diversity and frequent recombination of their genomes, as well as increasing human–animal interface activities, it is not uncommon for novel coronaviruses to emerge periodically in humans [1].

In 2002 and 2012, respectively, two highly pathogenic coronaviruses with zoonotic origin, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), emerged among humans and caused fatal respiratory illness, making coronaviruses a public health concern [2,5].

In late December 2019, a previously unknown coronavirus was discovered from a cluster of patients with pneumonia of unknown cause in Wuhan, a city in the Hubei province of China [1,4,6]. This virus, initially named 2019-nCoV, was identified as a highly transmissible and pathogenic coronavirus which affected the lung and had a rapid and worldwide spread [1,5,6]. On February 11, 2020, the International Committee on Taxonomy of Viruses (ICTV) named this novel coronavirus as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and on the same day the World Health Organization (WHO) officially designated the disease coronavirus disease 2019 (COVID-19) [1,4,5]. Later, on March 11, 2020, the WHO officially declared the disease a pandemic [6].

COVID-19 can range in severity, depending not only on the viral infection itself and/or secondary infections but is also conditioned by the immune system and the host's response. The disease is often associated with aggressive and uncontrolled inflammation that may lead to acute respiratory distress syndrome (ARDS), multiorgan damage and failure, and death [7,8]. This chapter aims to review the general characteristics of SARS-CoV-2 infection, its interaction with target cells and the resulting immune response, as well as current and potential therapeutic interventions.

Epidemiology

The initial outbreak, on December 2019, only occurred in Wuhan and its surroundings in Hubei Province. By the end of January 2020, COVID-19 had spread to all 31 provinces in mainland China [4]. The first case reported outside of China was on January 13, 2020, from a patient in Thailand that had been in Wuhan [9]. In the following months, the disease spread to all the continents and the WHO officially declared it a pandemic on March 11, 2020 [4,6].

Initial data showed that patients were mainly concentrated at the age of 30–79, accounting for more than 85% of confirmed cases. Prevalence was slightly higher on males and the proportion of infected healthcare workers was around 2% [4,10].

As of July 2021, the cumulative number of cases reported globally was over 187 million and the number of deaths exceeded four million. Cases have been reported from all five continents, most of them announced in America and Europe with 74 and 56 million cases, respectively, with 1.9 and 1.1 million deaths each. Because COVID-19 is an ongoing pandemic, geographic distribution is constantly evolving and situation reports are being released periodically [11,12].

As SARS-CoV-2 continued to circulate and evolve, variants of interest and concern were reported. A variant of interest (VOI) is one with genetic changes affecting virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; and with epidemiological impacts suggesting an emerging risk to global public health, like causing significant community transmission or clusters [11].

On the other hand, a variant of concern (VOC) is a SARS-CoV-2 variant that meets the definition of a VOI and has been demonstrated to possess increased transmissibility or detrimental change in COVID-19 epidemiology; or increased virulence or change in clinical disease presentation; or cause decreased effectiveness of public health and social measures or available diagnostics, vaccines and therapeutics. The four VOCs characterized to date are Alpha, Beta, Gamma, and Delta, all of which have demonstrated increased transmissibility. Of those aforementioned variants, Delta has been detected in at least 111 countries and is expected to rise and become the dominant variant globally in the following months [11,12].

Virology

SARS-CoV-2 is a coronavirus that belongs to the betacoronavirus genus in the Orthocoronavirinae subfamily. It is an enveloped, positive-sense single-stranded RNA virus with characteristic spikes projecting from its surface [[3], [4], [5]]. These viral particles are generally spherical, its diameter varying from about 60 to 140 nm, and their spikes measure about 9 to 12 nm. On electron micrographs, the negative-stained virions resemble a solar corona, typical of the Coronaviridae family [1,4,6].

Through full genome sequencing and phylogenetic analysis, it is known that SARS-CoV-2 is similar to a previously identified SARS-like coronavirus (bat-SL-CoVZC45, MG772933.1) found in bats and pangolins [1,13]. SARS-CoV-2 also shares 79.5% and 50% sequence identity to SARS-CoV and MERS-CoV, respectively [4].

SARS-CoV-2 virions consist of a nucleoprotein (N) which wraps the RNA genome forming a coiled tubular structure, packed by a phospholipid bilayer envelope that is associated with envelop (E) and matrix (M) proteins, and is covered with spike (S) and hemagglutinin-esterase (HE) proteins, the latter being found only in some coronaviruses [4,6].

The genome, 29.9 kb in size, shows the typical betacoronavirus organization consisting of 5′ and 3′ untranslated regions, a replicase complex (ORF1ab) that encodes proteins essential for viral replication/transcription such as RNA dependent RNA polymerase (RdRp), S, E, M, and N genes which are for their respective structural proteins, and several unidentified nonstructural open reading frames [1,6].

Transmission

Human coronaviruses are thought to be of zoonotic origin, and bats are most likely the natural hosts for all presently known CoVs. SARS-CoV-2 shows a high sequence identity to some bat coronaviruses such as RaTG13 previously detected in Rhinolophus affinis, a species widespread in China and Southeast Asia. However, bat habitats are generally far from human activity areas, and the virus was probably transmitted to humans by another animal host. Furthermore, bat SARS-like coronaviruses cannot directly infect humans unless they undergo mutation or recombination in animal hosts. For example, animal hosts of SARS-CoV and MERS-CoV are the civet and camel, respectively, before transmission to humans. Regarding the intermediate animal host of SARS-CoV-2, it has been reported that the sequence identity between pangolin origin CoVs and SARS-CoV-2 is very high, suggesting that SARS-CoV-2 may be of pangolin origin [4].

SARS-CoV-2 transmission is mainly person-to-person, through respiratory droplets or secretions which are distributed by coughing or sneezing from infected individuals [4,6,14,15]. Thus, COVID-19 patients are the main source of infection, and those severely ill are more contagious than mild ones. Incubation period is around 3 and 6 days [4,14]. In this period, even without signs or symptoms of respiratory disease, as well as those with asymptomatic infection, are potential sources of transmission [4]. The transmissibility of SARS-CoV-2 is not precisely known, but data show that basic reproduction number (R0) is expected to be around between 2 and 3 [6].

In general, respiratory viruses have the highest transmissibility when the patient is symptomatic, in alignment with the period of peak respiratory viral load. The exact point of transmission for SARS-CoV-2 remains unknown [6]. Moreover, the number of virus RNA copies in some asymptomatic cases can be comparable to those with manifest symptoms, and we can assume that transmission may occur with the illness onset and even with mild or no symptoms [6].

Procedures that induce production of aerosol, such as nebulizer treatment or intubation, are reported to increase the risk of transmission [6]. Transmission by direct and indirect contact may be possible, and recent studies showed that SARS-CoV-2 can remain viable on various surfaces such as stainless steel, plastic, glass, and cardboard at least several hours [6]. SARS-CoV-2 RNA has been detected in stool, whole blood and urine of COVID-19 patients, but whether transmission via such medium is possible is still not precise [4,6].

Pathogenesis

SARS‐CoV‐2 utilizes the angiotensin‐converting enzyme 2 (ACE2) receptor to enter the host cell, similar to SARS-CoV, but with up to 10–20-fold higher affinity [4,15]. ACE2 receptor is a cell membrane protein present in lung, heart, kidney, and intestine tissue. It is highly expressed in the epithelium of the upper respiratory tract, alveolar type II pneumocytes and the enterocytes in the small intestine. SARS-CoV-2 is able to cause respiratory and gastrointestinal symptoms [15]. Naturally, all other organs of the body that express the ACE2 receptor could also be infected and extrapulmonary spread may be observed [4].

However, the presence of the ACE2 receptor is not the sole factor that determines infection of the tissue [15,16]. Cell entry of coronaviruses depends on binding of the viral spike (S) proteins to cellular receptors and subsequent protein priming and fusion [2,4]. The S protein is comprised of two subunits, S1 and S2. The S1 fraction possesses a receptor‐binding domain (RBD) which interacts and binds to the ACE2 receptor, and then employs the host's serine protease (TMPRSS2) for S protein priming. The resulting S2 fraction is responsible for the fusion of the virus to the cell membrane and entry [2,4,6].

Once the virus enters the epithelial cells of the upper respiratory tract, it starts to replicate and as the disease progresses, transmits to the lower sections of the airway [4]. Alike SARS-CoV, lung cells once infected show decreased expression of ACE2 receptor [15]. The downregulation of ACE2 expression is associated with acute lung injury and is a pathological mechanism leading to acute lung injury and ARDS [17,18]. Pulmonary inflammation also increases capillary leakage that can cause ARDS [15,19].

In most cases, the immune system can eliminate the virus. However, deficient immunity or hyperinflammation can lead to severe respiratory failure. Thus, the immune response against SARS‐CoV‐2 and the severity of the inflammation are two major factors that define the outcome in patients with COVID‐19 [15,20].

Immune response against COVID-19

SARS-CoV-2 is first recognized by the innate immune system through the identification of pathogen‐associated molecular patterns and viral RNA by pathogen‐related receptors of the macrophages and epithelial cells. Then, toll‐like receptors 3 and 7, cytosolic RNA sensor, RIG-I, and MDA5 contribute to the identification of virus-infected cells and the activation of downstream inflammatory signaling pathways, such as the phosphorylation of nuclear factor‐κB (NF‐κB), phosphoinositide 3‐kinase, mitogen‐activated protein kinase, and IFN regulatory factor‐3 (IRF‐3) [15]. This cascade leads to the induction of innate immune response via production of type 1 interferon (IFN‐1) which possesses antiviral function, as well as release of proinflammatory cytokines such as IL‐1β, TNF‐α, IL‐6, and IL‐18, and activation of natural killer cells, the latter which exerts a major histocompatibility complex (MHC)‐independent immune response that can restrict the pathogenesis of the virus at the early stages of infection [15,[21], [22], [23]].

Through its downstream signaling pathways, IFN‐1 activates IFN‐induced transmembrane family proteins, which in turn inhibit the entrance of the virus to the host cell. This inhibits the replication of the virus and the infection of the further cells by SARS‐CoV‐2. It is important to note that although type I IFN‐based immune response is initially critical to restrict viral infection, its excessive production leads to severe inflammation and ARDS [15,21].

Dendritic cells that are antigen-presenting cells (APCs) process and present the viral antigen to naïve T cells via the human leukocyte antigens (HLAs), leading to adaptative immune system activation. HLA molecules are very polymorphic with more than 10,000 variants reported so far, these molecules determine the capacity of each individual to recognize and present specific portions of any proteic infectious agent. Accordingly, individual HLA variation has been linked to the efficiency of the immune response to a virus across a population [24]. APCs also produce cytokines that direct the antiviral immune response of the T cells, differentiating them into the different types of effector cells. The cytokines produced by APCs and T cells drive the cellular immune response to SARS‐CoV‐2 [15].

COVID-19 patients often present with lymphopenia, which demonstrates activation and recruitment to the lung tissue to inhibit the infection by SARS‐CoV‐2. T cells are the directors of the cellular immunity. Serum levels of Th1‐associated cytokines, including IFN‐γ, TNF‐α, and IL‐2, are reported to be increased and activate cytotoxic T cells which destroy virus-infected cells through production of perforin and granzyme. Also, T helper cells may present the viral antigen to the B lymphocytes, which subsequently produce neutralizing antibodies against the spike (S) protein of the virus. The neutralizing antibodies inhibit the replication of the virus and produce humoral immunity, which is one of the main concepts for vaccine design against SARS‐CoV‐2 [15].

During the cytokine storm, monocytes and Th1 cells produce granulocyte‐monocyte colony‐stimulating factor (GM‐CSF) and IL‐6. GM‐CSF and IL‐6 have a major role in the progression of mild to severe respiratory inflammation and ARDS, and higher serum concentrations of IL‐6 are associated with poor clinical outcomes [15,21].

The activation of B cells induces the differentiation of plasma cells and production of neutralizing antibodies that help the eradication of current infection, but also protect the host to further infections. The dynamics of the antibody response are complex, but in most of the patients, these antibodies are present three weeks after infection. First, B cells start their antibody response against the nucleocapsid (N) protein. Then, they produce anti‐spike (S) antibodies. These antibodies can be found in patient serum 9 days (IgM) and 14 days (IgG) after infection. Appropriate serum antibody levels prevent the patient from being reinfected.

Immune dysfunction in COVID-19

Dysfunctional immune activity, either as immunodeficiency as well as hyperimmunity with severe or excessive inflammatory response, can result in severe disease and increased mortality. Immunocompromised patients, like those with old age with multiple comorbidities, cancer, immunosuppressive drug therapy, or other immunodeficiencies, are unable to inhibit the replication of the virus and thus susceptible to severe disease. Consequently, SARS‐CoV‐2 can infect the lower respiratory tract faster and cause pneumonia that can be followed by severe inflammation and ARDS, leading to higher mortality [15].

In addition, SARS‐CoV‐2 possesses the capability to evade identification by the immune system, which could be the underlying reason for its prolonged incubation period in comparison to other respiratory viruses. Type I IFN, an important antiviral component of the immune system, is decreased in COVID‐19 patients as well as in those critically ill, through inhibition of IFN‐signal transduction pathways such as IRF‐3, resulting in the reduction of the power of the immune system. This mechanism is like the immune evasion acknowledged in SARS and MERS infections, which consists of disturbance in RNA‐sensing and type I IFN producing pathways [15,21,23].

The effects of interferons in COVID‐19 are time dependent. In the first stages, IFNs hinder disease progression by inhibiting the infection of new host cells. On the contrary, in later stages, IFNs might promote progression by inducing upregulation of ACE‐2 in airway epithelial cells, increasing the chance infection of these cells [15].

T lymphocyte cells are a major cellular immunity component and play a key role in the adaptive immune response. T cell exhaustion is associated with severe infection and poor antiviral immune response, and in COVID-19 patients two exhaustion markers, named programmed death‐1 (PD‐1) and T‐cell immunoglobulin and mucin‐domain containing‐3 (Tim‐3), were reported to be highly expressed. This is one of many mechanisms that contribute to severity and understanding the process in order to inhibit or prevent it from happening could lead to improved clinical results. Another plausible immune evasion mechanism is the escaping from the MHC‐dependent presentation of its antigens by APCs, thus avoiding the triggering of the adaptive immune response [15,23].

On the other hand, exaggerated immune response, severe inflammation, subsequent ARDS, and further fibrosis lead to lung damage and respiratory failure with bigger impact than the direct cytopathic effects of the virus. Damaged lung cells and macrophages produce chemotactic factors that recall innate immune cells and induce inflammatory response. Then, the inflammatory cells start an uncontrolled production of proinflammatory cytokines and chemokines, which is known as cytokine storm [23,25]. It results in extensive inflammation of the lungs, leakage of fluid to the alveoli and accumulation of inflammatory exudates, and the formation of hyaluronan, which in turn leads to hyaloid membrane formation, ARDS, and even multiple organ failure. CXCL‐8, 9, 10, and CCL‐2, 3, and 5 are the major produced chemokines in this process, and TGFβ, TNF‐α, IFN‐γ, IFN‐α, IL‐1β, 6, 12, 18, and 33, are cytokines that also contribute in its process [15,23,25].

Management of the cytokine storm can reduce lung tissue damage and lead to a better outcome in COVID‐19 patient. Multiple strategies, such as using immunomodulatory drugs or targeting inflammatory cytokines can potentially reduce its severity and are discussed in further sections [15,25].

Clinical features

COVID-19 has been considered as a type of self-limiting infectious disease, and most cases with mild symptoms can recover in 1–2 weeks. SARS-CoV-2 infection can cause five different outcomes: asymptomatically infected persons, mild to medium disease which comprises the majority of cases, severe disease, critical disease, and death [4].

Asymptomatic infection

Asymptomatic cases can account to at least one third of SARS-CoV-2 infections [14,26,27]. They can transmit the virus for an extended period, perhaps longer than 14 days, and play a significant role in the COVID-19 pandemic. A small fraction of individuals with positive PCR test but without symptoms may turn out to be presymptomatic and will eventually develop symptoms [26,27]. Both instances are often associated with subclinical lung abnormalities on the CT, which shows that absence of symptoms might not necessarily imply an absence of harm [26].

Clinical manifestations

The incubation period for most cases of COVID-19 is approximately five days, and nearly all infected persons who have symptoms are expected to do so within 12 days of infection [6,14,28,29]. Average duration of hospitalization is around 12 days and severe illness occurs in 15.7% of the patients after admission [29,30]. Duration of viral shedding ranges between 8 and 37 days, the median being at 20 days [30].

The most frequent symptoms are fever, cough, sputum production, and dyspnea. Other less common symptoms include fatigue, myalgia, nausea or vomiting, and diarrhea [6,14,[29], [30], [31], [32]] (Table 9.1 ). Fever may not always be present [6,29]. Older patients tend to have more systemic symptoms, extensive radiological ground-glass lung changes, lymphopenia, thrombocytopenia, and increased C-reactive protein and lactate dehydrogenase levels [14].

Table 9.1.

Common symptoms and laboratory findings on patients with COVID-19.

Common symptoms	Common laboratory findings
Fever	Lymphocytes	Decreased
Cough	Neutrophils	Elevated
Sputum production	C-reactive protein	Elevated
Dyspnea	Serum ferritin	Elevated
Fatigue or myalgia	Lactate dehydrogenase	Elevated
Nausea or vomiting	D-dimer	Elevated
Diarrhea	Erythrocyte sedimentation rate	Elevated
Headache	Lnterleukin-6	Elevated
	Aspartate aminotransferase	Elevated
	Alanine aminotransferase	Elevated

Risk factors for severe disease or death include individuals older in age or with coexisting illness (ages 60 or older), and medical comorbidity such as hypertension, diabetes mellitus, cardiovascular disease, chronic pulmonary disease, or malignancy [[29], [30], [31]]. Other risk factors associated with higher odds of in-hospital death are a higher Sequential Organ Failure Assessment (SOFA) score on admission, elevated D-dimer levels, as well as elevated levels of blood IL-6, high-sensitivity cardiac troponin I, lactate dehydrogenase, and lymphopenia. These findings could help clinicians to identify at an early stage patients with worse prognosis [30].

Approximately 15% of individuals affected by COVID-19 develop severe disease, and 5% to 6% are critically ill with respiratory failure and/or multiple organ dysfunction or failure [31]. Disease progression is usually seen in the form of pneumonia. Further worsening, over the course of 7 to 10 days after initiating symptoms, may translate into ARDS and respiratory failure, thromboembolic complications such as deep vein thrombosis or pulmonary embolism, acute kidney injury and sepsis, either attributed to secondary infection or directly caused by SARS-CoV-2 infection [29,30]. In some cases, marked inflammatory or autoimmune responses such as Guillain-Barré syndrome may appear [33,34].

Patients may need invasive mechanical ventilation, renal replacement therapy, vasopressor infusion, or other critical care measures. They also have elevations in leukocytes, neutrophils, and creatinine kinase, and in computed tomography extended ground-glass opacities, interstitial infiltration, and/or multiple patchy consolidations in both lung fields [31].

Complications

Several complications of COVID-19 have been described. ARDS is a major complication that arises in a median of eight days after symptom onset [32]. ARDS is a life-threatening lung condition that prevents enough oxygen from getting to the lungs and into the circulation, accounting for mortality of most respiratory disorders and acute lung injury [4].

Inflammatory complications may arise during SARS-CoV-2 infection. Clinical findings showed exuberant inflammatory responses, further resulting in uncontrolled pulmonary inflammation, likely a leading cause of case fatality. Rapid viral replication and cellular damage, virus-induced ACE2 downregulation and shedding, and antibody-dependent enhancement are responsible for aggressive inflammation caused by SARS-CoV-2. The initial onset of rapid viral replication may cause massive epithelial and endothelial cell death and vascular leakage, triggering the production of proinflammatory cytokines and chemokines. Loss of pulmonary ACE2 function has been proposed to be related to acute lung injury because ACE2 downregulation and shedding can lead to dysfunction of the renin-angiotensin system, and further enhance inflammation and cause vascular permeability [4].

Thromboembolic disease is another common complication among COVID-19 patients. In patients receiving at least standard doses of thromboprophylaxis, the incidence of the composite events venous and arterial thromboembolism, including deep vein thrombosis and pulmonary embolism, is around 31% [35]; most patients have elevated D-dimer and fibrinogen levels [36]. It is more frequent in severely ill patients and particularly in those in the intensive care unit (ICU). Pulmonary embolism is the most frequent thrombotic complication [35,36], and age and coagulopathy are independent predictors of thrombotic complications [35]. Unless contraindicated, pharmacological thrombosis prophylaxis should be started in all hospitalized patients, and physicians should be vigilant for signs of thrombotic complications and order appropriate diagnostic tests at a low threshold in order to promptly switch to high-prophylactic or therapeutic doses [35,36].

Laboratory findings

The most frequent laboratory abnormalities found on patients with COVID-19 are lymphocytopenia, neutrophilia, and thrombocytopenia [10,15,[37], [38], [39]]. The pulmonary infiltration of the lymphocytes, apoptosis/pyroptosis of the lymphocytes, lateral margination, and infection of the lymphocytes by SARS‐CoV‐2 are the most common reasons leading to lymphopenia [7,15] and has been proposed as a prognostic marker for COVID-19 [39]. Other findings include elevated inflammatory markers, like C-reactive protein (≥10 mg/L), lactate dehydrogenase (≥250 U/L), serum ferritin (>300 μg/L), and D-dimer (≥0.5 mg/L); liver and kidney dysfunction; and coagulopathies (Table 9.1), with patients with severe disease having more prominent laboratory abnormalities [14,29,30,38].

Imaging findings

The most frequent radiographic and CT patterns are ground-glass opacities (GGOs) and local or bilateral patchy shadowing. Interstitial abnormalities may also be present. In some cases, no abnormal images may be found; paired with the fact that not all patients develop fever, diagnosis in mild cases may be complicated [14,29]. Lung abnormalities are predominantly found in peripheral middle and lower regions, and often show a multiple or bilateral onset and an asynchronous process [40].

The imaging findings of COVID-19 can be classified broadly in three stages: an early rapid progressive stage (≤7 days), an advanced stage (8–14 days), and an absorption stage (>14 days) [40]. In the early rapid progressive stage, GGOs plus a reticular pattern, GGO plus consolidation, and GGO alone were all common signs. In the advanced stage, GGO plus reticular pattern or consolidation were the dominant findings. Finally, in the absorptive stage, repairing signs like subpleural lines, bronchus distortion, and fibrotic strips can be found [40] (Fig. 9.1 ).

Figure 9.1.

Chest CT images from a patient with COVID-19. (A) Early progressive stage with bilateral ground-glass. (B) Advanced stage with ground-glass opacities and consolidation.

Pathology findings

Histological examination of lung tissue shows involvement of alveoli and bronchioles with diffuse alveolar damage as the main finding, along with cellular fibromyxoid exudates filling its lumina, consisting in protein-rich edema fluid, fibrin, cellular debris, macrophages, neutrophils, and lymphocytes. Epithelial necrosis with desquamation of pneumocytes, hyaline membrane formation, and pulmonary edema can be observed and is suggestive of ARDS [4,19,31,41].

Multinucleated syncytial cells with atypical enlarged pneumocytes characterized by large nuclei, amphophilic granular cytoplasm, and prominent nucleoli can be identified in the intra-alveolar spaces, indicating viral cytopathic-like changes. In addition, interstitial involvement with mononuclear inflammatory infiltrates, dominated by lymphocytes, can be found in the lungs [4,31,41].

In areas with more advanced lesions, organizing-stage diffuse alveolar damage with pronounced fibroblastic proliferation, partial fibrosis, and pneumocyte hyperplasia result in interstitial thickening. Alveoli are collapsed and its walls are thickened and lined by cuboidal epithelial cells characteristic of type II pneumocyte hyperplasia. These pulmonary pathological findings resemble those seen in SARS and MERS [4,19,31,41].

Diagnosis

Diagnostic approach

COVID-19 is a viral respiratory disease and as such, it should be suspected in all febrile and/or respiratory symptomatic patients, especially if the person has had close contact (within six feet during more than a few minutes while not wearing a face mask or other personal protective equipment) or has recently been to a high SARS-CoV-2 infection prevalence location. There are no specific clinical features, and in the pandemic context, clinicians should have a low threshold for suspicion. In the absence of fever or pulmonary complications, COVID-19 should also be considered if the patient has disease-related symptoms like, for example, diarrhea, taste or olfactory loss, and thromboembolic events.

Ideally, all suspected cases should be tested as soon as possible after symptom onset. This is in order to control transmission, to monitor SARS-CoV-2 transmission rates and severity, to mitigate the impact of COVID-19 in healthcare and social care settings, to detect clusters or outbreaks in specific settings, and to maintain COVID-19 elimination status once achieved. If this is not possible, testing strategies or priorities should be established. When testing is limited or unavailable, patients with history of exposure, compatible clinical course, and no other evident explanation of symptoms, may be presumptively diagnosed as probable COVID-19. If hospitalization is not necessary, self-isolation at home and monitoring is an option.

Soon after initial outbreak, diagnosis based on the detection of the viral sequence by nucleic acid amplification testing (NAAT) via reverse-transcription polymerase chain reaction (RT-PCR) became available and is the main method of diagnosis [4,13]. It is used for qualitative and quantitative SARS-CoV-2 detection in samples collected from the upper respiratory tract, including nasal or nasopharyngeal swabs [42]. Another frequently used test is the detection of SARS-CoV-2 antigens. A positive RT-PCR for SARS-CoV-2 generally confirms the diagnosis of COVID-19. However, patients can have detectable SARS-CoV-2 RNA for weeks after the onset of symptoms, and furthermore this test does not determine time of infection [43]. Also, RNA detection does not necessarily indicate infectiousness, which is determined by viral load. For example, patients who are beyond day 10 of symptoms and have less than 100,000 viral RNA copies per ml of sputum are considered to have little residual risk of infectivity [44]. A negative RT-PCR for SARS-CoV-2 generally excludes the diagnosis of COVID-19. However, false-negative results may happen and if clinical suspicion is high, the test should be repeated. Many biotechnology companies have successfully developed nasopharyngeal swabs and nucleic acid detection kits [4]. It has been shown that patients with SARS-CoV-2 infection possess acute serological responses. Combined with immunochromatography, colloidal gold, and other technologies, relevant detection reagents have been developed rapidly [4].

Compatible laboratory or imaging findings can further support the diagnosis. With the rapid spread of COVID-19, CT is an especially important tool for establishing diagnosis and severity [40]. The majority of COVID-19 cases have similar features on CT images including bilateral distribution of patchy shadows and GGOs predominantly in middle and lower lung fields, as mentioned previously [4,31]. To note, there is a small proportion of COVID-19 patients with negative RT-PCR tests and lung abnormalities on CT imaging, suggesting that CT could detect lesions earlier in the disease [40]. However, clinical picture and thoracic imaging alone are not specific enough to make a definite diagnosis [42].

In some patients, a second-line investigation like bronchoalveolar lavage (BAL) is often required to diagnose or exclude SARS-CoV-2 infection [42]. In a study, BAL was performed on patients after at least one negative or indeterminate upper respiratory swab due to clinical or radiological suspicion for COVID-19 [42]. High concordance between swabs and BAL were observed, the latter being the gold standard to detect pathogens in the presence of pulmonary infiltrates [42]. It seems that BAL has a limited role in the diagnosis of COVID-19 if thoracic imaging and upper respiratory tract swabs are concordantly negative, but it might be necessary in patients with a negative swab to establish a different diagnosis [42].

Management

General management

Management of patients with COVID-19 is based mainly on symptomatic control and supportive therapy, including supplemental oxygen, mechanical ventilator support when needed, antibiotics for prevention of secondary bacterial infection, and body fluid management. In most cases, outpatient management is appropriate, since approximately 80% of patients develop a mild disease which does not warrant medical intervention or hospitalization [45].

Bacterial superinfection and pneumonia are not a prominent feature and empiric therapy is not routinely administered, but its clinical features may overlap with those of COVID-19, and treatment is reasonable when the diagnosis is uncertain or there is clinical suspicion. Because of higher risk of thromboembolic complications, all hospitalized patients should receive pharmacological thrombosis prophylaxis, unless contraindicated [35,36,46].

Based on the pathogenesis of COVID-19, many drugs—new and existing, those that target the virus itself or modulate the immune response—are being researched and clinical trials are being launched.

Dexamethasone and other glucocorticoids

In patients hospitalized with COVID-19, the use of dexamethasone, oral or intravenous, at a dose of 6 mg daily for up to 10 days or until discharge, has shown to lower 28-day mortality in patients who were receiving respiratory support [47]. When compared to usual care alone, there was an absolute reduction in mortality of 2.8% (22.9% vs. 25.7%; age-adjusted rate ratio, 0.83; 95% CI, 0.75 to 0.93) [47]. Incidence of death was lower among patients receiving invasive mechanical ventilation (29.3% vs. 41.4%; rate ratio, 0.64; 95% CI, 0.51 to 0.81) and among those receiving oxygen without invasive mechanical ventilation (23.3% vs. 26.2%; rate ratio, 0.82; 95% CI, 0.72 to 0.94) [47].

The use of dexamethasone in patients who are receiving oxygen was also associated with a lower risk of invasive mechanical ventilation or, for those already receiving invasive mechanical ventilation, a greater chance of successful cessation [47]. The benefit was also clear in patients who were being treated more than seven days after symptom onset, when inflammatory lung damage is more likely [47]. However, there was no found benefit among patients who did not require oxygen, and results were consistent with possible harm in this subgroup [47].

A prospective meta-analysis of clinical trials of critically ill patients with COVID-19 showed that administration of systemic corticosteroids was associated with lower 28-day all-cause mortality, when compared with usual care or placebo [48]. Other treatment strategies analyzed were dexamethasone intravenous 20 mg daily for five days followed up by 10 mg daily for five days; hydrocortisone intravenous 200 mg daily for seven days, continuous or in bolus dosing every 6 h; and methylprednisolone intravenous 40 mg every 12 h for seven days [48]. Therefore, when dexamethasone is not available, it is reasonable to use other glucocorticoids at equivalent doses.

The ORs for the association between corticosteroids and mortality were similar and the optimal dose and duration of treatment could not be assessed [48]. There was no suggestion of an increased risk of serious adverse events [48]. However, patients receiving glucocorticoids should be monitored due to risk of hyperglycemia and increased risk of infections, and prophylaxis treatment for Strongyloides is reasonable for patients from endemic areas. In the absence of compelling contraindications, a corticosteroid regimen should be a component of standard care for critically ill patients with COVID-19 [48].

Finally, inhaled corticosteroids [49] has been tested in a recent trial in patients with mild COVID-19 symptoms, showing that early administration of inhaled budesonide reduced the likelihood of needing urgent medical care and reduced time to recovery after early COVID-19. Further studies are necessary to confirm the routine use of inhaled corticosteroids in COVID-19.

Remdesivir

Remdesivir, recently recognized as a promising antiviral drug against a wide array of RNA viruses in-vitro, is an adenosine analog which incorporates into nascent viral RNA chains resulting in premature termination [50]. It is approved by the Food and Drug Administration (FDA) for the treatment of COVID-19 in hospitalized adult and pediatric patients and can be administered in a five-day course (200 mg day one, 100 mg daily days 2–5) or extended to a 10-day course (100 mg daily days 6–10) if there is no clinical improvement. Remdesivir is not recommended in patients with renal impairment with an estimated glomerular filtration rate (eGFR) < 30 mL/min per 1.73 m2 unless the potential benefit outweighs the potential risk [51].

In patients with nonsevere COVID-19 disease, hospitalized with peripheral capillary oxygen saturation (SpO₂) >94% on room air, remdesivir appeared to yield better clinical status and higher discharge rates, although not statistically significant. Treatment with remdesivir also failed to show or to exclude a statistically significant reduction in mortality or time to recovery when compared with no remdesivir [[52], [53], [54]].

In hospitalized patients with SpO₂ ≤94% on room air, including patients on supplemental oxygen, on mechanical ventilation, and extracorporeal membrane oxygenation (ECMO), initial data showed treatment with remdesivir trended toward greater clinical improvement at 28 days, a shorter median time to recovery and decreased need for mechanical ventilation [52,53,55,56]. According to the WHO-sponsored SOLIDARITY trial, there was no difference in overall 28-day mortality between patients randomly assigned to open-label remdesivir and those assigned to standard care [52]. In another study, ACTT-1, remdesivir resulted in a faster time to recovery, defined as discharge from the hospital or continued hospitalization without need for supplemental oxygen or ongoing medical care. Further analysis showed that recovery was only statistically significant among patients who were on low-flow oxygen at baseline [53]. A double-blind RCT in China involving patients with severe COVID-19, stopped early for poor enrollment, stated that time to clinical improvement was not statistically different with remdesivir compared with placebo for 10 days [55].

In a meta-analysis of four trials that included the trials mentioned above, remdesivir did not reduce mortality (OR 0.9, 95% CI 0.7–1.12) or need for mechanical ventilation (OR 0.90, 95% CI 0.76–1.03) compared with standard of care or placebo [57,58]. Among those who were not on mechanical ventilation at baseline, there appeared to be a trend toward lower mortality with remdesivir but without statistical significance. In this population, remdesivir is suggested over no antiviral treatment, prioritizing those requiring low-flow supplemental oxygen [51,59].

Baricitinib and JAK inhibitors

Janus kinase (JAK) is a family of intracellular tyrosine kinases that mediates intracellular transcription factors. It is involved in the phosphorylation of the signal transducer and activator of transcription (STAT) protein family in the JAK-STAT pathway, which results in the production of several proinflammatory cytokines, including IL‐6. Inhibition of JAK could reduce the production of proinflammatory cytokines and restrict cytokine storm in severe COVID‐19 patients [15,60].

Baricitinib is a selective inhibitor of JAK 1 and 2 and blocks the intracellular signaling pathway of inflammatory cytokines, including interleukin-2, interleukin-6, interleukin-10, interferon-γ, and granulocyte-macrophage colony-stimulating factor. In addition, it limits SARS-CoV-2 entry and infectivity by inhibiting adaptor‐associated protein kinase 1 receptor [61,62] and improves lymphocyte counts in patients with COVID-19 [62].

The US FDA has issued an emergency use authorization (EUA) to permit the emergency use of baricitinib, in combination with remdesivir, for treatment of suspected or laboratory confirmed COVID-19 in hospitalized adults and pediatric patients two years of age or older requiring supplemental oxygen, invasive mechanical ventilation, or ECMO. It is administered as a 4 mg daily dose, either orally or through a nasogastric tube, for 14 days or until hospital discharge. Patients with an eGFR of less than 60 mL per minute are recommended a dose of 2 mg once daily [62,63].

Baricitinib plus remdesivir was superior to remdesivir alone for the treatment of hospitalized patients with COVID-19, with a shorter time to recovery and a greater improvement in clinical status. However, it did not detect a difference in mortality. Because of this reason, added to the fact that dexamethasone showed a significant benefit in survival, and because baricitinib and dexamethasone have not been compared directly, it is not the first drug to be considered. The safety and efficacy of using both baricitinib and a glucocorticoid are uncertain, and there is no evidence supporting the use of baricitinib alone [62].

Tocilizumab and IL-6 pathway inhibitors

In response to cytokines, inflammatory cells are recruited, and an immune response is exerted. In some cases, these inflammatory immune cells lead to an uncontrolled production and cytokine storm, of which IL‐6 is one of the most important contributors [64].

Tocilizumab is a humanized monoclonal antibody against the interleukin-6 receptor (IL-6R) that can inhibit the inflammatory pathway induced by IL‐6. It was granted an EUA for the treatment of COVID-19 in the United States in June 2021 [15,65,66] and can be administered in hospitalized adults and pediatric patients (two years of age and older) who are receiving systemic corticosteroids and require supplemental oxygen, noninvasive or invasive mechanical ventilation, or ECMO. It is given 8 mg/kg up to 800 mg as a single dose and is recommended in individuals with severe or rapidly progressing disease, those who require high-flow oxygen or greater respiratory support and have either been admitted to the ICU within the prior 24 h or have significantly increased inflammatory markers [59,67].

Overall, it is an effective treatment for hospitalized COVID-19 patients who have hypoxia and evidence of inflammation (CRP ≥75 mg/L), and studies have shown that treatment reduces mortality at day 28, increases the chances of successful hospital discharge, and reduces the chances of requiring invasive mechanical ventilation, compared to standard care alone or placebo [[67], [68], [69]]. These benefits are consistent across all patient groups, including those receiving invasive mechanical ventilation, noninvasive respiratory support, or no respiratory support other than simple oxygen [67].

Although tocilizumab inhibits the destructive effects of the SARS‐CoV‐2 on lung tissue, like other immunosuppressive drugs, uncontrolled or unnecessary application could be associated with adverse effects, including an increase in hepatic enzymes and opportunistic infections [15,25].

Convalescent plasma and antibody-based therapies

Antibody-based treatments are a form of passive immunotherapy that can improve the immune response and inhibit SARS‐CoV‐2 infection and progression. This can be achieved by the infusion of the SARS‐CoV‐2 convalescent plasma from recovered patients, as demonstrated previously for the treatment of multiple diseases, including SARS [70] and MERS [71].

Convalescent plasma can restrict viral infection and modulate the immune response. It contains neutralizing IgM and IgG antibodies, which inhibit viral entry to the host cell activating the complement system, inducing phagocytosis of the virus, and activating antibody‐dependent cellular toxicity [72]. Convalescent plasma also contains immune‐modulatory cytokines and autoantibodies that control the hyperinflammatory process and the cytokine storm [15,73].

In the United States, EUA has been granted for high-titer convalescent plasma among hospitalized patients with COVID-19 who are early in the course of disease or have impaired humoral immunity [74].

Use of convalescent plasma in patients with COVID-19 has also been reported in numerous clinical trials [[75], [76], [77]], and data suggest that plasma with higher antibody titers administered earlier in the disease are associated with better outcomes, with lower 30-day mortality rates [76]. However, many studies, including a meta-analysis of four published RCTs, have not demonstrated a clear clinical benefit of convalescent plasma, and neither a difference in mortality, duration of hospitalization or use of mechanical ventilation were detected with convalescent plasma compared with placebo or standard of care [78,79].

It is uncertain whether convalescent plasma is beneficial in COVID-19, but it is safe and well tolerated and an early administration within the clinical course of the disease can potentially improve patient outcomes with relatively low risk [79,80]. Low antibody levels in some of the recovered patients, limited access to large doses of convalescent plasma, and the possibility of adverse reactions are the main limitations and challenges of convalescent plasma therapy [15].

Conclusion

COVID-19 is caused by SARS-CoV-2 infection and mainly affects the lung. Depending on the host's immune and inflammatory response, it may develop a disease that can range from asymptomatic or mild to severe and life-threatening. A competent immune system is crucial in eliminating the virus and controlling the disease, and either deficient immunity or hyperinflammation can lead to uncontrolled disease and progression, respiratory failure, and death. Since being declared a pandemic by the WHO on March 2020, a global effort is being made to research and develop potential treatment. By understanding the virus and its pathogenesis, including its structure, mechanism of entry, host's response, and immune and inflammatory mediators involved, targeted therapies can be designed and developed.

Take-home messages

SARS-CoV-2 emerged in late December 2019 and since then it has spread across the globe, resulting in an ongoing pandemic. The virus continues to circulate and evolve, with variants of interests and concern emerging periodically.

Entry to the host cell involves binding between the host's ACE2 receptor and the viral S protein. The S1 fraction possesses a RBD and the S2 fraction mediates fusion and entry.

The cytotoxic effects of the virus stimulate the release of proinflammatory cytokines in an attempt to control the infection. Deficient immunity or hyperinflammation can lead to severe and uncontrolled disease.

Several therapeutic interventions have been proposed and numerous clinical trials are being conducted. Remdesivir incorporates into nascent viral RNA and mediates premature termination. Dexamethasone, baricitinib, and tocilizumab aim to control the host's excessive inflammatory response by acting on different pathways. Finally, convalescent plasma, with its neutralizing IgM and IgG antibodies, restricts viral infection and modulates immune response.