An Updated Review on COVID-19: Variants, Long COVID, Diagnostics, and Therapeutic Strategies

The human body is exposed to a variety of infectious microorganisms, such as viruses, bacteria, fungi, protozoa, and helminths, which cause tissue damage through different mechanisms. Viruses are unique among these five types of infectious organisms in that they can manipulate the host-cell machinery in a unique way and continuously evolve to survive and prosper in all species [1].

COVID-19 is the disease caused by a new coronavirus called SARS-CoV-2. WHO first learned of this new virus on 31 December 2019, following a report of a cluster of cases of ‘viral pneumonia’ in Wuhan, People’s Republic of China [2]. Since December 2019, a novel coronavirus disease had rapidly spread throughout China, leading to a global outbreak, and causing considerable public health concern. World Health Organization (WHO) announced the outbreak of COVID-19 as a global public health emergency on 30 January 2020. In India, the first case of COVID-19 was reported on January 27, 2020, in Kerala district. Since then, there is a wide variation in the reporting of cases across the country. The case reporting is based on the SARS-CoV-2 antigen testing by Real-Time Reverse Transcription Polymerase Chain Reaction (RT-qPCR) or by Rapid Antigen Test (RAT) [3]. Coronavirus (Covid) is clustered under the viral family group that causes disease in mammals and birds. A pandemic novel coronavirus was named as ‘‘Corona Virus Disease 2019’’ (2019-nCoV) by World Health Organization (WHO) in Geneva, Switzerland. As its RNA pattern is closer to SARS, the 2019 Coronavirus is renamed as SARS-CoV-2- 2 pandemic. It belongs to the subfamily Orthocoronavirinae inside the family Coronaviridae, order Nidovirales, and the realm Riboviria [4]. A two-dimensional view of Corona beneath a transmission electron microscopy reveals a characteristic look of ‘‘paying homage to a crown’’ around the virions. This lead to naming the virus ‘‘Corona’’, meaning ‘‘crown’’ or ‘‘halo’’ in Latin This is the deadly third-generation virus in Corona family preceded by severe acute respiratory syndrome (SARS) in 2003, killed almost 10% of total affected patients (8429) across 29 international locations and Middle East Respiratory Syndrome (MERS) in 2012, even more lethal with a mortality rate of 30% of the infected patients [4].

HISTORY

Coronaviruses are enveloped positive sense RNA viruses ranging from 60 nm to 140 nm in diameter with spike like projections on its surface giving it a crown like appearance under the electron microscope; hence the name coronavirus [3]. Four corona viruses namely HKU1, NL63, 229E and OC43 have been in circulation in humans, and generally cause mild respiratory disease. There have been two events in the past two decades wherein crossover of animal beta corona viruses to humans has resulted in severe disease. The first such instance was in 2002–2003 when a new coronavirus of the β genera and with origin in bats crossed over to humans via the intermediary host of palm civet cats in the Guangdong province of China. This virus, designated as severe acute respiratory syndrome coronavirus affected 8422 people mostly in China and Hong Kong and caused 916 deaths (mortality rate 11%) before being contained. Almost a decade later in 2012, the Middle East respiratory syndrome coronavirus (MERS-Covid), also of bat origin, emerged in Saudi Arabia with dromedary camels as the intermediate host and affected 2494 people and caused 858 deaths (fatality rate 34%) [5].

COVID-19 was the third leading cause of death in the United States (USA) in 2020 after heart disease and cancer, with approximately 375,000 deaths. [34]  Individuals of all ages are at risk of contracting this infection. However, patients aged ≥60 and patients with underlying medical comorbidities (obesity, cardiovascular disease, chronic kidney disease, diabetes, chronic lung disease, smoking, cancer, solid organ or hematopoietic stem cell transplant patients) have an increased risk of developing severe COVID-19 infection. According to the CDC, age remains the strongest predictor of poor outcomes and severe illness in patients with COVID-19. Data from the National Vital Statistics System (NVSS) at CDC states that patients with COVID-19 aged 50 to 64 years have a 25 times higher risk of death when compared to adults infected with this illness and aged less than 30 years. In patients 65 to 74 years old, this risk increases to 60 times. In patients older than 85, the risk of death increases to 340 times. According to the CDC, these data include all deaths in the United States throughout the pandemic, from February 2020 to July 1, 2022, including deaths among unvaccinated individuals. The percentage of COVID-19 patients requiring hospitalization was 6 times higher in those with preexisting medical conditions than those without medical conditions (45.4% vs. 7.6%) based on an analysis by Stokes et al. of confirmed cases reported to the CDC from January 22 to May 30, 2020.[35] The study also reported that the percentage of patients who succumbed to this illness was 12 times higher in those with preexisting medical conditions than those without (19.5% vs 1.6%).[35]  Data regarding the gender-based differences in COVID-19 suggests that male patients have a higher risk of severe illness and increased mortality due to COVID-19 compared to female patients.[36][37] Results from a retrospective cohort study from March 1 to November 21, 2020, evaluating the mortality rate in 209 United States of America (USA) acute care hospitals that included 42604 patients with confirmed SARS-CoV-2 infection, reported a higher mortality rate in male patients (12.5%) compared to female patients (9.6%).[38] Racial and ethnic minority groups have been reported to have a higher percentage of COVID-19-related hospitalizations than White patients based on a recent CDC analysis of hospitalizations from an extensive administrative database that included approximately 300,000 COVID-19 patients hospitalized from March 2020 to December 2020. This high percentage of COVID-19-related hospitalizations among racial and ethnic groups was driven by a higher risk of exposure to SARS-CoV-2 and an increased risk of developing severe COVID-19 disease.[39] A meta-analysis of 50 studies from USA and UK researchers noted that people of Black, Hispanic, and Asian ethnic minority groups are at increased risk of contracting and dying from COVID-19 infection.[40] 

COVID-19-related death rates were the highest among Hispanic persons. [34] Another analysis by the CDC evaluating the risk of COVID-19 among sexual minority adults reported that underlying medical comorbidities which increase the risk of developing severe COVID-19 were more prevalent in sexual minority individuals than heterosexual individuals within the general population and within specific racial/ethnic groups. [41]

Pathophysiology

Structurally and phylogenetically, SARS-CoV-2 is similar to SARS-Covid and MERS-Covid and is composed of 4 main structural proteins: spike (S), envelope (E) glycoprotein, nucleocapsid (N), and membrane (M) protein. It also contains 16 nonstructural proteins and 5-8 accessory proteins.[42] 

The surface spike (S) glycoprotein, which resembles a crown, is located on the outer surface of the virion. It undergoes cleavage into an amino (N)-terminal S1 subunit, which facilitates the incorporation of the virus into the host cell. The carboxyl (C)-terminal S2 subunit contains a fusion peptide, a transmembrane domain, and a cytoplasmic domain responsible for virus-cell membrane fusion. [43][44] The S1 subunit is further divided into a receptor-binding domain (RBD) and an N-terminal domain (NTD), which facilitates viral entry into the host cell and serves as a potential target for neutralization in response to antisera or vaccines.[45] 

The RBD is a fundamental peptide in the pathogenesis of infection as it represents a binding site for the human angiotensin-converting enzyme 2 (ACE2) receptors. Inhibition of the renin-angiotensin-aldosterone system (RAAS) does not increase the risk of hospitalization for COVID-19 and severe disease. [46]

SARS-CoV-2 gains entry into the host cells by binding the SARS-CoV-2 spike or S protein (S1) to the ACE2 receptors in the respiratory epithelium. ACE2 receptors are also expressed by other organs such as the upper esophagus, enterocytes from the ileum, myocardial cells, proximal tubular cells of the kidney, and urothelial cells of the bladder. [47] The viral attachment process is followed by priming the spike protein S2 subunit by the host transmembrane serine protease 2 (TMPRSS2) that facilitates cell entry and subsequent viral replication. [48] In the early phase of the infection, viral replication results in direct virus-mediated tissue damage. In the late phase, the infected host cells trigger an immune response by recruiting T lymphocytes, monocytes, and neutrophils. Cytokines such as tumor necrosis factor-α (TNF α), granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-1 (IL-1), interleukin-6 (IL-6),), IL-1β, IL-8, IL-12 and interferon (IFN)-γ are released. In severe COVID-19 illness, a 'cytokine storm' is seen. This is due to the over-activation of the immune system and high levels of cytokines in circulation. This results in a local and systemic inflammatory response. [49][50] 

Effect of SARS-CoV-2 on the Respiratory System

Increased vascular permeability and subsequent development of pulmonary edema in patients with severe COVID-19 are explained by multiple mechanisms. [51][52][53] These mechanisms include:

• Endotheliosis as a result of direct viral injury and perivascular inflammation leading to microvascular and microthrombi deposition
• Dysregulation of RAAS due to increased binding of the virus to the ACE2 receptors
• Activation of the kallikrein-bradykinin pathway, the activation of which enhances vascular permeability
• Enhanced epithelial cell contraction causes swelling of cells and disturbance of intercellular junctions
• The binding of SARS-CoV-2 to the Toll-Like Receptor (TLR) induces the release of pro-IL-1β, which mediates lung inflammation until fibrosis. [54]

Effect of SARS-CoV-2 on Extrapulmonary Organ Systems

Although the respiratory system is the principal target for SARS-CoV-2, other major organ systems such as the gastrointestinal tract (GI), hepatobiliary, cardiovascular, renal, and central nervous systems may also be affected. SARS-CoV-2–induced organ dysfunction is likely due to a combination of mechanisms, such as direct viral toxicity, ischemic injury caused by vasculitis, thrombosis, immune dysregulation, and renin-angiotensin-aldosterone system (RAAS) dysregulation. [55]

Cardiac involvement in COVID-19 is common and likely multifactorial. ACE2 receptors exhibited by myocardial cells may cause direct cytotoxicity to the myocardium leading to myocarditis. Proinflammatory cytokines such as IL-6 can also lead to vascular inflammation, myocarditis, and cardiac arrhythmias.[56]

Acute coronary syndrome (ACS) is a well-recognized cardiac manifestation of COVID-19. It is likely due to multiple factors, including proinflammatory cytokines, worsening of preexisting severe coronary artery disease, coronary plaque destabilization, micro thrombogenesis, and reduced coronary blood flow. [57] 

SARS-CoV-2 has a significant effect on the hematological and hemostatic systems as well. The mechanism of leukopenia, one of the most common laboratory abnormalities encountered in COVID-19, is unknown. Several hypotheses have been postulated that include ACE 2 mediated lymphocyte destruction by direct invasion by the virus, lymphocyte apoptosis due to proinflammatory cytokines, and possible invasion of the virus in the lymphatic organs.[58] 

Thrombocytopenia is common in COVID-19 and is likely due to multiple factors, including virus-mediated suppression of platelets, autoantibodies formation, and coagulation cascade activation, resulting in platelet consumption.[59] 

Thrombocytopenia and neutrophilia are considered a hallmark of severe illness.[55] Although it is well known that COVID-19 is associated with a state of hypercoagulability, the exact mechanisms that lead to the activation of the coagulation system are unknown and likely attributed to the cytokine-induced inflammatory response. The pathogenesis of this associated hypercoagulability is multifactorial. The hypercoagulability is probably induced by direct viral-mediated damage or cytokine-induced injury of the vascular endothelium leading to the activation of platelets, monocytes, and macrophages, with increased expression of von Willebrand factor and Factor VIII that results in the generation of thrombin and formation of a fibrin clot.[59][60]  Other mechanisms that have been proposed include possible mononuclear phagocyte-induced prothrombotic sequelae, derangements in the renin-angiotensin system (RAS) pathways, and complement-mediated microangiopathy.[59]

Symptoms

A wide range of symptoms are found in COVID-19 patients, ranging from mild/moderate to severe, rapidly progressive, and fulminant disease. Symptoms of COVID-19 are non-specific and disease presentation can range from asymptomatic to severe pneumonia. Incidence of asymptomatic cases ranges from 1.6% to 51.7% and these people do not present typical clinical symptoms or signs and do not present apparent abnormalities in lung computed tomography. The most common symptoms of COVID-19 are fever, cough, myalgia, or fatigue and atypical symptoms include sputum, headache, haemoptysis, vomiting, and diarrhea. Some patients may present with sore throat, rhinorrhoea, headache, and confusion a few days before the onset of fever, indicating that fever is a critical symptom, but not the initial manifestation of infection. Furthermore, some patients experience loss of smell (hyposmia) or taste (hypogeusia), which are now being considered early warning signs and indications for self-isolation [6].

The most common symptoms of COVID-19 are

• Fever.

• Dry cough.

• Fatigue.

Other symptoms that are less common and may affect some patients include

• Loss of taste or smell.

• Nasal congestion.

• Conjunctivitis (also known as red eyes).

• Sore throat.

• Headache.

• Muscle or joint pain.

• Different types of skin rash.

• Nausea or vomiting.

• Diarrhea.

• Chills or dizziness.

Symptoms of severe COVID-19 disease include:

• Shortness of breath.

• Loss of appetite.

• Confusion.

• Persistent pain or pressure in the chest.

• High temperature (above 38 °C).

Other less common symptoms are

• Irritability.

• Confusion.

• Reduced consciousness (sometimes associated with seizures).

• Anxiety.

• Depression.

• Sleep disorders.

• More severe and rare neurological complications such as strokes, brain inflammation, delirium and nerve damage.

People of all ages who experience fever and/or cough associated with difficulty breathing or shortness of breath, chest pain or pressure, or loss of speech or movement should seek medical care immediately. If possible, call your health care provider, hotline or health facility first, so you can be directed to the right clinic [1]

Differential Diagnosis

The symptoms of the early stages of the disease are nonspecific. Differential diagnosis should include the possibility of a wide range of infectious and noninfectious respiratory disorders.

• Community-acquired bac   terial pneumonia
• Viral pneumonia 
• Influenza infection
• Aspiration pneumonia
• Pneumocystis jirovecii pneumonia
• Middle East respiratory syndrome (MERS)
• Avian influenza A (H7N9) viral infection
• Avian influenza A (H5N1) viral infection
• tuberculosis   

Clinical Features

• The clinical features of this ailment vary, extending from an asymptomatic state to acute respiratory distress syndrome to septic shock and multi-organ dysfunction. Ideally, this ailment is categorized depending on its severity and this include mild, moderate, severe, and critical. The shared symptoms of individuals with the disease include fever (98.6 per cent), tiredness (69.6 per cent), dry cough, and looseness of the bowels.

Asymptomatic infections

• Asymptomatic infections have been well documented [19-27]. One review estimated that 33 percent of people with SARS-CoV-2 infection never develop symptoms [28]. This estimate was based on four large population-based, cross-sectional surveys, among which the median proportion of individuals who had no symptoms at the time of a positive test was 46 percent (range 43 to 77 percent), and on 14 longitudinal studies, among which a median of 73 percent of initially asymptomatic individuals remained so on follow-up. However, there is still uncertainty around the proportion of asymptomatic infections, with a wide range reported across studies. Additionally, the definition of "asymptomatic" may vary across studies, depending on which specific symptoms were assessed. The range of findings in studies evaluating asymptomatic infections is reflected in the following examples:
• In a COVID-19 outbreak on a cruise ship where nearly all passengers and staff were screened for severe acute respiratory syndrome coronavirus 2 (SARSCoV- 2), approximately 19 percent of the population on board tested positive; 58 percent of the 712 confirmed COVID-19 cases were asymptomatic at the time of diagnosis [29,30]. In studies of subsets of those asymptomatic individuals, who were hospitalized and monitored, approximately 77 to 89 percent remained asymptomatic over time [30,31].
• In a smaller COVID-19 outbreak within a skilled nursing facility, 27 of the 48 residents (56 percent) who had a positive screening test were asymptomatic at the time of diagnosis, but 24 of them developed symptoms over the next seven days [32].
• Other studies, particularly those conducted among younger populations, have reported even higher proportions of infections that are asymptomatic [33-37]. As an example, in an outbreak on an aircraft carrier, a quarter of the crew, among whom the mean age was 27 years, tested positive for SARS-CoV-2 [36]. Among the 1271 cases, only 22 percent were symptomatic at the time of testing and 43 percent remained asymptomatic throughout the observation period. High rates of asymptomatic infection have also been reported among pregnant women presenting for delivery [2,34].
• Patients with asymptomatic infection may have objective clinical abnormalities [24,38]. As an example, in a study of 24 patients with asymptomatic infection who all underwent chest computed tomography (CT), 50 percent had typical ground-glass opacities or patchy shadowing, and another 20 percent had atypical imaging abnormalities [38]. Five patients developed low-grade fever, with or without other typical symptoms, a few days after diagnosis. In another study of 55 patients with asymptomatic infection identified through contact tracing, 67 percent had CT evidence of pneumonia on admission; only two patients developed hypoxia, and all recovered [24].
• As above, some individuals who are asymptomatic at the time of diagnosis go on to develop symptoms (i.e, they were actually presymptomatic). In one study, symptom onset occurred a median of four days (range of three to seven) after the initial positive RT-PCR test [30].

Severity of Symptomatic Infection

Spectrum of infection severity

• The spectrum of symptomatic infection ranges from mild to critical; most infections are not severe [19,39-44]. Specifically, in a report from the Chinese Centre for Disease Control and Prevention that included approximately 44,500 confirmed infections with an estimation of disease severity [45]:
• Mild disease (no or mild pneumonia) was reported in 81 percent.
• Severe disease (eg, with dyspnea, hypoxia, or >50 percent lung involvement on imaging within 24 to 48 hours) was reported in 14 percent.
• Critical disease (eg, with respiratory failure, shock, or multiorgan dysfunction) was reported in 5 percent.
• The overall case fatality rate was 2.3 percent; no deaths were reported among noncritical cases.
• Similarly, in a report of 1.3 million cases reported to the United States Centers for Disease Control and Prevention (CDC) through the end of May 2020, 14 percent were hospitalized, 2 percent were admitted to the intensive care unit (ICU), and 5 percent died [46]. The risk of severe illness varied by age and underlying comorbidities.

Infection fatality rates

• The case fatality rate only indicates the mortality rate among documented cases. Since many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are asymptomatic and many mild infections do not get diagnosed, the infection fatality rate (i.e., the estimated mortality rate among all individuals with infection) is considerably lower and has been estimated in some analyses to be between 0.15 and 1 percent, with substantial heterogeneity by location and across risk groups [47-50].

Fatality rates among hospitalized patients

• Among hospitalized patients, the risk of critical or fatal disease is high [51-57]. In a study from early in the pandemic that included 2741 patients who were hospitalized for COVID-19 in a New York City health care system, 665 patients (24 percent) died or were discharged to hospice [54]. Of the 647 patients who received invasive mechanical ventilation, 60 percent died, 13 percent were still ventilated, and 16 percent were discharged by the end of the study. The in-hospital fatality rate associated with COVID-19 has been higher than that for influenza [58-60]. As an example, in an analysis of hospital data from the United States Veterans Health Administration, patients with COVID-19 were five times more likely to die during the hospitalization than patients with influenza (21 versus 3.8 percent) [44].
• Over the course of the pandemic, declining in-hospital fatality rates have been reported [61-64]. As an example, in a retrospective study of a national surveillance database in England that included over 21,000 critical care patients with COVID-19, ICU survival improved from 58 percent in late March 2020 to 80 percent by June 2020 [61]. The reasons for this observation are uncertain, but potential explanations include improvements in hospital care of COVID-19 and better allocation of resources when hospitals were not overburdened.
• In resource-limited settings, in-hospital mortality rates may be higher than those reported elsewhere. As an example, in a study from 10 countries in Africa, where there was a median of two intensive care specialists in each hospital and a minority of facilities did not have pulse oximetry, the in-hospital 30-day mortality rate following critical care admission was 48 percent [65]. Mortality was associated with underlying comorbidities as well as resource shortages.

Excess deaths during the pandemic

• Neither the case fatality rate nor the infection fatality rate account for the full burden of the pandemic, which includes excess mortality from other conditions because of delayed care, overburdened health care systems, and social determinants of health [66-68].

Incubation period and serial interval

• The mean or median incubation period of the disease ranges from 5 to 6 days [69,70]. Lauer et al estimated that 2.5% of the patients will develop symptoms within 2.2 days (95% CI, 1.8 to 2.9 days) and 97.5% of patients will develop symptoms within 11.5 days (95% CI, 8.2– 15.6 days).
• Serial interval refers to the time interval between the onset of symptoms in the primary case and the secondary case. The mean serial interval is estimated to be approximately 4 to 5 days [71,72]. By analysing data from 468 infector–infectee pairs, Du et al noted that 59 secondary cases had symptoms earlier than their primary case. This suggested that there is a possibility that the transmission of the disease occurred during the asymptomatic phase of illness in this group of patients [73].

Period of Infectivity

• The duration for which a patient with COVID-19 remains infective is unclear. Viral load in the oropharyngeal secretions is highest during the early symptomatic stage of the disease [74]. The patient can continue to shed the virus even after symptom resolution. In a study from China, the median duration of virus shedding was 20 days (interquartile range [IQR] 17.0–24.0) amongst the survivors [75]. A study of viral dynamics in mild and severe cases revealed that mild cases tend to clear the viruses early, while severe cases can have prolonged viral shedding [76]. Data from studies using twin respiratory and fecal sampling have shown viral shedding can persist in stools for more than 4 weeks even when respiratory samples are negative [77]. Transmission during the asymptomatic phase has also been reported. In a study from Singapore, 6.4% of the 157 locally acquired cases of COVID-19 were attributed to transmission during the asymptomatic phase of the disease [78].

Initially, early in the pandemic, the understanding of COVID-19 and its therapeutic management was limited, creating an urgency to mitigate this new viral illness with experimental therapies and drug repurposing. Since then, due to the intense efforts of clinical researchers globally, significant progress has been made which has led to a better understanding of not only COVID-19 and its management but also has resulted in the development of novel therapeutics and vaccine development at an unprecedented speed [80].

Prevention

Preventive measures are the current strategy to limit the spread of cases. Early screening, diagnosis, isolation, and treatment are necessary to prevent further spread. Preventive strategies are focused on the isolation of patients and careful infection control, including appropriate measures to be adopted during the diagnosis and the provision of clinical care to an infected patient [81]. Important COVID-19 prevention and control measures in community are summarized in Table 1.

Table 1: COVID-19 prevention and control measures in community.

CONCLUSION