Emerging Variants of SARS-CoV-2

Coronavirus disease 2019 (COVID-19), the illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had a devastating effect on the world’s population resulting in more than 3.8 million deaths worldwide and emerging as the most significant global health crisis since the influenza pandemic of 1918.

Since being declared a global pandemic by the World Health Organization (WHO) on March 11, 2020, the virus continues to cause devastation, with many countries enduring a second or a third wave of outbreaks of this viral illness.

Adaptive mutations in the viral genome can alter the virus’s pathogenic potential. Even a single amino acid exchange can drastically affect a virus’s ability to evade the immune system and complicate the vaccine development progress against the virus.[1] 

SARS-CoV-2, like other RNA viruses, is prone to genetic evolution while adapting to their new human hosts with the development of mutations over time, resulting in the emergence of multiple variants that may have different characteristics compared to its ancestral strains. Periodic genomic sequencing of viral samples helps detect any new genetic variants of SARS-CoV-2 circulating in communities, especially in a global pandemic setting.

The genetic evolution of SARS-CoV-2 was minimal during the early phase of the pandemic with the emergence of a globally dominant variant called D614G, which was associated with higher transmissibility but without increased disease severity of its ancestral strain.[2] Another variant was identified in humans, attributed to transmission from infected farmed mink in Denmark, which was not associated with increased transmissibility.[3] 

Since then, multiple variants of SARS-CoV-2 have been described, of which a few are considered variants of concern (VOCs), given their impact on public health. VOCs are associated with enhanced transmissibility or virulence, reduction in neutralization by antibodies obtained through natural infection or vaccination, the ability to evade detection, or a decrease in therapeutics or vaccination effectiveness. Based on the recent epidemiological update by the WHO, as of June 22, 2021, four SARS-CoV-2 VOCs have been identified since the beginning of the pandemic:

• Alpha (B.1.1.7): first variant of concern described in the United Kingdom (UK) in late December 2020
• Beta (B.1.351): first reported in South Africa in December 2020
• Gamma(P.1): first reported in Brazil in early January 2021
• Delta (B.1.617.2): first reported in India in December 2020

All four reported VOCs -Alpha(B.1.1.7); Beta(B.1.351); and Gamma (P.1) and Delta(B.1.617.2) have mutations in the RBD and the NTD, of which N501Y mutation located on the RBD is common to all variants except the Delta variant which results in increased affinity of the spike protein to ACE 2 receptors enhancing the viral attachment and its subsequent entry into the host cells. Along with NBD, RBD serves as the dominant neutralization target and facilitates antibody production in response to antisera or vaccines.[4] 

Two recent preprint studies (not peer-reviewed) reported that a single mutation of N501Y alone increases the affinity between RBD and ACE2 approximately ten times more than the ancestral strain (N501-RBD). Interestingly the binding affinity of  Beta (B.1.351) variant and Gamma (P.1) variant with mutations N417/K848/Y501-RBD and ACE2 was much lower than that of N501Y-RBD and ACE2.[5][6]

Despite the extraordinary speed of vaccine development against COVID-19 and continued mass vaccination efforts across the world, the emergence of these new variant strains of SARS-CoV-2 threatens to overturn the significant progress made so far in halting the spread of SARS-CoV-2. This review article aims to comprehensively describe these new variants of concern, the latest therapeutics available in managing COVID-19 in adults, and the efficacy of different available vaccines against this virus and its new variants.

SARS-CoV-2 Variants of Concern (VOCs)

With the emergence of multiple variants, the CDC and the WHO have independently established a classification system for distinguishing the emerging variants of SARS-CoV-2 into variants of concern(VOCs) and variants of interest(VOIs).

• Alpha (B.1.1.7 lineage)
  • In late December 2020, a new SARS-CoV-2 variant of concern, B.1.1.7 lineage, also referred to as Alpha variant or GRY(formerly GR/501Y.V1), was reported in the UK based on whole-genome sequencing of samples from patients who tested positive for SARS-CoV-2.[7][8]
  • In addition to being detected by genomic sequencing, the B.1.1.7variantwas identified in a frequently used commercial assay characterized by the absence of the S gene (S-gene target failure, SGTF) PCR samples. The B.1.1.7 variant includes 17 mutations in the viral genome. Of these, eight mutations (Δ69-70 deletion, Δ144 deletion, N501Y, A570D, P681H, T716I, S982A, D1118H) are in the spike (S) protein. N501Y shows an increased affinity of the spike protein to ACE 2 receptors, enhancing the viral attachment and subsequent entry into host cells.[9][10][11]
  • This variant of concern was circulating in the UK as early as September 2020 and was based on various model projections. It was reported to be 43% to 82% more transmissible, surpassing preexisting variants of SARS-CoV-2 to emerge as the dominant SARS-CoV-2 variant in the UK.[10] The B.1.1.7 variant was reported in the United States (US) at the end of December 2020. An initial matched case-control study reported no significant difference in the risk of hospitalization or associated mortality with the B.1.1.7 lineage variant compared to other existing variants. However, subsequent studies have since reported that people infected with B.1.1.7 lineage variant had increased severity of disease compared to people infected with other circulating forms of virus variants.[12][8] A large matched cohort study performed in the UK reported that the mortality hazard ratio of patients infected with B.1.1.7 lineage variant was 1.64 (95% confidence interval 1.32 to 2.04, P<0.0001) patients with previously circulating strains.[13] Another study reported that the B 1.1.7 variant was associated with increased mortality compared to other SARS-CoV-2 variants (HR= 1.61, 95% CI 1.42-1.82).[14] The risk of death was reportedly greater (adjusted hazard ratio 1.67, 95% CI 1.34-2.09) among individuals with confirmed B.1.1.7 variant of concern compared with individuals with non-1.1.7 SARS-CoV-2.[15]
• Beta (B.1.351 lineage)
  • Tegally et al. reported a new variant of SARS-CoV-2 lineage B.1.351 also referred to as Beta variant or GH501Y.V2 with multiple spike mutations, which resulted in the second wave of COVID-19 infections in Nelson Mandela Bay in South Africa in October 2020.[16]
  • The B.1.351 variant includes nine mutations (L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, and A701V) in the spike protein, of which three mutations (K417N, E484K, and N501Y) are located in the RBD and increase the binding affinity for the ACE receptors.[17][9][18]SARS-CoV-2 501Y.V2(B.1.351 lineage) was reported in the US at the end of January 2021.
  • This variant is reported to have an increased risk of transmission and reduced neutralization by monoclonal antibody therapy, convalescent sera, and post-vaccination sera.[19]
• Gamma(P.1 lineage)
  • The third variant of concern, the P.1 variant also known as Gamma variant or GR/501Y.V3, was identified in December 2020 in Brazil and was first detected in the US in January 2021.[20] 
  • The B.1.1.28 variant harbors ten mutations in the spike protein (L18F, T20N, P26S, D138Y, R190S, H655Y, T1027I V1176, K417T, E484K, and N501Y). Three mutations (L18F, K417N, E484K) are located in the RBD, similar to the B.1.351 variant.[20] Based on the WHO epidemiological update on March 30, 2021, this variant has spread to 45 countries. Importantly, this variant may have reduced neutralization by monoclonal antibody therapies, convalescent sera, and post-vaccination sera.[19]
• Delta (B.1.617.2 lineage)
  • The fourth variant of concern, B.1.617.2 also referred to as the Delta variant was initially identified in December 2020 in India and was responsible for the deadly second wave of COVID-19 infections in April 2021 in India. In the United States, this variant was first detected in March 2021 and is o be the most dominant SARS-CoV-2 strains in the US in the coming weeks by researchers.
  • The Delta variant was initially considered a variant of interest. However, this variant rapidly spread around the world prompting the WHO to classify it as a VOC in May 2021
  • The B.1.617.2 variant harbors ten mutations ( T19R, (G142D*), 156del, 157del, R158G, L452R, T478K, D614G, P681R, D950N) in the spike protein

SARS-CoV-2 Variants of Interest (VOIs)

VOIs are defined as variants with specific genetic markers that have been associated with changes that may cause enhanced transmissibility or virulence, reduction in neutralization by antibodies obtained through natural infection or vaccination, the ability to evade detection, or a decrease in the effectiveness of therapeutics or vaccination. The WHO Weekly Epidemiological update on June 22, 2021, described seven variants of interest (VOIs), namely Epsilon (B.1.427 and B.1.429); Zeta (P.2); Eta( B.1.525); Theta (P.3); Iota (B.1.526); Kappa(B.1.617.1) and Lambda(C.37).

• Epsilon (B.1.427 and B.1.429) variants, also called CAL.20C/L452R, emerged in the US around June 2020 and increased from 0% to >50% of sequenced cases from September 1, 2020, to January 29, 2021, exhibiting an 18.6-24% increase in transmissibility relative to wild-type circulating strains. These variants harbor specific mutations (B.1.427: L452R, D614G; B.1.429: S13I, W152C, L452R, D614G). Due to its increased transmissibility, the CDC classified this strain as a variant of concern in the US.[21]
• Zeta (P.2) has key spike mutations (L18F; T20N; P26S; F157L; E484K; D614G; S929I; and V1176F) and was first detected in Brazil in April 2020.This variant classified as a VOI by the WHO and the CDC due to its potential reduction in neutralization by antibody treatments and vaccine sera.
• Eta (B.1.525) and Iota (B.1.526) variants harbor key spike mutations (B.1.525: A67V, Δ69/70, Δ144, E484K, D614G, Q677H, F888L; B.1.526: (L5F*), T95I, D253G, (S477N*), (E484K*), D614G, (A701V*)) and were first detected in New York in November 2020 and classified as a variant of interest by CDC and the WHO due to their potential reduction in neutralization by antibody treatments and vaccine sera.
• Theta (P.3) variant, also called GR/1092K.V1 carries key spike mutations (141-143 deletion E484K; N501Y; and P681H) and was first detected in the Philippines and Japan in February 2021 and is classified as a variant of interest by the WHO.
• Kappa(B.1.617.1) variant harbor key mutations ((T95I), G142D, E154K, L452R, E484Q, D614G, P681R, and Q1071H) and was first detected in India in December 2021 and is classified as a variant of interest by the WHO and the CDC.
• Lambda(C.37) variant was first detected in Peru and has been designated as a VOI by the WHO in June 2021 due to a heightened presence of this variant in the South American region.

The CDC  has designated the Epsilon (B.1.427 and B.1.429)variants as a VOC and Eta(B.1.525); Iota (B.1.526); Kappa(B.1.617.1); Zeta (P.2); B.1.526.1; B.1.617 and B.1.617.3 as VOIs.

Etiology

Coronaviruses (CoVs) are large, enveloped, positive-sense single-stranded RNA (+ssRNA) viruses that belong to the family within the Nidovirales order within the subfamily Coronaviridae. The genome encodes four or five proteins, including the spike (S) protein which projects through the viral envelope and forms the characteristic “crown” appearance of the virus, deriving its name from the Latin word corona, meaning crown. Based on their genomic structure, these viruses are classified into four different genera[22]:

• Alphacoronavirus (αCoV)
• Betacoronavirus (βCoV)
• Gammacoronavirus (γCoV)
• Deltacoronavirus (δCoV)

Coronaviruses are widespread among birds and mammals, but only the alpha coronaviruses and beta coronaviruses have been associated with human disease. The alpha coronaviruses include two human virus species, HCoV-229E, and HCoV-NL63, and the beta coronaviruses include five human virus species, HCoV-OC43, HCoV-HKU1, MERS-CoV, SARS-CoV, and now SARS-CoV-2. Most of these viruses involve the respiratory system, typically causing common cold symptoms[23]. Genomic characterization of the 2019 novel coronavirus demonstrated 89% nucleotide identity with bat SARS-like CoV and 82% with human SARS-CoV. Hence, it was termed SARS-CoV-2 by experts of the International Committee on Taxonomy of Viruses[24]. SARS-CoV-2 is a novel beta coronavirus belonging to the same subgenus as the severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which have been previously implicated in epidemics with mortality rates up to 10% and 35%, respectively.[25]

Epidemiology

Since the first cases of COVID-19 were reported in Wuhan, Hubei Province, China, in December 2019 and the subsequent declaration of COVID-19 as a global pandemic by the WHO in March 2020, this highly contagious infectious disease has spread to 223 countries with more than 178 million cases, and more than 3.8 million deaths reported globally. As per the CDC, COVID-19 was the third leading cause of death in the US in 2020. An epidemiological update by WHO 22 June 2021, reported that the Alpha(B.1.1.7) variant has spread to 170 countries, the Beta (B.1.351) variant has been reported in 119 countries, the Gamma (P.1) variant has been detected in 71 countries and the Delta variant(B.1.617.2) has spread to 85 countries around the world.

Persons of all ages are at risk for infection and severe disease. However, patients aged ≥60 years 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) are at an increased risk of developing severe COVID-19 infection. In fact, the percentage of COVID-19 patients requiring hospitalization was six 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 during January 22 to May 30, 2020. Notably, the study also showed that the percentage of patients who succumbed to this viral illness was 12 times higher in those with preexisting medical conditions than those without medical conditions (19.5% vs. 1.6%).[26]

Data regarding the gender-based differences in COVID-19 suggests that male patients are at risk of developing severe illness and increased mortality due to COVID-19 compared to female patients.[27][28] Similarly, the severity of infection and mortality related to COVID-19 differs between different ethnic groups.[29] Based on the results of a meta-analysis of 50 studies from the US 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.[30]

Pathophysiology

Structurally and phylogenetically, SARS-CoV-2 is similar to SARS-CoV and MERS-CoV and is composed of four main structural proteins: spike (S), envelope (E) glycoprotein, nucleocapsid (N), membrane (M) protein, along with 16 nonstructural proteins, and 5-8 accessory proteins.[31] The surface spike (S) glycoprotein, which resembles a crown, is located on the outer surface of the virion and undergoes cleavage into an amino (N)-terminal S1 subunit, which facilitates the incorporation of the virus into the host cell and a carboxyl (C)-terminal S2 subunit which is responsible for virus-cell membrane fusion.[32][33] The S1 subunit is further divided into a receptor-binding domain (RBD) and N-terminal domain (NTD), which is implicated in facilitating viral entry into the host cell and serves as a potential target for neutralization in response to antisera or vaccines.[34]

SARS-CoV-2 gains entry into the hosts’ cells by binding the SARS-CoV-2 spike or S protein (S1) to the angiotensin-converting enzyme 2 (ACE2) receptors abundantly on respiratory epithelium such as type II alveolar epithelial cells. Besides 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.[35] 

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 endocytosis with the assembly of virions.[36] Two phases explain the pathogenesis, an early phase characterized by viral replication followed by a late phase when the infected host cells trigger an immune response with the recruitment of T lymphocytes, monocytes, and neutrophil recruitment which releases cytokines such as tumor necrosis factor-α (TNF α), granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-1 (IL-1), interleukin-6 (IL-6), and interferon (IFN)-γ. As seen in severe COVID-19, the immune system’s overactivation results in a cytokine storm characterized by the release of high levels of cytokines, especially IL-6 and TNF-α, into the circulation, causing a local and systemic inflammatory response.[37][38] 

Genetic variation in the viral genes of SARS-CoV-2 can have implications in its pathogenesis, especially if it involves the RBD, which mediates viral entry into the host cells and is an essential target of vaccine sera monoclonal antibodies. As described previously, the three reported VOCs (B.1.1.7; B.1.351; and P.1) have mutations in the RBD and the NTD, of which N501Y mutation located on the RBD is common to all variants and results in increased affinity of the spike protein to ACE 2 receptors enhancing the viral attachment and its subsequent entry into the host cells. Although the respiratory system is the predominant target for SARS-CoV-2 as described above, it can affect other major organ systems such as the gastrointestinal tract (GI), hepatobiliary, cardiovascular, renal, and central nervous system. SARS-CoV-2–induced organ dysfunction, in general, is possibly explained by either one or a combination of the proposed mechanisms such as direct viral toxicity, ischemic injury caused by vasculitis, thrombosis, or thrombo-inflammation, immune dysregulation, and renin-angiotensin-aldosterone system (RAAS) dysregulation.[39]

• Effect of SARS-CoV-2 on the Central Nervous System (CNS)
  • There is emerging evidence of ACE2 receptors in human and mouse brains, indicating the potential infection of the brain by SARS-CoV-2. Zubair et al. outlined that neuroinvasion by SARS-CoV-2 can occur with various possible routes such as transsynaptic transfer across infected neurons via the olfactory nerve, vascular endothelial cell infection, or migration of leukocytes across the blood-brain barrier.[40]
• Effect of SARS-CoV-2 on the Cardiovascular system
  • The pathogenesis of CVS involvement in COVID-19 is unknown and is likely multifactorial, and several theories have been postulated. ACE2 receptors are also exhibited by myocardial cells implicating direct cytotoxicity by the SARS-CoV-2 on the myocardium leading to myocarditis. Conversely, the release of proinflammatory cytokines such as IL-6 can lead to vascular inflammation, myocarditis, and cardiac arrhythmias.[41]
  • Acute coronary syndrome (ACS) is also a well-recognized cardiac manifestation of COVID-19. It is likely multifactorial due to the associated thrombogenicity associated with this virus and possibly due to the release of inflammatory cytokines, which may reduce coronary blood flow, reduce oxygen supply resulting in the destabilization of coronary plaque microthrombogenesis.[42][43][42]
• Effect of SARS-CoV-2 on the Gastrointestinal (GI) Tract
  • The pathogenesis of GI manifestations of COVID-19 is unknown and is likely multifactorial. Several mechanisms have been proposed, including the direct ACE 2-mediated viral cytotoxicity of the intestinal mucosa, cytokine-induced inflammation, gut dysbiosis, and vascular abnormalities.[44]
• Effect of SARS-CoV-2 on the Hepatobiliary System
  • The pathogenesis of liver injury in COVID-19 patients is unknown. Liver injury is likely multifactorial and is explained by various hypotheses that include ACE-2-mediated viral replication in the liver and its resulting cytotoxicity, hypoxic or ischemic damage, immune-mediated inflammatory response, drug-induced liver injury (DILI), or worsening of pre-existing liver disease.
• Effect of SARS-CoV-2 on the Renal System
  • The pathogenesis of COVID-19 associated kidney injury is unknown and is likely multifactorial explained by a single or a combination of many factors such as direct cytotoxic injury from the virus, imbalance in the RAAS, associated cytokine-induced hyperinflammatory state, microvascular injury, and the prothrombotic state associated with COVID-19. Other factors such as associated hypovolemia, potential nephrotoxic agents, and nosocomial sepsis can also potentially contribute to kidney injury.[45]

Histopathology

Lungs: A multicenter analysis of lung tissue obtained during autopsies of patients who tested positive for COVID-19 demonstrated typical diffuse alveolar damage features in 87% of cases. Additionally, there was a frequent presence of type II pneumocyte hyperplasia, airway inflammation, and hyaline membranes in alveolar zones. Forty-two percent of patients were noted to have large vessel thrombi, platelet (CD61 positive), and/or fibrin microthrombi were present in 84% of cases.[46]

GI Tract: Endoscopic specimens demonstrated positive staining of the viral nucleocapsid protein in the gastric, duodenal, and rectal epithelium cytoplasm. Numerous infiltrating plasma cells and lymphocytes with interstitial edema were seen in the lamina propria of the stomach, duodenum, and rectum.[47] 

Liver: A prospective single-center clinicopathologic case series study involving the postmortem histopathological exam of major organs of 11 deceased patients with COVID-19 reported hepatic steatosis findings in all patients. The liver specimens of 73% of patients demonstrated chronic congestion. Different forms of hepatocyte necrosis were noted in 4 patients, and 70% showed nodular proliferation.[48]

Heart: Analysis of cardiac tissue from 39 autopsy cases of patients who tested positive for SARS-CoV-2 demonstrated the presence of SARS-CoV-2 viral genome within the myocardium.[49]

Brain: A single-center histopathological study of brain specimens obtained from 18 patients who succumbed to COVID-19 demonstrated acute hypoxic injury in all patients’ cerebrum and cerebellum. Notably, no features of encephalitis or other specific brain changes were seen. Additionally, immunohistochemical analysis of brain tissue did not show cytoplasmic viral staining.[50]

Kidney: Histopathology analysis of kidney specimens obtained from autopsies of 26 patients with confirmed COVID-19 demonstrated signs of diffuse proximal tubular injury with loss of brush border, non-isometric vacuolar degeneration, and necrosis. Additionally, electron microscopy showed clusters of coronavirus-like particles with spikes in the tubular epithelium and podocytes.[51]

History and Physical

COVID-19, the illness caused by SARS-CoV-2, primarily affects the respiratory system and is spread mainly from person to person through respiratory particles from activities such as coughing and sneezing. The majority of transmission occurs from close contact with presymptomatic, asymptomatic, or symptomatic carriers. Transmission with aerosol-generating procedures and contamination of inanimate surfaces with SARS-CoV-2 has also been implicated in the spread of COVID-19. Epidemiologic data from several case studies have reported that patients with SARS-CoV-2 infection have the live virus present in feces implying possible fecal-oral transmission.[52] A meta-analysis that included 936 neonates from mothers with COVID-19 showed vertical transmission is possible but occurs in a minority of cases.[53] 

The median incubation period for SARS-CoV-2 is estimated to be 5.1 days, and the majority of patients will develop symptoms within 11.5 days of infection.[54] It is estimated that 17.9% to 33.3% of infected patients will remain asymptomatic.[55][56] Patients with SARS-CoV-2 infection can experience a range of clinical manifestations ranging from no symptoms to critical illness associated with respiratory failure, septic shock, and multiorgan failure. The vast majority of symptomatic patients commonly present with fever, cough, and shortness of breath and less commonly with a sore throat, anosmia, dysgeusia, anorexia, nausea, malaise, myalgias, and diarrhea. Stokes et al. reported that among 373,883 confirmed symptomatic COVID-19 cases in the US, 70% of them experienced fever, cough, shortness of breath, 36% reported myalgia, and 34% reported headache.[26] 

Another large meta-analysis that aimed to summarize clinicopathological characteristics of 8697 patients with COVID-19 in China reported laboratory abnormalities that included lymphopenia (47.6%), elevated C-reactive protein levels (65.9%), elevated cardiac enzymes (49.4%), and abnormal liver function tests (26.4%).[57] Other laboratory abnormalities included leukopenia (23.5%), elevated D-dimer (20.4%), elevated erythrocyte sedimentation rate (20.4%), leukocytosis (9.9%), elevated procalcitonin (16.7%), and abnormal renal function (10.9%).[57] The common radiographic findings in patients with COVID-19 include bilateral multifocal opacities on chest X-rays and bilateral, peripheral ground-glass opacities, with or without areas of consolidation on chest CT.

Based on the severity of presenting illness, the National Institutes of Health (NIH) has issued guidelines that classify COVID-19 into five distinct types that adults with SARS-CoV-2 infection can be grouped in. It considers the severity of clinical symptoms, laboratory and radiographic abnormalities, hemodynamics, and organ function.

• Asymptomatic or Presymptomatic Infection: Individuals with positive SARS-CoV-2 test without any clinical symptoms consistent with COVID-19.
• Mild illness: Individuals who have any symptoms of COVID-19 such as fever, cough, sore throat, malaise, headache, muscle pain, nausea, vomiting, diarrhea, anosmia, or dysgeusia but without shortness of breath or abnormal chest imaging
• Moderate illness: Individuals who have clinical symptoms or radiologic evidence of lower respiratory tract disease and who have oxygen saturation (SpO2) ≥ 94% on room air
• Severe illness: Individuals who have (SpO2) ≤ 94% on room air; a ratio of partial pressure of arterial oxygen to fraction of inspired oxygen, (PaO2/FiO2) <300 with marked tachypnea with respiratory frequency >30 breaths/min or lung infiltrates >50%.Neutrophilia is also considered an essential hallmark of severe illness.[39]
• Critical illness: Individuals who have acute respiratory failure, septic shock, and/or multiple organ dysfunction. Patients with severe illness may become critically ill with the development of acute respiratory distress syndrome (ARDS) that tends to occur approximately one week after the onset of symptoms. A multicenter prospective observational study that analyzed 28-day mortality in mechanically ventilated patients with ARDS concluded that COVID-19 ARDS patients had similar ARDS features from other causes. The risk of 28-day mortality increased with ARDS severity.[58]

The frequency of the spectrum of disease was described in a report from the Chinese Center for Disease Control and Prevention that reported mild disease in 81% of patients, severe disease (with shortness of breath, hypoxia, or abnormal imaging) in 14%, critical disease (respiratory failure, shock, multiorgan dysfunction in 5%, and an overall case fatality rate of 2.3%.[59] A comprehensive systematic review and meta-analysis involving 212 studies comprising of 281,461 individuals from 11 countries/regions reported that severe disease course was noted in about 23% with a mortality rate of about 6% in patients infected COVID-19.[60]

Extrapulmonary Manifestations of COVID-19

• Neurologic manifestations: Besides anosmia and ageusia, other neurological findings include headache, stroke, impairment of consciousness, seizure disorder, and toxic metabolic encephalopathy. Five patients with COVID-19 developed Guillain-Barré syndrome (GBS) based on a case series report from Northern Italy.[61][62]
• Cardiac manifestations: Myocardial injury manifesting as myocardial ischemia/infarction (MI) and myocarditis are well-recognized cardiac manifestations in patients with COVID-19. Other common cardiac manifestations include arrhythmias, cardiomyopathy, and cardiogenic shock. A single-center retrospective study analysis of 187 patients with confirmed COVID-19 reported that 27.8% of patients exhibited myocardial injury indicated by elevated troponin levels. The study also noted that patients with elevated troponin levels had more frequent malignant arrhythmias and a high mechanical ventilation rate compared with patients with normal troponin levels. The pre-existing cardiovascular disease seems to be linked with worse outcomes and increased risk of death in patients with COVID-19.[63]
• Hematologic manifestations: Lymphopenia is a common laboratory finding in the vast majority of patients with COVID-19. Other laboratory abnormalities include thrombocytopenia, leukopenia, elevated ESR levels, C-reactive protein (CRP) lactate dehydrogenase (LDH), and leukocytosis.COVID-19 is also associated with a state of coagulopathy as evidenced by the high prevalence of venous and thromboembolic events such as PE, DVT, MI, ischemic strokes, and arterial thromboses that also occurred in patients despite being maintained on prophylactic or even therapeutic systemic anticoagulation. Notably, COVID-19 is associated with markedly elevated D-dimer, fibrinogen levels, prolonged prothrombin time (PT), and partial thromboplastin time(aPTT) patients at risk of developing arterial and venous thrombosis.[39][63] Clinical trials are required to determine the benefit of therapeutic anticoagulation in patients with COVID-19, especially at what stage of the illness.
• Renal manifestations: Patients hospitalized with severe COVID-19 are at risk for developing kidney injury, most commonly manifesting as acute kidney injury (AKI), which is likely multifactorial in the setting of hypervolemia, drug injury, vascular injury, and drug-related injury, and possibly direct cytotoxicity of the virus itself. AKI is the most frequently encountered extrapulmonary manifestation of COVID-19 and is associated with an increased risk of mortality.[64] A large multicenter cohort study of hospitalized patients with COVID-19 that involved 5,449 patients admitted with COVID-19 reported that 1993(36.6%) patients developed AKI during their hospitalization, of which 14.3% patients required renal replacement therapy(RRT).[65] Other clinical and laboratory manifestations include proteinuria, hematuria, electrolyte abnormalities such as hyperkalemia, hyponatremia, acid-base balance disturbance such as metabolic acidosis.[63][39]
• Gastrointestinal manifestations: Based on a meta-analysis by Elmunzer et al.; that involved 1992 patients across 36 centers,1052 patients (53%) experienced GI symptoms, with the most common reported symptoms being diarrhea (34%), nausea (27%), vomiting (16%), abdominal pain (11%).[66] Cases of acute mesenteric ischemia and portal vein thrombosis have also been described.[67]
• Hepatobiliary manifestations: Elevation in liver function tests are frequently noted in 14% to 53% of patients with COVID-19 infection.[68] Hepatic dysfunction occurs more frequently in patients with severe COVID-19 illness.
• Endocrinologic manifestations: Patients with pre-existing endocrinologic disorders such as diabetes mellitus are at increased risk of developing severe illness. Clinical manifestations such as abnormal blood glucose levels, euglycemic ketosis, and diabetic ketoacidosis have been noted in patients hospitalized with COVID-19.[63]

Evaluation

A detailed clinical history regarding the onset and duration of symptoms, travel history, exposure to people with COVID-19 infection, underlying medical comorbidities, and medication history should be obtained by treating providers. Patients with typical clinical signs suspicious of COVID-19 such as fever, cough, sore throat, loss of taste or smell, malaise, and myalgias should be promptly tested for SARS-CoV-2. Besides symptomatic patients, anyone with known high-risk exposure to SARS-CoV-2 should be tested for SARS-CoV-2 infection even in the absence of symptoms.

The standard diagnostic mode of testing is testing a nasopharyngeal swab for SARS-CoV-2 nucleic acid using a real-time PCR assay. Commercial PCR assays have been validated by the US Food and Drug Administration (FDA) with emergency use authorizations (EUAs) for the qualitative detection of nucleic acid from SARS-CoV-2 from specimens obtained from nasopharyngeal swabs as well as other sites such as oropharyngeal, anterior/mid-turbinate nasal swabs, nasopharyngeal aspirates, bronchoalveolar lavage (BAL) and saliva.

The sensitivity of PCR testing is dependent on multiple factors that include the adequacy of the specimen, technical specimen collection, time from exposure, and specimen source.[69] However, the specificity of most commercial FDA-approved SARS-CoV-2 PCR assays is nearly 100%, provided that there is no cross-contamination during specimen processing. SARS-CoV-2 antigen tests are less sensitive but have a faster turnaround time compared to molecular PCR testing.[70] Comprehensive testing for other respiratory viral pathogens should be considered for appropriate patients as well.

Routine laboratory assessment with complete blood count (CBC), a comprehensive metabolic panel (CMP) that includes testing for renal and liver function, and a coagulation panel should be performed in all hospitalized patients. Troponin levels and a baseline EKG to rule out cardiac injury should be performed if clinically indicated, especially in patients presenting with chest tightness or shortness of breath.

Additional tests such as testing for inflammatory markers such as ESR, C-reactive protein (CRP), ferritin, lactate dehydrogenase, D-dimer, and procalcitonin can be considered in hospitalized patients. However, their prognostic significance in COVID-19 is not clear. Imaging studies may include chest x-ray, lung ultrasound, or chest computed tomography (CT). The American College of Radiology recommends against computed tomography’s routine use as an initial imaging study or as screening. There are no guidelines available regarding the timing and choice of pulmonary imaging studies in patients with COVID-19, and the type of imaging should be considered based on clinical evaluation.

Treatment / Management

At the onset of this pandemic, there was an urgency to mitigate this new viral illness with experimental therapies and drug repurposing. Since then, significant progress has been made in the management of COVID-19 due to the intense clinical research efforts globally that have resulted in novel therapeutics and vaccine development at an unprecedented speed. Currently, a variety of therapeutic options are available that include antiviral medications (e.g., remdesivir), anti-SARS-CoV-2 monoclonal antibodies (e.g., bamlanivimab/etesevimab, casirivimab/imdevimab), anti-inflammatory drugs (e.g., dexamethasone), immunomodulators agents (e.g., baricitinib, tocilizumab) are available under EUA or being evaluated in the management of COVID-19.[39] 

However, not every patient with COVID-19 qualifies for treatment with any of these medications. The utility of these treatments is specific and based on the severity of illness or certain risk factors. The clinical course of the COVID-19 illness occurs in 2 phases, an early phase when SARS-CoV-2 replication is greatest before or soon after the onset of symptoms. Antiviral medications and antibody-based treatments are likely to be more effective during this stage of viral replication. The later phase of the illness is driven by a hyperinflammatory state induced by the release of cytokines and the coagulation system’s activation that induces a prothrombotic state. Anti-inflammatory drugs such as corticosteroids, immunomodulating therapies, or a combination of these therapies may help combat this hyperinflammatory state than antiviral therapy.[70] Below is a summary of the latest potential therapeutic options proposed, authorized, or approved for clinical use in the management of COVID-19.

Antiviral Agents 

• Remdesivir is a broad-spectrum antiviral agent that previously demonstrated antiviral activity against SARS-CoV-2 in vitro.[71] Based on results from three randomized, controlled clinical trials that showed that remdesivir was superior to placebo in shortening the time to recovery in adults who were hospitalized with mild-to-severe COVID-19, the U.S. Food and Drug Administration(FDA) approved remdesivir for clinical use in adults and pediatric patients (over age 12 years and weighing at least 40 kilograms or more) to treat hospitalized patients with COVID-19.[72][73][74] However, results from the WHO SOLIDARITY Trial conducted at 405 hospitals spanning across 40 countries involving 11,330 inpatients with COVID-19 who were randomized to receive remdesivir (2750) or no drug (4088) found that remdesivir had little or no effect on overall mortality, initiation of mechanical ventilation, and length of hospital stay.[75] There is no data available regarding the efficacy of remdesivir against the new SARS-CoV-2 variants; however, acquired resistance against mutant viruses is a potential concern and should be monitored.
• Hydroxychloroquine and chloroquine were proposed as antiviral treatments for COVID-19 during the early onset of the pandemic. However, data from randomized control trials evaluating the use of hydroxychloroquine with or without azithromycin in hospitalized patients did not improve the clinical status or overall mortality compared to placebo.[76][77][78][79] Data from randomized control trials of hydroxychloroquine used as postexposure prophylaxis did not prevent SARS-CoV-2 infection or symptomatic COVID-19 illness.
• Lopinavir/ritonavir is FDA approved combo therapy for treating HIV and was proposed as antiviral therapy against COVID-19 during the early onset of the pandemic. Data from a randomized control trial that reported no benefit was observed with lopinavir-ritonavir treatment compared to standard of care in patients hospitalized with severe COVID-19.[80]Lopinavir/Ritonavir is currently not indicated for the treatment of COVID-19 in hospitalized and non-hospitalized patients.
• Ivermectin isan FDA-approved anti-parasitic drug used worldwide in the treatment of COVID-19 based on an in vitro study that showed inhibition of SARS-CoV-2 replication.[81] A single-center double-blind, randomized control trial involving 476 adult patients with mild COVID-19 illness was randomized to receive ivermectin 300 mcg/kg body weight for five days or placebo did not achieve significant improvement or resolution of symptoms.[82]

Anti-SARS-CoV-2 Neutralizing Antibody Products

Individuals recovering from COVID-19 develop neutralizing antibodies against SARS-CoV-2, and the duration of how long this immunity lasts is unclear. Nevertheless, their role as therapeutic agents in the management of COVID-19 is extensively being pursued in clinical trials.

• Convalescent plasma therapy was evaluated during the SARS, MERS, and Ebola epidemics; however, it lacked randomized control trials to back its actual efficacy. The FDA approved convalescent plasma therapy under EUA for patients with severe life-threatening COVID-19.[83][84]Although it appeared promising, data from multiple studies evaluating the use of convalescent plasma in life-threatening COVID-19 has generated mixed results. One retrospective study based on a US national registry reported that among patients hospitalized with COVID-19, not on mechanical ventilation, there was a lower risk of death in patients who received a transfusion of convalescent plasma with higher anti-SARS-CoV-2 IgG antibody than patients who received a transfusion of convalescent plasma with low antibody levels. Data from three small randomized control trials showed no significant differences in clinical improvement or overall mortality in patients treated with convalescent plasma versus standard therapy.[85][86][87] An in vitro analysis of convalescent plasma obtained from individuals previously infected with the ancestral SARS-CoV-2 strains demonstrated significantly reduced neutralization against the beta (B.1.351).[88] Another in vitro study reported that the beta (B.1.351) variant exhibited markedly more resistance to neutralization by convalescent plasma obtained from individuals previously infected with the ancestral SARS-CoV-2 strains compared to the alpha( B.1.1.7) variant, which was not more resistant to neutralization.[89]
• REGN-COV2 (Casirivimab and Imdevimab): REGN-COV2 is an antibody cocktail containing two noncompeting IgG1 antibodies (casirivimab and imdevimab) that target the RBD on the SARS-CoV-2 spike protein that has been shown to decrease the viral load in vivo, preventing virus-induced pathological sequelae when administered prophylactically or therapeutically in non-human primates.[90] Results from an interim analysis of 275 patients from an ongoing double-blinded trial involving non hospitalized patients with COVID-19 who were randomized to receive placebo, 2.4 g of REGN-COV2 (casirivimab 1,200 mg and imdevimab 1,200 mg) or 8 g of REGN-COV2 COV2 (casirivimab 2,400 mg and imdevimab 2,400 mg) reported that the REGN-COV2 antibody cocktail reduced viral load compared to placebo. This interim analysis also established the safety profile of this cocktail antibody, similar to that of the placebo group.[91] Preliminary data from a Phase 3 trial of REGN-COV (casirivimab/imdevimab) revealed a 70% reduction in hospitalization or death in non-hospitalized patients with COVID-19. In vitro data is available regarding the effect of REGN-COV2 on the two SARS-CoV-2 variants of concern (B.1.1.7; B.1.351 variants) that reveal retained activity.[92]
• Bamlanivimab (LY-CoV555 or LY3819253): Bamlanivimab is a neutralizing monoclonal antibody derived from convalescent plasma obtained from a patient with COVID-19. Like REGN-COV2, it also targets the RBD of the spike protein of SARS-CoV-2 and has been shown to neutralize SARS-CoV-2 and reduce viral replication in non-human primates.[93][94] Results from the Phase 2 trial (BLAZE-1) involving outpatients with a recent diagnosis of mild to moderate COVID-19 who were randomized to receive 1 of 3 doses (700 mg, 2800 mg, or 7000 mg) of bamlanivimab or placebo reported that patients who received bamlanivimab monotherapy did not have a significant decline in viral load compared to placebo. However, in this cohort, bamlanivimab reduced the risk of COVID-19 hospitalization or emergency department (ED) visits by day 29 by 70%. This interim analysis also established the safety profile of bamlanivimab, which was similar to that of the placebo group at all three doses.[95] A preprint study (not peer-reviewed) reported that bamlanivimab still binds to the Y501-RBD of SARS-CoV-2 (B.1.1.7, 20I/501Y.V1) in vitro, as efficiently as the previous N501-RBD of the original strain.[5] A separate preprint study by the same authors reported that the B.1.351/501Y.V2 variant and P.1/501Y.V3 variant, which shares three similar mutations (K417N, E484K, and N501Y), completely lost binding to bamlanivimab in vitro, causing complete loss of efficacy of bamlanivimab.[6] On March 25th, the U.S. government stopped its distribution of bamlanivimab alone, citing that the increasing emergence of coronavirus variants makes the treatment ineffective.
• Bamlanivimab and Etesevimab (LY-CoV555 or LY3819253 and LY-CoV016 or LY3832479) are potent anti-spike combinations neutralizing monoclonal antibody treatment used to treated outpatients with a recent diagnosis of mild to moderate COVID-19 who have high-risk comorbidities for severe COVID-19 infection. In vitro experiments revealed that etesevimab binds to a different epitope than bamlanivimab and neutralizes resistant variants with mutations in the epitope bound by bamlanivimab. In Phase 2 of the BLAZE-1 trial, bamlanivimab/etesevimab was associated with a significant reduction in SARS-CoV-2 viral load compared to placebo.[95] Data from the Phase 3 portion of BLAZE-1 is pending release, but preliminary information indicates that therapy reduced the risk of hospitalization and death by 87%. On June 25, 2021, the Department of Health and Human Resources reported a pause in the distribution of the combination monoclonal antibodies bamlanivimab and etesevimab based on in vitro studies showing that these monoclonal antibodies were ineffective against the Beta(B.1.351); and Gamma (P.1) variants.
• Sotrovimab(VIR-7831) is a potent anti-spike neutralizing monoclonal antibody that demonstrated in vitro activity against all the four VOCs Alpha (B.1.1.7), Beta (B.1.351), Gamma(P1), and Delta (B.1.617.2). Results from a preplanned interim analysis(not yet peer-reviewed) of the multicenter, double-blind placebo-controlled Phase 3, COMET-ICE trial by Gupta et.al that evaluated the clinical efficacy and safety of sotrovimab demonstrated that one dose of sotrovimab(500 mg) reduced the risk of hospitalization or death by 85% in high-risk non hospitalized patients with mild to moderate COVID-19 compared with placebo.
• REGN-COV2 (casirivimab and imdevimab) and sotrovimab were approved for clinical use by the FDA under two separate EUAs issued in November 2020 and May 2021, respectively, that allowed the use of these drugs only in nonhospitalized patients (aged ≥12 years and weighing ≥40 kg) with laboratory-confirmed SARS-CoV-2 infection and mild to moderate COVID-19 who are at high risk for progressing to severe disease and/or hospitalization. On March 25th, the U.S. government stopped its distribution of bamlanivimab alone, citing that the increasing emergence of coronavirus variants makes the treatment ineffective. Ongoing local vigilance regarding the prevalence of emerging variants will be necessary to determine which antibody treatments retain efficacy.

Immunomodulatory Agents

• Corticosteroids: Severe COVID-19 is associated with inflammation-related lung injury driven by the release of cytokines characterized by an elevation in inflammatory markers. During the pandemic’s early course, glucocorticoids’ efficacy in patients with COVID-19 was not well described. It was a debate and uncertainty topic purely due to the lack of scientific data from large-scale randomized clinical trials. The Randomized Evaluation of Covid-19 Therapy (RECOVERY) trial, which included hospitalized patients with clinically suspected or laboratory-confirmed SARS-CoV-2 who were randomly assigned to received dexamethasone (n=2104) or usual care (n=4321), showed that the use of dexamethasone resulted in lower 28-day mortality in patients who were on invasive mechanical ventilation or oxygen support but not in patients who were not receiving any respiratory support[96]. Based on this landmark trial results, dexamethasone is currently considered the standard of care either alone or in combination with remdesivir based on the severity of illness in hospitalized patients who require supplemental oxygen or non-invasive or invasive mechanical ventilation.
• Interferon-β-1a (IFN- β-1a): Interferons are cytokines that are essential in mounting an immune response to a viral infection, and SARS-CoV-2 suppresses its release in vitro[97]. However, previous experience with IFN- β-1a in acute respiratory distress syndrome (ARDS) has not benefited [98]. Results from a small randomized, double-blind, placebo-controlled trial showed the use of inhaled IFN- β-1a had greater odds of clinical improvement and recovery compared to placebo[99]. Another small randomized clinical trial showed that the clinical response using inhaled IFN- β-1a was not significantly different from the control group. The authors reported when used early, this agent resulted in a shorter length of hospitalization stay and decreased 28-day mortality rate. However, four patients who died in the treatment group before completing therapy were excluded, thus making the interpretation of these results difficult[100]. Currently, there is no data available regarding the efficacy of interferon β-1a on the three new SARS-CoV-2 variants (B.1.1.7; B.1.351 and P.1). Given the insufficient and small amount of data regarding this agent’s use and the relative potential for toxicity, this therapy is currently not recommended to treat COVID-19 infection.
• Interleukin (IL)-1 Antagonists: Anakinra is an interleukin-1 receptor antagonist that is FDA approved to treat rheumatoid arthritis. Its off-label use in severe COVID-19 was assessed in a small case-control study trial based on the rationale that the severe COVID-19 is driven by cytokine production, including interleukin (IL)-1β. This trial revealed that of the 52 patients who received anakinra and 44 patients who received standard of care, anakinra reduced the need for invasive mechanical ventilation and mortality in patients with severe COVID-19[101]. There is no data available regarding the efficacy of interleukin-1 receptor antagonists on the three new SARS-CoV-2 variants (B.1.1.7; B.1.351, and P.1). Given the insufficient data regarding this treatment based on case series only, this is not currently recommended to treat COVID-19 infection.
• Anti-IL-6 receptor monoclonal antibodies: Interleukin-6 (IL-6) is a proinflammatory cytokine that is considered the key driver of the hyperinflammatory state associated with COVID-19. Targeting this cytokine with an IL-6 receptor inhibitor could slow down the process of inflammation based on case reports that showed favorable outcomes in patients with severe COVID-19[102][103][104]. The FDA approved three different types of IL-6 receptor inhibitors for various rheumatological conditions (Tocilizumab, Sarilumab) and a rare disorder called Castleman’s syndrome (Siltuximab).
  • Tocilizumab is an anti-interleukin-6 receptor alpha receptor monoclonal antibody that has been indicated for various rheumatological diseases. The data regarding the use of this agent is mixed. A randomized control trial involving 438 hospitalized patients with severe COVID-19 pneumonia, among which 294 were randomized to receive tocilizumab and 144 to placebo, showed that tocilizumab did not translate into a significant improvement in clinical status or lower the 28-day mortality compared to placebo.[105] Results from another randomized, double-blind placebo-controlled trial involving patients with confirmed severe COVID-19 that involved 243 patients randomized to receive tocilizumab or placebo showed that the use of tocilizumab was not effective in preventing intubation or death rate.[106] The REMAP-CAP and RECOVERY trials (not yet published), two large randomized controlled trials, showed evidence of a mortality benefit in patients exhibiting rapid respiratory decompensation.[107]
  • Sarilumab and Siltuximab are IL-6 receptor antagonists that may potentially have a similar effect on the hyperinflammatory state associated with COVID-19 as tocilizumab. Currently, no known published clinical trials are supporting the use of siltuximab in severe COVID-19. Conversely, a 60-day randomized, double-blind placebo control multinational phase 3 trial that evaluated the clinical efficacy, mortality, and safety of sarilumab in 431 patients did not show any significant improvement in clinical status or mortality rate.[108] Another randomized, double-blind placebo-controlled study on sarilumab’s clinical efficacy and safety in adult patients hospitalized with COVID-19 is currently ongoing (NCT04315298).
• Janus kinase (JAK) inhibitors 
  • Baricitinib is an oral selective inhibitor of Janus kinase (JAK) 1 and JAK 2 currently indicated for moderate to severely active rheumatoid arthritis patients. Baricitinib was considered a potential treatment for COVID-19 based on its inhibitory effect on SARS-CoV-2 endocytosis in vitro and on the intracellular signaling pathway of cytokines that cause the late-onset hyperinflammatory state that results in severe illness.[109][110] This dual inhibitory effect makes it a promising therapeutic drug against all stages of COVID-19. A multicenter observational, retrospective study of 113 hospitalized patients with COVID-19 pneumonia who received baricitinib combined with lopinavir/ritonavir (baricitinib arm, n=113) or hydroxychloroquine and lopinavir/ritonavir (control arm, n=78) reported significant improvement in clinical symptoms and 2-week mortality rate in the baricitinib arm compared with the control arm. Results from the ACTT-2 trial, a double-blind, randomized placebo-controlled trial evaluating baricitinib plus remdesivir in hospitalized adult patients with COVID-19, reported that the combination therapy of baricitinib plus remdesivir was superior to remdesivir therapy alone in not only reducing recovery time but also accelerating clinical improvement in hospitalized patients with COVID-19, particularly who were receiving high flow oxygen supplementation or noninvasive ventilation.[111] Baricitinib, in combination with remdesivir, has been approved for clinical use in hospitalized patients with COVID-19 under a EUA issued by the FDA. The efficacy of baricitinib alone or in combination with remdesivir has not been evaluated in the SARS-CoV-2 variants, and there is limited data on the use of baricitinib with dexamethasone.  
  • Ruxolitinib is another oral selective inhibitor of JAK 1 and 2 that is indicated for myeloproliferative disorders, polycythemia vera, and steroid-resistant GVHD. Similar to baricitinib, it has been hypothesized to have an inhibitory effect on cytokines’ intracellular signaling pathway, making it a potential treatment against COVID-19. Results from a small prospective multicenter randomized controlled phase 2 trial evaluating the efficacy and safety of ruxolitinib reported no statistical difference than the standard of care. However, most of the patients demonstrated significant chest CT improvement and faster recovery from lymphopenia.[112] A large randomized, double-blind, placebo-controlled multicenter trial (NCT04362137) is ongoing to assess ruxolitinib’s efficacy and safety in patients with severe COVID-19.
  • Tofacitinib is another oral selective inhibitor of JAK 1 and JAK3 that is indicated for moderate to severe RA, psoriatic arthritis, and moderate to severe ulcerative colitis. Given its inhibitory effect on the inflammatory cascade, it was hypothesized that its use could ameliorate the viral inflammation-mediated lung injury in patients with severe COVID-19. Results from a small randomized controlled trial that evaluated the efficacy involving 289 patients who were randomized to receive tofacitinib or placebo showed that tofacitinib led to a lower risk of respiratory failure or death (PMID:34133856).
• Bruton’s tyrosine kinase inhibitors such as acalabrutinib, ibrutinib, rilzabrutinib are tyrosine kinase inhibitors that regulate macrophage signaling and activation currently FDA approved for some hematologic malignancies. It is proposed that macrophage activation occurs during the hyperinflammatory immune response seen in severe COVID-19. Results from a small off-label study of 19 hospitalized patients with severe COVID-19 who received acalabrutinib highlighted the potential clinical benefit of BTK inhibition.[113]Clinical trials are in progress to validate the actual efficacy in severe COVID-19 illness.

Management of COVID-19 Based on the Severity of Illness 

• Asymptomatic or Presymptomatic Infection
• Individuals with a positive SARS-CoV-2 test without any clinical symptoms consistent with COVID-19 should be advised to isolate themselves and monitor clinical symptoms.
• Mild Illness

• Based on the NIH guidelines, individuals with mild illness can be managed in the ambulatory setting with supportive care and isolation. 
• Laboratory and radiographic evaluation are routinely not indicated.
• Elderly patients and those with pre-existing conditions should be monitored closely until clinical recovery is achieved.  
• SARS-CoV-2 neutralizing antibodies such as REGN-COV2 (Casirivimab and Imdevimab) or sotrovimab can be considered outpatients who are at risk of disease progression with a low threshold to consider hospitalization for closer monitoring. 
• The National Institutes of Health (NIH) Covid-19 Treatment Guidelines Panel recommends against dexamethasone in mild illness.
• Moderate Illness

• Patients with moderate COVID-19 illness should be hospitalized for close monitoring.
• Clinicians and healthcare staff should don appropriate personal protective equipment (PPE) while interacting or taking care of the patient. 
• All hospitalized patients should receive supportive care with isotonic fluid resuscitation if volume-depleted, and supplemental oxygen therapy must be initiated if SpO2 and be maintained no higher than 96%. Patients should be monitored by continuous pulse oximetry.[114]
• Empirical antibacterial therapy should be started only if there is a suspicion of bacterial infection and should be discontinued as early as possible if not indicated.
• Patients with COVID-19 are at risk of developing venous and thromboembolic events. Thus all hospitalized patients with COVID-19 should receive thromboembolic prophylaxis with appropriate anticoagulation.
• Remdesivir and dexamethasone can be considered for patients who are hospitalized and require supplemental oxygen.
• The National Institutes of Health (NIH) Covid-19 treatment guidelines panel recommends the use of either remdesivir alone or dexamethasone plus remdesivir or dexamethasone alone if combination therapy (remdesivir and dexamethasone) is not available in hospitalized patients who require supplemental oxygen provided they are not on high flow oxygen delivery or require noninvasive ventilation or receive invasive mechanical ventilation or ECMO
• Severe/Critical Illness[115][114][39]

• Patients with severe/critical COVID-19 illness require hospitalization.
• Considering that patients with severe COVID-19 are at increased risk of prolonged critical illness and death, discussions regarding goals of care, reviewing advanced directives, and identifying surrogate medical decision-makers must be made.
• All patients should be maintained on prophylactic anticoagulation, considering COVID-19 is associated with a prothrombotic state.
• Clinicians and other healthcare staff must wear appropriate PPE that include gowns, gloves, N95 masks, and eye protection when performing aerosol-generating procedures on patients with COVID-19 in the ICU, such as endotracheal intubation, bronchoscopy, tracheostomy, manual ventilation before intubation, physical proning of the patient or providing critical patient care such as nebulization, upper airway suctioning, disconnecting the patient from the ventilator, and non-invasive positive pressure ventilation that may potentially lead to the aerosol generation.[116]
• Renal replacement therapy should be considered in renal failure when indicated.
• High-flow nasal cannula oxygen or noninvasive ventilation can be considered in patients who do not require intubation.
• Having awake patients self-prone while receiving high flow nasal cannula oxygen can improve oxygenation if endotracheal intubation is not indicated. However, the efficacy of performing this maneuver on awake patients is not clear and more data from clinical trials is needed.
• The National Institutes of Health (NIH) Covid-19 Treatment Guidelines Panel strongly recommends using dexamethasone in hospitalized patients who require oxygen via noninvasive or invasive ventilation. Combination therapy with dexamethasone plus remdesivir or baricitinib or tocilizumab in combination with dexamethasone alone can also be considered. If corticosteroids cannot be used, baricitinib plus remdesivir may be used.
• The National Institutes of Health (NIH) Covid-19 Treatment Guidelines Panel also recommends tocilizumab (as a single intravenous dose) in recently hospitalized patients who are exhibiting rapid respiratory decompensation due to COVID-19.
• Impending respiratory failure should be recognized as early as possible, and a skilled operator must promptly perform endotracheal intubation to maximize first-pass success.
• Vasopressors should be started to maintain mean arterial pressure between 60 mmHg and 65 mmHg. Norepinephrine is the preferred initial vasopressor. 
• Empiric antibacterial therapy should be considered if there is a concern for a secondary bacterial infection. Antibiotic use must be reassessed daily for de-escalation, and the duration of the treatment must be evaluated for appropriateness based on the diagnosis.
• Management of COVID-19 patients with ARDS should be similar to classical ARDS management from other causes that include prone positioning as per The Surviving Sepsis Campaign guidelines for managing COVID-19.[114]
• ECMO should be considered in patients with refractory respiratory failure.

Prevention of COVID-19

Besides the importance of imposing public health and infection control measures to prevent or decrease the transmission of SARS-CoV-2, the key to containing this global pandemic is by vaccination to prevent SARS-CoV-2 infection in communities across the world. Extraordinary efforts in global research during this pandemic have resulted in the development of novel vaccines against SARS-CoV-2 at an unprecedented speed to contain this viral illness that has devastated communities worldwide and has had a downward spiraling effect on the global economy. Vaccination triggers the immune system leading to the production of neutralizing antibodies against SARS-CoV-2. As per the WHO Coronavirus (COVID-19) Dashboard, more than 2.4 billion doses of vaccine doses have been administered as of 22 June 2021 with approximately 22% of the world’s population receiving at least one dose of the vaccine.

Vaccination triggers the immune system leading to the production of neutralizing antibodies against SARS-CoV-2. Results of an ongoing multinational, placebo-controlled, observer-blinded, pivotal efficacy trial reported that individuals 16 years of age or older receiving two-dose regimen the trial vaccine BNT162b2 (mRNA-based, BioNTech/Pfizer) when given 21 days apart conferred 95% protection against COVID-19 with a safety profile similar to other viral vaccines.[117] Results from another multicenter, Phase 3, randomized, observer-blinded, placebo-controlled trial demonstrated that individuals who were randomized to receive two doses of mRNA-1273 (mRNA based, Moderna) vaccine given 28 days apart showed 94.1% efficacy at preventing COVID-19 illness, and no safety concerns were noted besides transient local and systemic reactions.[118]

Based on the results of these vaccine efficacy trials, the FDA issued two EUAs, one on December 11, 2020, granting the use of the BNT162b2 vaccine, and another on December 18, 2020, granting the use of the mRNA-1273 vaccine for the prevention of COVID-19. A third vaccine, Ad26.COV2.S for the prevention of COVID-19 received EUA by the FDA on February 27, 2021, based on a multicenter, placebo control, phase trial showed that a single dose of Ad26.COV2.S vaccine conferred 73% efficacy in the US in preventing COVID-19 (data not yet published).

Interim analysis of an ongoing multicenter randomized control trial demonstrated ChAdOx1 nCoV-19 demonstrated clinical efficacy against symptomatic COVID-19 and had an acceptable safety profile.[119] The ChAdOx1 nCoV-19 vaccine has been approved or granted emergency use authorization to prevent COVID-19 in many countries across the world but has not yet received a EUA or approval from the FDA for use in the US. Besides the vaccines mentioned above, as many as seven other vaccines that include protein-based and inactivated vaccines have been developed indigenously in India, Russia, and China and have been approved or granted emergency use authorization to prevent COVID-19 in many countries around the world.

Differential Diagnosis

• Influenza A and B
• Parainfluenza virus
• Respiratory syncytial virus
• Adenovirus
• Cytomegalovirus
• Rhinovirus

Pertinent Studies and Ongoing Trials

Efficacy of Available COVID-19 Vaccines in Prevention Against SARS-CoV-2 Variants of Concern

The three novel vaccines, BNT162b2 vaccine,mRNA-1273 vaccine, and ChAdOx1 nCoV-19, were developed to target the SARS-CoV-2 spike protein main site where these variants have developed mutations, raising concerns regarding the efficacy of these vaccines against the new variants.

• BNT162b2 vaccine: The efficacy of the BNT162b2 vaccine against the four SARS-CoV-2 variants is unknown. In vitro analysis of 20 serum samples obtained from 15 participants from the BNT162b2 clinical efficacy trial efficiently neutralized all SARS-CoV-2 variants. Neutralization of B.1.1.7 variant and P.1 was roughly equivalent. The neutralization of B.1.351 was vigorous but lower than the ancestral SARS-CoV-2 strain.[120][117] Clinical trials of the BNT162b2 vaccine against these four new SARS-CoV-2 variants are ongoing and are awaited.
• mRNA-1273 vaccine: The efficacy of the mRNA-1273 vaccine against the SARS-CoV-2 variants is unknown.In vitro analysis of serum samples obtained from participants of the mRNA-1273 vaccine, clinical efficacy trialdemonstrated that the mutations affecting the RBD of the B.1.1.7 variant had no significant effect on neutralization by serum obtained from participants who received the mRNA-1273 vaccine. Conversely, the analysis also showed a decrease in titers of neutralizing antibodies against the B.1.1.7+E484K variant, B.1.351 variant, P.1 variant, and the B.1.427/B.1.429 variants. The reduction in neutralizing titers was significantly lower in the B.1.351 variant.[118]
• Ad26.COV2.S vaccine: A single dose of this vaccine offers protection against COVID-19 consistently across many countries, including Brazil with a predominant percentage of strains from the P.2 lineage and across South Africa with a predominant percentage of strains from the B.1.135 lineage (data not yet reported). It is important to note that the vaccine’s efficacy in the US was higher by a factor of 1.3 compared to South Africa (72% versus 57%).[121]
• ChAdOx1 nCoV-19 vaccine: A two-dose regimen of the ChAdOx1 nCoV-19 vaccine did not confer protection against mild to moderate COVID-19 SARS-CoV-2 B.1.351 variant based on results from a multicenter, double-blind, randomized control trial 33725432. Results of another randomized control trial by Emary et al. published on March 30, 2021, in the Lancet regarding the ChAdOx1 nCoV-19 vaccine showed that in vitro neutralization activity against the B.1.1.7 variant was reduced compared with a non-B.1.1.7 variant and the clinical efficacy of the vaccine was 70.4 % for B.1.1.7 showed compared to 81.5 % efficacy noted in non-B.1.1.7 variants.[122]

Prognosis

The prognosis of COVID-19 is largely dependent on various factors that include the patient’s age, the severity of illness at presentation, pre-existing conditions, how quickly treatment can be implemented, and response to treatment. As previously described, the frequency of the spectrum of disease was described in a report from the Chinese Center for Disease Control and Prevention that reported mild disease in 81% of patients, severe disease (with shortness of breath, hypoxia, or abnormal imaging) in 14%, critical disease (respiratory failure, shock, multiorgan dysfunction in 5%, and an overall case fatality rate of 2.3%.[59] 

A comprehensive systematic review and meta-analysis involving 212 studies comprising of 281,461 individuals from 11 countries/regions reported that severe disease course was noted in about 23% with a mortality rate of about 6% in patients infected COVID-19.[60]

Complications

• COVID-19 can be regarded as a systemic viral illness based on the involvement of major organ systems.
• Patients with advanced age and comorbid conditions such as obesity, diabetes mellitus, chronic lung disease, cardiovascular disease, chronic kidney disease, chronic liver disease, and neoplastic conditions are at risk of developing severe COVID-19 and its associated complications. The most common complication of severe COVID-19 illness is progressive or sudden clinical deterioration leading to acute respiratory failure and ARDS and/or multiorgan failure leading to death.
• Patients with COVID-19 illness are also at increased risk of developing prothrombotic complications such as PE, DVT, MI, ischemic strokes, and arterial thrombosis.[39]
• Cardiovascular system involvement results in malignant arrhythmias, cardiomyopathy, and cardiogenic shock.
• Acute renal failure is the most frequently encountered extrapulmonary manifestation of COVID-19 and is associated with an increased risk of mortality.[64]
• More recent data have emerged regarding prolonged symptoms in patients who have recovered from COVID-19 infection, termed “post-acute COVID-19 syndrome.” A large cohort study of 1773 patients performed 6 months after hospitalization with COVID-19 revealed that most exhibited at least one persistent symptom: fatigue, muscle weakness, sleep difficulties, or anxiety. Patients with severe illness also had an increased risk of chronic lung issues.[123]

Deterrence and Patient Education

• Patients must be educated and encouraged to adhere to social distancing guidelines, use of facemasks and travel guidelines as per CDC guidelines, and social distancing state and local authorities’ social distancing protocols.
• Patients must be educated about frequent handwashing for a minimum of 20 seconds with soap and water when they come in contact with contaminated surfaces.
• Patients should be educated and encouraged to seeking emergency care when necessary.
• Patients should be educated and given an option for telehealth services in place of office visits if applicable.
• Patients must be educated about the efficacy of the available vaccines and the benefits of the vaccination.
• Patients should be encouraged to seek treatment early and be educated on new treatment options such as monoclonal antibodies.

Enhancing Healthcare Team Outcomes

• COVID-19 has wreaked havoc across the world and has overwhelmed many healthcare systems and economies of many countries. Three vaccines have been authorized for use in the US by the FDA under an Emergency Use Authorization (EUA).
• Until most of the world’s population gets vaccinated against this illness, COVID-19 will continue to remain a threat to global public health with the emergence of potentially treatment-resistant variants.
• Prevention and management of this highly transmissible respiratory viral illness require a holistic and interprofessional approach that includes physicians’ expertise across specialties, nurses, pharmacists, public health experts, and governmental authorities. There should be closed-loop communication between the clinical providers, pharmacists, and nursing staff while managing patients with COVID-19.
• Clinical providers managing COVID-19 patients on the frontlines should keep themselves periodically updated with the latest clinical guidelines about diagnostic and therapeutic options available in the management of COVID-19 especially considering the emergence of new SARS-CoV-2 variants, which could have a huge impact on morbidity and mortality.
• Clinicians should maintain a high index of suspicion in patients from a high risk of exposure area or recent travel to a high exposure area who present with extrapulmonary manifestations in the absence of pulmonary symptoms. These patients should be appropriately triaged and tested for SARS-CoV-2.
• Resources for contact tracing and testing must be enhanced to limit the spread of this virus. Patients must be educated and encouraged to adhere to social distancing guidelines, travel guidelines, and the use of facemasks as per CDC guidelines and COVID-19 protocols of state and local authorities.
• Clinical pharmacists must also keep themselves updated about the emergence of novel therapeutics that have been approved or granted emergency use authorization in the management of COVID-19.
• Hospitals and communities should have in place a plan to triage moderate and high-risk patients for additional therapy, such as monoclonal antibodies, on an outpatient basis.
• A strong focus must be made to educate the public about the importance of receiving the vaccination against COVID-19, and consideration must be made to establish mass vaccination sites.
• Continued viral surveillance of new variants must be performed at regular intervals with viral genomic sequencing given the possibility that more highly transmissible, more virulent variants and treatment-resistant variants could emerge that can have a more catastrophic effect on global health in addition to the current scenario.
• Such a multi-pronged approach enhances improved patient care and outcomes. It also reduces the burden of hospitalizations that could potentially lead to the exhaustion of healthcare resources.
• Such measures could immensely change the dynamic of healthcare infrastructure and go a long way in eradicating or eliminating this virus and limiting its devastating effect on socioeconomic and healthcare situations across the entire world.

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he SARS-CoV-2 lambda variant (lineage C.37) was designated by the World Health Organization as a variant of interest and is currently increasing in prevalence in South American and other countries. The lambda spike protein contains novel mutations within the receptor binding domain (L452Q and F490S) that may contribute to its increased transmissibility and could result in susceptibility to re-infection or a reduction in protection provided by current vaccines. In this study, the infectivity and susceptibility of viruses with the lambda variant spike protein to neutralization by convalescent sera and vaccine-elicited antibodies was tested. Virus with the lambda spike had higher infectivity and was neutralized by convalescent sera and vaccine-elicited antibodies with a relatively minor 2.3-3.3-fold decrease in titer on average. The virus was neutralized by the Regeneron therapeutic monoclonal antibody cocktail with no loss of titer. The results suggest that vaccines in current use will remain protective against the lambda variant and that monoclonal antibody therapy will remain effective.

Lambda spike protein-pseudotyped lentiviruses
The lambda spike protein has mutations L452Q and F490S in the RBD, and G75V, T76I mutations and 246-252 deletions in the N-terminal domain (NTD) (Figure S1A). To analyze antibody neutralization of the variant spike protein, we generated expression vectors for the variant and its constituent mutations and used these to produce pseudotyped lentiviral virions encoding GFP and nano-luciferase reporters. The use of such pseudotypes to determine antibody neutralizing titers has been shown to yield results consistent with those obtained with the live virus plaque reduction neutralization test10. Immunoblot analysis of transfected pseudotype virus producer cells and virus-containing supernatants showed that the variant spike proteins were well expressed, proteolytically processed and incorporated into lentiviral virions at a level similar to that of the parental D614G spike protein (Figure S1B). Analysis of the infectivity of the pseudotyped viruses on ACE2.293T cells, normalized for particle number, showed that the lambda spike protein increased infectivity by 2-fold. The increase was due to the L452Q mutation; the other mutations (G75V-T76I, F490S, T859N and Δ246-252) had no significant effect on infectivity (Figure S1C).

Neutralization of the lambda variants by convalescent sera and vaccine-elicited antibody

Analysis of serum specimens from convalescent patients who had been infected prior to the emergence of the variants showed that viruses with the lambda variant spike protein were 3.3-fold resistant to neutralization by convalescent sera as compared to neutralization of virus with the parental D614G spike, similar to the 4.9-fold resistance of the B.1.351 variant to neutralization (Figure 1A).

Analysis of serum samples from individuals vaccinated with Pfizer BNT162b2 showed that virus with the lambda spike was about 3-fold resistant to neutralization (Figure 1B). Serum samples from individuals vaccinated with the Moderna mRNA-1273 vaccine were on average 2.3-fold resistant to neutralization (Figure 1C). The resistance was attributed to the L452Q and F490S mutations in the lambda spike protein (Figure 1A, B, C).

L452Q increases spike protein affinity for ACE2

N501Y and L452R mutations in the RBD of earlier variants increase spike protein affinity for ACE2, an effect that most likely is a primary contributor to the increased transmissibility of the alpha, beta and delta variants11. To determine whether the lambda variant has an increased affinity for ACE2, we used a sACE2 neutralization assay in which pseudotyped virions were incubated with different concentrations of sACE2 and the infectivity of the treated virions was measured on ACE2.293T cells. The results showed that the lambda spike caused a 3-fold increase sACE2 binding. The increase was caused by the L452Q mutation and was similar to the increase provided by the N501Y mutation12,13 (Figure 1D). The F490S mutation did not have a detectable effect on sACE2 binding. The findings suggest that L452Q, like L452R in the delta variant, increases virus affinity for ACE2, likely contributing to increased transmissibility.

Neutralization by REGN10933 and REGN10987 monoclonal antibodies
Analysis of REGN10933 and REGN10987, the monoclonal antibodies that constitute the Regeneron REGN-COV2 therapy, showed that virus with the lambda variant spike protein was about 3.6-fold resistant to neutralization by REGN10987. The resistance was attributed to the L452Q mutation (Figure 2A and B). Virus with the lambda variant spike protein was neutralized by REGN10933 with no decrease in titer. The REGN10933 and REGN10987 cocktail neutralized the virus with no decrease in titer relative to virus with the D614G spike protein (Figure 2A and B).

Discussion

Virus with the lambda spike protein, like several VOC variant spike proteins showed a partial resistance to neutralization by vaccine-elicited antibodies and convalescent sera; however the average 3-fold decrease in neutralizing titer against the variant is not likely to cause a significant loss of protection against infection as the average neutralization IC50 titer by the sera of BNT162b2 and mRNA-1273 vaccinated individuals was about 1:600, a titer that is above that in the sera of individuals who recovered from infection with the parental D614G virus. A small fraction of vaccinated individuals had serum antibody titers less than average but whether this will lead to reduced protection from variant infection will need to be determined in epidemiological studies.

The resistance of the lambda variant to antibody neutralization was caused by the L452Q and F490S mutations. The L452R mutation of the California B.1.427/B.1.429 is associated with a 2-fold increase in virus shedding by infected individuals and a 4-6.7-fold and 2-fold decrease in neutralizing titer by the antibodies of convalescent and vaccinated donors, respectively14. The degree of neutralization resistance provided by L452Q was similar to that of L452R. Amino acid residues 490 and 484 lie close together on the top of the RBD and are therefore in a position to affect the binding of neutralizing antibody. The E484K mutation in the B.1.351, B.1.526, P.1 and P.3 spike proteins causes partial resistance to neutralization2–7. Similarly, the F490S mutation also caused a 2-3-fold resistance to neutralization, demonstrating the importance of the amino acid as an antibody recognition epitope. While the lambda variant was slightly resistant to REGN10987, it was neutralized well by the cocktail with REGN10933.

This study suggests that the L452Q and F490S mutations of the lambda variant spike protein caused a partial resistance to vaccine elicited serum and Regeneron monoclonal antibodies. While our findings suggest that current vaccines will provide protection against variants identified to date, the results do not preclude the possibility that novel variants will emerge that are more resistant to current vaccines. The findings highlight the importance of wide-spread adoption of vaccination which will protect individuals from disease, decrease virus spread and slow the emergence of novel variants.

reference link : https://www.biorxiv.org/content/10.1101/2021.07.02.450959v1.full

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reference link : https://www.ncbi.nlm.nih.gov/books/NBK570580/