key: cord-0740890-ygqed30x
authors: Fallah, Ali; Razavi Nikoo, Hadi; Abbasi, Hamidreza; Mohammad-Hasani, Azadeh; Hosseinzadeh Colagar, Abasalt; Khosravi, Ayyoob
title: Features of Pathobiology and Clinical Translation of Approved Treatments for Coronavirus Disease 2019
date: 2021-10-25
journal: Intervirology
DOI: 10.1159/000520234
sha: 9f566e33a4b262f24ba6a7ef486a7b27aa45f47f
doc_id: 740890
cord_uid: ygqed30x

BACKGROUND: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is currently the most important etiological agent of acute respiratory distress syndrome (ARDS) with millions of infections and deaths in the last 2 years worldwide. Several reasons and parameters are responsible for the difficult management of coronavirus disease-2019 (COVID-19) patients; the first is virus behavioral factors such as high transmission rate, and the different molecular and cellular mechanisms of pathogenesis remain a matter of controversy, which is another factor. SUMMARY: In the present review, we attempted to explain about features of SARS-COV-2, particularly focusing on the various aspects of pathogenesis and treatment strategies. KEY MESSAGES: We note evidence for the understanding of the precise molecular and cellular mechanisms of SARS-CoV-2 pathogenesis, which can help design the appropriate drug or vaccine. Additionally, and importantly, we reported the updated issues associated with the history and development of treatment strategies such as, drugs, vaccines, and other medications that have been approved or under consideration in clinics and markets worldwide.

The novel coronavirus-infected persons from Wuhan city, Hubei Province, China, were described in December 2019 [1] . To date, the acute respiratory distress syndrome (ARDS) related to novel coronavirus affected Ali Fallaha, Hadi Razavi Nikoob and Hamidreza Abbasid contributed equally.

SARS-CoV-2 includes pleomorphic spherical particles of 70-90 nm diameter with coronavirus-specific morphology that were derived from clinical samples and seen under a transmission electron microscope [9, 10] . Coronaviruses are enveloped viruses containing an unsegmented, single-stranded, positive-sense RNA genome of around 30 kb in length, which is enclosed by a 5′-cap and 3′-poly (A) tail [10, 11] . The genome organization of SARS-CoV-2 has similarities to that of other beta-coronaviruses. SARS-CoV-2 genome is demarcated by short RNA breakpoint sequences that lead to recombination at specific nonrandom locations within the viral genome, suggesting the evolutionary pattern of coronaviruses over vast distances in time [12] .

The genome and subgenome produce 6 open reading frames (ORFs). The majority of the 5′ end is occupied by ORF1a/b, encoding sixteen nonstructural proteins (NSP1-NSP16) [11, 13] . One large polyprotein is initially produced from ORF1a/b and cleaved by the papain-like protease encoded within NSP3 and the 3C-like protease, to produce replication-transcription complex, which are necessary for viral transcription and replication. The remaining ORFs encode for 9 putative accessory proteins and 4 structural proteins (Spike-S, Envelope-E, Membrane-M, and Nucleocapsid-N) (Fig. 1 ) [14] . The specific role and function of each protein in the life cycle of the virus are shown in Table 1 . Phylogenetic analysis of the SARS-CoV-2 S gene sequence illustrates that there are distinguished 27 amino acid substitutes in contrast to SARS-CoV-1/SARS-like coronaviruses. These substitutions are about higher infectivity and lower pathogenicity of SARS-CoV-2 than SARS-like coronaviruses [15] . SARS-CoV-2 evolved 2 major types L and S that differ in 2 SNPs. These are at positions of 8782 and 28114 that are located in ORF1ab (T8517C, synonymous) and ORF8 (C251T, S84L), respectively [16] . In addition, L type was the most prevalent, detected in 70% of the samples amplified, and S type was detected in 30% of the specimens. L and S types of SARS-CoV-2 have very small genetic differences and may not influence the immune response [4] .

Four major structural proteins in SARS-CoV-2 are mentioned in brief below:

(1) S is a large multifunctional transmembrane glycoprotein, and cleaved into S1 and S2 units. (2) Matrix glycoprotein (M) is the most abundant viral protein, which gave a definite shape to the viral envelope, and is essential for virus morphogenesis and assembly. (3) E is the smallest of the major structural proteins. It acts as a viroporin (ion channel) and is essential for various stages of the virus cycle, such as pathogenesis, assembly, and release of the virus. (4) N is the only structural protein that binds to the genomic RNA, and facilitates virion assembly, and enhances the transcription efficiency of the virus [17] [18] [19] [20] .

Binding to ACE2 and Entry The first SARS-CoV-2 targets human cells, such as nasal and bronchial epithelial cells and pneumocystis, SARS-CoV-2 (COVID-19) Virus 3 Intervirology DOI: 10.1159/000520234 through the binding of viral structural S glycoprotein to the angiotensin-converting enzyme 2 (ACE2), as a zinccontaining metalloenzyme, which is widely expressed in many cells [21] . The attachment of receptor-binding domain (RBD) located on the surface of S glycoprotein to ACE2 prompts endocytosis of the virus [22] . The S1 subunit binds to the ACE2 via its RBD, and the S2 subunit is responsible for membrane fusion (Fig. 2) [3] . Additionally, the priming of the virus S protein is mediated by different co-receptors and activators, including transmembrane serine protease 2 and endosomal/lysosomal cysteine proteases such as cathepsin B and L. Taken together, these events can cause downregulation of ACE2, through internalization and degradation of the protein, which in turn results in the loss of cilia and squamous metaplasia, which contribute to severe lung injury [23, 24] . In addition to the ACE2 receptor, SARS-CoV-2 could bind the putative alternative receptor CD147 to enter target cells. Research has shown that when CD147 protein expression is inhibited, cell infection with the new coronavirus is reduced by 50% [5, 25] .

According to the WHO and COVID-19 treatment guidelines, many antiviral agents are known today as "effective compounds" against the SARS-CoV-2, but here we investigated the NIH-or WHO-recommended antiviral agents that are available at https://www.covid19treatmentguidelines.nih.gov [26] for a better understanding of their antiviral properties on SARS-CoV-2. These drugs can target viral replication machinery, RNA polymerase, and viral protease, or modulate inflammatory responses against SARS-CoV-2 [27, 28] . Characteristics of approved and under development therapeutics options such as medication class, product name, clinical phase, manufacturing, mechanisms of action, dosage, and limitation are shown in Table 2 and Figure 3 .

Reduction of viral loads in COVID-19 patients treated with some antiviral agents that can inhibit the binding of SARS-CoV-2 to host cells was found in various phases of clinical trials, indicating the inhibitory effect of these molecules on viral envelope proteins and their host cell receptors/co-receptors [31, 32] . These are including antiviral drugs (ivermectin), neutralizing monoclonal anti- Genome properties of SARS-CoV-2. A The large replica polyproteins encoded by ORF1a/b are cleaved by the PL pro and the 3CL pro , to produce nonstructural proteins that are highly conserved throughout coronaviruses. B The S protein mainly contains the S1 and S2 subunits. The S1/S2 cleavage sites are highlighted. This scheme is a mixed conclusion from a previous study [15] [16] [17] [18] [19] [20] . bodies (bamlanivimab and etesevimab), recombinant human monoclonal antibodies (casirivimab, imdevimab, and sotrovimab), and convalescence plasma [33] . At the beginning of the pandemic, several studies reported data on the antiviral activity of ivermectin, hydroxychloroquine alone, or in combination with azithromycin against SARS-CoV-2 [34] [35] [36] . The updates obtained from different trials with thousands of COVID-19 patients indicated these drugs do not reduce mortality or the duration of mechanical ventilation, and even cause adverse drug reactions [37] . Convalescent plasma or serum from a patient who recovered from COVID-19 could be another option for prophylaxis of infection and treatment of CO-VID-19 patients, particularly after the onset of symptoms [38] . The antibody binds the S protein which prevents the entry of SARS-CoV-2 into the host cell and viral neutralization. In addition, the antibody modulates the inflammatory response, which is also more easily achieved during the initial immune response, a stage that may be asymptomatic [39] . There are reports that convalescent serum was used for the therapy of patients with CO-VID-19 in China during the current outbreak [40] . Recently, the connection of the SARS-CoV-specific human MAb CR3022 to SARS-CoV-2 RBD showed its potential as a remedial factor in the management of SARS-CoV-2. Indeed, it can be applied alone or in combination with other impressive treatments [41] . Interactions with some structural proteins and involved in virus release, apoptosis, and pathogenesis ORF3b

Apoptosis stimulator, and inhibits the antiviral innate immune response ORF6

Effective in viral pathogenesis, and inhibition of IFN induction ORF7a

Apoptosis induction ORF7b

Unknown (an integral membrane protein, expressed in viral-infected cells) ORF8

May enhance replication and shows interaction with some structural proteins ORF9b

Shows interaction with some NSPs and interferon antagonist ORF10

Its function is not clearly understood but may have an immune modulatory role ORF14

Unknown (consists of 73 amino acid residues) S protein Mediates attachment and viral entry into the host cell E protein It acts as a viroporin and is essential for stages of the virus cycle, such as pathogenesis, assembly, and release of the virus M protein It is essential for virus morphogenesis and assembly N protein It facilitates virion assembly and enhances the transcription efficiency of the virus 

After the attachment, the ACE2/S SARS-CoV-2 complex is internalized into the cytoplasm by receptor-mediated endocytosis and prompts uncoating of virion in the acidic endosomal vesicles to release of the single-stranded viral RNA [42] . The positive single-stranded viral RNA translated into replicase polyproteins pp1a/pp1b and other products such as nsp1-16 collectively constitute the functional replication-transcription complexes by the host cell machinery [43] . Ribosomal frame shifting during the translation process has been seen in the replication of SARS-CoV-2, which produces genomic and multiple copies of subgenomic RNA species [23, 44] . The assembly of viral particles takes place via the interaction of genomic RNA and viral envelope proteins (S, E, and M) at the endoplasmic reticulum and Golgi complex [45] . Finally, these virions are subsequently released out of the cells via exocytosis [46] . It has been shown that several antiviral drugs influence the viral replication machinery in different ways: (i) directly targeting the viral proteins, such as RdRp and viral protease, and (ii) interruption of viral replication machinery through modulating cellular factors [47, 48] . Remdesivir, favipiravir, ribavirin, sofosbuvir, and tenofovir revealed the interaction and inhibition of RdRp, resulting in the reduced viral RNA synthesis and mRNA capping [49] . Remdesivir is the best example of a novel nucleotide analog with strong therapeutic applications against a diverse range of human viruses such as Ebola virus disease, SARS-CoV-1 and MERS, and SARS-like coro-naviruses that inhibit viral RNA synthesis [50] . In addition, other inhibitors including lopinavir, ritonavir (Kaletra), and darunavir have been tested in clinical trials in the treatment of COVID-19 patients. This class of drugs interferes with the processing of the viral polyprotein by blocking the function of viral protease. Among these drugs, remdesivir is the only FDA-approved antiviral agent for the treatment of COVID-19 [51] .

Virus replication (Viral phase) in pneumocytes leads to the inflammatory response, including macrophages, natural killer cells, CD4+T cells, cytotoxic T lymphocytes/CTLs, and antibody responses [52] . In later stages of infection, epithelial-endothelial barrier integrity is compromised, which potentially mediates lung injury, as well as extrapulmonary systemic involvement caused by SARS-CoV-2 [53] . Viral replication and pathobiology of SARS-CoV-2 virus are shown in Figure 4A -D. Several therapeutics plans modulate inflammatory responses against SARS-CoV-2 by different mechanisms. Approved and under evaluation plans include (1) immunomodulatory (colchicine, corticosteroids, interleukin inhibitors [IL-1 and IL-6], and interferons) and (2) cell-based therapy (mesenchymal stem cell) [54] [55] [56] .

Pathophysiology of SARS-CoV-2-induced ARDS is a multifactorial process and is very similar to SARS-CoV-1 S protein 3D structure Viral envelope TM S2 S1 RBD ACE2 TMPRSSs Host cell Cell membrane Fig. 2 . The S protein of coronaviruses facilitates viral entry into target cells. The S protein of SARS-CoV-2 binds to ACE2 as the entry receptor, through its S2 subunit for viral attachment. The S protein is cleaved by the cellular serine protease that called TMPRSSs at the S1/S2 boundary or within the S1 subunit, which removes the structural constraint of S1 on S2, and releases the internal fusion peptide combined with the S TM domain for the viral fusion. This scheme is a mixed conclusion from a previous study [24] . S, spike; SARS-CoV-2, severe acute respiratory syndrome coronavirus-2; ACE2, angiotensin-converting enzyme 2;TMPRSSs, transmembrane serine proteases. and MERS infectious patients, with less severe pathogenesis [57, 58] . The clinical symptoms of SARS-CoV-2 can be asymptomatic, symptomatic, mild, and also lead to severe disease with multi-organ failure. In the symptomatic phase or Viral phase, in which the clinical manifestations of the disease usually start 5 days after exposure, patients may experience symptoms such as fever, dyspnea, sore throat, chest pain, expectoration, cough, and myalgia, but fever, cough, and fatigue are common symptoms of COVID-19 [59] . At the present, there are different confirming diagnostic methods for the detection of SARS-CoV-2 in patients, around the time of symptom onset, in laboratories, as follows: (1) nucleic acid tests like real-time RT-PCR or next-generation sequencing; (2) antibody or antigen detection tests, including enzymelinked immunosorbent assay; (3) chest computed tomography and spectroscopic techniques [60] [61] [62] [63] . Real-time RT-PCR on nasopharyngeal and oropharyngeal swabs is considered the "gold standard" for confirming the diagnosis in clinical cases of COVID-19 [64, 65] . Besides clinical symptoms, the blood biochemistry indexes such as the total white blood cell, lymphocyte, platelet, and thromboplastin time decline, while C-reactive protein, lactate dehydrogenase, aspartate transaminase, alanine aminotransferase, cytokine level, and bilirubin increase in most patients [66] . ARDS is a prevalent phenomenon in patients, followed by anemia, acute heart injury, and secondary infections [67] . Reports illustrate that middleaged and older people with chronic and underlying diseases, especially high blood pressure and diabetes, are susceptible to respiratory failure and have poorer prognoses, but it does not mean that children are lesser than old people susceptible to SARS-CoV-2 [68] [69] [70] . In the later stages of infection or the thrombo-inflammatory phase, ARDS is a common complication, and resulted from the occurrence of cytokine storms and immune regulatory network imbalance, which is finally followed by anemia, acute heart damage, multiple organ failure, and secondary bacterial infections [71] . Bilateral severe interstitial inflammation of the lungs is found in the chest computed tomography pictures or chest X-ray, which is named ground-glass opacity and involves a local lobe but later expands to multiple lung lobes [67] .

With the threat of millions of people being infected and health-care systems becoming overwhelmed, the race is on to develop a vaccine that will protect individuals and slow the spread of the disease [72] . S protein plays a significant role in the induction of protective immunity against SARS-CoV-2 by mediating T-cell responses and neutralizing antibody production [73] . In the past few decades, scientists would develop vaccines that induce the body to produce antibodies that recognize and block human coronaviruses with the use of S protein as the target [74] . Nonetheless, the expanded vaccines have minimal usage, even between strains close together of the virus, owing to an absence of cross-conservation [75] . Recently, researchers identified the at least target domain of the virus's S protein that is critical for docking with ACE2 receptor and this region or RBD located in the S1 subunit of the S protein [76] [77] [78] . Furthermore, several studies strongly reported that viral structural proteins such as N, M, and E proteins have the potential for inclusion within future vaccine candidates to stimulate T-cell responses, and may significantly contribute to the recovery from COVID-19 [1] .

In addition, inactivated and live attenuated vaccine platforms can induce broad and strong immune responses, in comparison to the other platforms, because they have the whole virion including structural and nonstructural proteins [1, 79, 80] . According to the vaccine tracker reported by the World Health Organization, October 2021, nearly 300 vaccine candidates are currently under various phases of development. In total candidate vaccines, 194 and 123 are in clinical and preclinical phases, respectively, that are available at https://www.who.int/ publications/m/item/draft-landscape-of-covid-19-candidate-vaccines. There are 10 platforms for COVID-19 vaccines including, PS, nonreplicating viral vector (VVnr), replicating viral vector (VVr), VVnr in combination with an antigen-presenting cell (VVnr + APC), VVr in combination with an antigen-presenting cell (VVr + APC), virus-like particle, inactivated virus, live attenuated virus, mRNA vaccine (RNA), and DNA [30, 81, 82] . Around 11 vaccine candidates have been authorized/approved up to now in clinics and markets worldwide. Additionally, their platforms, clinical phase, manufacturing, and dosage are shown in Table 3 and Figure 5 .

The pandemic of the newly identified coronavirus that is also known as COVID-19 is the third highly pathogenic human coronavirus. SARS-CoV-2 has less mortality than SARS-CoV-1 and MERS, but it has spread fast all over the world and has been declared a public health emergency of international concern by the WHO. Despite extensive research and a flood of articles published daily on SARS-CoV-2, and advances in effective management of COVID-19, we will require in-depth studies about SARS-COV-2 pathogenesis. For the discovery of an effective drugs and vaccines against SARS-CoV-2, identification and evaluation of the available data on different molecular and cellular mechanisms involved in SARS-CoV-2 pathogenesis is very promising.

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We are grateful to all the colleagues for critical reviews of the manuscript.

The authors declare that no conflict of interest exists.

No funding was received for this study. The authors declare no conflicts of in terests.

Ayyoob