key: cord-1003123-ln6695lf
authors: Khan, Suliman; Tombuloglu, Huseyin; Hassanein, Sameh E.; Rehman, Surya; Bozkurt, Ayhan; Cevik, Emre; Abdel-Ghany, Shaimaa; Nabi, Ghulam; Ali, Ashaq; Sabit, Hussein
title: Coronavirus diseases 2019: Current biological situation and potential therapeutic perspective
date: 2020-08-05
journal: Eur J Pharmacol
DOI: 10.1016/j.ejphar.2020.173447
sha: cef941427f6f33dc98afc99b4f3ae87bde67d850
doc_id: 1003123
cord_uid: ln6695lf

Coronavirus Disease 2019 (COVID-19) caused by a Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was first reported in Wuhan, China at the end of December 2019. SARS-CoV-2 is a highly pathogenic zoonotic virus and closely related to the Severe Acute Respiratory Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The COVID-19 was declared as a global pandemic due to its high infectiousness, and worldwide morbidities and mortalities. The Chinese scientists at the start of the outbreak reported genome sequences, which made the characterization of glycoproteins and other structural proteins possible. Moreover, researchers across the world have widely focused on understanding basic biology, developing vaccines, and therapeutic drugs against the COVID-19. However, until now, no promising treatment options, as well as vaccines, are available. In this review, we have described SARS-CoV-2's genome, transmission, and pathogenicity. We also discussed novel potential therapeutic agents that can help to treat the COVID-19 patients.

earlier claim that pangolin could be an intermediate source of transmission from bat to humans was later discredited (Khan et al., 2020a; Khan et al., 2020c) . The generated data indicated that SARS-CoV-2 is highly transmissible and can infect both lungs with atypical clinical symptoms, resulting in either misdiagnosis or missed diagnosis . These might be among the possible reasons for unstoppable spread, and high rates of mortalities and morbidities.

COVID-19 is transmitted from human to human through inhalation or contact with respiratory droplets of infected individuals. The time from infection to the manifestation of symptoms ranges from 2-14 days (Khan et al., 2020a) . Clinical manifestations represent a wide spectrum of diseases ranging from mild to severe respiratory syndrome influenza-like illness with lower respiratory tract symptoms, loss of taste and smell, and severe gastrointestinal symptoms. Although, COVID-19 is mild in most cases, however, it can be a life-threatening disease by developing severe pneumonia, acute respiratory distress syndrome (ARDS), high fever, headache, and multi-organ dysfunction (Singhal, 2020) . In this review, we have described the route of transmission and virus entry mediating cellular receptors. We further discussed therapeutic options, susceptibility to the disease, and immunological responses that could play a role in the prevention and eradication of COVID-19 infection.

sequencing of SARS-CoV-2 indicates a similarity score of 79.6% with SARS-CoV, relating its origin to bats, however, the transmission to humans through an unknown intermediate animal in Wuhan, China is still controversial (Khan et al., 2020a; Zaman et al., 2020) .

Bats are the natural reservoirs of highly pathogenic viruses especially, coronaviruses which constitute 31% of their virome. They are immune to viral infection and the characteristics such as higher species diversity (over 1400), roosting, longer life span (over 30 years), and migration transmit the viral pathogens across the political and geographical boundaries (Allocati et al.) . Globally, only 77 countries reported 5717 bat-associated animal viruses in 207 different bat species (Chan et al.) . However, in bats, the traits including roosting, grouping, and unique immune system can interfere with the genetic system of the viruses to generate novel mutant and recombinant viruses (Han et al.) . Han et al., (Han et al., 2019) , investigated 831 bats belonging to 15 species and reported 11 coronavirus strains in four bat species. Further investigation revealed that the four α-CoVs from bats species were similar to that previously isolated from porcine epidemic diarrhea virus (PEDV), indicating a common ancestor of the CoVs in both bats and pigs. Moreover, a synthesized CoV revealed that the PEDV possibly evolved from the CoV of bats, while another α-CoV (α-YN2018) might be originated from other bat species. These observations suggest that SARS-CoV-2 may have multiple host origins. An intensive study on immortalized bat cell lines indicated that human CoVs can spread via zoonotic-reverse zoonotic transmission cycles, and this might give some CoVs the chance to circulate and exchange segments of genetic material between strains detected in bats and other mammals, including humans. Furthermore, CoV can infect other vertebrates including ducks, geese, chickens, quails, pigeons, and sparrows, and use these hosts as a natural reservoir (Zhuang et al., 2020) .

To identify the type of CoV in the recent outbreak in Wuhan, China, Zhang et al., (Zhang et al., 2020c) analyzed 169 genomes of SARS-CoV-2 and classified them into two major genotypes; type I and Type II. Type I is further sub-divided into type IA and IB. Furthermore, phylogenetic analysis indicated that type IA is similar to the ancestral SARS-CoV-2, whereas type II was probably evolved from the type I and prevalent in the infections.

We generated a bioinformatic analysis for the coronavirus family to predict the potential origin of SARS-CoV-2. Gorbalenya et. al., (Gorbalenya et al., 2020) , reported that the emergence of SARS-CoV-2 as a human pathogen may be perceived completely independent from the other SARS-CoV outbreak. Although, SARS-CoV-2 is indeed not a descendent of SARS-CoV, and the introduction of each of these viruses into humans was likely facilitated by independent unknown external factors. Our findings indicated that SARS-CoV-2 is most 

In COVID-19, the immune response is less rigorous, as a result, the elder people and individuals with underlying conditions are prone to develop Acute Respiratory Distress Syndrome (ARDS) and death (Khan et al., 2020a) . However, fever associated with ARDS may lead to better outcomes among patients. COVID-19-infected individuals demonstrate increased levels of infection-related biomarkers and inflammatory cytokines. For example, attenuation or even reduction in the number of T cells was observed in severe cases. Moreover, suppressor T cells, regulatory T cells, memory helper T cells, and helper T cells were negatively affected J o u r n a l P r e -p r o o f while naive helper T cells showed an increased level in severe cases, suggesting that the primary target of COVID-19 infection is T lymphocytes (Qin et al., 2020) . Similarly, Shi et al., (2020) reported a comprehensive decline of lymphocytes including CD4+ and CD8+ T cells, B cells, and NK cells, and the elevation of interleukins (IL-2 and IL-6), which can be considered as reliable biomarkers in severe COVID-19 disease (Fig. 3) . Furthermore, analysis of ILs in the serum samples of critical, severe, and mild COVID-19 cases showed that the expression of Interleukins (IL-2 receptor and IL-6) was comparatively higher in the critical cases than severe and mild ones. However, no statistical differences in the expression of tumor necrosis factor-alpha (TNF-α), Interleukins (IL-1, IL-8, IL-10), High-sensitivity C-reactive Protein (hs-CRP), lymphocyte count, and lactate dehydrogenase (LDH) between the three patient groups were reported (Chen et al., 2020b) . Zhang et al. (Zhang et al., 2020a) suggested that the severity of COVID-19 is correlated with increased IgG response, where the blood group is linked with the susceptibility of SARS-CoV-2 infection. A recent study in COVID-19 patients (n=1,775) reported that individuals with blood group A have a substantially higher risk, whereas those with blood group O are comparatively at lower risk for contracting COVID-19 infection . Although it is very early to conclude, however, the results obtained in this study were similar to a previous study on SARS, where SARS-CoV was reported with a lower rate of infectiousness in individuals with blood group O .

Pneumonia appears to be the most frequent manifestation of SARS-CoV-2 infection, in 994) . They also reported less common symptoms including headache or dizziness (12.1%), diarrhea (4.8%), and nausea or vomiting (3.9%). Furthermore, laboratory tests indicated the presence of lymphocytopenia (64.5%) and an elevation in CRP (44.3%), LDH (28.3%), and leukocytopenia (29.4%). In the same study, Li et al., (Li et al., 2020d) found that lymphocytopenia, eosinophil cytopenia, and leukopenia were observed in 10 COVID-19

patients. In another study on 29 COVID-19 patients, Meng et al. observed decreased white blood cell count (79.3%), decreased lymphocyte count (68.9%), increased levels of hs-CRP (93.1%), and normal level of procalcitonin. Similarly, serum LDH was found increased (68.9%) while albumin was decreased (51.7%) in this study. Overall, these indications suggest that LDH and High-sensitivity C-reactive Protein (α-HBDH) could be reliable biomarkers for investigating COVID-19. Moreover, by investigating 140 COVID-19 patients, Zhang et al., (Zhang et al., 2020b) reported eosinopenia and lymphopenia as potential diagnostic factors for the disease while asthma and chronic obstructive pulmonary disease (COPD) are unlikely to be the risk factors. Older age and underlying health conditions including cardiovascular problems, hypertension, diabetes, and pulmonary aberrations were found to be associated with the development of severe symptoms in COVID-19 infected patients.

The overall risks associated with COVID-19 infection can be mitigated with effective eradication of the infection. Currently, no promising treatment options are available against COVID19 that can be recommended globally. However, Remdesivir, baricitinib, chloroquine, hydroxychloroquine, and favipiravir have been found with significant efficacy against COVID-J o u r n a l P r e -p r o o f 19. Among the trialed antiviral drugs, remdesivir alone or in combination with chloroquine or interferon beta showed effectiveness against COVID-19 infection (Sheahan et al., 2020) Researchers all over the globe are striving to develop effective vaccines or therapeutic molecules to combat the deadly COVID-19 infection. For the sake of developing novel drugs, the COVID-19 main protease was made publicly available to expedite the process. Ton et al., (Ton et al., 2020) have developed a tool, namely Deep Docking for the computer-based screening of a large number of molecules in a very short time. They identified 1,000 potential ligands for the main protease of COVID-19 from nearly 1.3 billion compounds available in the ZINC15 library. These generated compounds are available for further characterization and improvements. Since no specific antiviral agents are available, therefore, the provided treatment options to COVID-19 patients are all supportive in nature. Besides effective treatment options and preventive strategies must be developed and practiced as the COVID-19 has the highest potential to spread compared to its family members; SARS-CoV and MERS-CoV (Singhal, 2020 ).

Matsuyama et al., (Matsuyama et al., 2020) reported that VeroE6 cell line expressing -20000-29542, 29559, 29609, 29741, 29761, 29803, 29826, 29837, 29868, 29935, 29939, 29975, 29988, 29992, 30031, 30054, and 30417 ).

An inhaled corticosteroid compound, ciclesonide has been suggested as a potential drug against the COVID-19 (Matsuyama et al., 2020) (Matsuyama et al., 2020) (Matsuyama et al., 2020) (Matsuyama et al., 2020) (Matsuyama et al., 2020) . The compound suppressed SARS-CoV-2 replication in cultured cells, where the suppression was mainly related to the targeting viral nonstructural protein 15 (nsp15) (Matsuyama et al., 2020) . It is expected that inhaled ciclesonide can reduce viral replication and host inflammation in the lungs.

ACE2 negatively regulates the renin-angiotensin system (RAS) by converting Ang II to  where it functions as a carboxypeptidase. SARS-CoV-2 was found to attack cells using this type I integral membrane protein (Matsuyama et al., 2020) . Depletion of ACE2 by SARS-CoV-2inhibits the ACE2/Ang (1-7)/Mas receptor pathway, leading to disruption of the RAS, J o u r n a l P r e -p r o o f which then leads to the progression of acute severe pneumonia. Thus, inhibiting ACE2 may alleviate pneumonia in COVID-19 patients, provided that blood pressure is controlled (Fig. 4 ).

In terms of clinical manifestations , lung cancer and COVID-19 are similar, making it difficult for clinicians to differentiate (Yang et al., 2020a) . Lung cancer patients receiving systemic immunosuppressive agents are more prone to be infected with COVID-19 as compared to healthy individuals . Liang et al., (Liang et al., 2020) surveyed 1,590 COVID-19 cases, where 18 cases had a history of cancer, while five of these 18 cases had a history of lung cancer (Xia et al., 2020) . However, any conclusion to associate COVID-19 infection with cancer should be drawn carefully, as no convincing evidence is available to confirm that patients with cancer have an increased risk of being infected with COVID-19. To draw a clear conclusion, a reasonable sample size with less heterogeneity must be studied.

An animal model expressing DPP-IV receptor on the pulmonary alveolar cells has been designed to elucidate how diabetes worsens disease severity, and the obtained data indicated an association of diabetes with macrophage infiltrates (Bloomgarden, 2020) . Therefore, diabetic patients seem to be more susceptible to COVID-19 infection than others. Yang (Fang et al., 2020; Li et al., 2017) . In addition, ACE2 is not only expressed in the alveolar epithelial cells, but also in the heart, gastrointestinal tract, kidney, testis, and pancreas, and thus makes these tissues and organs susceptible to COVID-19 infection and damage to multiple organs Xu et al., 2020a) .

A meta-analysis study conducted by Li et al., (Li et al., 2020a) summarized the proportion of cardiovascular disease (16.4%), diabetes (9.7%), and hypertension (17.1%) in COVID-19 patients. They concluded that patients with previous cardiovascular diseases may have an increased risk of developing severe conditions, while, COVID-19 infection can exacerbate the damage of the heart. In COVID-19 patients with underlying cardiovascular disease, hypersensitive C-reactive protein, and serum creatinine levels were elevated compared with COVID-19 patients with no underlying cardiovascular disease. Overall these indications suggest that COVID-19 can affect cardiovascular function and lead to myocardial injury (Chen et al., 2020a) .

Genome of the SARS-CoV-2 consists of 29,900 nucleotides (nt), predicted with 14 open reading frames (ORFs) (5′ to 3′) such as nucleocapsid (N,1,260 nt) , spike (S, 3,822 nt), ORF1ab (P, 21,291 nt), membrane (M, 669 nt), envelope (E, 228 nt), ORF3a (828 nt), and ORF8 (366 nt) . The viral spike (S) glycoprotein encoded by spike gene facilitates viral binding J o u r n a l P r e -p r o o f to ACE2 receptor of the host cell membrane. After the viral fusion and entry through the ACE2 receptor, its RNA is translated to non-structural proteins (nsps) from ORF1a and ORF1b. The first ORF (1a) produces a 440-500 kDa polypeptide 1a (pp1a), undergoes cleavage to produce 11 nsps. Ribosome frameshift exits immediately upstream of the ORF1a stop codon, allowing translation of the second ORF (1b) to produce a 740-810 kDa large polypeptide (pp1ab), which is then cleaved and as result, 16 nsps are produced. This cleavage property is mediated by viral proteases nsp3 and nsp5 that contain a papain-like protease domain and a 3C-like protease domain, respectively (Kim et al., 2020) . The sequence of the spike gene is extremely divergent when compared with that of bat-SARSr-CoV RaTG13 (93.1% nucleotide identity) Wu et al., 2020) .

SARS-CoV-2 is a positive-sense single-stranded RNA (+)ssRNA) virus that can infect mammalian and avian hosts, where its nucleotide substitution rate is higher than their hosts (Lin et al., 2019). At the whole genome level, the sequence identity of the SARS-CoV-2 was 50% to MERS-CoV, 79% to SARS-CoV, 88% to Bat-SL-CoVZC45 and Bat-SL-CoVZXC21, and 96%

to Bat-SARSr-CoV RaTG13 . Genomic analyses of SARS-CoV-2 and 20 closely related coronavirus strains highlighted identical mutations in both the SARS-CoV-2 and RaTG13, which could indicate that SARS-CoV-2 is probably originated from the Bat-SARSr-CoV RaTG13 (Lv et al., 2020) .

For patients who meet specified criteria, in addition to testing for other respiratory pathogens, the CDC recommends collection of specimens to test for COVID-19 virus from the upper respiratory tract (nasopharyngeal and oropharyngeal swab) and, if possible, the lower J o u r n a l P r e -p r o o f respiratory tract (sputum, tracheal aspirate, or bronchoalveolar lavage). Additional specimens (eg, stool, urine) can also be collected (Patel and Jernigan, 2020) . The world health organization (WHO) has also provided detailed descriptions of approved methods being used for coronavirus detection (WHO, 2020), which is based on the detection of unique sequences of viral RNA. In routine-based testing for COVID-19 patients, the presence of SARS-COV-2 is determined through the detection of viral genes namely N, E, S, and RdRP using real-time polymerase chain reaction (RT-PCR). Moreover, the RNA-sequencing technique is also employed for further confirmation of SARS-CoV-2, if needed. However, these methods require expert personnel and expensive laboratory equipment whereas, low viral load in the throat or nasal swab of patients may give false-negative results during RT-PCR-based detection (Lucia et al., 2020) .

Besides PCR-based methods, researchers and clinical laboratory workers are making efforts to develop and use faster, reliable, and more efficient techniques for COVID-19 detection.

For instance, a CRISPR-Cas12-based method has been developed with an estimated detection limit of 10 copies/μL (Lucia et al., 2020) . Another method known as droplet digital PCR (ddPCR) has recently been developed to detect SARS-CoV-2 with a detection efficiency of at least 500 times higher than RT-PCR . More interestingly, Yang et al. (Yang et al., 2020b ) developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) method, using RNA reverse transcription and nucleic acid amplification in a single step within 30 minutes. According to Wang et al. (Wang et al., 2020) , nanopore target sequencing (NTS) method can be used to detect SARS-CoV-2 and other respiratory viruses simultaneously within 6-10 h. Nonetheless, an efficient, rapid, and cost-effective technique is still required to be developed so that testing procedures could become easy in low income and hardest hit countries. The need for a faster sensing process at a lower detection limit is an important but challenging strategy. Designing novel antibody conjugated composite electrodes is critical for more sensitive and rapid practical applications. It is clear that the electrical charge transport improves the sensing characteristics of the biosensor, thus, conducting polymers such as polyaniline (PAN) can be proposed as a host matrix. It is well known that the chain length and positive charge in its backbone are reversible with the applied electrical pulse (Chowdhury et al., 2019) . Doping gold nanoparticles with antibody onto PAN can accumulate more SARS-CoV-2 particles for rapid detection. These cost-effective and eco-friendly composite assays can be developed from disposable electrodes for multi detection purposes.

The deadly and highly infectious COVID-19 pandemic is spreading unstoppably in almost all countries of the world. Until now, no promising vaccines or drugs are available that could be recommended on a large scale. The actual numbers of the infected people may be larger than reported figures due to the lack of high testing capacity in some countries, accurate data recording systems in different countries, or the presence of weak systems for data collection.

This pandemic may get worsened in the near future if not effective treatment or vaccine is developed to combat or prevent the virus. The genome of SARS-CoV-2 and other CoVs have been sequenced and are available online, as well as all research reports on COVID-19 are freely available, therefore, the scientific community should take advantage of them in order to develop J o u r n a l P r e -p r o o f strategies to control the rapid spread of COVID-19 and eradicate the SARS-CoV-2. There is a possibility that more coronaviruses could emerge in the future and cause deadly outbreaks. Therefore, strategies should be developed that could prevent the emergence of new viruses and/or minimizing the health consequences if any new pathogenic virus emerges. Simultaneously, ssRNA is replicated via RNA-dependent RNA polymerase to produce viral RNA. Next step is to produce empty capsids and them to pack these capsids with RNA. The viral particles are ready depart via exocytosis. 

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Genome of the SARS-CoV-2 consists of 29,900 nucleotides and the viral spike glycoprotein encoded by spike gene facilitates viral binding to ACE2 receptor of the host cell membrane

CRISPR-Cas12-based method, droplet digital PCR (ddPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) method should be developed for the detection of SARS-CoV-2

Active hexose correlated compound (AHCC), an immune-stimulant can be tested against COVID-19

Bio-nanotechnology approaches should be used to develop various nano architectural electrochemical immunosensors that can be utilized for the detection of pathogenic viral organisms

The authors acknowledge the postdoctoral research grant from the Second Affiliated Hospital of Zhengzhou University and postdoctoral research grant from the Chinese Postdoctoral Science Foundation for SK.

The authors declare that there is no conflict of interest.