key: cord-0908142-n61gz7pi
authors: Samudrala, Pavan Kumar; Kumar, Pramod; Choudhary, Kamlesh; Thakur, Nagender; Wadekar, Gaurav Suresh; Dayaramani, Richa; Agrawal, Mukta; Alexander, Amit
title: Virology, pathogenesis, diagnosis and in-line treatment of COVID-19
date: 2020-07-17
journal: Eur J Pharmacol
DOI: 10.1016/j.ejphar.2020.173375
sha: 4f1ebe79adb858673d7b8d1e4150635cea50b3dd
doc_id: 908142
cord_uid: n61gz7pi

SARS-CoV-2, a newly emerged pathogen in December 2019, marked as one of the highly pathogenic Coronavirus, and altogether this is the third coronavirus attack that crossed the species barrier. As of 1(st) July 2020, it is spreading around 216 countries, areas or territories, and a total of 10,185,374 and 503,862 confirmed cases and death reports, respectively. The SARS-CoV-2 virus entered into the target cells by binding with the hACE2 receptors. Spike glycoprotein promotes the entry of the virus into host target cells. Literature reported a significant mutation in receptor binding sites and membrane proteins of the previous SARS-CoV to turned as SARS-CoV-2 virus, responsible for most dreadful pandemic COVID-19. These modifications may be the probable reason for the extreme transmission and pathogenicity of the virus. A hasty spread of COVID-19 throughout the world is highly threatening, but still, scientists do not have a proper therapeutic measure to fight with it. Scientists are endeavoring across the world to find effective therapy to combat COVID 19. Several drugs such as Remdesivir, Hydroxychloroquine, Chloroquine, Ribavirin, Ritonavir, Lopinavir, Favipiravir, Interferons, Bevacizumab, Azithromycin, etc. are currently under clinical trials. Vaccine development from various pharmaceutical companies and research institutes is under progress, and more than ten vaccine candidates are in the various phases of clinical trials. This review work highlighted the origin, emergence, structural features, pathogenesis, and clinical features of COVID-19. We have also discussed the in-line treatment strategies, preventive measures, and vaccines to combat the emergence of COVID-19.

The Coronavirus (CoV) as believed to be originated from bats, was known for 800 years, 79 confirmed by many works of literature. These are positive-sense single-strand RNA viruses 80 with around 24 similar species from the family of coronaviridae. This family of 81 coronaviridae is further categorized as α, β, λ, and δ based on its distinct genetic features. 82

However, among these, only alpha (α) and beta (β) coronavirus genera are pathogenic to 83 mammalian and humans (Chen et Africa is listed as a minimally affected region (297,290 cases and 6,010 deaths) till date 118 (WHO, 2020a) . During this outbreak of COVID-19, the world is frightened with an 119 unpredictable and hasty impact of the infection, and the data is changing day by day. 120 

Coronaviruses are crown shape peplomers, positive-sense ssRNA (single strand RNA) virus, 124 which was reported in the pleomorphic form with 80-160 nm size . It is a 125 nonsegmented and RNA virus ranging from 26 to 32 kb. Coronavirus comes under the order-126 nidovirus, family-coronaviridae, subfamily-coronavineae which were further divided into α, 127 β, ϒ and δ genus. Among these, α and β genus of Coronavirus mainly affect the human 128 population. The α genus contains HCoV-229E (Human Coronavirus) and NL63, while the β  129   genus consists of HKU1, 229E, OC43, MERS-CoV, SARS-CoV and latest outbreak SARS-130 CoV-2. Coronavirus has been mainly reported with single-strand RNA, nucleocapsid protein, 131 envelop protein, membrane protein, spike glycoprotein (S), etc., as shown in Figure 2 (Lei et 132 al., 2018) . 133 Spike (S) glycoprotein is responsible for the characteristic feature of the Coronavirus because 134 it forms the crown-like structure on the outer surface of the virus. The S-protein divides into 135 two subunits, namely, S1 and S2. The S1 subunit further classified into three domains, 136 particularly A, B, and C (Angeletti et al.) . Generally, domain A of the subunit S1 present on 137

CoV-OC43 and CoV-HKU1 is binding with the host receptors (Hulswit et al., 2019) . Interestingly, the structure of the S protein in both SARS-CoV and novel SARS-CoV-2 143 viruses is almost similar to a few differences. 144 

Recent literature reveals that RBD of the S1 subunit of the " S " protein is responsible for 154 binding with ACE2 (Angiotensin-converting enzyme) receptors (Letko et al., 2020) . This 155 RBD in coronaviruses is highly variable. Based on studies, six RBD amino acids that remain 156 present on the S1 subunit are very critical for binding to the receptors. Interestingly, different 157 structural and functional studies stated that five of these six residual proteins are distinct in 158 SARS-CoV-2 compared to SARS-CoV. Accordingly, the coordinates based on the COVID-159 19 (L455, F486, Q493, S494, N501, and Y505) compared to those found in SARS-CoV 160 (Y442, L472, N479, D480, T487, and Y4911) differ in only five distinct residues except 161 Y4911 (Andersen et al., 2020). These differences may be the probable reason for the high 162 affinity of SARS-CoV-2 with the receptors and therefore are optimal for receptor binding 163 

A polybasic cleavage site (RRAR) is present at the union site of S1 and S2 subunit of Spike 166

protein. In addition, proline residue is also introduced prior to this cleavage site, and the 167 sequence in SARS-CoV-2 becomes PRRA (Unique protein sequencing in SARS-CoV-2). insertion of the cleavage site has been seen but also the conversion of low pathogenicity virus 177 into highly pathogenic forms is well observed (Alexander and Brown, 2009; Ito et al., 2001) . 178

However, the function of the predicated O-linked glycans is still not clear, but based on the 179 literature, they may create a mucin-like domain that helps in immunoevasion ( are assembled into the nucleocapsid and viral envelope at the ER or ERGIC, followed by 250 release of virus by exocytosis or by fusing with the plasma membrane. 251

Although the pathogenesis behind COVID-19 is not well understood, the pathogenesis of 253 MERS-CoV and SARS-CoV still can be the best source of information regarding COVID-19 254 (Li et al., 2020b) . 255

Recent literature suggests that the modified residues of RBD of S1 subunit, presence of 256 RRAR and partially opened state of 'S' trimer may be a reason for high pathogenicity and 257 transmission capacity of COVID-19. These RBD of S1 subunit on Spike proteins binds to the 258 hACE2 receptor which are mainly present in the lungs, particularly type-2 pneumocytes. This 

The clinical symptoms of COVID-19 infection can be seen after 5 to 6 days of incubation 272 which mainly differs from age and immune system of the person. Males are more susceptible 273 to SARS-CoV-2 as compare to females. People with the age of more than 60 are more 274 sensitive to SARS-CoV-2 (Li et al., 2020a; The, 2020). 275

The most common clinical features of SARS-CoV-2 infection are fever (more than 80% 276 cases), cough (more than 60% cases), fatigue (more than 35% cases), sputum production 277 (more than 30% cases), and shortness of breath (more than 15% cases). However, less 278 common features include headache, muscle weakness, breathlessness, sore throat, and 279 pleuritic pain (10-15%). Apart from this nausea, vomiting, chest tightness is the rare features 

Pro-inflammatory cytokines are secreted by alveolar macrophages results in the recruitment 320 of neutrophil and monocyte or macrophage along with activation of T-cells of epithelial cells, 321 which further starts inflammation and tissue injury (Ritchie and Singanayagam, 2020). In 322 medical term, ARD is called "diffuse alveolar damage," or epithelial-cell hyperplasia. The 323 diagnostic parameter for ARD is hypoxia, which mainly decides based on the ratio between 324 the blood pressure of oxygen and the percentage of oxygen supply, formulated as PaO2/FiO2 325 mmHg. In severe cases, PaO2/FiO2 found to be ≤100 mmHg while in moderate cases, found 326 to be ≤ 200. This ratio falls from 200 to 300 in mild cases of ARD due to SARS-CoV-2 327 . Other parameters that can distinguish ARD are bilateral opacities 328 followed by the collapse of lungs, which can be diagnosed through CT scan or ultrasound, 329 where lung infiltration found to be >50% (Lai et al., 2020a) . 330 

It is a reliable technique to isolate the affected population from the large population. It is also 350 essential for initial screening for auxiliary diagnosis. A thermal camera was first introduced at 351 hospital entrances and in the emergency department to recognize any persons with 352 incremental body temperature. The scanning distance required for such cameras is 10 meters. However, numerous potential pre-analytical and analytical risks are associated with RT-373 PCR. Such risks are false (-) identification, sample preparation, specificity, sensitivity, 374 stability issues, and also, it is a time-consuming process. Although calibration of the 375 instruments is also a matter of great concern, as it may provide false or misleading results, 376 therefore it is highly recommended to calibrate the RT-PCR regularly to avoid any 377 misleading readings. Besides, the diagnostic kit should also be pre-validated in terms of the 378 accuracy and reliability of the data (Lippi et al., 2020) . 379 

During the outbreak, remdesivir was tested on three COVID-19 infected patients in the U.S., 422 which showed improvement of symptoms with no significant side effects, and also FDA has 423

given permission about 250 patients to use this product. As far as safety is a major concern, 424 Gilead Sciences announced phase III clinical trial of remdesivir to prove its safety and 425 efficacy in COVID-19 infection (Keown, 16 .03.2020). After a preliminary investigation, 426

Gilead announced the results of the initial Phase 3 simple trial. The drug significantly 427 reduced the mortality rate upon 14 days of treatment and showed improvement in 64 % of 428 cases (Gilead, 2020) . Based on these results, the FDA issued Emergency Use Authorizations 429 for the use of remdesivir against COVID-19; however, full approval is still not provided 430 anywhere in the world (FDA, 2020). 431

The FDA already approves the drug chloroquine for treating malaria, arthritis and lupus 433 Hydroxychloroquine and Azithromycin. They reviewed the data of 84 patients, they treated 499 with Hydroxychloroquine on the first day at a dose of 400 mg twice a day, followed by 200 500 mg twice daily. Azithromycin was given at a dose of 500 mg per day. They observed 501 prolongation of QT interval from day 4 of therapy. Very importantly, severely prolonged QT 502 interval was observed in a subset of nine patients with more than 500 mg against the baseline 503 average of 435±24 mg (Mean ± SD). QT interval prolongation is a known marker for the 504 high risk of sudden cardiac death (Chorin et al., 2020) 505

In the latest news, on 18 th March 2020, reported that Favipiravir marketed as Avigan found 507 effective against COVID-19. Xinmin Zhang from the Ministry of Science and Technology, 508

China, said that Favipiravir gives positive results in a clinical trial on 340 patients in 509

Shenzhen and Wuhan city. The drug was developed by Toyama Chemicals and prescribed for 510 influenza infection. In February 2020, it got approval for the experimental treatment of novel 511 coronavirus infection. In the Wuhan trial, the treatment with favipiravir improved the 512 symptoms of infection and reduced the duration of fever. According to the Guardian Report, 513 some patients with early COVID-19 symptoms showed recovery; however, the patients with 514 severe or advanced symptoms do not show a similar response (Bryner, 2020) . 515

Bevacizumab, a recombinant humanized monoclonal antibody against VEGF, was first 517 approved by USFDA on 26 th February 2004 for the first-line treatment for metastatic 518 colorectal cancer (Cowling and Leung, 2020) . Subsequently, the FDA approved this product 519 along with chemotherapy to treat many cancers like lung cancer, renal cancer, cervical 520 cancer, ovarian cancer, etc. (Zhang and Zhou, 2018 ). In addition, recent studies suggest that 521 higher levels of blood VEGF in COVID-19 patients compared with normal and also 522 pulmonary edema, dyspnea, acute respiratory distress and acute lung injury are the most 523 detrimental symptoms of COVID-19. Numerous studies reported that VEGF was a critical 524 factor in pulmonary edema, acute respiratory distress and acute lung injury (Schoeman and 525 Fielding, 2019). Based on this evidences, Qilu Hospital of Shandong University has also 526 initiated clinical trials on this product for treating the COVID-19 (Clinical trials.gov). 527

Protease inhibitors are approved by USFDA to treat HIV, and also, these drugs previously 529 Immunodeficiency Virus) (Pronker et al., 2013) . Usually, successful development of a 572 vaccine takes around ten years. In this pandemic crisis of COVID-19, the world is sorely 573 needed a potential vaccine to combat this threatful situation. As per the available data, around 574 ten vaccines are presently under clinical trial against SARS-CoV-2 from which the scientists 575 from Oxford University and AstraZeneca expected to have the data of phase III trial by this 576 summer (as shown in table 1). However, many experts around the globe suspect the 577 credibility of this work as it takes a minimum of 18 months to develop the first vaccine even 578 after tremendous efforts. While some presume that a huge dose of vaccines (around hundreds 579 of million) will be ready to launch by the end of this year (Iserson, 2020) . 580 

PPEs are being used by health care professionals to protect from the infection of SAR-CoV-2 623 to avoid secondary transmission in hospitals. PPE should cover the whole body to prevent the 624 chances of infection through the patient. Health care professionals should also wear respirator 625 masks such as N95 (filters >95% of airborne particles), FFP2 (filters > 94% of airborne 626 particles), and FFP3 (filters > 99% of airborne particles) to avoid infection. Adequate training 627 of PPEs handling should be given to health care workers to avoid careless handling. Also, 628

proper care should be taken for the disposal of used PPEs (Kraemer et al., 2020) . 629

Many health advisory bodies have compelled the use of masks across the world as a 631 preventive measure to avoid the spread of COVID-19. Mask control the virus spread through 632 the droplets of an infected person by acting as a shield/barrier to prevent the exposure of the 633 critical body parts responsible for the spreading of the COVID-19. However, in the absence 634 of a mask, it is advisable to cover the face with bending elbow over the face or to cover with 635 a handkerchief/tissue paper while sneezing or coughing (Adhikari et al., 2020; WHO, 2020b). 636

Cleaning of hands from time to time with alcohol-based sanitizers is advisable to protect 638 individuals against coronavirus disease. Washing hands with soap and water before and after 639 meals must be practiced as a preventive measure. As suggested, the content of alcohol should 640 be more than 70% in hand sanitizes, and therefore children should be kept away from 641 alcohol-based sanitizers (WHO, 2020b). Although, there is a great need to produce sufficient evidence by successful clinical studies to 667 assure the safety and efficacy of these drug substances. The development of a vaccine for the 668 prevention and cure of COVID-19 and a promising diagnostic tool is also essential. 669

Hopefully, the constant scientific efforts and thorough understanding of SARS-CoV-2 670 pathogenesis and life cycle will soon find out the solution for this. 

Gaurav Suresh Wadekar: Writing-Original Draft

Epidemiology, causes, clinical manifestation and 687 diagnosis, prevention and control of coronavirus disease (COVID-19) during the early 688 outbreak period: a scoping review

690 Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease

Permeation Enhancers: Specialized Components of Mucoadhesives

History of highly pathogenic avian influenza. Revue 696 scientifique et technique

Membrane binding proteins of coronaviruses

The proximal 700 origin of SARS-CoV-2

How will 702 country-based mitigation measures influence the course of the COVID-19 epidemic?

The role of the nsp2 and nsp3 in its pathogenesis

Global aspects of viral glycosylation

710 COVID-19: towards controlling of a pandemic

Activation of the SARS coronavirus spike 712 protein via sequential proteolytic cleavage at two distinct sites

Identification of new respiratory viruses in 715 the new millennium. Viruses

Coronavirus infections reported by ProMED

Flu drug used in Japan shows promise in treating COVID-19

Human 722 immunopathogenesis of severe acute respiratory syndrome (SARS)

Zhejiang da xue xue bao. Yi xue ban = Journal of 728 Zhejiang University

Emerging coronaviruses: Genome structure, replication, 730 and pathogenesis

The 733 QT interval in patients with COVID-19 treated with hydroxychloroquine and azithromycin. 734 Nature medicine

Role of lopinavir/ritonavir in the 737 treatment of SARS: initial virological and clinical findings

Epidemiological research priorities for public health 739 control of the ongoing global novel coronavirus (2019-nCoV) outbreak. Euro surveillance : 740 bulletin Europeen sur les maladies transmissibles

Origin and evolution of pathogenic coronaviruses

CT Imaging and Differential Diagnosis of COVID-19. Canadian 746 Association of Radiologists journal = Journal l'Association canadienne des radiologistes

Screening of an 750 FDA-approved compound library identifies four small-molecule inhibitors of Middle East 751 respiratory syndrome coronavirus replication in cell culture

Roche coronavirus test receives emergency use authorisation from 754 FDA

Coronaviruses: an overview of their replication and 760 pathogenesis

Breakthrough: Chloroquine phosphate has shown apparent 762 efficacy in treatment of COVID-19 associated pneumonia in clinical studies

Hydroxychloroquine and 767 azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical 768 trial

Hydroxychloroquine and 772 azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical 773 trial

Observational Study of 776 Hydroxychloroquine in Hospitalized Patients with Covid-19. The New England journal of 777 medicine

First known person-to-784 person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 785 the USA

Gilead Announces Results From Phase 3 Trial of Investigational Antiviral 787 Remdesivir in Patients With Severe COVID-19

Clinical Characteristics of Coronavirus Disease

Coronavirus Disease 2019 (COVID-19): What we know? 795

COVID-19: what is next for public health?

Azithromycin-induced torsade de 799 pointes

Clinical 803 features of patients infected with 2019 novel coronavirus in Wuhan

Use 806 of Chest CT in Combination with Negative RT-PCR Assay for the 2019 Novel Coronavirus 807 but High Clinical Suspicion

Human 810 coronaviruses OC43 and HKU1 bind to 9-<em>O</em>-acetylated sialic acids via a 811 conserved receptor-binding site in spike protein domain A

Angiotensin-converting enzyme 2 protects from severe 815 acute lung failure

SARS-CoV-2 (COVID-19) Vaccine Development and Production: An 817

Cambridge quarterly of healthcare ethics : CQ : the international 818 journal of healthcare ethics committees

Generation of a highly pathogenic avian influenza A virus from an avirulent 821 field isolate by passaging in chickens

A Paper Raises Some Safety Concerns for Gilead's COVID-19 823 Treatment

Azithromycin as a 825 cause of QT-interval prolongation and torsade de pointes in the absence of other known 826 precipitating factors

SARS-coronavirus replication is supported by a 830 reticulovesicular network of modified endoplasmic reticulum

The effect of human mobility and control 834 measures on the COVID-19 epidemic in China

A 838 crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung 839 injury

Asymptomatic carrier state, acute respiratory disease, and pneumonia due to 842 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths

Severe acute respiratory 845 syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The 846 epidemic and the challenges

Effective 848 strategies to prevent coronavirus disease-2019 (COVID-19) outbreak in hospital. The Journal 849 of hospital infection

Nsp3 of coronaviruses: Structures and functions of a 851 large multi-domain protein

Functional assessment of cell entry and receptor 853 usage for SARS-CoV-2 and other lineage B betacoronaviruses

Structure of SARS coronavirus spike 856 receptor-binding domain complexed with receptor

Molecular immune pathogenesis and 862 diagnosis of COVID-19

Development and Clinical Application of 866 A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis

Potential preanalytical and analytical 869 vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19)

Receptor usage and cell entry of porcine epidemic diarrhea coronavirus

Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting 876 SARS-CoV-2 infection in vitro

Overlapping and discrete aspects of the pathology and pathogenesis of the 879 emerging human pathogenic coronaviruses SARS-CoV, MERS-CoV, and 2019-nCoV

COVID-19 vaccines: knowing the unknown

Neurological Manifestations of Hospitalized Patients with

China: a retrospective case series study

Coronavirus (COVID-19): managing stress and anxiety

Trypsin Treatment Unlocks Barrier for Zoonotic Bat Coronavirus 891 Infection

Clinical management of severe acute respiratory infection when 893 novel coronavirus (nCoV) infection is suspected

Structures of MERS-CoV spike glycoprotein in complex with 896 sialoside attachment receptors

Coronavirus Infections-More Than Just the 898 Common Cold

Findings of lung ultrasonography of novel 900 corona virus pneumonia during the 2019-2020 epidemic

Coronaviruses post-SARS: update on replication and 902 pathogenesis

Risk 904 in vaccine research and development quantified

Immunosuppression for hyperinflammation in 906 COVID-19: a double-edged sword? The Lancet

Roche's cobas SARS-CoV-2 Test to detect novel coronavirus receives FDA 908

Emergency Use Authorization and is available in markets accepting the CE mark

The epidemiology and pathogenesis of coronavirus 910 disease (COVID-19) outbreak

Coronavirus envelope protein: current knowledge

Structure of mouse coronavirus spike protein complexed with receptor 915 reveals mechanism for viral entry

A Review of Coronavirus Disease-2019 (COVID-19)

Regulatory updates and 919 analytical methodologies for nitrosamine impurities detection in sartans, ranitidine, nizatidine 920 and metformin along with sample preparation techniques

Animal Models and Novel Therapeutic 924 Interventions for Middle East Respiratory Syndrome Coronavirus Infections. Frontiers in 925 microbiology 10

Chloroquine and its analogs: A new promise of an old drug for 927 effective and safe cancer therapies

Genetic Recombination, and Pathogenesis of Coronaviruses. Trends in 930 microbiology

The COVID-19 vaccine development landscape

COVID-19: fighting panic with information

Of chloroquine and COVID-19

Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Receptor Recognition by the Novel 943 Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS 944 Coronavirus

Xiao, 946 G., 2020a. Remdesivir and chloroquine effectively inhibit the recently emerged novel 947 coronavirus (2019-nCoV) in vitro

Unique epidemiological and clinical features 949 of the emerging 2019 novel coronavirus pneumonia (COVID-19) implicate special control 950 measures

WHO, 2020a. Coronavirus disease 2019 (COVID-19): Situation Report -144

Coronavirus disease (COVID-19) advice for the public, Advice for Public. 954 World Health Organization

Cryo-EM structure of the 2019-nCoV spike in the prefusion 957 conformation

Overview of The 2019 Novel Coronavirus (2019-959 nCoV): The Pathogen of Severe Specific Contagious Pneumonia (SSCP)

Pathological 963 findings of COVID-19 associated with acute respiratory distress syndrome. The Lancet. 964 Respiratory medicine

The 966 deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in 967 China

The 969 deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in 970 China

974 Clinical characteristics of 82 death cases with COVID-19

Bevacizumab with dose-dense paclitaxel/carboplatin as first-line 976 chemotherapy for advanced ovarian cancer

A pneumonia outbreak associated 981 with a new coronavirus of probable bat origin

COVID-19): A Perspective from China

☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.☐The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:None