Submitted: June 08, 2021 | Approved: July 03, 2021 | Published: July 05, 2021
How to cite this article: Khan AA, Dutta T, Mondal P, Mandal M, Chowdhury SK, et al. Novel Coronavirus Disease (COVID-19): An extensive study on evolution, global health, drug targets and vaccines. Int J Clin Virol. 2021; 5: 054-069.
Copyright License: © 2021 Khan AA, et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Novel Coronaviruses (nCoVs); World Health Organization; MERS-CoV; SARS-CoV; RNA-dependent RNA polymerase
The Coronavirus disease-2019 (COVID-19), has become a worldwide pandemic and the scientific communities are struggling to find out the ultimate treatment strategies against this lethal virus, Severe Acute Respiratory Syndrome Coronavirus–2 (SARS-CoV-2). Presently, there is no potential chemically proven antiviral therapy available in the market which can effectively combat the infection caused by this deadly virus. Few vaccines are already developed but it is not clear to the scientific community how much efficient they are to combat SARS-CoV-2. Mode of transmission and symptoms of the disease are two important factors in this regard. Rapid diagnosis of the COVID-19 is very much important to stop its spreading. In this scenario, a complete study starting from symptoms of the disease to vaccine development including various SARS-CoV-2 detection techniques is very much required. In this review article, we have made a partial analysis on the origin, virology, global health, detection techniques, replication pathways, doses, mode of actions of probable drugs, and vaccine development for SARS-CoV-2.
On 31st Dec 2019, a bunch of cases for some unknown types of pneumonia were reported by the hospitals of Wuhan, Hubei, China, knocking the world with an indication of imminent danger . On 1st January 2020, Wuhan public health care authorities closed down the Huanan seafood wholesale market, where live wild animals were sold, due to a suspected link with that outbreak . At the same time, scientists confirmed the 2019 novel coronavirus (2019-nCoV, rechristened as SARS-CoV-2) from the infected pneumonia patients on 7th January, 2020 . On 30th January, 2020, the World Health Organization (WHO) confirmed COVID-19, to be a Public Health Emergency of International Concern (PHEIC), and declared as an epidemic . As on 7th June, 2021, globally 173,937,118 affected and 3,741,055 death cases were confirmed by the WHO. Similar symptoms like, common cold, fever in human beings, caused by Coronavirus, were reported in the middle of the year 1960 . Coronavirus (CoVs), a genus of the Coronaviridae family, is likely one of the major pathogens by which the human respiratory system is affected. Two classes of CoVs were first isolated i.e. HCoV-229E and HCoV-OC43 . The HCoV-229E straining was related to symptoms of common cold . An outbreak also occurred in the Guangdong province of southern China, caused by a similar pathogen SARS-CoV in 2002, where approximately 38% of all patients suffered from acute breathing problems and hence required artificial respirators [7,8]. The overall mortality rate of SARS-CoV in 2002 was approximately 10%, where older people accounted for approximately 50% of the cases, while middle aged and children comprised the other 50% . In the September 2012, another viral infection occurred in Saudi Arabia which subsequently spread to the Middle East countries like Qatar, Germany, Jordan, France and Britain and it was named as Middle East Respiratory Syndrome (MERS) . Symptoms were almost similar to the previous one (SARS-CoV-2002) like fever, diarrhea, cough and breathing problem . Recently, SARS-CoV zoonotic pathogens have mutated to form themselves a new virus “2019 novel Coronavirus” (2019-nCoV) or SARS-CoV-2 formally named by the World Committee on Virus Classification. Erstwhile, 2019-nCoV was also known as “Novel Coronavirus Pneumonia (NCP)” in China till 8th February 2020 and subsequently has spread abruptly to all over the world [12-14]. It is explained by the research group of Ji, et al. in their investigation that the codon usage of 2019-nCoV is very similar to the host, snakes than any additional hosts for cross-species transmission of the pathogens to human . The transmission of this respiratory pathogens is associated with three main primary modes e.g. “airborne”, “contact,” and “droplet” transmission but the research-based literature and the guidance from the public health agencies are still paradoxical . As per the research based studies, physical touch is mainly responsible for the contact transmission and indirectly can transmit by settled droplets . COVID-19 spreads by human-to-human close contact [17,18]. The symptoms of COVID-19 infection may appear in 5-14 days . The time duration from the onset of COVID-19 symptoms to eventual death of the patients ranges between 6 to 41 days . This period varies from patient to patient depending on their age and immune response of the system. The period is shorter for patients above 70 years old compared to those less than 70 years old . The general symptoms of COVID-19 are fever, fatigue, cough, while additional symptoms like diarrhea, sputum production, headache, lymphopenia, haemoptysis, dyspneamay manifest, varying from patient to patient [17,21]. COVID-19 infection showed a few unique clinical features like targeting the lower airway which causes the upper respiratory tract infection like a runny nose, a sore throat and sneezing . It has been observed in per month analysis that the worldwide growth rate of infection and the death rate of COVID-19 patients has increased aggressively whereas the recovery rate of the patients from this disease is quite low with such rates (Figure 1). CoVs are transmitted as SARS-CoV and MERS-CoV to alternate host civet cats and camels respectively, prior to affecting the humans, but presently, there is no clear evidence of the origin of SARS-CoV-2 (2019-nCOV) [23,24].
According to the WHO, there are no recommended medicines available in the market and hence maintaining social distance, along with proper hygiene, is the only way to stop the spread of COVID-19 . Though there are a few myths regarding the medicine of COVID-19 (mixture of different kinds of herbals) but it is not approved by the FDA [25,26]. Since January 2020, at least 37 bio-pharmaceutical companies worldwide are involved for the development of the drug and protective vaccine with multiple platforms including adenoviral vector, mRNA, recombinant protein and DNA . Researchers are also trying to use some natural compounds against this virus [28-30]. Some drugs which are under investigation viz. Hydroxychloroquine, Carfilzombic, Eravacycline, Valrubicin, Lopinavir needs to be successful during in-vivo analysis [28,31-36].
The objective of this review article is to summarize all the aspects of COVID-19, starting from its history to the present scenario and develop a clear understanding of the transmission, detection, precaution, symptoms, and virology along with the ways of treatment of COVID-19 via probable drugs.
Previously, the CoVs like SARS-CoV and MERS-CoV pathogens were transmitted from different animals including bats, cats, cattle and camels to the human body as shown in figure 2. Over the years, much has been learned from the global outbreak pattern for similar pathogens occurring in China, South Africa, Saudi Arabia (Middle East Countries) and the pandemic spread, affected from severe respiratory diseases.
The recent outbreak of 2019-nCoV, its origin and its transmission to the human body is under debate. However, from the epidemiologic investigation at the starting point of this global outbreak, it was reported that 2019-nCoV infected patients were seafood vendors, visitors or were close to the infection at the seafood market of Wuhan . Till now the detailed host source of SARS-CoV-2 and its transmission to human body is not clear (Figure 2). SARS-CoV is transmitted by respiratory droplets (coughs or sneezes), resembling the spread of influenza from infected persons . It may also spread through an airborne route at a close distance, eg., person-to-person . The transmission rate (R0) (reproductive number or the usual number of persons to that a single infected person shall spread the pathogens) of COVID-19 initially is between 1.4 to 2.5 projected by the WHO and higher values of R0 varies in the range of 3.6 to 4.0 reported by different literature . Accordingly, these values would be associated to the R0 of 1.3 for common flu and R0 of 2.0 for SARS-CoV. If the R0 value is not more than 1, the virus may disappear, else the epidemic shall remain in the environment [41,42].
The 2019-nCoV infection is very contagious, known to all that the virus can spread rapidly from one person to other and in many instances the virus can spread even prior to becoming symptomatic .The growth factor of COVID-19 cases over the globe is shown in figure 3. Growth factor related to the number of months where a quantity reproduces itself over time. The formula used here is: every day’s new cases divided by fresh instances on the preceding day.
The virus comes in the bronchial secretions with a droplet transmission, where one having infectious cough, sneezing can infect another in close contact, directly through the mucous membranes. Infections to an otherwise healthy individual can also spread by facial touch (touching one’s mouth, nose, and eyes by their hands, which are already exposed to the infection). 2019-nCoV persisted in the aerosols during experiments at least three hours as described in a letter of an editor .
The structure of SARS-CoV-2 is composed of four different types of proteins viz. spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins. According to the cryo-electron microscopy analysis, coronavirus genome is a large, linear single stranded, positive-sense RNA molecule that contains all information necessary for the making of viral replication. In positive sense, the size of the SARS-CoV depends on its proteins (S, E, M, N) and the other helper proteins and it varies from 29.0 kb to 30.2 kb and the molecular weight is usually 5.5 x 106 to 6.1x 106. There are total seven genes of CoVs RNA genome that are preserved in the following order: ORF1a, ORF1b, S, OEF3, E, M, N in 5′ to 3′ direction. Major part of the RNA genome is coated by ORF and rest of the part of the genome shield by mRNA and other necessary proteins. ORF1a/b develops replicase proteins PP1a and PP1ab through ribosomal frame shifting and simultaneously both these proteins produce sixteen non-structural proteins (NSPs). These NSPs also carry on the process of various viral activities including the reproduction of the replicase transcriptase compound. The mRNA part is responsible for the formation of structural proteins (S,E,M,N) and other accessory proteins as shown in figure 4.
Furthermore, there is a protein envelope named HE protein and the RNA packed nucleocapsid protected by the protein embedded lipid layers [45,46]. The outer and inner portion of SARS-CoV-2 is shown in figure 5.
The nature and the structure of the RNA genome of SARS-CoV-2, is very similar to that of the family of beta-CoV, which occurred as pandemic previously. However, the contamination of SARS-CoV-2, spreads rapidly through the droplets and person to person and the integrity of the envelope is crucial for viral infection but the lipid layer enveloped of SARS-CoV-2 can be easily destroyed by lipid solvents such as detergents, alcohol and some another disinfectants [47-49].
To infect a host cell, first the spike glycoprotein (S) of corona virus must bind the host cell surface with the help of a receptor called angiotensin converting enzyme‑2 (ACE‑2)  and the conformational changes occurring that allows the virus to get inside by the process known as endocytosis. After that virus genome enters into the host cell cytoplasm and release nucleocapsid or ssRNA(+) followed by replication transcription complex . Translation process is carried out by involvement of produced pp1a and pp1b from the ribosomal shifting of viral genome ORF1a and ORF1b and producing dsRNA genome from the genomic ssRNA(+) [51,52]. The dsRNA genome is transcribed or replicated and providing viral mRNAs or new ssRNA(+) genomes by the 16NSPs. Total 16 NSPs which are produced from PPs involving in specific functions mainly for the replication process such as suppression of host cell by NSP1 and NSP2. The production of multi-domain complex by NSP3, replication by M protease (NSP5),  transmembrane (TM) proteins (NSP4 & NSP6), NSP7 & NSP8 acting as primase  and R-binding protein NSP9 is efficient for viral infection in the dimeric mode [54,55]. NSP10 acts as co-catalyst at the beginning of replicative enzyme and NSP11 & NSP15 shows endo-ribonuclease activity [56,57]. NSP12, NSP13, NS14 and NSP16 showed RNA‑dependent RNA polymerase activity, helicase activity, exoribonuclease activity and methyl transferase activity respectively . Synthesis of structural proteins encoded by subgenomic mRNAs, the central organiser of CoV assembly actually determine the shape of viral envelope after synthesis of proteins such as M, E and S by entering into the endoplasmic reticulum (ER) i.e. Golgi intermediate compartment (ERGIC) complex . At the same time, ribonucleoprotein is formed by the complexion of replicated genome and N protein and new virions are released by exocytosis from ERGIC [59,60]. The step by step translation and replication process of CoV in the host cell is depicted in figure 6.
The extremely non-specific symptoms of the COVID-19 include fever, respiratory symptoms like- cough, viral pneumonia and dyspnea . During the whole course of disease COVID-19 different patients came across different problems like gastrointestinal disorders, diarrhea, and respiratory problems . In most of the cases, the delay in detection at early stage is the main reason of the high spread of this virus. Recent reports on the Diamond Princess Cruise ship quarantined in Yokohama, Japan, showed that 454 infected cases identified out of 3700 passengers and crew, as they did not have enough diagnosis kits . Rapid screening and early detection of SARS-CoV-2 in suspected patients has become necessary to control the lethal effect of the COVID-19 outbreak [64,65]. The Point of Care (POC) device, which is very efficient and cost-effective will be helpful for early stage detection . Some modern detection techniques are summarized as follows.
Polymerase Chain Reaction (PCR) assay for COVID-19
Real time reverse transcription polymerase chain reaction (rRT-PCR) is currently used as standard molecular technique for the detection of COVID-19 . Sophisticated laboratory equipment are required for rRT-PCR technique (Bio-safety level 2 or above) . Commercial PCR based techniques are usually time taking and expensive and it requires experts as the existence of RNA pathogen does not always reflect the disease [69-71]. Another problem with Commercial PCR system is that other respiratory viruses are also encountered at the time of detection ofCOVID-19 that reflects positive CoV PCR result .
Loop Mediated Isothermal Amplification Assay (LAMP) for COVID-19
It is a new method where nucleic acid (DNA) is amplified with high efficiency, rapidity and specificity in isothermal condition. A set of four designed primers with a DNA polymerase are utilised. By this method the stand displacement activity synthesize the targeted DNA up to 109 copies below 60 °C within one hour . With several reversed replications of the target stem loop DNAs are obtained as final product and appears like a cauliflower. LAMP is very much popular for pathogen detection and it is more simple than PCR . Though LAMP is very much faster and sensitive than PCR but its establishment is in early stage.
When SARS-CoV-2 was first identified, many scientists redirected their focus to CRISPR (Clustered regularly interspaced short palindromic repeats)-based diagnostics to detect SARS-CoV-2. The use of Cas12/Cas13 enzymes is the key principle of this approach and it is initially determined as the components of ‘bacterial immune system’ coupled to RNAs with specific binding to certain regions of the target DNA or RNA . STOP Covid (SHERLOCK Testing in One Pot COVID) and DNA Endonuclease-Targeted CRISPR Trans Reporter are two commonly used CRISPR-based detection methods for SARS-CoV-2 . The first technique is targeted to the N-gene and E-gene of SARS-CoV-2 and engages the Cas12a enzyme, on the other hand, the second one is targeted at the N gene with the utilization of Cas12b enzyme. PCR-based tests take center stage to maintain the standard of diagnostic tests [76,77]. However, a labor-intensive protocol with long waiting for results, and a dwindling reagents supply has led to many scientists looking for alternative CRISPR test. For mass testing, many have turned to CRISPR test, as its nucleotide-targeting ability makes it optimal for the detection of the presence of viral RNA.
LFIA detection method
Lateral Flow Immunoassay (LFIA) is another conventional method for the detection of COVID-19 disease. After the addition of the sample, specific IgM and IgG antibodies flow with the capillary action and specific immunoglobulins bind with SARS-CoV-2 gold conjugated antigens. The main advantage of this method is that it is suitable to detect COVID-19 disease at the different stages of the infection due to the combined determination of IgM and IgG .
Virus-proteins or specific antibodies against these SARS-CoV-2 virus-proteins
It is the modern method for the detection of COVID-19 including antibody and antigen tests. Here the interaction between SARS-CoV-2 virus proteins and specific antibodies is performed. As a result, an intermediate complex is formed which gives pieces of information regarding the kinetics of SCoV2-rN/anti-SCoV2-rN composite formation which gives the SCoV-rN and anti- SCoV-rN Gibbs free energy (DGAssoc). The results are very helpful for the design of new diagnostic systems for the development of new anti-SARS-CoV-2 medicine .
The early symptoms of COVID-19 infection are fever, sore throat, tiredness, fatigue, dry cough, aches and pains, pneumonia, dyspnea, swollen eyes and sometimes diarrhea, nausea or a runny nose and sneezing, for a low percentage of people [21,79]. These symptoms are shown within five to six days after the infection transmission of SARS-CoV-2 but the incubation period may last upto 14 days [70,80,81][70,80,81]70, 80, 8169, 79, 8068, 78, 7967, 77, 7867, 77, 7868, 78, 7968, 78, 79. The virus particles spread through the droplet transmitted and largely affect the nasal and mucous membranes in the throat and surroundings, which infect the neighbouring cells. They crawl progressively down and affect the bronchial tubes mucous membranes and lungs. They can damage the alveoli or the lung sacs, and the lung function, since the lung is filled with fluid, pus and dead cells. Patients suffering from excessive breathing trouble may need ventilation support (Acute Respiratory Distress Syndrome). Extreme condition may results death 82818079798080.
Sometime it may affect the rectum of the infected individual. It may enter the cells of gastrointestinal system hence causing symptoms like diarrhea or indigestion. The pathogen may directly damage the bloodstream, blood vessels, bone marrow and organs like the liver, the heart, the kidney. This may result in inflammation and malfunction of all the organs. Some patients may tolerate the damage of organs and the infection with immune system. It is not reported that 2019-nCoV could not damage the brain but could insinuate the brain in some patients. The 2019-nCoV may infect some nerve cells also .
COVID-19 is a respiratory disease by which people are being affected with minor to modest symptoms and may get cured without any specific treatment. Most of the patients infected with SARS-CoV-2 take 1 to 14 days to grow symptoms . The SARS-CoV-2 can infect individual in different ways. It is observed that the people whose aged are more than 60 years, with pre-existing diseases, may have higher risk of getting affected. The symptoms of COVID-19 may appear after exposure as MERS-COV virus and incubations period of SARS-COV-2 is approximately 5.2 days .
Emergency warning signs of COVID-19 such as acute breathing trouble, tremendous chest pain or pressure, new confusion or inability to arouse, bluish lips or face, if developed, required immediately medication. The situation report - 95 from the World Health Organization reveals 84570 and 1716078 confirmed cases in China and USA respectively as on 31st May, 2020. The effect of corona virus on human body is shown in figure 7.
Individual exhibiting COVID-19 symptoms must undertake a few necessary precautions to prevent the human-to-human transmission. The expert recommendations related to precaution for avoiding COVID-19, by the WHO and the CDC are i) Anyone who has COVID-19 symptoms, must stay at home and avoid large or any mass gathering, occasions, or programmes & public areas. Avoid public transportation, taxis or ride-sharing, and maintain distance (about 6 feet) from others. Keep away from affected area or community with COVID-19 cases. ii) Wash hands frequently with soap-water for more than 20 seconds or use hand sanitizer containing alcohol (not less than 60%) and cover mouth & nose with a tissue or the elbow while sneezing or coughing. Used tissue must be thrown into covered dustbin or lined trashcan. Also stop touching mouth, nose and eyes with unless hand sanitize. iii) Wash and disinfect surfaces frequently on regular basis, do not take raw or undercooked meat, and do not share household items like glasses, cups, dishes, eating utensils, bedding and towels etc. Use separate bathroom if possible and finally, stay isolated in a particular room (termed home quarantine) away from the other members of family and with limited access to pets. iv) Visit a doctor immediately in case of any COVID-19 symptoms, informed the clinic beforehand so that they can take necessary precautions, and disclosed to the doctor any travel history or contact with contaminated or infected people.
The authorities of the health departments of different countries have appealed to and instructed all concerned regarding epidemic precaution, prevention, protection, treatment, medicine and diagnostic techniques; including awareness and information, education and communication (IEC) activities, for prevention of such severe respiratory diseases due to CoVs .
Though COVID-19 can affect any age group, its deadliest effect is mostly found in middle and older age group. Recent investigations reveal that it has a profound effect in the age range of 49 to 56 years  and 77.8% of confirmed patient were within the age of between 30 to 79 years among 44672 patients for period of 16th to 20th February 2020 . Recent reports showed that the mortality rate is 0.2% for the 10-39 years age group, 0.4% for 40-49 years age group, 1.30% for 50-59 years age group, 3.6% for 60-69 years age group, 8% for 70-79 years age group and highest rate of 14.8% is realized for 80+ age group as shown in figure 8. Presently, the limited data available pertaining to age-related risk-factors is insufficient in case of COVID-19.
Recent data shows people with aged above 65 years and suffering from chronic bronchial diseases or mild to severe asthma, severe chronic cardiac disease, high obesity (body mass index [BMI] ≥ 40) have a high risk of COVID-19 infection. Furthermore, people with certain uncontrolled diseases like diabetes, chronic kidney diseases, or hepatic diseases, immunity disorder, bone marrow or organ transplantation, HIV or AIDS also have an elevated risk of getting affected by COVID-19 [42,43][42,43]42, 4341, 4240, 4139, 4039, 4040, 4140, 41.
At present vaccines or drugs are not available in the market that can effectively combat the COVID-19 disease . Since COVID-19 is a viral infection, antibiotics readily available are not effective. Different drugs were experimented through in vitro trails on the human-based SARS-CoV and MERS-CoV, but they are initial stages. Interferon-beta (IFNb) has potential to reduce the replication of MERS-CoV only but there are no appropriate drugs available in the market for SARS-CoV-2 . Initially, usage of the drug with the combination of Anti-HIV drugs Lopinavir/Ritonavir (LPV/RTV), ribavirin and pegylated interferon resulted a success report to cure MERS-CoV infected patients in South Korea [40,88]. Furthermore, in vitro studies with the drug remdesivir, a powerful terminator of RNA viral transcription is at beginning stage for the diseases caused by SARS-CoV, MERS-CoV and related zoonotic bat CoVs [89-91]. There are few drugs such as captopril, perindopril, ramipril, lisinopril, benazepril and moexipril also tested for effectiveness toward ACE2 as the similarity found with ACE .
Genomic information and replication process of SARS-CoV-2 is almost similar to the SARS-CoV, but the only difference is that it has higher binding affinity to host cell. To discover potential drugs for SARS-CoV-2 we need to analyse systemic replication and transcription pathways of the virus in the host cell. The replication of SARS-CoV-2 begins with the binding of its spike protein (S) on the cell-surface molecules of the host. This receptor recognition is important for initiating virus entry into the host cells, thereby playing a major part in the tissue and host species tropism of viruses. Therefore inhibitory effect of the communication between the spike proteins to the human related proteins specifically enzymes viz. humanACE2 and type-II trans-membrane serine protease (TMPRSS2) enzymes is the key step for drug development. Secondly inhibition of the viral enzyme and proteins that are involved for the synthesis and replication of RNA is important for designing potential drugs. Based on the homology there are total 18 viral proteins (Figure 4) viz. Nsp1, Nsp3 (Nsp3b, Nsp3c, PLpro and Nsp3e), Nsp7-Nsp8 complex, Nsp9–Nsp10 and Nsp14–Nsp16, 3CLpro, E-channel (E-protein), ORF7a, Spike, N-terminal RNA binding domain (NRBD), C-terminal RNA binding domain (CRBD), RdRp, helicase and 2 human enzymes viz. ACE2 and TMPRSSS2 that are involved from the endocytosis to the exocytosis of SARS-CoV-2. Interrupting endocytosis and exocytosis processes would be potential for development and discovery of new drugs therapeutics.
Before going to in details of the drugs related to the SARS-CoV-2, herein we note some approved drugs that are reported for the treatment of SARS-CoV (2002). These are the following drugs: Ribavirin (inhibits viral polymerase) , E64-d,glycyrrhizin (inhibits replication process) .
Drugs that effectively block the host specific receptor or enzymes
ACE-2 enzyme inhibitors: ACE2 enzyme, a human host spike receptor helps for cross species transmission. The spikes of SARS-CoV-2 have more affinity to ACE2 receptor binding domain (RBD) as compared to previous MERS & SARS CoV. There is a strong interaction between several key amino acid residues of RBD receptor and ACE2 enzyme . The drugs that showed inhibitory activity against ACE-2 enzyme areeprosartan (Tevetan), irbesartan (Avapro), losartan (Cozaar), olmesartan (Benicar), telmisartan (Micardis), valsartan (Diovan) and chloroquine along with their mode of action and side effects are shown in the table 1. Among these drugs only Cholroquine is reported to have potential activity against the interface between the ACE-2 and spike protein . Few ACE-2 enzyme blocker drugs are shown in figure 9.