COVID-19: Prospective Challenges and Potential Vaccines

Muhammad Shahid Nadeem, PhD; Akbar Ali, PhD; Maryam A. Al-Ghamdi, PhD; Jalaluddin Azam Khan, PhD; Markus Depfenhart, MD, PhD, LLM; Mazin A. Zamzami, PhD; Bibi Nazia Murtaza, PhD; Imran Kazmi, PhD; Mujadid Ur Rehman, PhD

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ABSTRACT

Context • RNA viruses exhibit an extraordinary ability to evolve in a changing environment and to switch from animal hosts to humans. The ongoing COVID-19 pandemic, recognized as a respiratory disease, is an example of zoonotic transmission of the RNA virus known as SARS-CoV-2. The development and regulatory approval of a vaccine against SARS-CoV-2 pose multiple preventive and therapeutic challenges, especially during an ongoing pandemic.

Objective • The review intended to examine the challenges and recent achievements in the development of vaccine candidates against COVID-19.

Design • The research team performed a literature review, searching relevant and up to date information from the literature. The sources of data included Google Scholar, PubMed, NCBI, and Yahoo. The search terms used were COVID-19 challenges, SARS-CoV-2 prospective challenges, RNA viruses adoptability, host switching by RNA viruses, COVID-19 vaccines.

Setting • The study took place at the digital libraries of contributing institutions. The data was combined, selected for further analysis and manuscript preparation at King Abdulaziz University.

Results • RNA viruses with high rate of genome alterations and evolution have better chances to survive in the adverse environmental conditions by adopting the alternate host species. The recent epidemics such as SARS, MERS, and COVID-19 are examples of zoonotic transmission of RNA viruses from animal species to the humans. However, the mechanisms involved in the switching-on to new host species need further investigations to control the zoonotic transmissions in near future. As of April 2020, 115 candidate vaccines were being evaluated; 78 of them had been found to be active, and a few of them are in Phase I trials. In the development of different types of vaccine candidates against COVID-19, multiple international pharmaceutical and biotechnology companies are involved.

Conclusions • Emerging and re-emerging pathogenic RNA viruses pose a serious threat to human health. Little is known about the human-host adoptive mechanism for zoonotic transmission. Deep insights into the molecular mechanism responsible for the switching of animal or bird viruses to humans could provide target molecules or events to prevent such transmissions in the near future. Fast development and approval of efficacious and safe vaccines is key to the effort to provide preventive measures against COVID-19 and future viruses. However, the development and availability of a vaccine candidate is a time-consuming  process and often can’t be completed during an epidemic. Currently, several types of vaccines are under development, and most of them won’t realistically be available in time for the present COVID-19 pandemic. (Altern Ther Health Med. 2020;26(S2):72-78)

Muhammad Shahid Nadeem, PhD, Assistant Professor; Maryam A. Al-Ghamdi, PhD, Associate Professor; Jalaluddin Azam Khan, PhD, Professor; Mazin A. Zamzami,  PhD, Associate Professor; and Imran Kazmi, PhD, Associate Professor, Department of Biochemistry, Faculty of Science, King Abdulaziz University Jeddah, Saudi Arabia. Akbar Ali, PhD, Assistant Professor, College of Pharmacy, Northern Border University, Rafha, Saudi Arabia. Bibi Nazia Murtaza, PhD, Assistant Professor; and Mujadid Ur Rehman, PhD, Professor; Department of Microbiology, Abbottabad University of Science and Technology (AUST), Abbottabad, Pakistan. Markus Depfenhart, MD, PhD, LLM, Faculty of Medicine, Venlo University B.V, Venlo, Netherlands and Medical One Clinic Hamburg, Hamburg, Germany.

Corresponding author: Muhammad Shahid Nadeem, PhD
E-mail address: [email protected] 

A rapidly increasing human population has created a human-dominated ecosystem, and human activities pose a serious threat to animal populations. Gradually, the limiting of the number of or the extinction of many animal species has resulted in host switching by genetically modifiable RNA viruses because they have the ability to adopt new hosts in the altered ecosystems.^1,2 This rapid evolution of zoonotic RNA viruses has resulted in modifications in the virulence and disease patterns in the changing ecosystem.^3-5

The sudden outbreak and unusually rapid spread of COVID-19 has caught most of the world unprepared. Like other respiratory coronavirus infections in the recent past, the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS), COVID-19 has been reported as a zoonotic transmission.^6-9

The causative agent of COVID-19 is SARS-CoV-2, a β-coronavirus characterized by a 27.9-kb, single-stranded, sense RNA genome.^10,11 It codes for 10 genes and 26 proteins; one polyprotein coded by orf1a/b is subsequently cleaved into 16 proteins, including the viral protease and RNA polymerase.¹²

The genome of SARS-CoV-2 also codes for the surface glycoprotein known as spike protein (S-protein), which interacts with the human angiotensin-converting enzyme 2 (ACE2) receptor on cell membranes and promotes viral entry into cells.¹³ In general, the large genome discriminates coronaviruses from other RNA viruses.

The genome codes for an exonuclease, known as ExoN, exhibit proofreading activity and stabilize the genome structure by reducing the mutation rate.¹⁴ However, alignment studies of the genomic sequences of SARS-CoV-2, isolated in samples from various countries, have shown 93 mutations. These include 3 mutations in the receptor binding domain of the S-protein: (1) N (354)→D, (2) D (364)→Y, and (3) V (367)→F.¹⁵

The S-protein defines the host selection and tropism; it also remains the major target for neutralizing antibodies. The mutations in the S-protein may lead to conformational changes in the protein and subsequent alterations in antigenicity.^15-17

COVID-19 is a stark reminder of the challenges that exist in preventing and intervening in prospective viral infections. It has imposed a clear understanding of the molecular mechanisms behind the host-adaptation strategies of these viruses that can help in selecting potential targets against zoonotic invasions.

Vaccination is considered to be an ideal protective or preventive measure against viral infections. An enormous amount of funds, time, and effort have been entailed for the development and careful assessment of an array of SARS-CoV-2 vaccines. Various vaccine development technologies are being considered, including recombinant protein subunit vaccines, nucleic acid vaccines, and whole virus vaccines. Several vaccine candidates are being considered for all 3 types, and all candidates are in trial stages.

However, development and approval of vaccine candidates is a tedious task that requires significant funding and is very risky, with limited chances of success.

The development and regulatory approval of a vaccine against SARS-CoV-2 contains multiple preventive and therapeutic challenges for international biomedical research and development groups, especially during an ongoing pandemic. The current review intended to examine the challenges and recent achievements in the development of vaccine candidates against COVID-19.

Methods

The study took place at the digital libraries of contributing institutions. No human or animal subjects were directly involved in this study. No consent form was involved, and ethical approval of this study wasn’t needed.

Procedures

The sources of data mainly included Google Scholars, PuBMed, NCBI and Yahoo. The search terms uses were COVID-19, SARS-CoV-2 vaccines, RNA virus host adoptability. Extensive data were collected using the online search engines, combined and evaluated. The information obtained from peer reviewed articles published in the reputed journals and from the websites of biopharmaceutical companies were included in the present study. The information extracted from research articles published in the journals without peer review and data from internet websites other than the original sources were excluded. The information obtained from research and review articles on RNA viruses, problems in the vaccine development during SARS and MERS were also included in the present study due to similarity of these viruses with SARS-CoV-2. Total 95 information sources (research/review articles, and websites) were combined and only 78 were included in the present study.

Results

Preventive and Therapeutic Challenges

The recent emergence of COVID-19 was not unexpected or accidental. For many years, global health experts have clearly sounded the alarm about the possibility of a robust and severe pandemic episode that would be worse than the influenza epidemic in 1918.^18,19 The occurrence of the epidemics of influenza in 1985, SARS in 2003, and MERS in 2012 and the currently ongoing pandemic of COVID-19 are stark reminders that health experts need to develop countermeasures against emerging and re-emerging pathogens.

In particular, the RNA viruses predominantly found in mammalian and avian host species impose a challenge of continuous surveillance, through investigations and deep insights into their genetics, host adoptability, and pathophysiology.²⁰ A modified version of viral epidemics threatens humans almost every 10 years, and health authorities are always caught with a limited arsenal to combat the deadly infections.

SARS-CoV-2 has been reported to be a coronavirus of animal—bat or pangolin—origin that has switched to the human host.^6,21 The determination of the molecular mechanism behind the adaptation of such animal viruses to humans has tremendous importance for the intervention and prevention of future zoonotic transmissions.

An efficient vaccination can induce protective immunity against a specific disease in future. However, the efficacy and safety of a newly developed vaccine candidate requires a careful and complete evaluation before its application at a population scale.

Sometimes, vaccination can exacerbate a natural infection with its corresponding pathogen; the phenomenon is known as immunopotentiation. The phenomenon has been observed in the case of coronavirus vaccines. An N-protein-based vaccine developed against SARS-CoV has shown an enhanced lung immunopathology.^22,23 The vaccine not only failed to protect against the SARS-CoV infection but also led to a condition called antibody dependent enhancement (ADE), which enables an antibody-mediated, nonspecific entry of viruses into cells.

A similar response occurred with a SARS-CoV vaccine candidate that used a formalin-inactivated whole virus.²⁴ Due to COVID-19’s similarity to SARS, the need for concern about the effects of vaccines against it is obvious.

The most severe pathology from SARS-CoV-2 has been found in individuals above 50 years of age. These individuals also respond poorly to the vaccine due to immune senescence.²⁵ This issue needs to be addressed in the
SARS-CoV-2 vaccine for older individuals. If a vaccine can stop the transmission of disease, it can indirectly help older individuals.

Various types of vaccines against SARS-CoV were in development when the epidemic waned.^26-28 Furthermore, the development was curtailed by a lack of interest by vaccine companies and funding agencies.

Vaccine development involves an expensive and lengthy process, from formulation to evaluation to trials to a vaccine’s availability as a licensed product. In a vaccine project, the chance of failure remains at about 94%.^29,30

The vaccines against epidemic diseases have a very limited market as compared to adult and childhood vaccines and receive less attention from multinational pharmaceutical companies. At present, no licensed vaccine exists in the market against human coronaviruses.

Many vaccination options against COVID-19 have been proposed or are under development,³¹ but conventional procedures for protein production are too slow to respond to an epidemic. The effort needs rapid, safe, and low-cost procedures to produce bulk quantities of recombinant viral proteins and to manage the subsequent immune-response investigations.¹⁹

The preclinical trials require animal models with human ACE2 because SARS-CoV-2 doesn’t infect wild-type rats or mice. The development of such animal models is a costly, tedious, and time consuming process,³² and even if the preclinical studies are successful, clinical trials with controlled placebo groups are rarely acceptable to human populations under a pandemic situation of high mortality.

A time-saving strategy might be simultaneous application of a few candidate vaccines in a single, shared group trial, but such procedures are statistically and logistically complex. Also, vaccine developers usually avoid the generation of direct comparative data of their products that such a trial would create.^33,34 Even if health authorities can overcome all the above obstacles, the provision of funds to provide several million vaccine doses in a short time poses a big challenge.

Potential Vaccines Against COVID-19

As a result of the current COVID-19 pandemic, research and development institutions from different countries are racing to develop vaccines. However, a typical vaccine development can take from several to many years, with a success rate lower than 10% overall. For example, the US FDA has approved about 3000 candidate vaccines for clinical trials during the last 30 years, and fewer than
20 vaccines received final approval and certification.³⁵

The Coalition for Epidemic Preparedness Innovations (CEPI) has organized huge funds, 2 billion USD, for the development of a vaccine against SARS-CoV-2.³⁶ The key players in the field of innovation have been activated, and some of those may eventually succeed in developing a vaccine against SARS-CoV-2. However, most of these institutions and companies have neither an established pipeline to swiftly provide a vaccine for clinical trials nor the capacity to prepare the millions of required doses. Vaccines of various types have been reported to be in different developmental stages, and CEPI expects a need for at least one-million doses of SARS-CoV-2 vaccine during the next year or so.³⁶

Vaccines Under Development

Table 1 discusses a selection of vaccines now under development.

Table 1. Candidate Vaccines Against COVID-19, With Relevant Pharmaceutical and Biotechnology Companies and Trial Stages.

Whole virus vaccines. Whole virus vaccines-live-attenuated or inactivated-are a classic strategy in the fight against COVID-19. The advantages of whole virus vaccines include their ability to be developed rapidly and their excellence in inducting a B and T cell response and stimulating toll like receptors (TLRs).³⁷

However, they have some serious disadvantages as well. In general, live-attenuated virus vaccines pose a risk of reversion to virulent strains. They aren’t suitable for sensitive populations, such as infants, the elderly, and immune-compromised individuals. The inactivated virus vaccines can cause hypersensitivity reactions and can possibly result in T helper 2 (Th2) bias. Whole virus vaccines need extensive safety evaluations before use in a general population.^37-39

Janssen, a pharmaceutical division of Johnson & Johnson, has announced a collaboration with the Biomedical Advanced Research and Development Authority (BARDA) on a promising whole virus vaccine candidate for COVID-19.⁴⁰ In the past, Janssen has used adenoviral vector, AdVac, for the synthesis of Ebola vaccine in the PER.C6 cell line. The same technology will be used for the COVID-19 vaccine development and production.⁴⁰

Researchers at the University of Hong Kong also have produced a whole virus vaccine by inserting a part of the surface antigen of COVID-19 into live influenza virus.⁴¹ The influenza virus had been previously developed by the same team and used as a nasal-spray vaccine. Therefore, the new vaccine will provide immunity against influenza as well as COVID-19.

ChAdOx1 nCoV-19, a vaccine under development has been evaluated for initial trials, it exhibited encouraging results and now in process for human trials.⁴²

Codagenix, a Chinese biotechnology company, uses the codon de-optimization technology to develop live attenuated vaccines against viruses.⁴³ In this technology, relatively harmless viruses are produced by rewriting viral genes using statistically under-represented codon pairs.³⁷ CanSino Biological have produced an active vaccine Ad5-nCoV that is under final trial stages.^44,45 This technology has been used to produce vaccines against various pathogenic viruses.^46-50 Using this technology, a live-attenuated COVID-19 vaccine is in process that will carry all structural and nonstructural proteins including the S-protein.

Viral S-protein and receptor binding domain (RBD). Vaccines based on recombinants of complete viral proteins or their specific domains are well accepted and cost effective, with no risk for incomplete inactivation. Also, the aluminium salts or squalene emulsions can be easily added as adjuvants to these protein formulations to enhance immunogenic impact.⁵¹

Previous studies on the SARS and MERS coronaviruses have shown that S-protein is an ideal target for vaccine development and for intervention into the host-virus interaction. Studies on nonhuman primates have shown some protective as well as disease-enhancing epitopes in SARS-CoV S-protein.⁵² However, in all cases, an S-protein-based vaccination has been associated with the greater survival of animals.

Similar findings have been reported for MERS-CoV S-protein-based vaccines.^53,54 SARS-CoV-2 was identified soon after the detection of infection, and its genome sequence was made available swiftly by Chinese groups.^10,11 The high-resolution structure of SARS-CoV-2 S-protein has been described for a better understanding of its major structural and functional domains.^13,55 S-protein has a 1273-amino-acid (MW 140 kDa) polypeptide that exists as a homotrimer. The protein consists of 2 subunits, S1 and S2. S1 has 2 domains—the C-terminal domain (CTD) and the N-terminal domain (NTD); the RBD is located in the CTD. S2 consists of
2 hepatic repeats (HRs)—the transmembrane domain (TM) and the fusion domain (FD).^13,55,56

Research groups have already been investigating the S-protein or its components from the known coronaviruses, SARS and MERS, for vaccine development.⁵⁷ These efforts have been recently directed to S-protein vaccine development for SARS-CoV-2.⁵⁸

Recently, it has been reported that antibodies raised against the SARS-CoV-2 RBD can successfully react with the SARS-CoV-2 RBD protein, suggesting a preventive measure against SARS-CoV-2 infection.⁵⁹ Similarly, vaccines comprising 13 major histocompatibility complex class I (MHC‐I) and 3 MHC‐II epitopes of S-protein have also been suggested.⁶⁰

Although the S-protein-derived vaccines against the related coronaviruses SARS and MERS have shown considerable efficacy in animal models, the safety of vaccines produced against SARS-CoV-2 by a similar procedure requires further evaluations and clinical trials.61 University of Queensland (Australia), CEPI, Clover Bipharmaceuticals have been working on viral protein component based vaccines, good initial results have been reported.^36,62,63 Fudan University, Chinese Academy of Sciences, and an American biopharmaceutical company (Vaxart, Inc.) have also started vaccine development projects based on the recombinant S-protein or RBD.^43,64 S-protein based highly immunogenic vaccine has successfully gone through the preclinical trials on monkeys.⁶⁵

Nucleic-acid vaccines. Ribonucleic acid (RNA)-based vaccines are a new type of vaccine in which mRNA coding for a protein of a pathogen, such as that of a virus, gets delivered in vivo into human cells, such as with the help of liposomes, nanoparticles, or peptide carriers. Like other types of vaccines, the purpose of RNA vaccines is to induce the synthesis of antibodies against the target pathogen.

Inside the cells, the RNA is translated into protein(s) of the pathogen, which are expressed on the cell membrane of antigen-presenting cells and provoke the defense cells to make antibodies through acquired immunity.^66,67 Unlike other types of vaccines, the process doesn’t require the introduction of the whole killed/attenuated pathogen or any specific antigenic epitopes in RNA-based vaccines. Rather, the antigens are produced inside the host body based on the instructions present in the RNA code.

These vaccines can be introduced directly into the blood or muscles, under the skin, or in the lymph nodes of a host body. After the cells start making antigens, the rest of the mechanism is similar to that of other classes of vaccines.^68,69

RNA-based vaccines are new, and no researchers have had clinical experience from them yet, not even in the veterinarian field. But these vaccine candidates seem to have theoretical  advantages over some other classes of vaccines because they are simple to produce in a shorter period of time than for other vaccines, can be easily administered, and have no known adverse effects to date.^36,70

The major advantage of using pathogen mRNA as a vaccine candidate is that it can be synthesized directly in the lab in a matter of days, which bypasses the difficulty of standardization of the production and purification of the viral protein of interest, which can take months or years. CEPI indicates that these vaccines have shown promising results -n clinical trials. CEPI believes that mRNA-based vaccines against COVID-19 can trigger a robust immune response.³⁶

These vaccines will be easy to assess and stable over longer periods of time than other vaccines and can be prepared at a bulk scale.^71,72 Many companies have been engaged in the development of RNA vaccines against COVID-19, and a few of them are in clinical trials.

Moderna, a biotechnology company, has produced the first batch of mRNA vaccine for COVID-19, called mRNA 1273, under a CEPI-funded project.^44,72 The vaccine is in Phase 1 clinical trials in humans and is being tested with 45 participants at the National Institutes of Health (NIH). According to the plans, the vaccine will finally be available in the market by spring 2021.^73,74 CureVac and Tonix Pharmaceuticals have also developed mRNA based vaccine that has entered the clinical trials.^75,76

Deoxyribonucleic acid (DNA) vaccines mostly comprise recombinant plasmids that code for antigens. These are better than RNA vaccines for efficacy in delivery and stability of the formulations. However, the DNA molecules have to interact with the host-cell nucleus, which could theoretically result in incorporation into the host genome. This has never been observed in the history of animal vaccination, and therefore, DNA vaccines have to be considered to be safe.⁷⁷

Soon after the availability of SARS-CoV-2 genome, Inovio Pharmaceuticals started development of a DNA vaccine known as INO-4800, by application of synthetic biology procedures. Applied DNA Sciences Subsidiary and 2 other companies have started development of a linear DNA vaccine against SARS-CoV-2. All these vaccines are at preclinical or Phase I clinical stages.^35,78 A ncleic acid based vaccine BNT162 has been produced by BioNTech / Pfizer that has shown encouraging results at preclinical stages.⁷⁹

As of April 2020, 115 candidate vaccines were being evaluated; 78 of them had been found to be active, and a few of them are in Phase I trials. In the development of different types of vaccine candidates against COVID-19, multiple international pharmaceutical and biotechnology companies are involved.

Conclusions

Emerging and re-emerging pathogenic RNA viruses pose a serious threat to human health. Little is known about the human-host adoptive mechanism for zoonotic transmission. Deep insights into the molecular mechanism responsible for the switching of animal or bird viruses to humans can provide target molecules or events to prevent such transmissions in near future. Fast development and approval of efficacious and safe vaccines is key to the effort to provide preventive measures against COVID-19 and future viruses. However, the development and availability of a vaccine candidate is a time-consuming  process and often can’t be completed during an epidemic. Currently, several types of vaccines are under development, and most of them won´t realistically be available in time for the present COVID-19 pandemic.

Acknowledgments

To the frontline doctors and paramedical staff struggling against COVID-19 worldwide.

Authors’ disclosure statement 

The authors have no conflict of interest.

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