key: cord-344006-0iq9s94n
authors: Atzrodt, Cassandra L.; Maknojia, Insha; McCarthy, Robert D.P.; Oldfield, Tiara M.; Po, Jonathan; Ta, Kenny T.L.; Stepp, Hannah E.; Clements, Thomas P.
title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2
date: 2020-05-23
journal: FEBS J
DOI: 10.1111/febs.15375
sha: 
doc_id: 344006
cord_uid: 0iq9s94n

The emergence of the SARS‐CoV‐2 strain of the human coronavirus has thrown the world into the midst of a new pandemic. In the human body, the virus causes COVID‐19, a disease characterized by shortness of breath, fever, and pneumonia, which can be fatal in vulnerable individuals. SARS‐CoV‐2 has characteristics of past human coronaviruses, with close genomic similarities to SARS‐CoV, the virus that causes the disease SARS. Like these related coronaviruses, SARS‐CoV‐2 is transmitted through the inhalation of droplets and interaction with contaminated surfaces. Across the world, laboratories are developing candidate vaccines for the virus – with vaccine trials underway in the US and the United Kingdom ‐ and considering various drugs for possible treatments and prophylaxis. Here, we provide an overview of SARS‐CoV‐2 by analyzing its virology, epidemiology, and modes of transmission while examining the current progress of testing procedures and possible treatments through drugs and vaccines.

human transmission, causing the number of cases to skyrocket and outweigh both MERS and SARS [43] . The R 0 for SARS is about 3, MERS to be 0.45, and early estimates placed this value for COVID-19 at 2.2 to 3.11 [32, 44, 45] . While both SARS and COVID-19 appear to have similar R 0 , COVID-19 has a higher viral load in the nose and throat of patients before symptoms develop whereas SARS has a presence more directly tied to symptoms [46] . This suggests that COVID-19 can be transmitted before the development of symptoms, making it harder to isolate and control [46] .

In over 80% of cases of COVID-19, symptoms present as a mild fever, dry cough, and shortness of breath. Severe cases displayed symptoms such as dyspnea (shortness of breath) in 44% of patients, hypoxia (oxygen depletion in body tissues) in about 50% of patients, and a high fever in around 14% of total patients [47] [48] [49] [50] . Depending on the age, hospitalization rates in the United States range from 0.1% for ages 5-17 to 17.2% for others 85 years or older with five percent of total cases experiencing critical conditions such as shock and multi-organ failure [47, 51] . There are two main clinical symptoms that appear for critically ill patients with COVID-19: low levels of oxygen due to poor breathing (Acute Respiratory Distress Syndrome) and fevers [52, 53] . This lack of oxygen is usually addressed through mechanical ventilation in non COVID-19 patients [54] . Additionally, it is thought that later phases of COVID-19 brings a lack of oxygen due to low long compliance and sedation has been suggested in support of mechanical ventilation due to the large demand of drugs such as oxycodone and hydromorphone [54] [55] [56] [57] .

However, in some cases, those confirmed with COVID-19 are asymptomatic yet can still spread the disease [58] . For this reason and the long incubation period of up to two weeks, COVID-19 has demanded extreme safety precautions to be implemented to minimize transmission and morbidity.

This "flattens the curve" of the projected number of infections and aims to stop healthcare services to be overwhelmed with so many new cases at once. Such precautions include social distancing (upholding 2m distance from others), which would reduce the median estimated number of infections

This article is protected by copyright. All rights reserved by 78% by some models [59, 60] . Despite the implementation of these measures, many countries are still experiencing infections at an exponential rate.

Notably, infection and death rates are not the same between countries, age groups, or even races [61] .

Despite the worldwide mortality rate of 6.9%, death rates range from ~.1% in Chile and Israel to 14% in Italy (note these are estimates based on numbers reported by the WHO as of May 8 th , 2020 and doesn't take account for asymptomatic or those infected who have not been tested) [44] . Countries are in various stages of their outbreaks, but there are still many factors that lead to the infection and death rate disparity such as population density, healthcare system, testing policy, and age structure of the country. Testing alone has proved to be a major determinant of the success of a country's response to this outbreak. The decision on whether to engage in mass testing has contributed to the quick control of the outbreak in countries like Germany and South Korea, whereas the reluctance to provide mass testing of those exhibiting symptoms of infection done in the UK and United States has, arguably, prolonged the outbreak [62, 63] . A nation's testing system is especially pertinent given the possibility of disease transmission through asymptomatic carriers [64] .

Moreover, the severity and onset of COVID-19 varies dramatically for different ages with worsening symptoms with age [65] . The lowest risk is observed in those under 19 years of age with a mortality rate ranging from 0 to 0.1%, whereas those 75 to 84 years of age have mortality rates ranging from 4.3 to 10.5%. The highest risk is seen in those 85 years old or older, with a mortality rate of 10.4% to 27.3% [65] . Underlying health conditions including diabetes, cardiovascular disease, or a suppressed immune system also increase the fatality rate [66] .

Considering its high mortality rate in certain groups and high transmission rate, without proper treatment, the thousands of reported deaths from this virus might turn into millions without a coordinated and strategy-based, world-wide response.

This article is protected by copyright. All rights reserved Like other coronaviruses, SARS-CoV-2 is a single-stranded, positive-sense RNA virus that uses spike proteins to bind to human lung epithelial cells (Fig. 2) [67] . The structure of the receptor-binding region that the virus binds to, the angiotensin-converting enzyme 2 (ACE2) receptor (Fig. 3) , is the same target of the SARS-CoV outbreak of 2003 [68] . It's these receptors that act as docking sites for the spike proteins of SARS-CoV-2 to bind to, allowing the viral and cellular membranes to fuse (Fig.   3 ). From there, the virus "hijacks" the cell; it integrates its RNA into the cell's own replication machinery, facilitating propagation of the virus. The virus is then able to proliferate throughout the body, creating immune responses, and causing the person to become infected [69, 70] .

A commonality amongst coronaviruses is the use of their envelope-anchored homotrimeric spike glycoprotein (S protein) to mediate binding with host cell receptors ( Fig. 3 ) [71] . The S protein is cleaved into two subunits during cell infection -the S1 subunit, which contains two receptor-binding domains (RBDs) that allow the virus to bind to its host cell, and the S2 subunit, which is critical for membrane fusion [72] .

The host cell receptor for the S1 subunit of the S protein, ACE2, is a transmembrane protein located on the cells of epithelial tissue in the lungs, heart, kidneys, and intestine [73] . Its primary physiological function is to regulate the maturation of the peptide hormone angiotensin, which helps regulate vasoconstriction and blood pressure [74] . Thus, the expression of ACE2 has antiinflammatory effects that can protect against lung injury, while its downregulation by the binding of SARS-CoV or SARS-CoV-2 has pro-inflammatory effects, which promote the severe acute lung injury symptomatic of infection by these viruses [75, 76] . Beyond its potential role in the pathology of COVID-19, this receptor is directly linked to the infectivity and transmissibility of the SARS-CoV-2 virus. The fact that infectivity and transmissibility of SARS-CoV-2 are higher than that of SARS-CoV is a result of the 10-to 20-fold higher binding affinity of the SARS-CoV-2 RBD to the ACE2 receptor due to differences in the amino acid sequence of the SARS-CoV-2 RBD region which allow more interactions between the S protein and the host cell receptor [77, 78] . The binding affinity of the virus to host cell ACE2 receptors also dictates the pathway of intermediate host organisms that the virus

This article is protected by copyright. All rights reserved could infect before being transmitted to humans and, therefore, which organisms could be used to study the virus [79, 80] .

After the S1 subunit binds to the ACE2 receptor of the target cell, the heptad repeat 1 (HR1) and 2 (HR2) domains of the S2 subunit combine to create a six-helix bundle core that brings the viral and host cell membranes within close proximity of each other for fusion to take place [80, 81] . Upon membrane fusion, the RNA of the coronavirus genome is released into the host cell cytoplasm via an early endosome -unlike SARS-CoV, which employs a late endosome and therefore must cross higher barriers of antiviral host immunity -where it is translated into a replication-translation complex that in turn translates sub-genomic RNA into accessory and structural proteins (Fig. 3) [82-84]. These proteins form viral particle buds that are exocytosed to spread the virus to surrounding cells, thus spreading the infection throughout the host organism.

Between infected hosts, COVID-19 is primarily transmitted through contact with droplets that contain viral particles [85] . Droplets are any medium in which a human can release the virus, such as coughs, sneezes, and mucous. They generally cannot travel more than 2 meters from their origin, though simulations investigating the effects of aerodynamics on the spread of these droplets suggest that fast physical activity, such as running or cycling, increases the distance they can travel [86, 87] . While it is generally thought that droplets do not linger in the air, in one study, SARS-CoV-2 was found to last in the air for 3 hours in experimental conditions [88] . This disease can also spread by a person touching contaminated surfaces then subsequently touching their facial area (fomite-mediated transmission).

Depending on the material, the surfaces were shown to be infectious from several hours on cardboard to 3 days on plastics or stainless steel [88] . Despite these similarities to previous outbreaks and viruses, the ability of SARS-CoV-2 to stay on surfaces and affected individuals to not immediately display symptoms has made it difficult to contain and trace the virus, leading to the current global situation.

An understanding of the molecular mechanisms of this virus not only explains its increased transmissibility and the subsequent symptoms of infections, but also opens the door for a wide range of testing and treatment mechanisms that target the entry mechanism or epitopes of the virus.

The most prevalent form of testing right now utilizes quantitative reverse transcription polymerase chain reaction (RT-qPCR) [89] . This form of testing is widely used to combat the outbreak in places like the US, Hong Kong, Germany, Italy, and South Korea [90] [91] [92] . The test requires a nasopharyngeal swab to gather genetic material that will reveal whether or not the patient has the virus. The testing mechanism first requires the isolation of RNA, then the production of a singlestrand complementary DNA (cDNA) copy of the RNA [93] . Finally, PCR is performed to amplify the cDNA for analysis, which, in all, takes hours to complete [94] .

An important consideration for this testing method is navigating potential false negative and false positive results, which generally result from sample contamination [95] . In some instances, cases that have been suspected to be positive for COVID-19 via computed tomography (CT) images were not diagnosed as positive by RT-qPCR [95] . China has employed a high-resolution CT to supplement their testing to ward out false negatives [96] .

The challenge with carrying out this procedure on a global scale is that the current supply for swabs is limited and hard to distribute. Swab production facility locations can lead to delays and shipment issues, inhibiting the volume of testing [6] . Some countries, including the US and Iceland are struggling to find suppliers that will provide authorized nasal swabs for mass testing [97] .

Recently, molecular testing has been made more accessible to organizations that are outside of the traditional hospital setting through the US-based biotechnology company Abbott and the German Accepted Article technology company Bosch Healthcare Solutions. The Abbott RealTime SARS-CoV-2 assay, which is their new automation systematic machine, reduces processing time from a few days to 15 minutes, because it reduces hands-on time and increases patient analysis flexibility. Each test conducted for this machine is one cartridge and each cartridge elicits one test, which means that there will be a low throughput [98, 99] . The Vivalytic VRI (viral respiratory tract infections) COVID-19 Test System pioneered by Bosch and Randox Laboratories is similar to the Abbott RealTime SARS-CoV-2 assay in that it reduces hands-on time and can confirm a positive test within 2.5 hours with a reported 95% accuracy [100].

One of the most common and fastest forms of testing is the lateral flow immunoassay, which takes a genetic sample from the patient and measures whether or not they have antibodies against a virus [101] . This test, however, is not for determining whether the patient has the disease currently, but instead it measures whether an individual has antibodies for a disease, which would indicate that they have mounted an immune response against the pathogen in the past. Companies like Abbott also have antibody test and recently England has approved a serological test pioneered by the Swiss biotechnology company Roche Diagnostics [102, 103] . Serological tests have a much higher success rate with these companies both boasting successes above 99% accuracy [104] .

Another viable option is the Enzyme-Linked Immunosorbent Assay (ELISA)-based testing, because it is sensitive and is amenable to high-throughput assays [105] . However, some of these serological assays introduced early in the pandemic lacked specificity, which may result in the generation of false positives, leading to overestimates of rates of infection [106] . More specific assays have now emerged that are proving very useful in providing a fuller picture of the rates of asymptomatic or mild SARS-Cov2 infection, through detection of anti-viral antibodies that persist for months and even years after the virus has been cleared [107] .

Altogether, serological tests can serve as an indicator for how widespread the virus is, while RT-qPCR tests can show who currently has the disease.

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Clustered regularly interspaced short palindromic repeats (CRISPR) technology has promise as a tool for disease detection [108] . Two enzymes that work in conjunction with CRISPR, Cas13 and Cas12, can be activated when specific sequences of RNA are detected. Once the enzymes are activated, they exhibit local RNAse or DNAse behavior, respectively, breaking down strands of RNA or singlestranded DNA nearby; in a test scenario, this is usually measured with a fluorescent signal or activity on a lateral flow strip, which acts similarly to a pregnancy test. If the CRISPR-Cas complex is combined with a reporter molecule, the enzyme breaks down the nearby reporter molecule, triggering a response.

When Cas13 is used, a process called SHERLOCK can detect the presence of an RNA virus such as SARS-CoV-2 [109]. Cas13 is activated when it is guided to the specified sequence and starts to breakdown nearby RNA strands. When a RNA sequence reporter molecule is combined with the CRISPR-Cas13 sequence, Cas13 will break it down, signaling the presence of a specific RNA strand, such as a virus, through fluorescence or a lateral flow strip. Cas12 can also be used, in a process very similar to SHERLOCK, called DETECTR, that shows the presence of a virus by activating Cas12 to break down a DNA-based reporter molecule [110] . DETECTR technology is faster than SHERLOCK, but both are being researched and tried as future testing methods. Recently, the company Sherlock Biosciences has received FDA emergency-use approval (EUA) for its SHERLOCK based COVID-19 test, which the first EUA with CRISPR technology [111] .

Currently, there is no available cure or vaccine for COVID-19 and the fastest timescale for development of a vaccine is estimated to be between 12-18 months [112] . In the absence of these long-term and sustainable treatments, doctors and healthcare professionals are working on managing critical respiratory symptoms (dyspnea and hypoxia) from COVID-19 through the use of mechanical ventilation [113] . In a case study on 2634 hospitalized patients in New York, about 12% of the

This article is protected by copyright. All rights reserved patients required ventilation and the mortality among those receiving ventilation was 88% [113] . The repurposing of drugs has also shown promising results for a possible treatment of COVID-19 symptoms: The WHO has outlined four drugs as potential therapeutic candidates for COVID-19 in their Solidarity project: remdesivir, lopinavir/ritonavir, interferon beta-1a, and hydroxychloroquine/chloroquine [114] . Of these, remdesivir currently shows the most promise [115] .

However, further studies have shown the promise of other drugs -EIDD-2801 and Favipiravir [116, 117] . Analyzing the pathways of these drugs not only provides a greater depth of understanding of the virus, but also reveals possible targets for the creation of an antiviral drug.

A drug originally created to be used against the Ebola virus, remdesivir has recently been discovered to be effective in preventing the proliferation of SARS-CoV and MERS-CoV [115] . The structure of remdesivir prevents the propagation of viruses by blocking a crucial piece of RNA duplication machinery -the RNA-dependent RNA polymerase (RdRp) [118] .

In a study of remdesivir, the drug was administered to mouse cell lines infected with SARS-CoV, MERS-CoV, and SARS-CoV-2, and was able to inhibit the spread of the SARS-CoV-2 virus [115] .

For this reason, there is excitement about the potential of this drug. Currently, several phase II/III trials are underway with one highly powered (large sample size) trial sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) in the US, reporting patients had a 31% faster time to recover when taken compared to a placebo [119, 120] . This has been one of the few trials highly powered with a use of a placebo to generate positive results leading to its Emergency Authorization Use by the FDA [121] . As a result, remdesivir has become one of the most promising drugs to fight COVID-19, being tested around the world by countries such as China, Germany, Italy, South Korea, among others [122] . Further studies and results will be needed to determine its efficacy.

Favipriavir (also known as Avigan) similarly selectively inhibits RdRp through preventing it from binding to its energy source (ATP), thus making it non-functional [118] . Its efficacy is promising,

This article is protected by copyright. All rights reserved with China's science and technology ministry calling it an "effective treatment" with "a high degree of safety", as many symptoms such as fever and cough subsided quicker when taking the drug [122] .

Even given these positive results, Japan is one of few countries heavily evaluating the drug with Fujita Health University performing phase II trials on the drug [122] .

Hydroxychloroquine and chloroquine are two safe, inexpensive drugs known mainly for their FDAapproved treatment against malaria and autoimmune diseases, but also been found to have antiviral activity [123, 124] . Viruses usually enter the body and infect cells through endocytosis, which packages the virus and brings it into the cell via an endosome. However, hydroxychloroquine/chloroquine increases the endosome's pH, making it too basic for other viruses to survive and replicate [115] . Given its hydrophobic structure, the drug can circulate throughout the blood and the effects can spread throughout the body including the lungs, making it a strong candidate for treatment against COVID-19 [115] . Tests of hydroxychloroquine and chloroquine against COVID-19 in China and France have proven promising but only studied small sample sizes [125] .

Nevertheless, due to the minimal known side effects of the drug, the FDA has authorized for emergency use by healthcare professionals [126] . There are future hopes that this is a drug that everyone could take to prevent COVID-19 (prophylaxis approach) and federal regulators in the US have removed many regulations that have allowed for testing to hit "warp speed" [127] . However, there are other studies suggesting no/limited effect of chloroquine, or even severe side effects [128] [129] [130] [131] . Some hospitals have also stopped using this drug for these reasons.

Lopinavir and ritonavir, referred to as Kaletra when combined, are mainly used to combat human immunodeficiency virus (HIV) infection by acting as a protease inhibitor that would prevent the cutting of certain proteins needed for HIV replication [132] . After initial reports of success from China and South Korea, scientists were excited by the potential of lopinavir/ritonavir as a treatment against COVID-19 [133] . Yet, when tested on hospitalized infected adults in isolation from other

This article is protected by copyright. All rights reserved drugs, lopinavir/ritonavir showed no significant benefit/improvement, indicating that the protease inhibition was not the same for SARS-CoV-2 as for HIV, ceasing future testing of the drug [132, 133] .

Interferons are a natural component of the immune system that activate antiviral machinery in order to inhibit replication and increase immune response [134] . This process can be sped up via interferon injection [134] . Given its ability to stimulate active immunity, previous studies have tested alpha and beta types of interferons against MERS and SARS [135] . It was identified that the type 1 interferon of a beta subtype was most effective against coronaviruses as it upregulates anti-inflammatory cells in the lungs [135] . Early testing of interferons in human epithelial cell lines showed a reduction of viral concentration by injection and a reduction in infection rates by administration of interferons by spray, in support of interferon-based prophylaxis [135, 136] . Currently, interferon beta-1a is a specific type of interferon available in the market to help mitigate the symptoms of multiple sclerosis, but further research is needed to see its effects in humans [135] .

EIDD-2801 can both serve as a preventable and treatable medicine through oral intake. In contrast to remdesivir, which may treat COVID-19 by inhibiting RdRp [102] , EIDD-2801 induces lethal mutagenesis by accumulating deleterious transition mutations in the viral RNA while having many off-target effects [116] . The results of EIDD-2801 have shown the greatest promise out of all these drugs, having been shown to reduce the concentration of SARS-CoV-2 as well as other coronaviruses (MERS and SARS) when taken prophylactically [116] . While these results have only been observed in mice, its ability to be easily taken orally and as a potential preventative treatment makes it a strong candidate for continued research. As of April 7 th , 2020, the FDA has given the company responsible for EIDD-2801 approval to perform human trials [137] .

Overall, the antiviral activities of these drugs, with the exception of lopinavir/ritonavir, have shown some level of efficacy against COVID-19 using different pathways. EIDD-2801, remdesivir, and Favipriavir all mitigate SARS-CoV-2 by stopping the RNA-dependent-RNA-polymerase from replicating the virus further. By contrast, hydroxychloroquine/chloroquine targets endosomes, while

This article is protected by copyright. All rights reserved interferon beta-1a takes advantage of the body's innate immunity increasing inflammatory responses.

Trying to evaluate the level of success these drugs can be against COVID-19 is difficult due to their different points of research; however, remdesivir is the one of the few drug to have a high-powered experiment that favors positive results, which has led it to become one of the more promising and frequently tested drug around the world [122] . While there is no definite answer yet, testing of these drugs has garnered greater understanding of the viral mechanism that could further aid other drug repurposing or synthesis for a possible cure.

CRISPR Along with possible drugs, new technologies have been utilized preemptively to counter the symptoms of SARS-CoV-2. CRISPR-Cas13 has been utilized to target essential parts of the SARs-CoV-2 virus, through an approach called PACMAN (Prophylactic Antiviral CRISPR in huMAN cells) [138] . Similar to SHERLOCK-based virus detection, PACMAN utilizes Cas13, which has RNAse activity that can be used for both the detection (see above) and the destruction of SARS-CoV-2 ( Fig. 4) [139] . This aspect of Cas13 can be utilized to destroy the virus with pinpoint accuracy, while also knocking out the RdRps. The main roadblock to using this technology is delivery. Some of the problems associated with the delivery of CRISPR-Cas13 have been researched and possible liposomal delivery systems have been established [138] . While these treatments still require further testing, there is promising research in the use of CRISPR as a means of targeting the virus and stopping symptoms, as well as utilizing PACMAN to prevent future pandemics.

While antibodies indicate that a person has developed an immune response to the virus, there is no evidence that shows how long the person will be protected, if they are protected at all, from reinfection of COVID-19. However, in a study of 23 patients that recovered from COVID-19, it was found using ELISA that antibody concentration was associated with neutralizing activity [140] . This has led healthcare professionals to consider blood transfusion of convalescent plasma as a possible treatment. In a case study of five critically ill patients treated with plasma, four out of the five patients

This article is protected by copyright. All rights reserved exhibited normalized body temperatures and decreased viral load, suggesting that the antibodies have antiviral activity [141] .

Using ELISA, scientists from Utrecht University in the Netherlands were able to identify a reactive human monoclonal antibody (47D11) that blocks SARS-CoV-2 infection [141] . Similar to the antibodies found in the blood plasma transfusions, 47D11 antibody is able to reduce viral activity, while also having the capability to be synthesized in a lab. This leads to significant advantages compared to plasma as nothing has to be stored and there isn't a limit to availability. With the recent evidence of 47D11's efficacy in cells, pharmaceutical companies are in a rush to produce a monoclonal antibody treatment as the world waits for an answer.

The vaccine development processes is known to take years for full approval for mass production.

However, many leaders in this area such as Dr. Anthony Fauci, the director of the US National Institute of Allergy and Infectious Diseases, has recently suggested that this process could take less than a year given the current the need to combat COVID-19. Meanwhile, researchers at Oxford University's Edward Jenner Institute for Vaccine Research have started testing a vaccine in humans and could have results of its efficacy by June [142, 143] . For most vaccines, this rapid progression would be seen as unrealistic, but the pressure needed to put this pandemic to halt has led to many regulatory agencies to speed up their approval process.

Typically, vaccine trials are three-phase processes that are run over the course of several years. The first phase is meant to assess the safety of a vaccine, and so it is injected into a small group of healthy volunteers. Next, in the second phase, the efficacy of the vaccine is tested in several hundred volunteers, including at-risk groups. Finally, the third phase moves to testing in thousands of patients if the results are promising and only then can a vaccine be mass-produced. However, governments worldwide have encouraged companies to launch production of vaccine candidates despite the fact

This article is protected by copyright. All rights reserved that none of them have completed the clinical trial process [144] . There are several different types of vaccines that scientists are researching to combat COVID-19.

This type of vaccine aims to provoke an immune response in vaccinated people by introducing a weakened version of the virus into their bodies. These live, attenuated vaccines are the closest thing to a natural infection, and so they are very effective at creating an immune response [145] . The vaccines for measles, mumps, and chickenpox use this approach. However, children and immunocompromised individuals can have difficulties handling the live attenuated vaccines and evoking an immune response [146] .

Another method of vaccination is to use a dead or inactivated virus, like in the polio vaccine. One upside to these vaccines is that there is no concern about the virus regaining pathogenicity and causing disease. However, booster shots are needed for continued protection because these vaccines trigger smaller immune responses [147] .

Rather than include the entire virus, subunit vaccines work by including only parts of the virus' structure, or subunits [148] . For example, a subunit vaccine for a coronavirus strain may only include the S protein or parts of the S protein (Fig. 2) . Similar to the inactivated vaccine, side effects are less common but booster shots are needed. Additionally, subunit vaccines may not be the most costeffective method of acquiring immunity against the coronavirus since their production is very costly.

The previously mentioned approaches to vaccine development are labor-intensive, and require scientists to work long hours cultivating and modifying the specific virus in the lab. Due to the urgency for a SARS-CoV-2 vaccine, researchers are trying novel approaches to vaccine development, with one such being a nucleic acid vaccine.

This article is protected by copyright. All rights reserved One of the first COVID-19 vaccines to be approved for clinical trials was a RNA vaccine first tested in Seattle [149] . Rather injecting a weakened or other altered form of the virus into patients, this vaccine works by injecting mRNA directly into the patient. The mRNA then codes for viral proteins that would lead to an immune response from the body and thus giving individual protection from the disease should they come into contact with the virus again. Other types of nucleic acid based vaccines code for material that interfere protein translation that is essential to the virus' propagation [150] .

However, despite the fact that this technology has been around for about 30 years, nucleic acid vaccines have not yet earned approval since an effective delivery system is needed in order for these vaccines to match the efficacy of a live vaccine [151] .

In clinical trials, research is also being conducted for viral vector vaccines for COVID-19 [152] . In this particular vaccine, scientists engineer non-pathogenic viruses -or a viral vector -with the particular sequence that codes for the virus' antigen. This approach is being used by researchers at Oxford University, who engineered a non-replicating chimpanzee adenovirus with the spike sequence of the SARS-CoV-2 spike protein [153] . This vaccine is particularly promising since it can elicit a strong immune response [154] . However, patients may have pre-existing immunity to the vector, rendering the vaccine useless.

Even with all of these options available, developing a vaccine that can be distributed in mass to combat COVID-19 is not without its challenges. Vaccines are developed from scratch for each target and vaccines against similar coronaviruses cannot be simply repurposed for new uses.

It is important to note that while vaccines were developed for both the SARS-CoV and MERS-CoV outbreaks, they were not utilized in the public sphere because they did not complete clinical trials.

Both of the SARS-CoV and MERS-CoV outbreaks were largely controlled due to containment, patient isolation, and social distancing. Nonetheless, as the SARS-CoV-2 continues to spread farther than its predecessors, the need for a vaccine only becomes more urgent.

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The 2020 SARS-CoV-2 pandemic has sparked advancement in coronavirus research. Data from previous coronavirus outbreaks has been used to enhance the study of treatment and prevention measures for COVID-19. Studying the structure of the virus has allowed scientists to design testing processes rapidly, and new systems of testing are currently being designed to increase the speed and specificity of the process. The testing process is rapidly improving, yielding greater knowledge of who is or has been infected. This data could greatly advance regional decision-making concerning when to lift restrictions and deciding when individuals can resume their usual day-to-day activities.

Treatments for COVID-19 are also being rapidly developed to treat the symptoms of the disease, since no vaccine has currently been approved for mass distribution. Out of all the drugs tested, remdesivir has shown the most promising results. This drug has shown potential in low-powered studies, but hopefully further research will shine light on its efficacy in the short term. Vaccine production is underway, and many types of vaccines are currently being researched and tested so that a vaccine can be available as soon as possible. There are many options for possible treatments of COVID-19, and, ultimately, it boils down to what is most effective, efficient, and available in the near future.

The combination of increased testing and efficient symptom treatment is an encouraging response to the pandemic. Currently, the spread of this virus shows promising decline, but this data will become more accurate as more people are tested and more time has passed. It is essential for governments to consider these factors before initiating the return to normal life.

This article is protected by copyright. All rights reserved CLA, IM, RDPM, TMO, JP, KTLT, and HES reviewed the literature, wrote the text, and revised the manuscript. CLA, IM, RDPM, TMO, JP, KTLT, and HES contributed equally to this manuscript.

TPC carefully revised and co-wrote the manuscript. 

This article is protected by copyright. All rights reserved the merging of the viral and cellular membranes, causing the viral genomic RNA to be inserted into the host cell and thus allowing the virus to replicate. The binding of SARS-CoV-2 to the ACE2 receptor causes a down-regulation of this receptor, disrupting its normal function in maintaining immune homeostasis and leading to pro-inflammatory effects that can cause lung injury. Figure 4 . The top of the drawing represents the DNA encoding for the Cas 13 protein and the CRISPR array, which contains the targets for Cas13 cleavage and subsequent degradation. This array is transcribed into pre-crRNA. The Cas13 protein turns this transcript into mature crRNAs, forming a crRNA-Cas13 complex that in turns searches along existing RNA transcripts for matching sequences known as protospacers. Once this complementary protospacer is found, Cas13 undergoes a conformational change to enhance binding and activates the RNA cleavage activity of Cas13, which can then be used to degrade foreign viral RNA entering the cell as shown on the right side of the image. Adapted from [156] .

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Hospitalization Rates and Characteristics of Patients Hospitalized with Laboratory-Confirmed Coronavirus Disease 2019 -COVID-NET, 14 States

Stavropoulou C In patients of COVID-19, what are the symptoms and clinical features of mild and moderate cases?

Auwaerter Coronavirus COVID-19 (SARS-CoV-2) | Johns Hopkins ABX Guide

Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study

Covid-19 in Critically Ill Patients in the Seattle Region -Case Series

Testing recommendation for COVID-19 (SARS-CoV-2) in patients planned for surgery -continuing the service and 'suppressing' the pandemic

Asymptomatic Transmission, the Achilles' Heel of Current Strategies to Control Covid-19

Case-Fatality Rate and Characteristics of Patients Dying in Relation to COVID-19 in Italy

CDC People Who Are at Higher Risk for Severe Illness | CDC

RNA Viruses: RNA Roles in Pathogenesis, Coreplication and Viral Load

Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

Coronaviruses: an overview of their replication and pathogenesis

Mechanisms of severe acute respiratory syndrome pathogenesis and innate immunomodulation

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response

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

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2

Angiotensin-converting enzyme 2 in lung diseases

CDC (2020) Coronavirus Disease 2019 (COVID-19) -Transmission. Cent Dis Control Prev

& Marchal T Towards aerodynamically equivalent COVID19 1.5 m social distancing for walking and running

Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1

Reverse transcription-polymerase chain reaction molecular testing of cytology specimens: Pre-analytic and analytic factors

Risk of nosocomial transmission of coronavirus disease 2019: an experience in a general ward setting in Hong Kong

Ackermann N & Sing A (2020) Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria

A "One-Health" approach for diagnosis and molecular characterization of SARS-CoV-2 in Italy

Quantitative RT-PCR: Pitfalls and Potential

Rapid PCR of STR markers: Applications to human identification

Real-time RT-PCR in COVID-19 detection: issues affecting the results

Small Solitary Ground-Glass Nodule on CT as an Initial Manifestation of Coronavirus Disease 2019 (COVID-19) Pneumonia

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From Iceland -COVID-19 Screening Swab Shortage Continues

Comparison of two commercial molecular tests and a laboratory-developed modification of the CDC 2019-nCOV RT-PCR assay for the qualitative detection of SARS-CoV-2 from upper respiratory tract specimens | medRxiv

Assay (EUA) | Abbott Molecular 100 VRI multiplex test Vivalytic

Lateral flow based immunobiosensors for detection of food contaminants

Abbott Launches COVID-19 Antibody Test

Roche's COVID-19 antibody test receives FDA Emergency Use Authorization and is available in markets accepting the CE mark Diagnostics

Poon LL & Peiris M (2020) Serological assays for severe acute respiratory syndrome coronavirus

Benucci M & Manfredi M (2020) Serological Assays for SARS-CoV-2 Infectious Disease: Benefits, Limitations and Perspectives

A serological assay to detect SARS-CoV-2 seroconversion in humans

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

Sherlock Biosciences Receives FDA Emergency Use Authorization for CRISPR SARS-CoV-2 Rapid Diagnostic • Sherlock Biosciences

CDC (2020) Coronavirus Disease 2019 (COVID-19) Situation Summary. Cent Dis Control Prev

Qiu M & Zanos TP (2020) Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the

Race to find COVID-19 treatments accelerates

Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro

An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice

Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase

Accepted Article RNA-Dependent RNA Polymerase by Remdesivir

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

Some FDA Approved drugs exhibit binding affinity as high as

kcal/mol against COVID-19 Main Protease (Mpro): A Molecular Docking Study IndiaRxiv

Major ongoing clinical trials for COVID-19 treatment and studies currently being conducted or scheduled in Japan. Glob Health Med advpub

CDC (2020) Coronavirus Disease 2019 (COVID-19). Cent Dis Control Prev

New insights into the antiviral effects of chloroquine

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

FDA Emergency Use Authorization | FDA

Pre-Exposure Prophylaxis with Hydroxychloroquine for COVID-19 Disease

Review of Current Evidence of Hydroxychloroquine in Pharmacotherapy of COVID-19. medRxiv

Hydroxychloroquine Versus COVID-19: A Rapid Systematic Review and Meta-Analysis

No evidence of clinical efficacy of hydroxychloroquine in patients hospitalized for COVID-19 infection with oxygen requirement: results of a study using routinely collected data to emulate a

Outcomes of hydroxychloroquine usage in United States veterans hospitalized with Covid-19

Lopinavir/ritonavir: a review of its use in the management of HIV infection

A Trial of Lopinavir-Ritonavir in Adults Hospitalized with Severe Covid-19

Interferon pathway in SLE: one key to unlocking the mystery of the disease

Type 1 interferons as a potential treatment against COVID-19

SARS-CoV-2 is sensitive to type I interferon pretreatment

Halford B An emerging antiviral takes aim at COVID-19

Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza

Molecular Mechanisms of RNA Targeting by Cas13-containing Type VI CRISPR-Cas Systems

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Ng AC

Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study

A human monoclonal antibody blocking SARS-CoV-2 infection

Kuznia R The timetable for a coronavirus vaccine is 18 months. Experts say that's risky. CNN

Kamisar B Oxford scientist says its vaccine is making headway, could show efficacy by

WSJ News Exclusive | Drugmaker Moderna Delivers First Experimental Coronavirus Vaccine for Human Testing

Long-term protection from SARS coronavirus infection conferred by a single immunization with an attenuated VSV-based vaccine

Live bacterial vaccines -a review and identification of potential hazards. Microb Cell Factories 5

Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic

Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine

Accepted Article This article is protected by copyright. All rights reserved

Induction of Th1 type response by DNA vaccinations with N, M, and E genes against SARS-CoV in mice

Recent advances in mRNA vaccine delivery

SARS-CoV-2 Vaccines: Status Report

About the COVID-19 Vaccine Trials Univ Oxf COVID-19 Oxf Vaccine Tral

Vaccine delivery methods using viral vectors

CDC (2020) International Locations with Confirmed COVID-19 Cases. Cent Dis Control Prev

RNA-Targeting CRISPR-Cas Systems and Their Applications

Before this pandemic occurred, all of these authors were undergraduate students in a discovery-based research lab focused on projects centered on performing novel CRISPR-Cas9 genetic knockouts in zebrafish under the discretion of Senior Lecturer Dr. Thomas Clements at Vanderbilt University.When the Spring 2020 semester went online, the class decided to focus their efforts on learning everything they could about COVID-19. We would like to thank Dr. James Pask, the Introductory Biology Lab Coordinator, for creating and fostering an environment that encourages us to explore these endeavors. Additionally, we are grateful for the Biological Sciences Department at Vanderbilt University for funding our experiments. Lastly, we would like to thank the Ta Family for helping revise the citations.

This article is protected by copyright. All rights reserved

This article is protected by copyright. All rights reserved