Overview of SARS-CoV-2 Genome and Protein Constituents

SARS-CoV, MERS-CoV, and SARS-CoV-2 belong to the Betacoronavirus genus, whose genomes typically contain 5′-methylated caps at the N terminus and a 3′-poly-A tail at the C terminus with a highly conserved order of genes related to replication/transcription and structural components. The replication and transcription–related gene is translated into two large nonstructural polyproteins by two distinct but overlapping open reading frames translated by ribosomal frameshifting (Tu et al., 2020). The overlapping open reading frame, composing two-thirds of the coronavirus genome, encodes the large replicase polyproteins 1a and 1b, which are cleaved by papain-like cysteine protease and 3C-like serine protease (3CLpro, also called Mpro). This cleavage produces 16 nonstructural proteins (NSPs) including important enzymes involved in the transcription and replication of coronaviruses such as RdRP, helicase (Nsp13), and exonuclease (Nsp14) (Tang et al., 2020). The 3′ one-third of the coronavirus genome is translated from subgenomic RNAs and encodes the structural proteins spike (S), envelope (E), and membrane (M) that constitute the viral coat and the nucleocapsid (N) protein that packages the viral genome (Tu et al., 2020). These structural proteins are essential for virus–host cell binding and virus assembly. Upon translation, the S, E, and M structural proteins are inserted into the rough endoplasmic reticulum to travel along the secretory pathway to the endoplasmic reticulum–Golgi apparatus intermediate compartment or coronavirus particle assembly and subsequent release from the cell via exocytosis (Tang et al., 2020).

Viral Entry Through the Binding of SARS-CoV-2 Spike Proteins to Angiotensin Converting Enzyme 2 Receptor

The S proteins of SARS-CoV, required for viral entry into the host target cell, are synthesized as inactive precursors and become activated only upon proteolysis (Gierer et al., 2013). The S protein has two functional domains called S1 and S2. S1 contains an N-terminal domain and a receptor-binding domain (RBD). The receptor-binding motif (RBM) is located within the carboxy-terminal half of the RBD and contains residues that enable attachment of the S protein to a host cell receptor (Letko et al., 2020). The S2 subunit drives the fusion of viral and host membrane subsequent to cleavage, or “priming,” by cellular proteases. SARS-CoV is known to gain entry into permissive host cells through interactions of the SARS-CoV S protein RBD with the cell surface receptor angiotensin converting enzyme (ACE) 2 (Wang et al., 2008). ACE2 is a negative regulator of the renin-angiotensin system and counterbalances the function of ACE, thereby maintaining blood pressure homeostasis (Kuba et al., 2005). It was shown in animal models that ACE2 promotes anti-inflammation, antifibrosis, and vasodilation, whereas ACE promotes proinflammation, fibrosis, vasoconstriction, and severe lung injury (Kuba et al., 2005). Furthermore, through S protein binding, SARS-CoV downregulates ACE2 receptor, and therefore this process not only leads to viral entry but also potentially contributes to severe lung injury, as the ACE2 pathway has protective functions in many organs. Since 83% of ACE2-expressing cells are alveolar epithelial type II cells and these cells contain high levels of multiple viral process-related genes, including regulatory genes for viral processes, viral life cycle, viral assembly, and viral genome replication, they can facilitate coronaviral replication in the lung (Y. Zhao et al., preprint, DOI: https://doi.org/10.1101/2020.01.26.919985). Sequence analysis showed that SARS-CoV-2 genome is very similar to SARS-CoV with a only a few differences in their complement of 3′ open reading frames that do not encode structural proteins (D. E. Gordon et al., preprint, DOI: https://doi.org/10.1101/2020.03.22.002386). Specifically, the S proteins of SARS-CoV-2 and SARS-CoV share 76.5% identity in amino acid sequences and have a high degree of homology (Xu et al., 2020b). SARS-CoV-2 also uses ACE2 as a cellular entry receptor because, in cells that are otherwise not susceptible to SARS-CoV-2 infection, overexpressing human or bat ACE2 mediates SARS-CoV-2 infection and replication (Hoffmann et al., 2020a; Zhou et al., 2020). In addition, SARS-CoV-2 does not use other receptors such as dipeptidyl peptidase 4, used by MERS-CoV, or the human aminopeptidase N used by human coronavirus strain 229E (Ou et al., 2020; Zhou et al., 2020). Several groups have now identified the RBD in SARS-CoV-2 and have confirmed by biochemical analyses as well as crystal structure prediction analyses that this domain binds strongly to both human and bat ACE2 receptor with a binding affinity significantly higher than that of SARS-CoV to the ACE2 receptor (Tai et al., 2020; Wan et al., 2020; Wrapp et al., 2020; Xu et al., 2020b). There has been much speculation that the high affinity binding of SARS-CoV-2 to ACE2 could mediate the increased potential for transmissibility and severity of infection. For instance, the coronavirus strain NL63 also uses the same ACE2 receptor for entry into the host cell as SARS-CoV, but the virus entry and outcome are vastly different, with SARS resulting in severe respiratory distress and NL63 resulting in only a mild respiratory infection (Mathewson et al., 2008). This led the authors to suggest that a lower-affinity interaction with NL63 for ACE2 may partially explain the different pathologic consequences of infection. It has been speculated that in addition to the ACE2 receptor, SARS-CoV-2 could employ other receptors for host cell entry. For example, the S protein of SARS-CoV-2 has a conserved RGD motif known to bind integrins, which is not found in other coronaviruses (Sigrist et al., 2020). This motif lies within the RBD of the S proteins of SARS-CoV-2, close to the ACE2 receptor-binding region (Sigrist et al., 2020). SARS-CoV-2 S protein can also interact with sialic acid receptors of the cells in the upper airways similar to MERS-CoV (E. Milanetti et al., preprint, DOI: https://doi.org/10.1101/2020.03.24.006197). Although the functional importance of integrins or sialic acid receptors in mediating SARS-CoV-2 S protein entry remains to be determined, these may potentially increase cell tropism, viral pathogenicity, and transmission of SARS-CoV-2.

SARS-CoV-2 Has Multiple Viral Entry Mechanisms

In general, coronaviruses deliver their genomes to the host cytosol by two known methods: directly fusing with the plasma membrane at the cell surface in a pH-independent manner or utilizing the host cell’s endocytic machinery in which the endocytosed virions are subjected to an activation step in the endosome. Endocytic activation is typically mediated by the acidic endosomal pH, resulting in the fusion of the viral and endosomal membranes and release of the viral genome into the cytosol (Wang et al., 2008). Fusion with the cell membrane requires that the S2 domain of the S protein be primed by cellular proteases at the S’ site. SARS-CoV is known to be able to enter host cells by directly fusing with the host membrane as well as through the endosomal pathway via cathepsin B and L (Matsuyama et al., 2010). SARS-CoV can also use the cell surface protease transmembrane protease serine type 2 (TMPRSS2) that belongs to the type II transmembrane serine protease family. Although SARS-CoV utilizes both host cell entry pathways, it appears that the TMPRSS2 pathway is the major route of infection of SARS-CoV in the lungs. However, in the absence of TMPRSS2, SARS-CoV can also employ the endosomal late entry route for infection, as SARS-CoV viral spread is still detected in the alveoli of TMPRSS2 knockout mice (Iwata-Yoshikawa et al., 2019). Unlike other soluble serine proteases, TMPRSS2 is anchored on the plasma membrane and localized with ACE2 receptors on the surface of airway epithelial cells (Shulla et al., 2011). This colocalization makes the lungs particularly susceptible to infection. TMPRSS2 cleavage of S protein might also promote viral spread and pathogenesis by diminishing viral recognition by neutralizing antibodies. The cleavage of S protein can result in shedding of SARS S protein fragments that could act as antibody decoys (Glowacka et al., 2011). Although TMPRSS2 affects the entry of virus but not the other phases of virus replication, only a small amount of S protein needs to be cleaved to enable viral or cell-cell membrane fusion, even when minute or undetectable amounts of ACE2 is available (Shulla et al., 2011). In keeping with this, the expression and distribution of TMPRSS2, but not ACE2, correlates with SARS-CoV infection in the lungs. SARS-CoV studies have shown that TMPRSS2 cleaves the S protein after receptor binding, which causes conformational changes that expose the S’ cleavage site (Glowacka et al., 2011). This confers a great advantage to the viral protein by protecting the activating cleavage site from premature proteolysis and yet ensuring that efficient cleavage occurs upon binding to the receptor on target cells (Shulla et al., 2011). Similarly, in the case of SARS-CoV-2, the host cell TMPRSS2 primes the S protein and enhances entry and infection (Hoffmann et al., 2020a; Matsuyama et al., 2020). SARS-CoV-2 may also use other host proteases such as trypsin for S protein activation (Ou et al., 2020). Similar to SARS-CoV, SARS-CoV-2 can also enter host cells through the endosomal pathway via cathepsins (Hoffmann et al., 2020a; Ou et al., 2020). Unlike SARS-CoV, the S protein of SARS-CoV-2 has a furin cleavage site at the S1/S2 boundary similar to MERS-CoV (Hoffmann et al., 2020a; Walls et al., 2020), which likely sensitizes S proteins to the subsequent activating proteolysis occurring on susceptible target cells, facilitates virus entry and infection, and potentially increases viral transmissibility (Qing and Gallagher, 2020). Since SARS-CoV-2 can be activated by an extensive range of proteases, and given that a varied number of proteases exist on the cell surface of different cell types, SARS-CoV-2 has the capacity to infect a wide range of cells (Tang et al., 2020). Thus, it is an opportunistic virus that can use multiple pathways of host cell entry and infection. It is conceivable that successful treatment of COVID-19 may require a cocktail of drugs that target multiple mechanisms of action as historically seen for the treatment of human immunodeficiency virus (HIV) infection; see the review by Maeda et al. (2019).

Drug Development Strategies

For negative-sense RNA viruses, approved therapies are currently available only for rabies virus, respiratory syncytial virus, and influenza virus (Hoenen et al., 2019). Since there are many functional similarities between SARS-CoV, SARS-CoV-2, and MERS-CoV, it is reasonable to screen drugs that were even moderately effective against SARS-CoV and MERS-CoV for SARS-CoV-2. These broad-spectrum anticoronavirus drugs could also be used against future emerging coronavirus infections. In particular, any such drugs that have an IC₅₀ in the low nanomolar range (preferably less than 100 nM) with high efficacy in inhibiting viral infection in vitro would be most advantageous. Drug repurposing has been used in response to emerging infectious diseases to rapidly identify potential therapeutics. If FDA-approved drugs currently on the market for other diseases demonstrate anti–SARS-CoV-2 activity, they could be repurposed for COVID-19 treatment. Several groups have identified compounds with anti–SARS-CoV-2 activity by repurposing select FDA-approved drugs (Choy et al., 2020; Jeon et al., 2020; Wang et al., 2020b). In addition, high-throughput drug repurposing screens have also been successfully used to identify such compounds (Table 1). The National Center for Advancing Translational Sciences also provides an online open science data portal for COVID-19 drug repurposing (https://ncats.nih.gov/expertise/covid19-open-data-portal; K. R. Brimacombe et al., preprint, DOI: https://doi.org/10.1101/2020.06.04.135046).

For compound screening with large-scale libraries and molecular target-based assays, biosafety level (BSL)-2 laboratories are commonly used. These assays take longer to develop but are usually without risk of infectivity to humans and are capable of higher throughput than live SARS-CoV-2 virus assays requiring BSL-3 facilities. However, the efficacy of active compounds identified from such high-throughput screening needs to be confirmed with live SARS-CoV-2 virus assays done in the BSL-3 environment. For example, virus pseudoparticles that contain viral structural proteins without the viral genome can be used to assay viral entry mechanisms. Cell lines expressing viral replicons that contain portions of the viral genome with reporter genes but without viral structure genes can also be used to assay viral replication mechanisms. These nonviral assays used for viral entry or replication are not infectious and can be used in a BSL-2 facility for screening large compound collections. This strategy has been used to screen compounds for BSL-3/4 viruses such as EBOV (Tscherne et al., 2010; Kouznetsova et al., 2014), Lassa virus (Cubitt et al., 2020), SARS, and MERS-CoV (de Wilde et al., 2014; Dyall et al., 2014). Recently, Letko et al. (2020) showed chimeric S proteins containing RBD of SARS-CoV-2 can confer receptor specificity to the full S protein sequence. This approach of nonconventional pseudotyping method is cost effective and can provide a faster way to screen viral-host interactions.

Therapeutic targets for COVID-19 can be directed toward the SARS-CoV-2 virus and its proteins or the host cell targets. Prevention of virus-host associations can fall in either of the two categories. Drugs targeting viral proteins have a major advantage, as they could potentially have higher specificity against the virus while having minimal adverse effects on humans. However, drug resistance may develop rapidly after treatment, particularly in RNA viruses where mutations occur frequently. Conversely, therapeutics targeting host cells may slow the development of drug resistance, as mutations in host cells are relatively rare (Hoenen et al., 2019). Importantly, drugs targeting host cells have greater potential for adverse effects. Possible treatment options under investigation for the prevention and control of SARS-CoV-2 infections in both categories are discussed below.

SARS-CoV-2 Viral Entry Inhibitors

Viral Replication Inhibitors

Inhibitors of viral nucleic acid synthesis are the best represented class of antiviral drugs that suppress viral replication in host cells (Hoenen et al., 2019). The most successful 3CLpro inhibitor is lopinavir, a protease inhibitor used to treat HIV infections that is usually marketed as a ritonavir-boosted form (lopinavir-ritonavir) (Zumla et al., 2016). Preliminary in vitro studies with ritonavir on SARS-CoV-2 infection have not shown much promise (Choy et al., 2020). However, there are clinical trials underway to test the efficacy of this drug in humans (Table 2). Specifically repurposing any inhibitors designed against SARS-CoV or MERS-CoV 3CLpro for SARS-CoV-2 may prove challenging. Although there is a high degree of sequence conservation in the active sites of SARS-CoV and MERS-CoV 3CLpro enzymes, most SARS-CoV 3CLpro inhibitors are inactive against MERS-CoV, indicating other important structural differences (Needle et al., 2015).

RdRP is another target for SARS-CoV-2 drug development. The sequences encoding the structure of RdRP in SARS-CoV, MERS-CoV, and SARS-CoV2 were found to be remarkably similar (Morse et al., 2020). Several RdRP inhibitors originally developed for other viruses are in active clinical trials to treat COVID-19 infections (Table 2). Remdesivir, a prodrug of an adenosine analog, was originally developed for the treatment of EBOV and has broad-spectrum antiviral activities against RNA viruses. Remdesivir successfully improved outcomes when used prophylactically and therapeutically in animal models of MERS-CoV (de Wit et al., 2020) as well as SARS (Sheahan et al., 2017). Treatment with remdesivir during early infection also showed significant clinical benefits in nonhuman primates infected with SARS-CoV-2 (Williamson et al., 2020). In patients with COVID-19, clinical improvements without adverse effects were noted in patients treated with remdesivir on a compassionate-use basis (Grein et al., 2020). In a randomized, controlled trial known as the Adaptive COVID-19 Treatment Trial, patients with COVID-19 who received remdesivir had significantly shorter recovery and mortality rates with no serious adverse events (Beigel et al., 2020). Due to these preliminary reports, FDA recently granted remdesivir emergency use authorization for the treatment of severely ill COVID-19 patients.

Other RdRP inhibitors include favipiravir and ribavirin. Favipiravir, a prodrug guanosine analog, is approved for the treatment of influenza in Japan and China. Favipiravir is not reported to have significant adverse effects; however, it may increase the risk for teratogenicity and embryotoxicity (Furuta et al., 2017). Ribavirin, another guanosine analog prodrug, is used for the treatment of severe respiratory syncytial virus infection, hepatitis C viral infection, and viral hemorrhagic fevers (Zumla et al., 2016; Tu et al., 2020). However, when used as a treatment for SARS-CoV infection in both preclinical (Day et al., 2009) and clinical settings (Stockman et al., 2006), ribavirin did not improve outcomes but instead had adverse effects. In addition, of these three drugs, only remdesivir has shown potent inhibition of SARS-CoV-2 infection in vitro (Choy et al., 2020; Wang et al., 2020a). Therefore, pursuing specific SARS-CoV-2 RdRP inhibitors is a valid approach for COVID-19 drug development, but the efficacy and toxicities of these drugs will need to be closely scrutinized in clinical trials.

Recently, ivermectin was shown to potently inhibit SARS-CoV-2 in vitro with a single treatment (Caly et al., 2020). Ivermectin is an FDA-approved drug for the treatment of parasitic infections. However, its suitability as a COVID-19 treatment is currently being examined in several clinical trials, including one that will test asymptomatic patients (ClinicalTrials.gov identifier: NCT04407507).

Four additional enzymes specific to SARS-CoV-2—helicase (Nsp13), 3′-5′ exonuclease (Nsp14), uridine-specific endoribonuclease (Nsp15), and RNA-cap methyltransferase (Nsp16)—may be considered as key targets for drug discovery (Gordon et al., 2020). In single-stranded positive-sense RNA viruses such as SARS-CoV-2, RNA helicases are essential for viral genome transcription and protein translation. Thus, inhibitors of viral helicases are attractive as therapeutic agents. At least one molecule inhibitor of SARS-CoV helicase without cell toxicity has been previously identified (Cho et al., 2015). However, despite significant efforts being made toward their development, helicase inhibitors are currently not available for clinical use (Briguglio et al., 2011). The SARS-CoV-2 exonuclease (Nsp14) cleaves nucleotides at 3′ end of RNA strand and is required for RNA replication (Romano et al., 2020). Uridine-specific endoribonuclease (Nsp15, EndoU) is an endoribonuclease that hydrolyzes single-stranded as well as double-stranded RNA at uridine residues. EndoU is highly conserved in all coronaviruses, which suggests its functional importance (Hackbart et al., 2020). Although its precise role in viral pathogenesis is not well established, it likely plays a role in evading host recognition (Deng and Baker, 2018). A recent study confirmed that EndoU contributes to delayed type I interferon response by cleaving 5′-polyuridines from negative-sense viral RNAs, which otherwise activate host immune sensors (Hackbart et al., 2020). There are currently no approved inhibitors for viral-specific 3′–5′ exonuclease or EndoU. In coronaviruses, RNA-cap methyltransferase (Nsp16) forms a complex with its cofactor Nsp10 (a 2-O-methyltransferase) for the addition of a cap to the 5′-end of viral RNA. This addition enables the virus to escape innate immune recognition in host cells as well as enhance viral RNA translation (Wang et al., 2015). Unfortunately, there are currently no effective inhibitors or approved drugs for these enzymes that may be used as targets for antiviral drug development.

Host Cell and Viral Targets for Antiviral Drug Development

Viral replication requires a number of cellular proteins and machinery. Inhibiting host cell protein function may effectively combat viral infection. These host targets include the host cell proteases TMPRSS2, furin, and cathepsin and ACE2 receptor discussed above. Additionally, the host cell autophagy pathway is used by some coronaviruses for viral replication and viral assembly. Since coronaviruses may hijack autophagy mechanisms for viral double membrane vesicle formation and replication, the inhibition of cellular autophagy may be a useful antiviral strategy (Abdoli et al., 2018; Yang and Shen, 2020). Although the drugs targeting host cell proteins are more likely to cause adverse effects, patients might tolerate a short 7–14-day treatment regimen. Other complicating factors for targeting host proteins is the redundancy of human cellular function pathways and variations in different cells or tissues, which may reduce correlations between in vitro and in vivo efficacy studies. This issue could be overcome by utilizing a drug combination therapy with different mechanisms of action such as that seen with the successful treatment of HIV; see the review by Maeda et al. (2019). Alternatively, a single drug with multiple activities against both viral targets and host viral replication machineries may be more effective in treating SARS-CoV-2 infection than drugs acting on one viral target. These drugs with polypharmacology against SARS-CoV-2 infection are discussed below.

Chloroquine (CQ) or hydroxychloroquine (HCQ) is a well known FDA-approved antimalarial drug that can inhibit viral infections via multiple mechanisms. The mechanism of inhibition likely involves the prevention of endocytosis or rapid elevation of the endosomal pH and abrogation of virus-endosome fusion (Devaux et al., 2020). CQ/HCQ also has anti-inflammatory properties, which has led to its clinical use in conditions such as rheumatoid arthritis, lupus, and sarcoidosis (Savarino et al., 2003). After the advent of SARS in 2003, Savarino et al. (2003) postulated that the antiviral as well as anti-inflammatory properties of CQ/HCQ might be beneficial for SARS treatment. In addition, viruses may engage host autophagic processes to enhance replication (Yang and Shen, 2020). Since CQ is a known inhibitor of autophagic flux, it may be beneficial in inhibiting viral replication. CQ was shown to be highly effective in the control of SARS-CoV-2 infection in vitro (Wang et al., 2020a). It can also potentially interfere with the terminal glycosylation of ACE2 receptor expression, thereby preventing SARS-CoV-2 receptor binding and subsequent spread of infection (Barlow et al., 2020). Andreani et al. (2020) found that HCQ significantly suppresses virus replication, and a combination of HCQ and azithromycin exhibits synergistic effects. However, the FDA has warned that the use of CQ/HCQ, particularly when used in conjunction with azithromycin, can cause abnormal heart rhythms such as QT interval prolongation and ventricular tachycardia. As of June 15, 2020, FDA has revoked the emergency use authorization of these drugs for the treatment of COVID-19. Several clinical trials are underway to test the efficacy of CQ/HCQ in different settings, although a few have been withdrawn. In addition, a drug repurposing screen performed in different cell lines indicates that viral entry in lung epithelial Calu-3 cells is pH-independent (M. Dittmar et al., preprint, DOI: https://doi.org/10.1101/2020.06.19.161042). Therefore, CQ may not be effective as a treatment against SARS-CoV-2.

Emetine, approved for amoebiasis, has broad antiviral activity against Zika virus, EBOV, Dengue virus, human cytomegalovirus, and HIV in vitro and in vivo. Emetine may elicit cardiotoxic and myotoxic effects with high doses; however, its potency as an antiviral is significantly lower than doses that cause toxicity (Yang et al., 2018). Emetine can act on multiple mechanisms such as viral RdRp inhibition, host cell lysosomal function, and blocking viral protein synthesis via inhibition of host cell 40S ribosomal protein S14 (Yang et al., 2018). A combination of 6.25 μM remdesivir and 0.195 μM emetine showed synergistic effects in vitro against SARS-CoV-2 infection, but some of the compounds currently undergoing clinical trials such as ribavirin and favipiravir did not show clear antiviral effects (Choy et al., 2020). This suggests that combination therapy may be a superior therapeutic option for the treatment of COVID-19 due to synergistic effects.

Niclosamide, an antiparasitic drug approved by FDA, has shown great potential for repurposing to treat a variety of viral infections including SARS-CoV and MERS-CoV by targeting both host and viral components (Xu et al., 2020a). Preliminary studies showed that niclosamide has potent antiviral activity against SARS-CoV-2 in vitro with an IC₅₀ of 0.28 μM (Jeon et al., 2020). In addition, niclosasmide exhibits very low toxicities in vitro and in vivo (Chen et al., 2018), making it an attractive candidate.

Nitazoxanide is another antiparasitic prodrug approved by FDA with antiviral properties and is reportedly well tolerated in patients. Although the mechanisms of viral inhibition are not well understood, it is thought to target host-regulated pathways and not viral machinery (Rossignol, 2016). In keeping with this, it was shown that nitazoxanide significantly inhibits EBOV in vitro by enhancing host antiviral responses (Jasenosky et al., 2019). An in vitro study determined that nitazoxanide can inhibit SARS-CoV-2 at low-micromolar concentrations with an EC₅₀ value of 2.12 μM (Wang et al., 2020a). Several trials are currently ongoing to determine its clinical efficacy as a treatment of patients with COVID-19 or as a postexposure prophylaxis therapy.

Prophylactic Treatment of SARS-CoV-2 Infection

SARS-CoV-2 infects humans mainly through inhalation of virally contaminated aerosol droplets from infected subjects. Thus, nasal sprays containing agents that can neutralize the virus or block viral entry into host cells are one approach to prevent SARS-CoV-2 infection. There are preliminary reports that an antihistamine nasal spray can inhibit SARS-CoV-2 infection in vitro (G. Ferrer and J. Westover, preprint, DOI: https://doi.org/10.21203/rs.3.rs-25854/v1). In rhesus monkeys, a nasal spray formulation of interferon-α2b was successful in decreasing the severity of SARS-CoV viral infection (Gao et al., 2005). Meng and colleagues also reported that a nasal drop formula of recombinant human interferon-α1b prevented SARS-CoV-2 infection in an open label clinical trial (Z. Meng et al., preprint, DOI: https://doi.org/10.1101/2020.04.11.20061473). Additionally, it might be possible to achieve high local drug concentrations for drugs with low systemic distribution and/or dose limiting toxicity when delivered systemically. Therefore, nasal administration of drugs merits further studies as a useful strategy in preventing or reducing SARS-CoV-2 infection. Phytochemicals from naturally occurring plants, particularly lectins and polyphenols, might also prove to be valuable candidates as prophylactic or therapeutic treatment against SARS-CoV-2 (recently reviewed in Mani et al. (2020)).

Other Treatments in Clinical Trials for COVID-19

Several drugs that target viral life cycles directly as well as host biology are currently being investigated for COVID-19 and are summarized in Table 2 and depicted in Figure 1. As previously discussed, in patients with severe cases of COVID-19, excessive inflammatory responses and cytokine release likely contributes to the severity of disease stimulating lung and other systemic injuries. The early modulation of these responses may help reduce the risk of acute respiratory distress (Barlow et al., 2020). To this end, therapies such as inhibitory human monoclonal antibodies against cytokines such as interleukin-6 (IL-6) are also being considered to help diminish the severity of excessive physiologic response to SARS-CoV-2. The efficacy of glucocorticoids, such as methylprednisolone or dexamethasone, for the treatment of COVID-19 is yet to be determined. However, preliminary reports indicate that dexamethasone may be beneficial in critically ill patients with COVID-19 (P. Horby et al., preprint, DOI: https://doi.org/10.1101/2020.06.22.20137273). In addition, ciclesonide, an inhaled corticosteroid might also prove an effective therapy as it has low cytotoxicity and can potently suppress SARS-CoV-2 growth in vitro (Jeon et al., 2020; S. Matsuyama et al., preprint, DOI: https://doi.org/10.1101/2020.03.11.987016).

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Fig. 1.

SARS-CoV-2 spike (S) protein binds the cell surface receptor ACE2 on host cells. Viral genome is delivered into the host cytosol by 1) directly fusing with the plasma membrane after being cleaved and activated by the serine protease TMPRSS2 or 2) using the host cell’s endocytic machinery in which the endocytosed virions are subjected to an activation step in the endosome. The viral genome also functions as the messenger RNA, which is translated into proteins, such as 3CLPro, papain-like cysteine protease (PLpro), and RdRp, by host cell machineries. The SARS-CoV-2 genome also encodes the structural proteins (S), envelope (E), membrane (M), and nucleocapsid (N). RdRP is essential for viral replication and therefore is an attractive target for anti–SARS-CoV-2 drugs. Drugs that are currently in clinical trials are shown here in red, along with their targets of viral life cycle or viral-host interactions. Figure created in BioRender.

Vaccines for SARS-CoV-2

Treating COVID-19 with drugs or convalescent plasma does not confer immunity; hence, there remains an unmet need for immediate and long-term disease prevention in the form of a vaccine. According to the World Health Organization, there are over 100 SARS-CoV-2 vaccine candidates under preclinical development, including 1) DNA-based vaccines, which contain DNA encoding immunogen in plasmids; 2) inactivated whole virus vaccines, which are heat or chemically inactivated; 3) live-attenuated vaccines, which contain viable but weakened virus; 4) RNA-based vaccines, where an RNA encoding the immunogen is directly introduced into the host; 5) replicating and nonreplicating viral vector-based vaccines, where viral vectors are used to introduce DNA-encoding immunogenic into the host; 6) protein subunits, which contain portions of a pathogen; and 7) virus-like particle-based vaccines, which contain nonpathogenic virus-like nanoparticles similar in composition to the virus of interest (https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidate-vaccines). Several vaccines from these categories are also under clinical investigation. The types of vaccines and their platforms used are summarized in Table 3. The advantages and disadvantages of using different platforms of vaccines vary and are reviewed elsewhere (Amanat and Krammer, 2020).

There are high expectations for these vaccines to be available for distribution within a year. Undoubtedly, an effective vaccine is the ultimate tool for COVID-19 disease prevention, but there are some important aspects to consider. SARS-CoV and MERS-CoV emerged almost 20 and 10 years ago, respectively. To this date, there are no approved vaccinations to prevent either of these diseases, although there are several candidates in the unlicensed preclinical stage. Effective vaccines are still not available for many infectious diseases such as malaria, HIV, EBOV, and Zika virus. Vaccine development typically takes 10–15 years and is associated with high costs (Zheng et al., 2018). In addition, rapid mutations arising in viral RNA could potentially render these vaccines ineffective. RNA viruses are known to mutate with high frequency, but thus far there do not seem to be many differences in the S protein amino acid residue sequences in emergent SARS-CoV-2 variants from different countries (Robson, 2020). Antibodies induced by vaccination could also potentially increase the risk and severity of disease in subsequent host-pathogen encounters (Kulkarni, 2020). The production of these antibodies may sometimes prove beneficial to the virus instead of the host by facilitating viral entry and replication in the target cell in a phenomenon known as antibody-dependent enhancement (ADE) of infection (Kulkarni, 2020). ADE has been noted in cases of dengue virus, HIV, respiratory syncytial virus, and influenza virus but has not been confirmed for SARS or EBOV (Kulkarni, 2020). However, preliminary results in animal models of SARS-CoV-2 infection are promising. In both rodents (K. S. Corbett et al., preprint, DOI: https://doi.org/10.1101/2020.06.11.145920) and nonhuman primates (Gao et al., 2020), vaccinations against SARS-CoV-2 have shown protection without any observable ADE. In addition, positive outcomes have been noted in participants of small study in terms of tolerability and immunogenicity (Zhu et al., 2020).

Perspectives and Conclusion

Safe and effective viral therapeutics or vaccine development necessitates that data initially be obtained from preclinical in vitro or animal models. However, preclinically developed drug candidates often fail in human clinical trials (Seyhan, 2019). For example, remdesivir efficiently suppressed EBOV replication in vitro with nanomolar activity and also protected 100% of infected animals from mortality (Warren et al., 2016). However, these results were not recapitulated in humans for the treatment of EBOV infections, and the remdesivir treatment group was terminated due to low efficacy and increased toxicities (Mulangu et al., 2019). In general, viral infections are highly dependent on host cells. Therefore, successful clinical translation of SARS-CoV-2 drugs would require careful considerations of the testing platform. These might include suitable cell models for in vitro viral infection assays as well as human induced pluripotent stem cell–derived airway and gut organoids.

SARS-CoV infection was curtailed by rigorous isolation, but MERS-CoV infection is still a concern, albeit at lower infectious rate than SARS-CoV-2. SARS-CoV-2 infections present a clinical challenge as they are highly transmissible in part due to asymptomatic transmission. Therefore, the approach taken with SARS-CoV would certainly help curtail the spread of SARS-CoV-2, but with the current spread of disease, such large-scale isolation and quarantine efforts have proven difficult. Therefore, better therapeutic options are essential. Multitarget treatment approaches of drug combination therapy have been successful with HIV treatment and will likely be a viable therapeutic strategy for the treatment of COVID-19. Combination drug therapy has been extensively used for the treatment of HIV, cancer, and severe bacterial and fungal infections. Recently, patients with COVID-19 treated with the triple antiviral drug cocktail lopinavir-ritonavir-ribavirin with interferon beta-1b compared with lopinavir-ritonavir alone showed significant improvements in clinical outcomes (Hung et al., 2020). In addition, the combination drugs elicited no further side effects compared with the two-drug controls. Combination drug therapy may increase toxicity compared with single drug treatment. A meta-analysis of published trials evaluated the efficacy and toxicity of two-drug full dose combination therapy versus a single full dose drug for the treatment of rheumatoid arthritis (Felson et al., 1994). The study concluded that combination therapy led to a 9% patient withdrawal rate due to significant increases in adverse effects. Therefore, with combination therapy approaches, drugs with dose limiting toxicity as monotherapies can be used with lower individual drug doses, thereby reducing toxicity and synergistically enhancing therapeutic efficacy (Sun et al., 2016; Hoenen et al., 2019). As an example, several FDA-approved drugs found in a drug repurposing screen showed activity against EBOV but were not clinically useful, as their plasma concentrations were not high enough to inhibit infection in humans (Kouznetsova et al., 2014). However, drug combination therapy using three of these drugs at low concentrations was able to effectively block EBOV infection in vitro (Sun et al., 2017). Thus, synergistic drug combinations can be particularly useful for drug repurposing (Zheng et al., 2018). For COVID-19, drug combination therapies with multiple agents that have different mechanisms of action, including inhibition of viral entry and replication, as well as inhibition of host immune responses, would be a practical and useful approach for disease intervention.