Discussion
We have argued that the selectivity of anti-viral therapy can be significantly enhanced by exploiting matching of the drug based on its purported mechanism of action with the viral cell cycle dynamics.Table 2 summarizes the association of the mechanism of action of currently tested repurposed molecules for COVID-19 with the specific rate constants. It is interesting to note that of these drugs, those drugs that target the conversion rate constant alone, such as those that target viral proteolysis, RNA dependent RNA polymerase, and those that act nonspecifically such as ivermectin, cyclosporine and nitrozoxanide are least likely to result in meaningful efficacy based on the model described in this manuscript. This is supported by weight of evidence (clinical trial or white paper based arguments) that has been generated so far on remdesivir [7, 8], protease inhibitors [20], and ivermectin [21], that either indicates that the effects are likely to be negligible to modest at best.
Our simulations demonstrated some important themes for consideration of combination treatments targeting the SARS-CoV-2 cell cycle. In general, antivirals should be initiated as early in the course of infection as possible to maximize impact on viral load AUC, duration of viral shedding and number of epithelial cells infected. This was a common theme across the scenarios and endpoints evaluated. Indeed, beginning treatment beyond 3 days after peak viral load is unlikely to have any meaningful impact on endpoints that may correlate with patient symptoms according to our simulations, but benefit for later intervention may persist beyond for clinical and public health endpoints associated with duration of viral shedding. As prolonged viral shedding phenotypes are described for influenza [22] and COVID-19 [23], we performed sensitivity analyses with c and δ. We observed in prolonged viral shedder phenotypes that cessation of viral shedding benefit persists for therapeutics that promote virion kill (c), infected cell death (δ) and inhibit virion release (ρ). Such interventions would be preferred to address so-called SARS-CoV-2 super spreaders [24, 25].
To illustrate the potential benefit of combinations of repurposed drugs, example combinations were drawn from the current trial literature (Table 3 ).
We assumed modest effect (0.333 log10 effect, 53.6% inhibition, 1.15 fold increase) for each target. Single target interventions were selected as β, δ, ρ, c; two target intervention was selected as δρ; three target interventions were selected as δρc and βδρ; four target interventions was selected as βδρc. Figure 4 shows the output of these simulations at different intervention times. Supplemental Figure3 and
Figure 4A shows the predicted impact on viral and infected epithelial cell kinetics assuming intervention three days before peak viral load. For the single interventions (top row) β, δ, ρ, c, no single intervention is sufficient to halt viral growth, but each blunts the peak and may shift the timing of peak viral load. However, a meaningful (> 2 log10) improvement in epithelial cells infected is expected. The combination interventions (bottom row) δρ, βδρ, cδρ, βδρc follow. The two-target intervention, δρ, shows a similar “blunting and delaying” quality on viral load as the single-target interventions, but better overall suppression of viral load and epithelial cell infection. In contrast, the three- and four-target interventions halt viral growth and (nearly) abolish epithelial cell infection. As a reminder, each element of each intervention is assumed to have a modest effect, so the results shown for the multiple-target combinations express their cooperative/synergistic effect on viral load and infected epithelial cells.
Figure 4B shows the predicted impact on viral and infected epithelial cell kinetics assuming intervention at peak viral load. As above, the single interventions have modest effect on viral load, with δ identified as ideal for reducing duration of viral shedding and c identified as ideal for reducing viral load AUC (Table 1 ). A three log10 reduction in uninfected epithelial cells is expected. The three- and four-target interventions somewhat improve duration of viral shedding, but the biggest gain is observed in a one log10 improvement in uninfected epithelial cells, with β identified as ideal for reducing infected epithelial cells (Table 1 ).
Figure 4C shows the predicted impact on viral and infected epithelial cell kinetics assuming intervention three days before peak viral load. Some modest gains are possible for duration of viral shedding, with δ identified as ideal for reducing duration of viral shedding and c identified as ideal for reducing viral load AUC (Table 1 ). Very little improvement in infected epithelial cells is predicted, reinforcing the primary finding of this work and others that early intervention is critical. Here, we explicitly report the effect on host cell damage, which has been underappreciated in prior efforts.
Table 1 captures the primary results of this simulation study, reporting that interventions targeting the host-cell “factories” forde novo virions are broadly effective in reducing the magnitude of viral load and infected epithelial cells and reducing the duration of viral shedding. Mechanisms that promote infected cell death (δ) and/or reduce copies of virions per infection (ρ) achieve this goal. Simulations results suggest interchangeability of these effects, with the noted exception of reducing duration of viral shedding where δ is superior to ρ. Interchangeability suggests additive effects, from simplistic anergy/additivity/synergy perspective, but also offers an opportunity to combine two low-potency agents, each targeting one mechanism, to boost the overall potency of the combination. Within the host cells, simply delaying the viral replication machinery (k) is not a good strategy.
Outside or on the border of host cells, Table 1reports differing strategies that depend on the objective of the intervention. Mechanisms that remove circulating virus (c) are broadly effective in reducing the viral load AUC and infected epithelial cells and reducing the duration of viral shedding. Mechanisms that prevent viral entry and infection of host cells (β) are only effective prior to peak viral load or if only focused on sparing host cell infection. Put simply, killing virus (c) both removes virus and prevents infection. Vaccines and antibodies fall into the category of removing circulating virus (c), and are predicted to have strong effects even at low potency if administered early (or before, in the case of vaccines) in the course of infection.
Given that the full time course is rarely measured in clinical evaluations with the exception of PEP studies, viral load AUC is a largely insensitive endpoint to evaluate potential therapeutic interventions. This is because of their dependence on the pre-intervention viral load values. For a therapeutic intervention to work in this regard, it needs to exhibit a rapid pharmacological onset (e.g., loading dose, direct rather than indirect pharmacology) and needs to be effective at clearing the virus. Treatments targeting c (killing of released virions) were the most effective, meaning that interventions like convalescent plasma, or investigational antibodies would be anticipated to be most likely to impact total viral load meaningfully.
Of the therapies being investigated, remdesivir was recently shown in hospitalized adults with moderate disease to provide a 31% faster time to recovery than those who received placebo (p<0.001) [8], but no virologic information was reported. However, in the study by Wang et al. [7], remdesivir had no meaningful effect on viral load. Remdesivir is thought to play a role in the incorporation into new viral RNA, leading to the inability of the viral polymerase to add new RNA.  In the absence of key mechanistic information, we assumed that remdesivir reduces the production of new virions by halting replication of its genome, and thus its effect is proximally associated with ρ.  It is possible that remdesivir may show meaningful efficacy if studied in more early infection phase. Future data on remdesivir in early onset mild patients with COVID-19, combined with suitable therapeutics will likely inform on the benefits of early intervention for this molecule.
Duration of viral shedding is less time sensitive to perturbation than viral load AUC and epithelial cells infected and is also influenced by a broader array of pharmacological interventions in the SARS-CoV2 cell cycle. Unlike both epithelial cells and viral load AUC, treatments targeting δ (death of infected cells) were the most effective against duration of viral shedding. The concept of early intervention with combination treatments targeting δ was validated in the clinic recently, where an open label, prospective, randomized early treatment study (median 5 days, [IQR 3-7 days] since symptom onset) showed triple combination of ribavirin, lopinavir/ritonavir, interferon (which all target δ) reduced viral shedding by 5 days sooner versus Lop/r alone [9]. Such findings may translate into meaningful benefits for patients and society, as duration of viral shedding may impact duration of hospital stay or isolation for an individual, and risk of transmission to others and the associated costs from a public health perspective [17].
The SARS-CoV-2 cell cycle provides some foundational basis for the selection of existing treatments with pharmacological plausibility within a set of combination regimens. To maximize sparing of epithelial cells and potential consequences of downstream cytotoxicity and pulmonary inflammation, a treatment regimen should include treatment(s) that maximize pharmacology on β (inhibition of new epithelial cell infection) like camostat, chloroquine and hydroxychloroquine, or influence rho as evidenced via remdesivir. To reduce duration of viral shedding, treatment regimens should include components that effectively reduce δ (death of infected cells) such as ribavirin, lopinavir/ritonavir and/or interferon. Interventions like convalescent plasma, or investigational antibodies such as RGN-COV2 and other investigational antibody treatments targeting c (killing of released virions) have the most significant promise in rapidly reducing viral load and will be a welcome addition to the combination armamentarium.