Antiviral therapies for the management of persistent coronavirus disease 2019 in immunocompromised hosts: A narrative review

Antiviral agents with activity against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) have played a critical role in disease management; however, little is known regarding the efficacy of these medications in the treatment of SARS‐CoV‐2 infection in immunocompromised patients, particularly in the management of persistent SARS‐CoV‐2 positivity.


INTRODUCTION
The coronavirus disease 2019 (COVID-19) therapeutic landscape has undergone significant changes since the onset of the pandemic.Initially, prevention and treatment options were limited, resulting in unfavorable outcomes.Over time, multifaceted interventions including public health measures, widespread vaccine campaigns, and therapeutic agents for the management of symptomatic disease have played a pivotal role in altering the outcomes of those with COVID-19.Additionally, the evolution of the aetiologic agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), over time has resulted in the rise of variants with purported reduced pathogenicity compared to ancestral viruses. 1,2The combination of these factors has resulted in improved patient outcomes.Despite these advances, immunocompromised patients remain at increased risk.
Two particular groups at increased risk of adverse outcomes due to a high degree of immunosuppression are those who have undergone solid organ transplantation (SOT) and those with haematologic malignancies.In relation to clinical outcomes, there is conflicting evidence in recipients of solid organ transplants, with some studies showing no difference compared to non-SOT recipients even early in the pandemic, while others demonstrated higher mortality rates that have declined over time. 3,4In contrast, patients with haematologic malignancies have consistently been shown to have poorer outcomes after SARS-CoV-2 infection, with higher rates of hospitalization, intensive care admission, mechanical ventilation, and death. 5,6deed, even patients without hematological malignancies who receive anti-CD20 therapies have been associated with increased COVID-19 severity. 7Therefore, patients with haematologic malignancies receiving anti-CD20 antibody therapy may be at particularly high risk. 5,8tiviral agents with activity against SARS-CoV-2 have played a critical role in disease management, with several randomized controlled trials showing reductions in disease severity, hospitalization, and death (discussed below).Despite the abundance of trial data for these drugs, immunocompromised patients represent only a small proportion of, or were excluded from, early trials of SARS-CoV-2-directed therapies. 9ing to their increased risk profile, antiviral therapy is likely to play a significant role in the management of immunocompromised patients for the foreseeable future.However, owing to the paucity of randomized controlled trial (RCT) data in this population, little is known regarding the efficacy of these medications in the treatment of SARS-CoV-2 infection.

Prolonged SARS-CoV-2 test positivity
In addition to the increased rates of adverse outcomes as outlined above, persistent rapid antigen test, polymerase chain reaction (PCR), and viral culture positivity after primary SARS-CoV-2 infection have been well described in immunocompromised hosts 11 and can result in ongoing debilitating symptoms in some individuals.Even in asymptomatic individuals, ongoing containment measures may result in barriers to providing appropriate and timely medical care, resulting in psychological harm.Immunocompromised patients more frequently remain positive for longer on testing, 12 but the rates vary according to the underlying cause of immunosuppression.Prolonged viral shedding is particularly common in patients with hematological malignancies. 13,14In their study, Hettle et al. described 183 cases of persistently positive PCR tests, six of whom were confirmed to have protracted COVID-19, and all of them had an underlying haematologic malignancy.Additionally, in their accompanying literature review which identified 60 cases from the literature, 80 percent of identified cases with prolonged positivity had an underlying hematologic malignancy. 15In another cohort of 382 patients with haematologic malignancies, 13.9% continued to be PCR-positive beyond day 30. 16is is unsurprising, with in vitro data showing abnormal humoral immune responses to SARS-CoV-2 antigens in this population, 17 and that overall B-cell counts have been shown to correlate with failed viral clearance. 18In vivo data also demonstrated prolonged viral clearance in patients with severe immunocompromise, including the hematooncology population. 19Prolonged positivity in SOT recipients is less frequently described; however, it is unclear whether this represents a lower burden of prolonged positivity in this population or publication bias.Some multicentre studies have demonstrated higher numbers of SOT recipients than those with haematologic malignancies, but this may reflect the underlying patient populations seen at these institutions. 20The degree of immunosuppression in those receiving SOT can be reduced in the short term, which may account for the lower rates of reporting.Data on immune response in SOT recipients suggest that responses are similar to non-SOT recipients, but data is derived from small studies, with multiple confounders including variation in organs transplanted, nature and degree of immunosuppression, and time since transplantation. 21,22Additionally, in a multicentre study based in the United States, transplant patients accounted for one-third of all cases in immunocompromised hosts (ICH) with prolonged positivity, with significant numbers from other groups including autoimmune and autoinflammatory disorders, other malignancies, and AIDS. 23ptimal management approaches for this difficult condition are undefined, and it is uncertain whether additional prolonged courses of antiviral therapy or combination therapy with antiviral agents are beneficial.Here, we review the evidence thus far for antiviral therapy in the immunocompromised population, and resistance to antiviral agents with a focus on the treatment of prolonged COVID-19 positivity.

METHODS
To better understand the potential benefit of these treatments a literature review was undertaken of the published literature available in PubMed and EMBASE using the search-terms "COVID-19", "immunocompromised" and "antiviral" on 27 Feb 2024.Articles included were those printed in full which were available in English and pertained to the treatment of adult populations.Articles that described treatment with standard-course therapies were excluded.Standard course therapies were defined as 5 days of ritonavir-nirmatrelvir or molnupiravir or up to 10 days of remdesivir.A total of 1,324 abstracts were screened for inclusion, leading to the inclusion of 14 case series and 25 case reports (Table 1).In relation to novel therapeutic approaches, evidence from the literature can be summarised into three general categories: 1. Use of extended courses of antiviral therapy 2. Combination antiviral therapy 3. Multi-modal therapy with an antiviral in combination with neutralizing antibodies

Evidence for antiviral agents for the treatment of SARS-CoV-2 infection in ICH
Currently, available antivirals for the treatment of COVID-19 have been well-studied in immunocompetent patients; however, data on their role in the management of immunocompromised patients are scarce.
The PINETREE study 24 which showed benefits early in disease onset, enrolled 562 patients; however, only 23 were immunocompromised.
7][28][29][30][31] Data on the treatment of immunocompromised hosts is therefore largely limited to observational studies.Such studies in solid organ transplant recipients have reported worse outcomes in those treated with remdesivir than in those who received supportive care without remdesivir. 32Observational studies of this nature are at a high risk of bias, as remdesivir therapy may be adminis-  34 Later, data from the PANORAMIC trial published in early 2023 which enrolled high-risk participants, most of whom were vaccinated, did not show any benefit compared to the standard of care 35 .Further data suggest that molnupiravir may be efficacious only in the very early stages of the disease, which may limit its efficacy in real-world situations owing to late presentation/administration. 36post-hoc analysis of the MOVe-OUT trial, focusing on immunocompromised patients, was performed by Johnson et al. 37 Only 55 of the 1048 enrolled patients were considered immunosuppressed (HIV, hematopoietic cell transplant, active cancer, or receiving immunosuppressing medications).Compared to the Placebo, there were fewer hospitalizations and deaths in the molnupiravir group, and the treatment effect was more pronounced than in those who were nonimmunocompromised (−14.2% vs. −2.4%)but with low overall numbers of those who were hospitalized or died (n = 9); these findings were not statistically significant (p = 0.294).Furthermore, the PANORAMIC trial enrolled 2181 patients with 'weakened immune systems' and 125 transplant recipients.The adjusted odds ratio for hospitalization or death favored usual care over molnupiravir therapy in immunocompromised patients but was not statistically significant (Odds ratio 1.89, 95% confidence interval 0.99-3.73). 35Importantly, molnupiravir has been shown to increase the clearance of infectious viruses, which may support its use in persistent infection.degree of immunocompromise, and specific outcomes in this population have not been reported.In a Canadian real-world assessment, antiviral therapy with r/nirmatrelvir reduced hospitalization in immunocompromised patients even in the presence of a complete vaccination history. 38Similarly, a large cohort study from Israel conducted in the Omicron era demonstrated the ongoing benefit of r/nirmatrelvir in reducing severe COVID-19 and death. 39A retrospective study from China demonstrated that in 35 immunocompromised patients treated with r/nirmatrelvir, there was a shorter time to PCR negativity (defined as a cycle threshold [CT] value > 35) when administered within 5 days of disease onset. 40Furthermore, a smaller RCT questioned the benefit of r/nirmatrelvir in a high-risk, but largely unvaccinated, population in the omicron era which did not demonstrate a reduction in mortality or RNA clearance at day 28.However, the number of immunocompromised patients included in this study was low. 41The main limitation of r/nirmatrelvir is its extensive drug-drug interaction profile which may limit its application in co-morbid patients.This is particularly important in the transplant population, with significant interactions occurring between calcineurin inhibitors, mTOR inhibitors, and other adjunctive medications commonly prescribed in this population. 42Furthermore, viral load rebound has been observed, but the significance of this phenomenon is uncertain, as it has been observed to occur during the course of SARS-CoV-2 infection in the absence of r/nirmatrelvir. 43

Antiviral therapy for persistent COVID-19
Our literature review identified 14 case series and 25 case reports detailing 84 cases of persistent COVID-19 that were treated with antiviral therapy beyond the standard course or in combination.Sixtyseven of the 84 patients had an underlying haematologic malignancy and 51 received anti-CD20 therapy (Figure 1A and Table 1).Of the 62 cases for which vaccination status was known, 51 received several doses of a COVID-19 vaccine.The median duration of positivity was 74 days (range, 14-901 days) (Figure 1B).Success was reported in 70 of the 84 cases.Only 18 cases reported monitoring for resistance to antiviral therapy, with resistance identified in two cases.Further details are provided below.

Extended courses of antiviral therapy
It has been hypothesized that the rationale for 5-day therapy courses was more attractive early in the pandemic when the scale of drug production and distribution may have resulted in drug shortages, making short-course therapy preferable to long-course therapy. 44Owing to its long half-life, it has been demonstrated in vitro that longer courses of remdesivir may result in higher intracellular concentrations, ensuring that drug levels are sufficient to reach 50% effective concentration (EC50) and 90% effective concentration (EC90). 44Additionally, early trials on 5-versus 10-day treatment regimens failed to show benefits at the population level; however, immunocompromised patients represent a unique population to which this finding may not apply.None of these trials addressed prolonged positivity.Therefore, a longer course of therapy may be beneficial for immunocompromised hosts.
In total, seven publications described the treatment of 11 cases of persistently positive COVID-19 with extended courses of antivirals, as summarised in Table 1.Eleven cases, including a case series by Breeden et al., 45 described four patients with haematologic malignancy treated with an extended course of r/nirmatrelvir (15-26 days), with success in all cases (Figure 1C).Two further case reports described prolonged therapy with remdesivir, which was successful in both cases.Adverse events were reported in only one of the seven cases, with an ALT increase occurring during a prolonged course of remdesivir. 46Two of the included studies monitored the emergence of genotypic resistance markers, which were not found.

Combination antiviral therapy
8][49][50][51] Furthermore, there are concerns that ongoing viral replication in ICH may lead to antiviral resistance when antiviral monotherapy is used, 18,52 as observed in other viruses, such as influenza.Indeed, standard-course remdesivir therapy in immunocompromised patients has been associated with the emergence of remdesivir-resistant mutations after prolonged COVID-19 positivity. 53However, it is worth noting that these resistance mutations may occur in immunocompromised patients even in the absence of administration of the associated agent, 15 and may be selected after administration of remdesivir.
Our literature search uncovered three case series and six case reports describing the use of combination antivirals for the treatment of persistent positivity in 13 individuals (Table 2).Many of these patients also received previous lines of therapy, including monoclonal antibodies, but did not receive these concurrently with antivirals.An underlying haematologic malignancy was present in all 13 patients, and all 13 patients received anti-CD20 therapy.In relation to antiviral agents chosen for combination therapy, all patients received r/nirmatrelvir, 11/13 (85%) received remdesivir, and 3/13 (23%) received molnupiravir.Considering all publications, success was achieved in 12 of 13 (92%) patients (Figure 1C).
This success rate is encouraging; however, another series by Brosh-Nissimov et al. 54 described a series of 14 patients, 11 of whom were treated with remdesivir and r/nirmatrelvir for 5 days in combination with a monoclonal antibody with success in only 5 of the 11 individuals in this cohort, suggesting an overall success rate of < 50%.
This illustrates the importance of publication bias in these studies, and escalating therapies for unsuccessful attempts at viral clearance, with successful attempts more likely to be published.Importantly, two renal transplant recipients were described in this publication but did not receive a second antiviral (r/nirmatrelvir) owing to drug-drug interactions with transplant medications, again highlighting that this strategy may not be suitable for all patients.
Resistance monitoring was performed in three of the 13 cases included in this review, with resistance mutations associated with remdesivir treatment failure noted in one, who was treated with a combination of r/NIR and MOL, but who had received multiple courses of remdesivir previously.No adverse effects were reported in any cases.

Multi-modal therapy with an antiviral in combination with neutralizing antibodies
Most examples of novel therapeutic approaches from the literature involve antiviral therapy in combination with additional treatments aimed at boosting neutralizing antibody levels, including monoclonal antibodies (mAbs), COVID-19 convalescent plasma (CCP), and pooled intravenous immunoglobulin (IVIG) (see Table 3).Several monoclonal antibodies or antibody cocktails have reached the market for the treatment of COVID-19 in patients who are at high risk of progressing to severe disease.Although monoclonal antibodies can be successful in clearing prolonged positivity in up to 80% of cases in some series 15 , limited availability and viral evolution to reduce the neutralization of these therapeutics have invariably resulted in the loss of efficacy of these treatments over time. 55CCP has been proposed as an alternative treatment to monoclonal antibodies.The benefits of CCP include the polyvalent nature of products, the ability to select high-titer donors, and activity against currently circulating variants.

Drawbacks of convalescent plasma include the potential transmission
of blood-borne viruses and variable epitope specificity.Furthermore, treatment of immunocompromised patients with convalescent plasma has been shown to select 'escape mutants' , which demonstrate reduced sensitivity to convalescent plasma. 56IVIG is another product available to boost neutralizing antibody titers in patients with prolonged positivity.IVIG in combination with antiviral therapy has been successful in the clearance of virus when directed monoclonal antibodies have failed.This is an important consideration when variant assignments are unavailable. 57r literature review revealed ten case series and 14 case reports detailing the treatment of 60 patients with antiviral plus antibody therapy (Table 3).The reported populations were similar to those receiving prolonged or combination antiviral agents, with a high proportionate representation of haematologic malignancies and anti-CD20 therapy CCP, and IVIG have been described with an overall success rate of 47/60 (78%) (Figure 1d).13/60 cases (22%) were tested for resistance markers, with 1/13 (8%) detecting resistance mutations to monoclonal antibodies.No adverse events were reported in any of the 60 cases.
In relation to combination therapy using monoclonal antibodies, our review revealed several case reports and a case series by Lanzafame 58 which reported high rates of success (22/29, 75%).Although not included in our summary due to limited available data, Wada et al.
described a similar approach in a cohort of 10 immunocompromised patients with prolonged COVID-19 disease with some success; however, the definition of prolonged COVID in this study was not clear.
Additionally, 50% of their cohort did not respond to combination therapy, requiring the addition of a second antiviral for success, which was measured as an increase in the PCR cycle threshold to an undefined level. 59Also worthy of particular note, Mikulska et al. 60 described the largest case series yet of 22 immunocompromised patients treated with a combination of antiviral and monoclonal antibody therapy for severe or persistent COVID-19 with high success rates (82% clinical response and 73% virologic response).Adverse events were reported in two of the 22 cases (myocardial infarction and bradycardia in one case each), serving as an important reminder of potential harm from these unproven therapies.An important consideration in relation to mAb-based therapy is the reduced availability of effective antibodies owing to ongoing viral evolution.
Antiviral therapy in combination with convalescent plasma was described in 11 individuals, five of whom were cohorts of patients with B-cell malignancy treated with r/nirmatrelvir and CCP, as described by Huygens et al., 61 and had a high success rate of 80% (4 of 5 cases).Considering all cases, the success rates for this approach were similar, with 8/11 (73%) patients responding.No adverse events were reported, and no resistance to antiviral agents was reported in 5/11 cases in which monitoring was performed.
The difficulty in obtaining CCP and the potential for blood-borne virus transmission make IVIG an attractive alternative.In a study by Upasani et al., 62 it was demonstrated that numerous commercially available IVIG products contain high titers of neutralizing antibodies but with a significant batch-to-batch variation.Furthermore, the characterization of recipient-neutralizing antibody titers before and after transfusion demonstrated a marked increase in neutralization, similar to that in healthy donors.They administered IVIG products in combination with remdesivir to nine individuals with sustained clearance in all cases.This case series provides compelling evidence of the effectiveness of this approach, but once again, the overall number was low.Our literature review revealed five additional cases of antiviral therapy in combination with IVIG for prolonged positivity which was successful in four of five.Therefore, success was achieved in 13 (93%) of the 14 patients included in this study.Monitoring for resistance was reported in one of the 14 cases which was not detected, and there were no adverse events reported.
Lastly, several authors have described combination approaches of more than one antibody type (see Table 3).Success was achieved in only 3/6 (50%) cases using this approach; however, this may be reflective of the underlying host factors that led to sequential escalating therapies.
The abundance of case reports and series describing antivirals in combination with antibody therapy, compared to extended or combination antivirals, indicates clinician preference for addressing underlying immunodeficiency.In a survey on the management of prolonged COVID-19, UK physicians reported combination therapy with antibodies more frequently than with remdesivir alone and with higher success rates. 63Controlling for age, sex, and underlying diagnosis, the odds ratio of clearing infection with remdesivir combined with antibody therapy compared with remdesivir alone was 23.1, with a wide 95% confidence interval of 1.3-424.9 (p = 0.035).

Resistance to antiviral agents
Immunocompromised hosts represent the perfect milieu for the emergence of resistant viruses.This has been well-documented in relation to monoclonal antibody therapy.In prolonged SARS-CoV-2 positivity, mutations preferentially accumulate in the spike and receptor-binding domains, which account for only 13% and 2% of the genome, respectively, yet account for 57% and 38% of the observed mutations. 64 one observational prospective study, 32% of immunocompromised individuals developed resistance to sotrovimab after therapy, 12 whereas in another case series, resistance to monoclonal antibodies occurred in more than two-thirds of immunocompromised patients with prolonged viral positivity. 65Similarly, the use of convalescent plasma in immunocompromised patients has been associated with the selection of immune escape viral variants. 18rtunately, data regarding the emergence of resistance to antiviral agents are comparatively limited.The Stanford Coronavirus Antiviral and Resistance database reports a number of mutations conferring resistance to remdesivir which have been identified in clinical specimens. 66,67The phase 3 PINETREE study conducted in late 2020/early 2021, detected the emergence of a mutation associated with a 12-fold increase in EC50 to remdesivir, notwithstanding which the patient recovered clinically.The de novo emergence of resistance to remdesivir in immunocompromised patients has been described 53,68 such as that reported by Gandhi et al., in which resistance occurred in a patient with prolonged positivity after single-agent remdesivir therapy. 69The mutation in question arose only after the administration of remdesivir and subsequently disappeared from the sequential positive specimens.In-vitro experimental data demonstrated that this mutation had an associated fitness cost compared with that of the wild-type virus 70 .
Numerous mutations in the main protease have been identified in vitro which confer resistance to nirmatrelvir, 52,66 including prior to the Food and Drug Administration emergency use authorization. 52ny of these are associated with only low-level resistance, 66 but one in particular, E166V, is associated with a 100x fold increase in IC-50 and has been isolated from clinical samples, including one of the cases in this review. 71This mutation is accompanied by a significant loss of replicative fitness; however, concurrent mutations may offset this fitness cost. 72,73Nonetheless, Zuckerman et al. described a case of clinical failure with antiviral therapy which they attributed to this mutation in combination with another mutation (L50F). 71 the time of writing, no reports of resistance to molnupiravir were found, a quality which has been attributed to the allegedly high barrier to resistance. 74Additionally, molnupiravir has demonstrated retained antiviral activity against SARS-CoV-2 with resistance markers to remdesivir, 75 furthering the case for combination therapy to prevent this occurrence in immunocompromised hosts.

SUMMARY AND RECOMMENDATIONS
The three antivirals licensed for the treatment of COVID-19 have shown benefits in improving the outcomes of unvaccinated individuals.The degree of the effect of these therapies on vaccinated cohorts and newer variants is less well characterized.There is less data still on how these therapies impact the disease process in immunocompromised hosts, particularly the effect on persistent SARS-CoV-2 positivity.
The paucity of data on the management of persistent COVID-19 in immunocompromised hosts is reflected in clinical guidelines and prescribing practices.The World Health Organization guidelines do not specifically mention immunocompromised populations or management of prolonged positivity. 76Guidelines from the National Institute for Health acknowledge that immunocompromised cohorts are a unique population, but there is insufficient evidence regarding the use of combination antiviral agents to make recommendations. 77The lack of evidence-based guidelines has resulted in great uncertainty regarding the best management for persistent SARS-CoV-2 positivity.This is reflected in a survey of Australian ID physicians regarding prescribing practices for immunocompromised patients, which showed a high degree of heterogeneity in approaches. 78inicians caring for immunocompromised hosts should attempt to reconstitute the host's immune system where possible.In the case of SOT, the net state of immunosuppression may be decreased on a caseby-case basis, considering the individual's risk profile for rejection. 79r patients with primary or secondary hypogammaglobulinemia, particularly those with haematologic malignancy, therapies that increase the levels of neutralizing antibodies are desirable.The combination of antiviral therapy and intravenous immunoglobulin is promising, with high success rates reported in small case series.The optimal timing for the introduction of these therapies and the combinations that are most efficacious are also uncertain.Uncertainty also exists surrounding the utility of further immunosuppression with anti-OL6 and anti-JAK therapies in an already immunocompromised host who was excluded from trials of these therapies.
The data presented here have numerous limitations.Foremost among these limitations are the small sample size of reported studies, the lack of a control group that allows assessment of the natural history of these infections, and the poor quality of data which is limited to case reports and small case series.Notably, a small case series showed that r/nirmatrelvir as a single agent can be successful in the treatment of prolonged COVID-19, highlighting the importance of a greater understanding of the natural history of this condition. 80Furthermore, our search criteria may have excluded additional reports of off-label treatments that were not clearly described in the accompanying abstracts.
Combination therapy may reduce the emergence of antiviral resistance.Reports of antiviral resistance are rare but have been described.
Expert opinion and in vitro evidence support the use of combination antivirals to safeguard the efficacy of the few currently available antiviral treatments.
Although randomized trials are currently underway to improve the evidence base in novel approaches for immunocompromised hosts, many questions remain unanswered.Persistent SARS-CoV-2 is an uncommon clinical scenario, and with declining testing rates, it may go unrecognized, limiting trial recruitment.Until such data are available, any off-label approach should be mindful of the potential side effects of medication and monitor the emergence of resistance to these treatments.