Zanamivir and baloxavir combination to cure persistent influenza and coronavirus infections after hematopoietic stem cell transplant

Abstract

Objectives: Immunocompromised patients may experience prolonged shedding of influenza virus potentially leading to severe infections. Alternatives to monotherapy with neuraminidase inhibitors should be evaluated to entirely suppress viral replication and prevent drug-resistant mutations.

Methods: We investigated the clinical and virological evolution in a case of persistent influenza A and human coronavirus OC43 (HCoV-OC43) coinfection in a hematopoietic stem cell transplant recipient after different therapeutic strategies.

Results: Successive oseltamivir and zanamivir monotherapies failed to control both infections, with positive results persisting for over 110 days each. This led to the emergence of highly resistant oseltamivir strains due to neuraminidase mutations (E119V and R292K) followed by a deletion (del245-248), while maintaining sensitivity to zanamivir. The intra-host viral diversity data showed that the treatments impacted viral diversity of influenza virus, but not of HCoV-OC43. Considering the patient's underlying condition and the impact of prolonged viral shedding on pulmonary function, eradicating the influenza virus was necessary. A 10-day regimen combining zanamivir and baloxavir-marboxil effectively controlled influenza virus replication and was associated with the clearance of HCoV-OC43, finally resulting in comprehensive respiratory recovery.

Conclusion: These observations underscore the importance of further investigating combination treatments as the primary approach to achieve influenza eradication in immunocompromised patients.

Keywords: Baloxavir-marboxil; Drug-resistant; Influenza; Neuraminidase inhibitor; Transplantation.

Fig. 1.

Virus detection, antiviral treatments and neuraminidase mutations. Panel A. Timeline of virus detection, antiviral drugs administration and neuraminidase sequencing results. HCoV-OC43 and Influenza were detected using the BioFire^® Respiratory Panel 2.1 plus (bioMerieux, Marcy-l’Etoile, France). Positive results are indicated by cyan dots, negative results are marked with red crosses. Anti-viral treatments are represented by yellow squares. Mutations in the neuraminidase (A/H3N2 NA) and their frequencies are noted in white squares. Panel B. Monitoring influenza infection and blood cell counts. Influenza A levels (blue circles) plotted on the left y-axis were estimated using cycle threshold (Ct) values from specific real-time PCR assays (Xpert^® Xpress CoV-2/Flu/RSV, Cepheid, Sunnyvale, CA). The negative threshold value of 40 is represented by the dotted line. White blood cells (pink squares) and lymphocytes (green triangles), expressed in billions of cells per litre in whole blood (G/L), are plotted on the right y-axis. Influenza treatment timing is illustrated by yellow bars and corresponding molecules are indicated above. Day 0 corresponds to the date when HCoV-OC43 was first detected.

Fig. 2.

Evolution of intra-host viral diversity. Diversity index estimated from the intra-host single nucleotide variations (iSNVs) data for the complete genome of OC43 (A) and the influenza H3N2 NA gene segment (D) for the respective snapshots captured over time. Number of sites with were detected iSNVs along the complete genome of OC43 (B) and the influenza H3N2 NA gene segment (E) for the respective snapshots captured over time. Violin plots representing the distribution of iSNVs frequencies the complete genome of OC43 (B) and the influenza H3N2 NA gene segment (E) for the respective snapshots captured over time.

Fig. 3.

Antiviral susceptibility. The 50% Inhibitory concentration (IC50) of oseltamivir for viruses isolated prior to (A/PARIS/05458i/2023, WT) and at the end (A/PARIS/05459i/2023) of the oseltamivir treatment. Metatranscriptomic sequencing revealed that the A/PARIS/05459i/2023 isolate contains a viral population with 84% of the E119V substitution (up from 36% in the primary sample), and below 1% of R292K (down from 56% in the primary sample), suggesting a replication advantage of E119V in vitro, and compatible with previous reports indicating that the R292K negatively impact viral fitness in vitro.