Persistent SARS-CoV-2 PCR positivity despite treatment in immunodeficient patients (preprint)

ABSTRACT

Purpose:  COVID-19 infection in immunodeficient individuals can result in chronically poor health, persistent or relapsing SARS-CoV-2 PCR positivity, and long-term infectious potential. While clinical trials have demonstrated promising outcomes using anti-SARS-CoV-2 medicines in immunocompetent hosts, their ability to achieve sustained viral clearance in immunodeficient patients remains unknown. We therefore aimed to study longer term virological outcomes in patients treated at our centre. Methods: We followed up immunocompromised inpatients treated with casirivimab-imdevimab (Ronapreve) between September and December 2021, and immunocompromised patients who received sotrovimab, molnupiravir, nirmatrelvir/ritonavir (Paxlovid), or no treatment from December 2021 to March 2022. Nasopharyngeal swab and sputum samples were obtained either in hospital or in the community until sustained viral clearance, defined as 3 consecutive negative samples, was achieved. Positive samples were sequenced and analysed for mutations of interest. Results: We observed sustained viral clearance in 64 of 103 patients, none of whom died. Of the 39/103 patients where sustained clearance was not confirmed, 6 died (between 2 and 34 days from treatment). Notably, we observed 23 cases of sputum positivity despite negative NPS samples, as well as recurrence of SARS-CoV-2 positivity following a negative sample in 12 cases. Patients with viral clearance were then divided into those who cleared within 28 days and those with PCR positivity beyond 28 days. We noted lower B cell counts in the group with persistent PCR positivity (mean (SD) 0.08 (0.10) x109/L vs 0.22 (0.29) x109/L, p=0.01) as well as lower IgA (median (IQR) 0.00 (0.00-0.30) g/L vs 0.30 (0.00-0.90) g/L, p=0.03) and IgM (median (IQR) 0.10 (0.00-0.30) g/L vs 0.30 (0.10-0.75) g/L, p=0.007). No differences were seen in CD4+ or CD8+ T cell counts. Antiviral treatment did not impact risk of persistent PCR positivity. Conclusion: Persistent SARS-CoV-2 PCR positivity is common among immunodeficient individuals, especially those with antibody deficiencies, regardless of anti-viral treatment. Peripheral B cell count and serum IgA and IgM levels are predictors of viral persistence.