Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution

Abstract

Background: Recent data suggest that human coronavirus (HCoV) pneumonia is associated with significant mortality in hematopoietic cell transplant (HCT) recipients. Investigation of risk factors for prolonged shedding and intrahost genome evolution may provide critical information for development of novel therapeutics.

Methods: We retrospectively reviewed HCT recipients with HCoV detected in nasal samples by polymerase chain reaction (PCR). HCoV strains were identified using strain-specific PCR. Shedding duration was defined as time between first positive and first negative sample. Logistic regression analyses were performed to evaluate factors for prolonged shedding (≥21 days). Metagenomic next-generation sequencing (mNGS) was conducted when ≥4 samples with cycle threshold values of <28 were available.

Results: Seventeen of 44 patients had prolonged shedding. Among 31 available samples, 35% were OC43, 32% were NL63, 19% were HKU1, and 13% were 229E; median shedding duration was similar between strains (P = .79). Bivariable logistic regression analyses suggested that high viral load, receipt of high-dose steroids, and myeloablative conditioning were associated with prolonged shedding. mNGS among 5 subjects showed single-nucleotide polymorphisms from OC43 and NL63 starting 1 month following onset of shedding.

Conclusions: High viral load, high-dose steroids, and myeloablative conditioning were associated with prolonged shedding of HCoV in HCT recipients. Genome changes were consistent with the expected molecular clock of HCoV.

Keywords: genome evolution; hematopoietic cell transplant; human coronavirus; shedding; whole genome sequencing.

Figure 1.

Duration of shedding according to human coronavirus strain. The bars indicate median values and first and third quartiles (P = .79 by Kruskal-Wallis test).

Figure 2.

Genome evolution of human coronavirus over time. Single-nucleotide variants in the consensus genome for patient 1 (A), 2 (B), and 3 (C) are depicted. Patients 4 and 5 showed no variants over time for the same coronavirus species (Table 3). Both nonsynonymous and synonymous variants are depicted relative to the day 0 genome recovered. Majority consensus nonsynonymous changes at allele frequency >50% are indicted in red, while majority consensus synonymous changes at allele frequency >50% are shown in green. Allele frequencies for variant sites are depicted when the majority allele had <95% frequency. Nonsynonymous changes are shown for the amino acid of a given gene, while synonymous changes are shown for the nucleotide of that gene. Allele frequencies alone are shown when the majority consensus base is not a variant relative to the day 0 genome but the majority allele frequency at that base is <95% (in flux). Abbreviations: HE, hemagglutinin esterase; M, membrane protein; N, nucleocapsid protein.