Deciphering an Adenovirus F41 Outbreak in Pediatric Hematopoietic Stem Cell Transplant Recipients by Whole-Genome Sequencing

Abstract

Human adenovirus (HAdV) represents a major cause of mortality and morbidity in pediatric recipients of allogeneic hematopoietic stem cell transplants (HSCT). HAdV species F type 41 (HAdV-F41) infections in HSCT patients are scarce, whereas HAdV-F41 circulates commonly in healthy individuals. Between March and July 2018, HAdV-F41 infections were identified in four children (A, B, C, and E) who received allogeneic HSCT and one child before HSCT (D) at Robert Debré Hospital, Paris, France. We report here the clinical course of HAdV-F41 infection and the phylogenetic investigation to identify interpatient transmission. HAdV DNA was quantified in stool and plasma samples by real-time PCR. HAdV type was determined by sequencing of the fiber and hexon genes. Phylogenetic investigation was done with whole-genome sequences obtained by next-generation sequencing. HAdV loads in stool samples ranged from 6.60 to 10.10 log₁₀ copies/ml. HAdV-F41 detection in plasma was observed in four patients, but no disseminated disease was reported. Two patients died, but neither death was attributed to HAdV. While sequencing limited to the fiber gene suggested a cluster with four patients, phylogenetic analysis with whole-genome sequencing (WGS) and HVR7 revealed a cluster that included three patients (C, D, and E), suggesting an interpatient transmission in that cluster and two other independent infections. HAdV-F41 levels in stool specimens of pediatric HSCT patients are high and represent a risk of interpatient transmission. WGS helped to identify related cases. Prompt detection of HAdV in stool and control measures are warranted to limit any risk of nosocomial transmission.

Keywords: WGS; adenovirus; adenovirus disease; hematopoietic stem cell transplantation; next-generation sequencing; outbreak; phylogeny; plasma; stools; whole genome.

FIG 1

Map of three medical wards, A, B, and C, and rooms in the hematology pediatric department of Robert Debré Hospital, Paris, France. Ward A is divided in three spaces, namely A1, with 7 single rooms each with an anteroom (rooms 1 to 7); A2, with three units, each with two single rooms and a common anteroom and a laminar flow hood (rooms 8 and 9, 12 and 13, and 14 and 15); and A3, with four rooms and a common anteroom and a laminar flow hood. Ward B includes four single rooms. Ward A and B are located on the same floor (5th floor) but are separated by corridors. Wards A and B have specific entrances under positive pressure. Ward C is located on the 4th floor and includes 21 beds in 19 rooms without anterooms.

FIG 2

Timeline of HAdV outbreak (between March and July 2018) in the hematology pediatric department. Tracking of patients in wards A, B, and C (salmon color, ward A; purple, ward B; blue, ward C; pink, intensive care unit; gray, outpatient or day hospital or other hospitals) according to the weeks of hospitalization. Red and green correspond to positive and negative HAdV PCR results, respectively. Black arrows correspond to the dates of HSCT.

FIG 3

Monitoring of HAdV viral loads in stools and plasma for patients A, B, C, and E and in stools only for patient D. Patients A, B, and E received CDV only. Patients A and B had three injections and patient E two injections. Patient C received three injections of CDV (including one CDV injection on 9 May 2018 that is not mentioned in the figure) and then 11 doses of BCV. For patient C, HAdV replication started on 23 April 2018 with an HAdV load of >9 log copies/ml from 30 April 2018 to 7 May 2018 (data not shown in the figure). Patient D did not receive any treatment and did not have any monitoring of HAdV in plasma. Patient B died on 10 August 2018 and patient C on 2 September 2018. Brown and orange lines correspond to viral load in stools and plasma, respectively. Gray and red arrows represent CDV and BCV administration, respectively.

FIG 4

Phylogenetic tree of alignment of the fiber gene sequences (sequence positions 413 to 1072) (A), of the hexon gene sequences (sequence positions 1905 to 2459) (B), and of the whole-genome sequences (C) obtained from the five HAdV-F41 strains of the present study and other HAdV-F41 strain sequences from published NCBI sequences. For whole-genome sequencing, a mean of 5,668,405 150-bp paired-end reads were sequenced per sample.