Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease

Abstract

Background Viral infections are common complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT recipients with steroid-refractory/dependent graft-versus-host disease (GvHD) are highly immunosuppressed and are more vulnerable to infections with weakly pathogenic or commensal viruses. Here, twenty-five adult allo-HSCT recipients from 2016 to 2019 with acute or chronic steroid-refractory/dependent GvHD were enrolled in a prospective cohort at Geneva University Hospitals. We performed metagenomics next-generation sequencing (mNGS) analysis using a validated pipeline and de novo analysis on pooled routine plasma samples collected throughout the period of intensive steroid treatment or second-line GvHD therapy to identify weakly pathogenic, commensal, and unexpected viruses. Results Median duration of intensive immunosuppression was 5.1 months (IQR 5.5). GvHD-related mortality rate was 36%. mNGS analysis detected viral nucleotide sequences in 24/25 patients. Sequences of ≥ 3 distinct viruses were detected in 16/25 patients; Anelloviridae (24/25) and human pegivirus-1 (9/25) were the most prevalent. In 7 patients with fatal outcomes, viral sequences not assessed by routine investigations were identified with mNGS and confirmed by RT-PCR. These cases included Usutu virus (1), rubella virus (1 vaccine strain and 1 wild-type), novel human astrovirus (HAstV) MLB2 (1), classic HAstV (1), human polyomavirus 6 and 7 (2), cutavirus (1), and bufavirus (1). Conclusions Clinically unrecognized viral infections were identified in 28% of highly immunocompromised allo-HSCT recipients with steroid-refractory/dependent GvHD in consecutive samples. These identified viruses have all been previously described in humans, but have poorly understood clinical significance. Rubella virus identification raises the possibility of re-emergence from past infections or vaccinations, or re-infection.

Investigation of Bufavirus and Parvovirus 4 in Patients with Gastro-Enteritis from the South-East of France

“…In BuV-positive patients with available blood samples, BuV was more frequently detected in blood samples of patients who died (2/6 patients vs. 1/24 patients) ( Table 2 ). In Switzerland, BuV nucleic acids were detected in 1/25 plasma samples; this patient presented with acute leukemia who underwent bone marrow transplantation and the issue was fatal 2 months later; the same patient had also a BuV-positive stool sample [ 29 ]. Together with our results, this supports that BuV could be involved in extra-intestinal clinical manifestations.…”

Metagenomic next-generation sequencing-guided antimicrobial treatment versus conventional antimicrobial treatment in early severe community-acquired pneumonia among immunocompromised patients (MATESHIP): A study protocol

“…mNGS tests using plasma or LRT samples had clinical impacts via new diagnoses, early diagnoses, and initiation of therapy for fungal infection; de-escalation of therapies; and by ruling out infectious etiologies ( Hogan et al, 2021 ; Sun et al, 2021 ; Zhan et al, 2021 ). Moreover, mNGS has been implemented to detect viruses in blood plasma samples of immunocompromised patients in recent years ( Zanella et al, 2021 ). Although mNGS is usually used as a tool to detect pathogens in the infectious disease, it can also be used to discover the drug resistance genes by analyzing the microbial nucleic acid sequence messages, which will help clinicians to choose precise antimicrobial agents ( Chiu and Miller, 2019 ; Casto et al, 2021 ).…”

A Paired Comparison of Plasma and Bronchoalveolar Lavage Fluid for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Suspected Severe Pneumonia

“…A previous study reported that anelloviruses (including TTV) could be identified in 96% of adult human blood samples during steroid-refractory/dependent graft-versus host disease. 17 The clinical significance of these viruses is poorly understood; however, anelloviruses were reported as non-pathogenic endogenous markers of the immune function, 45 and the quantification of TTV can guide immunosuppression to reduce graft rejection and infection. 46 We suggest that routine and simultaneous BALF and plasma mNGS is unnecessary, as doing so will not be more beneficial to patients and only increase the hospital expenses.…”