Better detection of Torque teno virus in children with leukemia by metagenomic sequencing than by quantitative PCR

Abstract

Torque teno virus (TTV) is a group of chronically persisting viruses with a short circular DNA genome. TTV demonstrates a wide sequence diversity and a large majority of humans are chronically infected by one or more types of TTV. As TTV is ubiquitous, and viral replication correlates with immune status, TTV has been studied as a marker to assess global functional immune competence in transplant recipients. Most studies of the prevalence, amounts, and variation in TTV have been performed using PCR assays. We here present a comparison of the most frequently used quantitative PCR (qPCR) assay for TTV with shotgun metagenomic sequencing for detection and characterization of TTV in a cohort of pediatric cancer patients.The results show that TTV is more common than the qPCR assays indicate, and analysis of the TTV genome sequences indicate that a qPCR with primers and probe designed on a conserved region of the TTV genome may fail to detect some of the TTV strains found in this study.

Human Anelloviruses: Influence of Demographic Factors, Recombination, and Worldwide Diversity

“…This problem did not exist in our work, since random amplification and massive sequencing were carried out, in addition to a first step of enrichment of the viral fraction. In line with this, recent evidence suggests that anellovirus detection by metagenomics is more reliable than that by quantitative PCR-based methods ( 31 ). In addition, most of the anellovirus-positive samples in our study had coinfections with variants of two or even all three human anellovirus genera, resulting in a distinctive anellovirus profile for each subject ( 16 ).…”

Identification of Torquetenovirus Species in Patients with Kawasaki Disease Using a Newly Developed Species-Specific PCR Method

“…However, as this study showed, a primer set may not detect all the TTV variants, whereas NGS sequencing can detect the variants. This disadvantage of PCR has been reported previously [38]. Meanwhile, NGS results should also be interpreted with caution because a large number of reads mapped to the reference sequence of a virus does not necessarily confirm the presence of the virus.…”

Rapid diagnosis of non-tuberculous mycobacterial pulmonary diseases by metagenomic next-generation sequencing in non-referral hospitals

“…In this study, qPCR was applied to validate the results of mNGS in nine patients, and only six samples were detected to be positive. Several articles have also indicated that the positive rate of mNGS was higher than qPCR in the ability to detect specific pathogens; for example, the Torque teno virus in children with leukemia ( Leijonhufvud et al., 2022 ) and Orientia tsutsugamushi ( Liu et al., 2021 ). Besides the positive rate, mNGS also exhibited several other advantages over qPCR in the detection of infectious diseases.…”