Viral metagenomics and blood safety

Abstract

The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new potential threats for blood transfusion safety. Currently, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) can be considered as under control in high-resource countries. However, other viruses unknown or unsuspected may be transmitted to recipients by blood-derived products. This is particularly relevant considering that a significant proportion of transfused patients are immunocompromised and more frequently subjected to fatal outcomes. Several measures to prevent transfusion transmission of unknown viruses have been implemented including the exclusion of at-risk donors, leukocyte reduction of donor blood, and physicochemical treatment of the different blood components. However, up to now there is no universal method for pathogen inactivation, which would be applicable for all types of blood components and, equally effective for all viral families. In addition, among available inactivation procedures of viral genomes, some of them are recognized to be less effective on non-enveloped viruses, and inadequate to inactivate higher viral titers in plasma pools or derivatives. Given this, there is the need to implement new methodologies for the discovery of unknown viruses that may affect blood transfusion. Viral metagenomics combined with High Throughput Sequencing appears as a promising approach for the identification and global surveillance of new and/or unexpected viruses that could impair blood transfusion safety.

Clinical and biological insights from viral genome sequencing

“…Total DNA and/or RNA, including from the host, bacteria, viruses, fungi and other pathogens, are extracted from a sample, and a library is prepared and sequenced by shotgun sequencing or RNA sequencing (RNA-seq). BOX 1 explores the diagnostic applications for metagenomics and RNA-seq; for example, in encephalitis of unknown aetiology [62][63][64] , for which conventional methods such as PCR are often not diagnostic, metagenomics and RNA-seq have detected viral infections [65][66][67] and other DNA (cDNA)-amplified fragment length polymorphism (AFLP), abbreviated to VIDISCA), filtration, ultracentrifugation and the depletion of free nucleic acids, which mostly come from the host, have all been tried [74][75][76][77] ; however, these methods may also decrease the total amount of viral nucleic acids so that it is insufficient for preparing a sequencing library. Non-specific amplification methods, such as multiple displacement amplification (MDA), which make use of random primers and Φ29 polymerases, can increase the DNA yield.…”

The blood DNA virome in 8,000 humans

“…The study of the human virome is particularly relevant in the context of current discussions of next-generation sequencing for surveillance of viruses in blood and for transfusion safety [11, 15, 16]. Only viruses that are both pathogenic and transfusion-transmissible are routinely tested for and excluded from blood-derived products.…”

Metagenomics analysis of red blood cell and fresh‐frozen plasma units

“…High‐throughput sequencing (HTS) has enabled studies of viral landscapes in clinical specimens including blood . Some sequences of Anelloviridae , Herpesviridae , Picornaviridae , and Flaviviridae were found in blood of individuals ineligible for transfusion and the presence of Anelloviridae and HPgV was reported in pooled plasma samples collected from high‐risk subjects . Anelloviridae and HPgV were also identified in plasma fractionation pools assembled from blood donors, with additional signatures corresponding to papillomavirus and gemycircularvirus …”