Human virome

The human virome is the total collection of viruses in and on the human body. Viruses in the human body may infect both human cells and other microbes such as bacteria (as with bacteriophages). Some viruses cause disease, while others may be asymptomatic. Certain viruses are also integrated into the human genome as proviruses, or endogenized as endogenous viral elements. Viruses evolve rapidly and hence the human virome changes constantly. Every human being has a unique virome with a unique balance of species. Lifestyle, age, geographic location, and even the season of the year can affect an individual's exposure to viruses, and one's susceptibility to any disease that might be caused by those viruses is also affected by pre-existing immunity and both viral and human genetics. The human virome is far from being completely explored and new viruses are discovered frequently. Unlike the roughly 40 trillion bacteria in a typical human microbiome, an estimate of the number of viral particles in a healthy adult human is not yet available, although virions generally outnumber individual bacteria 10:1 in nature. Studying the virome is thought to provide an understanding of microbes in general and how they affect human health and disease. In January 2024, biologists reported the discovery of "obelisks", a new class of viroid-like elements, and "oblins", their related group of proteins, in the human microbiome.

Methods and tools Multiple methods are available for the isolation and study of human viruses:

Deep sequencing is a rapid DNA sequencing technique that is useful for characterizing virome richness, stability, gene function and the association with disease phenotypes. This technology creates large amounts of sequence information and is capable of detecting rare components of a microbial community. Current methods combining the removal of human and bacterial DNA from samples, large scale sequencing, and bioinformatics are very efficient in the identification of unknown viruses. Unlike other discovery methods, viruses do not need to be grown in cell cultures. Without any prior knowledge of genome sequence or growth methods, novel viruses can be discovered. Therefore, deep sequencing is well suited for rapid identification of an unknown or unexpected viruses involved in a disease outbreak or associated with conditions not thought to be caused by viruses. Deep sequencing also allows for large scale screenings with minimal hands on effort. A systematic exploration of the viruses that infect humans (the human virome) is important and feasible with these methods. Polymerase chain reaction is a tool to amplify and detect specific DNA sequences. It can be used to help characterize the virome, but it is limited by the need for at least partial DNA sequence information. The human metagenome includes all organisms that live on or in the human body. Viruses contribute to the metagenome and establish chronic infection that infest chromosomes; this method will formulate new estimate of the number of genes that confer susceptibility to a given virus and specify alleles for some viruses. Large scale antibody studies with ELISA using donated blood could help to determine human exposure to particular viruses in different geographic regions.

Diversity of human viruses

The human virome is not stable and may change over time. In fact, new viruses are discovered constantly. With an increasing number of known viruses, diagnosis and treatment of novel viral-associated conditions will become easier as well. Studying the virome could help improve drug development and limit antibiotic usage. One of the first studies that used high-throughput DNA sequencing to describe the diversity of eukaryotic dsDNA viruses in normal individuals included 706 samples from 102 subjects. This study detected an average of 5.5 viral genera in each individual and these viruses included herpesviruses, papillomaviruses, polyomaviruses, adenoviruses, anelloviruses, parvoviruses, and circoviruses.

Each individual had a distinct viral profile, demonstrating the high interpersonal diversity of the virome. One to 15 viral genera (average 5.5) were detected in 92% of the 102 individuals sampled (Figure 2). Figure 3 illustrates the viromes of the 102 individuals defined by sampling up to five major body habitats, showing that a broad range of viruses was detected in healthy people (Figure 3). The 102 individuals carried seven distinct families of human DNA viruses (Figure 4A). Sequences were detected predominantly in the nose and skin, similarity to 17 papillomavirus genera(Figure 4B). Roseoloviruses, predominantly HHV-7 and to a lesser extent HHV-6, were present among 98% of the individuals who provided mouth samples. In addition, the same viruses were prevalent in multiple body habitats within individuals. For instance, the beta- and gamma-papillomaviruses were the viruses most commonly found in the skin and the nose (anterior nares; see Figure 4A,B), which may reflect proximity and similarities in microenvironments that support infection with these viruses.

The human blood virome Whole-genome sequencing data of blood from 8,240 individuals without any clear infectious disease revealed 94 different viruses in 42% of the study participants. The sequences included 19 human DNA viruses, proviruses and RNA viruses (herpesviruses, anelloviruses, papillomaviruses, three polyomaviruses, adenovirus, HIV, HTLV, hepatitis B, hepatitis C, parvovirus B19, and influenza virus). Of possible relevance to transfusion medicine, this study identified Merkel cell polyomavirus in 49 individuals, papillomavirus in blood of 13 individuals, parvovirus B19 in 6 individuals, and the presence of herpesvirus 8 in 3 individuals.

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