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User: Coy Tuner/The Human Virome

The Human Virome is a collection of viruses in the human body . Viruses are the most abundant infectious agents on the planet. These include viruses that cause acute self-limiting or uncontrolled infections, persistent and chronic infections that may or may not be asymptomatic, or latent infections, they also include viruses that are integrated in the human genome. Humans are constantly exposed to a variety of viruses that are genetically diverse and have new genotypes, strains and species that evolve rapidly. Every human being has a unique virome with a unique balance of species that can change quickly. Lifestyle, age, geographic location, and even the season of the year affects an individual's exposure to viruses; while their susceptibility to disease is effected by preexisting immunity and both viral and human genetics. The first virus that was discovered was the Tobacco mosaic virus in 1892 and viruses are still being discovered today. With today's technological advances, more viruses are rapidly being discovered.

Health Effects
The human virome is a part of our bodies and will not always cause harm. Through one's immune system, the body has the ability to rid itself of the virus. Sometimes, the immune system does not work properly which then viruses cause harm by infecting the cells in the body, this can affect cell division by rapidly dividing. It is much harder to identify viruses than it is to identify bacteria. There are multiple hosts that a virus can infect including bacteria and fungi. The physiological impact which is the host antiviral response and host proteins are dictated in part by genetics and can vary with genetic polymorphisms across the population. The human virome affects human health, human immunity, and response to human coinfections.

The Diet Effect
The human microbiome can be altered via diet, but more experiments need to be done. There was a study done that concluded with a significant relationship between diet and the human virome. This was done by comparing the distance between Virus-like particle communities in individuals both before and after they started their controlled diet. The results were that the distance between the gut viromes of individuals on the same diet was significantly smaller at the end of their dietary treatment than it was at the start, while there was no increase in virome similarity for individuals on different diets over time. The article concluded with a statement of the need to continue studies to understand the attainment of gut viral communities.

Plan
Human survey of the viruses in the human body is an important next step. Defining the virome will help understand microbes and how they affect human health and disease. A study of currently recognized species is a starting point for attempts to characterize and interpret patterns of virus diversity. Samples can be collected from human serum, plasma, saliva, gastrointestinal tract, urine, skin swabs and more. Samples from children and immunocompromised patients would yield the most exposure to new viruses because the viral loads are expected to be higher and last longer. Although several projects have been proposed no study has yet characterized the virome of human pathogens in a comprehensive and systematic way.

Purpose
The objective of analyzing the human virome is to monitor which agents change over time, find undiscovered agents already present, and detect new viruses when they appear . It is important to study viruses because they are crtical determinants of bacterial community structure and function in all habitats. . Viruses disperse quickly, meaning a global surveillance network is essential to ensure rapid detection. "A better understanding of the emergence of new human viruses as a biological and ecological process will allow refinement of the current notion of the kinds of pathogens, or the kinds of circumstances, that are of most concern, and so direct efforts at detection and prevention (would be the most efficient) . " As the depths of sequencing expands and the availability of viral genomes are complete, the easier and more accessible diagnosis can become. Future investigations of host-virome interactions hold great promise for providing new approaches to combating complex diseases. Lastly, studying the virome could help improve drug development and limit antibiotic usage.

Research Methods and Tools
Multiple methods are available for the classification and isolation of all classes of viruses.

Deep sequencing
Deep sequencing is a type of technology that would be useful for characterizing virome richness, stability, gene function and the association with disease phenotypes. This technology will detect rare components of a microbial community.

Polymerase chain reaction
Polymerase chain reactionis a tool to help characterize the virome, but is limited by the need of the investigator to determine which viruses to look for.

The Human Metagenome
The Human Metagenome includes all organisms that live on or in us. 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.

ELISA
Large scale antibody studies with ELISA using donated blood will help to determine exposure in different geographic regions.

Sequencing
Another method is Massive parallel sequencing where DNA sequencing is generated and then cloned by Polymerase chain reaction.

"The combination of host DNA depletion, optimized nucleic acid amplification, large scale sequencing and bioinformatics is an efficient procedure for the identification of unknown viruses. Unlike other discovery methods, there is no requirement for virus replication in cell culture, design of group-specific primers, or selected pairs of pre-infection and post-infection samples. Therefore, it is well suited for rapid identification of an unknown or unexpected virus involved in a disease outbreak. These procedures allow for large scale screenings with minimal hands on effort. It can easily be scaled up only by increasing sequencing capacity ." Therefore, a systematic exploration of the viruses that infect humans (the human virome) is important.

Challanges
The knowledge of viruses that infect humans is incomplete. Most studies are limited to the investigation of already known viruses. "Viruses do not contain a conserved genomic region that can be used to identify them . Viral genomic material can be a small proportion of the total nucleic acid in microbial connections because of the small genome sizes of most viruses and their low level presence ."