Abstract
The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome in various sites in the human body, as well as interactions between the human host and the virome with regard to health and disease. However, there have been few studies of direct causal relationships. Viral metagenomic analyses often lack standard references and are potentially subject to bias. Moreover, most virome-related review articles have focused on the gut virome and did not investigate the roles of the virome in other sites of the body in human disease. This review presents an overview of viral metagenomics, with updates regarding the relations between alterations in the human virome and the pathogenesis of human diseases, recent findings related to COVID-19, and therapeutic applications related to the human virome.
Highlights
Several direct causal relationships remain to be elucidated, we present a summary of current evidence for associations between the virome and human diseases, including SARS-CoV-2 infection, human immunodeficiency virus (HIV) infection, Clostridioides difficile infection (CDI), inflammatory bowel disease (IBD), graft-versus-host disease (GVHD), type 1 diabetes (T1D), type 2 diabetes (T2D), obesity, hypertension, asthma, chronic obstructive pulmonary disease (COPD), and colorectal cancer (CRC), in Tables 1 and 2 and Figure 3
Another study showed that the transfer of fecal filtrate containing bacterial components, metabolites, and bacteriophages that contribute to the normal intestinal microenvironment rather than fecal microbiota transplantation (FMT) was sufficient to restore normal stool habits and eliminate symptoms in CDI patients [124], suggesting that the gut virome of FMT donors should be considered in future
Advances in technology and updating of viral genome databases have accelerated the pace of virus identification, resulting in increased interest in the human virome
Summary
A wide range of microorganisms are found in the human body, including viruses, bacteria, archaea, fungi, and protozoa. The virome is the viral fraction of the microbiome, and it is dominated by bacteriophages that infect bacteria as well as eukaryotic viruses that infect human cells. Several cost-effective approaches have since been developed, including metagenomic next-generation sequencing (mNGS), to identify known or novel microorganisms via the sequencing of DNA or RNA from samples. In addition to viruses that can cause infection, virome dysbiosis is thought to be related to several human diseases. Pandemic, a large proportion of people infected with the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were asymptomatic, whereas others developed severe disease. We review the utility of the viral mNGS approach in identifying and characterizing viruses, the composition of the human virome, relationships of human diseases with gut as well as oral and respiratory viromes, and therapeutic approaches related to the human virome
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