The Experts below are selected from a list of 1551 Experts worldwide ranked by ideXlab platform
Mart Krupovic - One of the best experts on this subject based on the ideXlab platform.
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The healthy Human Virome: from virus–host symbiosis to disease
Current Opinion in Virology, 2021Co-Authors: Eugene Koonin, Valerian V Dolja, Mart KrupovicAbstract:Viruses are ubiquitous, essential components of any ecosystem, and of multicellular organism holobionts. Numerous viruses cause acute infection, killing the host or being cleared by immune system. In many other cases, viruses coexist with the host as symbionts, either temporarily or for the duration of the host's life. Apparently, virus-host relationships span the entire range from aggressive parasitism to mutualism. Here we attempt to delineate the healthy Human Virome, that is, the entirety of viruses that are present in a healthy Human body. The bulk of the healthy Virome consists of bacteriophages infecting bacteria in the intestine and other locations. However, a variety of viruses, such as anelloviruses and herpesviruses, and the numerous endogenous retroviruses, persist by replicating in Human cells, and these are our primary focus. Crucially, the boundary between symbiotic and pathogenic viruses is fluid such that members of the healthy Virome can become pathogens under changing conditions.
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The healthy Human Virome: from virus-host symbiosis to disease.
Current opinion in virology, 2021Co-Authors: Eugene V Koonin, Valerian V Dolja, Mart KrupovicAbstract:Viruses are ubiquitous, essential components of any ecosystem, and of multicellular organism holobionts. Numerous viruses cause acute infection, killing the host or being cleared by immune system. In many other cases, viruses coexist with the host as symbionts, either temporarily or for the duration of the host's life. Apparently, virus-host relationships span the entire range from aggressive parasitism to mutualism. Here we attempt to delineate the healthy Human Virome, that is, the entirety of viruses that are present in a healthy Human body. The bulk of the healthy Virome consists of bacteriophages infecting bacteria in the intestine and other locations. However, a variety of viruses, such as anelloviruses and herpesviruses, and the numerous endogenous retroviruses, persist by replicating in Human cells, and these are our primary focus. Crucially, the boundary between symbiotic and pathogenic viruses is fluid such that members of the healthy Virome can become pathogens under changing conditions.
Gregory A. Storch - One of the best experts on this subject based on the ideXlab platform.
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The Human Virome in Health and Disease
Molecular Microbiology, 2016Co-Authors: Kristine M. Wylie, Gregory A. StorchAbstract:Early studies of the Human microbiome were directed at bacteria. However, just as the bacterial microbiota affects Human health and disease, viruses have analogous interactions. Thus, the Human microbiome should be thought of as having a viral component, which is designated the Human Virome (Fig. 1 and Table 1). The definition of the Human Virome is complicated by the complexity of viruses and their life cycles. Viruses may be associated with acute infections that may or may not produce manifestations of disease and in which the presence of the viral etiologic agent is transient. In other cases, viral infections are persistent with prolonged presence of the implicated virus and ongoing replication. Persistent infections may or may not be associated with disease. In addition, some viruses become latent following acute infection. During latency, the viral genome persists, but viral replication does not occur, although transcription of some viral genes may take place. Another component of the Virome consists of sequences within the Human genome that appear to have resulted from remote incorporation of viral elements into the Human genome. Designated as endogenous Human retroviruses, these sequences cannot generate infectious viral particles. They occupy approximately 4.8% of the Human genome (1). Finally, bacteriophages are viruses that infect the bacteria that make up the Human endogenous microbiota. While all of the forms of viral infection described above may legitimately be considered part of the Human Virome, this chapter will focus on the first three groups: namely, viruses that infect eukaryotic cells and are capable of independent replication. The reason for that focus is that these are the viruses that have been associated to date with Human disease and are the targets of diagnostic testing.
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Metagenomic analysis of double-stranded DNA viruses in healthy adults
BMC biology, 2014Co-Authors: Kristine M. Wylie, Gregory A. Storch, Kathie A. Mihindukulasuriya, Yanjiao Zhou, Erica Sodergren, George M. WeinstockAbstract:The Human Microbiome Project (HMP) was undertaken with the goal of defining microbial communities in and on the bodies of healthy individuals using high-throughput, metagenomic sequencing analysis. The viruses present in these microbial communities, the 'Human Virome', are an important aspect of the Human microbiome that is particularly understudied in the absence of overt disease. We analyzed eukaryotic double-stranded DNA (dsDNA) viruses, together with dsDNA replicative intermediates of single-stranded DNA viruses, in metagenomic sequence data generated by the HMP. 706 samples from 102 subjects were studied, with each subject sampled at up to five major body habitats: nose, skin, mouth, vagina, and stool. Fifty-one individuals had samples taken at two or three time points 30 to 359 days apart from at least one of the body habitats. We detected an average of 5.5 viral genera in each individual. At least 1 virus was detected in 92% of the individuals sampled. 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. Some components of the Virome were stable over time. This study is the first to use high-throughput DNA sequencing to describe the diversity of eukaryotic dsDNA viruses in a large cohort of normal individuals who were sampled at multiple body sites. Our results show that the Human Virome is a complex component of the microbial flora. Some viruses establish long-term infections that may be associated with increased risk or possibly with protection from disease. A better understanding of the composition and dynamics of the Virome may hold important keys to Human health.
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Virome genomics: a tool for defining the Human Virome
Current opinion in microbiology, 2013Co-Authors: Kristine M. Wylie, George M. Weinstock, Gregory A. StorchAbstract:High throughput, deep sequencing assays are powerful tools for gaining insights into virus–host interactions. Sequencing assays can discover novel viruses and describe the genomes of novel and known viruses. Genomic information can predict viral proteins that can be characterized, describe important genes in the host that control infections, and evaluate gene expression of viruses and hosts during infection. Sequencing can also describe variation and evolution of viruses during replication and transmission. This review recounts some of the major advances in the studies of virus–host interactions from the last two years, and discusses the uses of sequencing technologies relating to these studies.
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Sequence analysis of the Human Virome in febrile and afebrile children.
PloS one, 2012Co-Authors: Kristine M. Wylie, George M. Weinstock, Kathie A. Mihindukulasuriya, Erica Sodergren, Gregory A. StorchAbstract:Unexplained fever (UF) is a common problem in children under 3 years old. Although virus infection is suspected to be the cause of most of these fevers, a comprehensive analysis of viruses in samples from children with fever and healthy controls is important for establishing a relationship between viruses and UF. We used unbiased, deep sequencing to analyze 176 nasopharyngeal swabs (NP) and plasma samples from children with UF and afebrile controls, generating an average of 4.6 million sequences per sample. An analysis pipeline was developed to detect viral sequences, which resulted in the identification of sequences from 25 viral genera. These genera included expected pathogens, such as adenoviruses, enteroviruses, and roseoloviruses, plus viruses with unknown pathogenicity. Viruses that were unexpected in NP and plasma samples, such as the astrovirus MLB-2, were also detected. Sequencing allowed identification of virus subtype for some viruses, including roseoloviruses. Highly sensitive PCR assays detected low levels of viruses that were not detected in approximately 5 million sequences, but greater sequencing depth improved sensitivity. On average NP and plasma samples from febrile children contained 1.5- to 5-fold more viral sequences, respectively, than samples from afebrile children. Samples from febrile children contained a broader range of viral genera and contained multiple viral genera more frequently than samples from children without fever. Differences between febrile and afebrile groups were most striking in the plasma samples, where detection of viral sequence may be associated with a disseminated infection. These data indicate that virus infection is associated with UF. Further studies are important in order to establish the range of viral pathogens associated with fever and to understand of the role of viral infection in fever. Ultimately these studies may improve the medical treatment of children with UF by helping avoid antibiotic therapy for children with viral infections.
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Emerging View of the Human Virome
Translational research : the journal of laboratory and clinical medicine, 2012Co-Authors: Kristine M. Wylie, George M. Weinstock, Gregory A. StorchAbstract:The Human Virome is the collection of all viruses that are found in or on Humans, including both eukaryotic and prokaryotic viruses. Eukaryotic viruses clearly have important effects on Human health, ranging from mild, self-limited acute or chronic infections to those with serious or fatal consequences. Prokaryotic viruses can also influence Human health by affecting bacterial community structure and function. Therefore, definition of the Virome is an important step toward understanding how microbes affect Human health and disease. We review progress in Virome analysis, which has been driven by advances in high-throughput, deep sequencing technology. Highlights from these studies include the association of viruses with clinical phenotypes and description of novel viruses that may be important pathogens. Together these studies indicate that analysis of the Human Virome is critical as we aim to understand how microbial communities influence Human health and disease. Descriptions of the Human Virome will stimulate future work to understand how the Virome affects long-term Human health, immunity, and response to coinfections. Analysis of the Virome ultimately may affect the treatment of patients with a variety of clinical syndromes.
Yujin Hoshida - One of the best experts on this subject based on the ideXlab platform.
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Viral Exposure Signature Associated with Liver Cancer Risk.
Trends in molecular medicine, 2020Co-Authors: Naoto Fujiwara, Yujin HoshidaAbstract:Virus infection is known to increase the risk of various cancers, including hepatocellular carcinoma (HCC). In a recent article in Cell, Liu et al. report a blood-based viral exposure signature (VES) based on a synthetic Human Virome to capture the history of virus exposure that is associated with future HCC occurrence.
Tobias Allander - One of the best experts on this subject based on the ideXlab platform.
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Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing.
PloS one, 2012Co-Authors: Fredrik Lysholm, Tobias Allander, Annelie Bjerkner, Anna Wetterbom, Cecilia Lindau, Hamid Darban, Kristina Fahlander, A. Michael Lindberg, Bengt Persson, Björn AnderssonAbstract:The Human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the Human Virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract Virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.
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Cloning of a Human parvovirus by molecular screening of respiratory tract samples
Proceedings of the National Academy of Sciences of the United States of America, 2005Co-Authors: Tobias Allander, Martti T. Tammi, Margareta Eriksson, Annelie Bjerkner, Annika Tiveljung-lindell, Björn AnderssonAbstract:The identification of new virus species is a key issue for the study of infectious disease but is technically very difficult. We developed a system for large-scale molecular virus screening of clinical samples based on host DNA depletion, random PCR amplification, large-scale sequencing, and bioinformatics. The technology was applied to pooled Human respiratory tract samples. The first experiments detected seven Human virus species without the use of any specific reagent. Among the detected viruses were one coronavirus and one parvovirus, both of which were at that time uncharacterized. The parvovirus, provisionally named Human bocavirus, was in a retrospective clinical study detected in 17 additional patients and associated with lower respiratory tract infections in children. The molecular virus screening procedure provides a general culture-independent solution to the problem of detecting unknown virus species in single or pooled samples. We suggest that a systematic exploration of the viruses that infect Humans, “the Human Virome,” can be initiated.
Björn Andersson - One of the best experts on this subject based on the ideXlab platform.
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Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing.
PloS one, 2012Co-Authors: Fredrik Lysholm, Tobias Allander, Annelie Bjerkner, Anna Wetterbom, Cecilia Lindau, Hamid Darban, Kristina Fahlander, A. Michael Lindberg, Bengt Persson, Björn AnderssonAbstract:The Human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the Human Virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract Virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.