Abstract:
:Next generation sequencing (NGS) technologies provide an increasingly important avenue for detecting known viruses, and for discovering novel viruses present in clinical or environmental samples. Several computational pipelines capable of identifying and classifying viral sequences in NGS data have been developed and used to search for viruses in human or animal samples, microbiomes, and in various environments. In this review we summarize the different approaches used to determine viral presence in sequence data. Strategies for avoiding confounding factors such as physical contamination and computational artifacts that lead to false virus identification are discussed. The application of these methodologies to cancer data sets has led to important insights on viruses both as drivers of and biomarkers for specific tumors.
journal_name
Curr Opin Viroljournal_title
Current opinion in virologyauthors
Cantalupo PG,Pipas JMdoi
10.1016/j.coviro.2019.07.010subject
Has Abstractpub_date
2019-12-01 00:00:00pages
41-48eissn
1879-6257issn
1879-6265pii
S1879-6257(19)30062-8journal_volume
39pub_type
杂志文章,评审abstract::Vaccines are the gold standard for the control and prevention of infectious diseases, but a number of important human diseases remain challenging targets for vaccine development. An influenza vaccine that confers broad spectrum, long-term protection remains elusive. Several broadly neutralizing antibodies have been id...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2012.02.005
更新日期:2012-04-01 00:00:00
abstract::Human alphaherpesviruses (αHHV) - herpes simplex virus type 1 (HSV-1), HSV-2, and varicella-zoster virus (VZV) - infect mucosal epithelial cells, establish a lifelong latent infection of sensory neurons, and reactivate intermittingly to cause recrudescent disease. Although chronic αHHV infections co-exist with brisk T...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2013.04.004
更新日期:2013-08-01 00:00:00
abstract::The rVSV-ZEBOV vaccine is currently the only Ebola vaccine with demonstrated clinical efficacy in a ring-vaccination clinical trial. It has been shown to be reactogenic but immunogenic and safe in several Phase I clinical studies. However, its mechanisms of protection are unknown and available immunogenicity data are ...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2017.03.008
更新日期:2017-04-01 00:00:00
abstract::Memory T cells are an important component of the adaptive immune response. Tissue-resident memory T cells (TRM) are a recently described subset of memory T cells that reside in peripheral tissues and are maintained independently of circulating subsets of memory T cells. Importantly, TRM are frequently found in barrier...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2017.11.001
更新日期:2018-02-01 00:00:00
abstract::High-risk human papilloma virus (hrHPV) infections are associated with the development of anogenital cancers, in particular cervical cancer, and a subset of head and neck cancers. Previous studies have shown that microRNAs (miRNAs) contribute to the development and progression of HPV-induced malignancies. miRNAs are s...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2019.07.002
更新日期:2019-12-01 00:00:00
abstract::Viral proteins have enabled the design of selective and efficacious treatments for viral diseases. While focus in this area has been on viral enzymes, it appears that multifunctional viral proteins may be even more susceptible to small molecule interference. As exemplified by HIV capsid, small molecule inhibitors can ...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2014.02.002
更新日期:2014-04-01 00:00:00
abstract::Lassa virus (LASV) is an emerging zoonotic virus endemic in West Africa that can cause severe haemorrhagic Lassa fever (LF) in humans. LF recently gained international attention as a prominent infectious disease, leading to increasingly severe outbreaks in Nigeria over the past three years. Morbidity and mortality ass...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2019.06.010
更新日期:2019-08-01 00:00:00
abstract::Once considered an inevitable consequence of HIV treatment, drug resistance is declining. This decline supports the hypothesis that antiretroviral therapy can arrest replication and prevent the evolution of resistance. Further support comes from excellent clinical outcomes, the failure of treatment intensification to ...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2013.08.007
更新日期:2013-10-01 00:00:00
abstract::The evolution of virulence has been studied from a number of theoretical perspectives, and a few experimental systems. Although there is no consensus on an overarching framework that covers all situations, the 'trade-off' hypothesis is a useful framework for examining the nature of symbiotic relationships between viru...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2012.06.010
更新日期:2012-10-01 00:00:00
abstract::Epicutaneous delivery of vaccinia virus (VacV) by scarification of the skin generates robust and durable protective immunity, which was ultimately responsible for eradicating smallpox from the human race. Therefore, infection of the skin with VacV is often used in experimental model systems to study the activation of ...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2017.10.001
更新日期:2018-02-01 00:00:00
abstract::Although two oral rotavirus vaccines are licensed in many countries, multiple factors may affect decision-making regarding introduction into national immunization programs in developing countries. Financial and logistic challenges to introduction of rotavirus vaccines in countries with limited infrastructure and resou...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2012.05.005
更新日期:2012-08-01 00:00:00
abstract::The generation of humanized mouse models in which immune deficient mice are engrafted with human tissues allows for the direct in vivo investigation of human-restricted viruses. These humanized mouse models have been developed and improved over the past 30 years. It is now possible to achieve high levels of human cell...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2015.06.006
更新日期:2015-08-01 00:00:00
abstract::The central nervous system (CNS) is an immunologically specialized organ where restrictive barrier structures protect the parenchyma from inflammation and infection. This protection is important in preventing damage to non-renewable resident cell populations, such as neurons, responsible for functions ranging from exe...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2017.12.003
更新日期:2018-02-01 00:00:00
abstract::The aetiologic association between infection with certain human papillomavirus (HPV) types, high-grade squamous neoplasia, and cancer at different epithelial sites is well established. In this review we briefly discuss recent breakthroughs in the regulation of squamous epithelia in homeostasis and disease, and provide...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2016.08.011
更新日期:2016-10-01 00:00:00
abstract::Structural information can inform our understanding of virus origins and evolution. The herpesviruses and tailed bacteriophages constitute two large families of dsDNA viruses which infect vertebrates and prokaryotes respectively. A relationship between these disparate groups was initially suggested by similarities in ...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2014.02.003
更新日期:2014-04-01 00:00:00
abstract::Despite remarkable therapeutic advances in the past two decades, the elimination of human immunodeficiency virus type 1 (HIV-1) from latent reservoirs constitutes a major barrier to eradication and preventing neurological disease associated with HIV/AIDS. Invasion of the central nervous system (CNS) by HIV-1 occurs ea...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2019.06.004
更新日期:2019-10-01 00:00:00
abstract::The Bunyavirales order is the largest group of RNA viruses, which includes important human and animal pathogens, that cause serious diseases. Licensed vaccines are often not available for many of these pathogens. The establishment of bunyavirus reverse genetics systems has facilitated the generation of recombinant inf...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2020.05.004
更新日期:2020-10-01 00:00:00
abstract::The ability to recognize invading viral pathogens and to distinguish their components from those of the host cell is critical to initiate the innate immune response. The efficiency of this detection is an important factor in determining the susceptibility of the cell to viral infection. Innate sensing of viruses is, t...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2016.11.012
更新日期:2017-02-01 00:00:00
abstract::Noroviruses are rapidly evolving RNA viruses and are generally known as the main cause of viral gastroenteritis worldwide. Particle stability is of special interest as transmission occurs via the faecal-oral route and virions are able to persist in the environment. Studies on norovirus capsid assembly and disassembly ...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2018.05.003
更新日期:2018-08-01 00:00:00
abstract::A common characteristic of virus capsids is icosahedral symmetry, yet these highly symmetric structures can display asymmetric features within their virions and undergo asymmetric dynamics. The fields of structural and computational biology have entered a new realm in the investigation of virus infection mechanisms, w...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2020.06.002
更新日期:2020-12-01 00:00:00
abstract::Latent HIV reservoirs are the greatest challenge facing an HIV cure. Here, we review recent evidence supporting an important role for the host immune response, in particular HLA class I-restricted CD8+ T lymphocytes, in modulating HIV reservoirs during natural infection. These observations indicate that factors govern...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2012.08.003
更新日期:2012-10-01 00:00:00
abstract::Type I interferons (IFN-I) were first described over 50 years ago as factors produced by cells that interfere with virus replication and promote an antiviral state. Innate and adaptive immune responses to viruses are also greatly influenced by IFN-I. In this article we discuss the diversity of cellular sources of IFN-...
journal_title:Current opinion in virology
pub_type: 杂志文章
doi:10.1016/j.coviro.2011.10.026
更新日期:2011-12-01 00:00:00
abstract::Recent technological advances have led to an explosion in the system-wide profiling of biological processes in the study of herpesvirus biology, herein referred to as '-omics'. In many cases these approaches have revealed novel virus-induced changes to host cell biology that can be targeted with new antiviral therapeu...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2014.09.021
更新日期:2014-12-01 00:00:00
abstract::The human roseoloviruses, human herpesviruses 6A (HHV-6A), HHV-6B, and HHV-7, are highly prevalent viruses that typically cause fever/rash illnesses such as roseola during early life primary infections. They also cause significant neurologic disease and complications following stem cell and solid organ transplantation...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2014.10.005
更新日期:2014-12-01 00:00:00
abstract::A number of new vaccines are being developed against microbial pathogens that might be used as bioweapons. For some of these vaccines, because of the lack of endemic disease and the lethal nature of the disease, human efficacy studies would not be ethical or feasible to conduct. In such cases, a regulation, known as t...
journal_title:Current opinion in virology
pub_type: 杂志文章
doi:10.1016/j.coviro.2012.01.004
更新日期:2012-06-01 00:00:00
abstract::While viral latency remains one of the biggest challenges for successful antiviral therapy, it has also inspired mathematical modelers to develop dynamical system approaches with the aim of predicting the impact of drug efficacy on disease progression and the persistence of latent viral reservoirs. In this review we p...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2013.06.015
更新日期:2013-08-01 00:00:00
abstract::Viruses are ubiquitous parasites of cellular life forms and the most abundant biological entities on earth. The relationships between viruses and their hosts involve the continuous arms race but are by no account limited to it. Growing evidence shows that, in the course of evolution, viruses and their components are r...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2018.07.011
更新日期:2018-08-01 00:00:00
abstract::Merkel cell polyomavirus (MCPyV) is the only human polyomavirus known to be involved in tumorigenesis. Like other human polyomaviruses, MCPyV is highly prevalent in the healthy population, yet the MCPyV-associated Merkel cell carcinoma (MCC) is a very rare disease. Although in vitro and in vivo models have provided si...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2015.08.010
更新日期:2015-10-01 00:00:00
abstract::Effective vaccines are the cornerstone of our defenses against acute influenza virus infections that result in ∼500 000 annual deaths worldwide. For decades, an on-going concerted effort has been to develop a universal influenza vaccine to combat the looming threat of potentially pandemic emerging and re-emerging infl...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2018.11.005
更新日期:2019-02-01 00:00:00
abstract::A model is described that predicts patterns of polyomavirus SV40 infections and associated cancers in humans. The model proposes that SV40 infections were established in humans primarily by exposure to contaminated oral poliovaccines and that infections persist today in geographic regions where poor sanitation or livi...
journal_title:Current opinion in virology
pub_type: 杂志文章,评审
doi:10.1016/j.coviro.2012.06.004
更新日期:2012-08-01 00:00:00