Virus nomenclature below the species level: A standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA, .
Archives of Virology (Impact Factor: 2.39). 01/2013; 158(1):301-311. DOI: 10.1007/s00705-012-1454-0



The task of international expert groups is to recommend the classification and naming of viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and nomenclature for filoviruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length virus names (such as "Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621") is proposed. These names contain information on the identity of the virus (e.g., Ebola virus), isolation host (e.g., members of the species Homo sapiens), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzavirus nomenclature and the nomenclature recently proposed for rotaviruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this nomenclature would increase the general understanding of filovirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.

Download full-text


Available from: Manfred Weidmann
  • Source
    • "Blood transfusion or needle exchange[21]. Human-human contact as well as via post-mortem contact Wildlife-Human, Blood transfusion or needle exchange44454647Incubation 2-4 weeks to 3 months. However vary depending on the host immune response system. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Human immunodeficiency virus (HIV) and the re-emerging Ebola virus disease (EVD) are closely intertwined and remain a persistent public health threat and global challenge. Their origin and rapid transmission and spread have similar boundaries and share overlapping impact characteristics, including related symptoms and other interactions. The controversies and global threat of these viruses require rapid response policy and evidence-based implementation findings. The constraints and dual burden inflicted by Ebola and HIV infections are highly characterized by similar socio-demographics, socio-economic and political factors. EVD has similar effects and burdens to HIV infection. This study seeks to understand EVD in the context of HIV epidemic despite the challenges in developing an effective vaccine against HIV and EVD. Our findings show that early understanding, prevention and treatment of these diseases a global health threat mainly in Africa is important and valuable. The lessons learned so far from HIV and Ebola epidemics are crucial in health programming and execution of rapid response interventions and continued vigilance against EVD before it become another worldwide health menace. Therefore, the current regional West Africa EVD requires strengthening healthcare systems and building preparedness and response capacity. Importantly, appropriate community participation, health education and resilience coupled with deployment of effective novel diagnostic approaches in early warning and surveillance of threats and emerging diseases. Therefore, there is an urgent need to develop novel key strategies are crucial in curbing the constant viral resurgence, persistence transmission dynamics and spread, as well in accelerating Ebola vaccines regimen (immunization) development and national implementation plans in achieving sustained control, and eventual elimination.
    Full-text · Article · Jan 2016
  • Source
    • "The genus Marburgvirus has two subspecies: Marburg virus (MARV) and Ravn virus (RAVV). The genus Ebolavirus is divided into five distinct species, Zaire ebolavirus (Ebola virus, EBOV), Sudan ebolavirus (Sudan virus, SUDV), Tai Forest ebolavirus (Tai Forest virus, TAFV), Bundibugyo ebolavirus (Bundibugyo virus, BDBV), and Reston ebolavirus (Reston virus, RESTV; Kuhn et al., 2013). EBOV is highly virulent to humans and NHPs with a mortality rate of up to 90% in African epidemics . "
    [Show abstract] [Hide abstract]
    ABSTRACT: Ebola and Marburg hemorrhagic fevers (EHF and MHF) are caused by the Filoviridae family, Ebolavirus and Marburgvirus (ebolavirus and marburgvirus), respectively. These severe diseases have high mortality rates in humans. Although EHF and MHF are endemic to sub-Saharan Africa. A novel filovirus, Lloviu virus, which is genetically distinct from ebolavirus and marburgvirus, was recently discovered in Spain where filoviral hemorrhagic fever had never been reported. The virulence of this virus has not been determined. Ebolavirus and marburgvirus are classified as biosafety level-4 (BSL-4) pathogens and Category A agents, for which the US government requires preparedness in case of bioterrorism. Therefore, preventive measures against these viral hemorrhagic fevers should be prepared, not only in disease-endemic regions, but also in disease-free countries. Diagnostics, vaccines, and therapeutics need to be developed, and therefore the establishment of animal models for EHF and MHF is invaluable. Several animal models have been developed for EHF and MHF using non-human primates (NHPs) and rodents, which are crucial to understand pathophysiology and to develop diagnostics, vaccines, and therapeutics. Rhesus and cynomolgus macaques are representative models of filovirus infection as they exhibit remarkably similar symptoms to those observed in humans. However, the NHP models have practical and ethical problems that limit their experimental use. Furthermore, there are no inbred and genetically manipulated strains of NHP. Rodent models such as mouse, guinea pig, and hamster, have also been developed. However, these rodent models require adaptation of the virus to produce lethal disease and do not mirror all symptoms of human filovirus infection. This review article provides an outline of the clinical features of EHF and MHF in animals, including humans, and discusses how the animal models have been developed to study pathophysiology, vaccines, and therapeutics.
    Full-text · Article · Sep 2013 · Frontiers in Microbiology
  • Source
    • "Bekal et al., 2011 [3] emend. Kuhn et al., 2013 Etymology of soybean cyst nematode virus 1: derived from the host of the virus (the soybean cyst nematode); and Lat. n. neut. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Nyamanini virus (NYMV) and Midway virus (MIDWV) are unclassified tick-borne agents that infect land birds and seabirds, respectively. The recent molecular characterization of both viruses confirmed their already known close serological relationship and revealed them to be nonsegmented, single- and negative-stranded RNA viruses that are clearly related to, but quite distinct from, members of the order Mononegavirales (bornaviruses, filoviruses, paramyxoviruses, and rhabdoviruses). A third agent, soybean cyst nematode virus 1 (SbCNV-1, previously named soybean cyst nematode nyavirus), was recently found to be an additional member of this new virus group. Here, we review the current knowledge about all three viruses and propose classifying them as members of a new mononegaviral family, Nyamiviridae.
    Full-text · Article · May 2013 · Archives of Virology
Show more