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Virus nomenclature below the species level: A standardized nomenclature for filovirus strains and variants rescued from cDNA

Authors:
  • NIH/NIAID Integrated Research Facility at Fort Detrick (IRF-Frederick)
  • China National Center for Bioinformation

Abstract

Specific alterations (mutations, deletions, insertions) of virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified virus genomes or parts thereof. A systematic nomenclature for such recombinant viruses is necessary to set them apart from wild-type and laboratory-adapted viruses, and to improve communication and collaborations among researchers who may want to use recombinant viruses or create novel viruses based on them. A large group of filovirus experts has recently proposed nomenclatures for natural and laboratory animal-adapted filoviruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include nomenclature for filoviruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filovirus genetic variant naming, ( /) / / / - , is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoviruses. For instance, the full-length designation of an Ebola virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to "Ebola virus H.sapiens-rec/COD/1995/Kikwit-abc1" (with the suffix "rec" identifying the recombinant nature of the virus and "abc1" being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as "EBOV H.sap/COD/95/Kik-abc1") and abbreviations (such as "EBOV/Kik-abc1") could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. "EBOV" would suffice if only one EBOV strain/variant/isolate is addressed.
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... The Filoviridae family is divided into three genera: Ebolavirus, Marburgvirus, and Cuevavirus. The genus Ebolavirus contains five distinct species, namely, Zaire ebolavirus, Sudan ebolavirus, Taï forest ebolavirus, Bundibugyo ebolavirus, and Reston ebolavirus, which is represented by EBOV, Sudan virus (SUDV), Taï forest virus, Bundibugyo virus (BDBV), and Reston virus, respectively [78]. In the most recent decade, EBOV, SUDV, and BDBV have produced Ebola virus disease (EVD) epidemics in Central and West Africa with increased frequency, and the case fatality rates range from 30% to 90% [79]. ...
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... The Filoviridae family is divided into three genera: Ebolavirus, Marburgvirus, and Cuevavirus. The genus Ebolavirus contains five distinct species, namely, Zaire ebolavirus, Sudan ebolavirus, Taï forest ebolavirus, Bundibugyo ebolavirus, and Reston ebolavirus, which is represented by EBOV, Sudan virus (SUDV), Taï forest virus, Bundibugyo virus (BDBV), and Reston virus, respectively [78]. In the most recent decade, EBOV, SUDV, and BDBV have produced Ebola virus disease (EVD) epidemics in Central and West Africa with increased frequency, and the case fatality rates range from 30% to 90% [79]. ...
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Population growth and industrialization have led to a race for greater food and supplyproductivity. As a result, the occupation and population of forest areas, contact with wildlife andtheir respective parasites and vectors, the trafficking and consumption of wildlife, the pollution ofwater sources, and the accumulation of waste occur more frequently. Concurrently, the agriculturaland livestock production for human consumption has accelerated, often in a disorderly way, leadingto the deforestation of areas that are essential for the planet’s climatic and ecological balance. Theeffects of human actions on other ecosystems such as the marine ecosystem cause equally seriousdamage, such as the pollution of this habitat, and the reduction of the supply of fish and otheranimals, causing the coastal population to move to the continent. The sum of these factors leadsto an increase in the demands such as housing, basic sanitation, and medical assistance, makingthese populations underserved and vulnerable to the effects of global warming and to the emergenceof emerging and re-emerging diseases. In this article, we discuss the anthropic actions such asclimate changes, urbanization, deforestation, the trafficking and eating of wild animals, as well asunsustainable agricultural intensification which are drivers for emerging and re-emerging of zoonoticpathogens such as viral (Ebola virus, hantaviruses, Hendravirus, Nipah virus, rabies, and severeacute respiratory syndrome coronavirus disease-2), bacterial (leptospirosis, Lyme borreliosis, andtuberculosis), parasitic (leishmaniasis) and fungal pathogens, which pose a substantial threat to theglobal community. Finally, we shed light on the urgent demand for the implementation of the OneHealth concept as a collaborative global approach to raise awareness and educate people about thescience behind and the battle against zoonotic pathogens to mitigate the threat for both humansand animals.
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Es wird über die Isolierung, Identifizierung und Darstellung des Erregers einer bisher unbekannten, kürzlich von Affen ausgegangenen menschlichen Infektionskrankheit berichtet. Zusätzliche Angabenfolgen in einer späteren Mitteilung. Summary A number of laboratory technicians and animal-house attendants at the Behringwerke in Marburg and the Paul-Ehrlich Institute in Frankfurt, in contact with monkeys, their blood or tissues, contracted an infection similar to “haemorrhagic fever”, but differing from it in several important aspects. Isolation, identification and structure of the causative virus (“Marburg virus”) of this previously unknown disease are reported. Resumen Acerca de la etiología de una enfermedad infecciosa transmitida del mono al hombre Se informa sobre el aislamiento, identificación y presentación del agente patógeno productor de una enfermedad infecciosa, hasta ahora desconocida, recientemente transmitida del mono a las personas. En una información posterior se comunicarán datos complementarios.