Updates of the SARS-CoV-2 life-cycle, its interactome and variants page


Update on SARS-CoV-2 / COVID-19 March 2021
One page describes the SARS circulating variants with list of variations. The SARS-CoV-2 replication cycle has been updated to add fusion directly at the cell surface, and host inhibitions by the virus.

Virosaurus update April 2020
Virosaurus (from virus thesaurus) is a curated virus genome database, aimed at facilitating clinical metagenomics analysis. The database has been updated, adding last SARS-Cov-2 sequences. It provides also non vertebrates viruses (insects, fungus, eukaryotic microorgansims) and plant virus sections.

Update on SARS-CoV-2 / COVID-19 March 2020
The nCoV virus has received an official name: SARS coronavirus 2 (SARS-CoV-2). WHO has named the disesae COVID-19. Coronavirus pages have been updated. Spike protein analysis has allowed predicting integrin binding: A potential role for integrins in host cell entry by SARS-CoV-2 Antiviral Res. 2020 Mar 1:104759

Novel Coronavirus (SARS-Cov-2) February 2020
The annotated proteome is accessible at SARS-CoV-2 proteome. UniProt provides pre-release access to these sequences from the current public health emergency. The data will become part of a future UniProt release and may be subject to further changes.

Wuhan Coronavirus January 2020
Wuhan 2020 Coronavirus (nCoV) belongs to the Betacoronavirus. These viruses are spread in many vertebrate species and cause respiratory diseases. SARS and Wuhan 2020 nCoV are Zoonosis causing pneumonia with risk of fatal cases. Human Coronavirus OC43 (or Betacoronavirus 1) is widespread and may cause 10-15% of common colds.

Antiviral drugs May 2019
Most common antiviral drugs have been added to ViralZone pages: EboV, HBV, HCV, HHV-1, HHV-5, ... HIV resource has been expanded with HIV antiretroviral drugs

Baltimore classification update June 2018
Upon taxonomy update presented by ICTV in early 2018, a new order called retrovirales (ortervirales) has been created. It contains viruses from Baltimore classification ssRNA(RT) and dsDNA(RT). To simplify our classification and include this new order, the "ssRNA(RT)" and "dsDNA(RT)" Baltimore classification have been merged into "reverse transcribing viruses". The official Baltimore classification has not changed.

Taxonomy update June 2018
The International Committee on Taxonomy of Viruses (ICTV) has ratified in january 2018 the creation of 1 order, 7 families, 10 sub-families and 58 genera. ViralZone has been updated accordingly, and in taxonomy pages these new nodes are tagged as .

Virus Acronyms February 2018

Most named virus have an associated acronym to facilitate communication. Hence Human Immunodeficiency Virus-1 can be shortened as HIV-1. We have compiled a document that keeps track of the history and acronyms of vertebrate viruses names, based on the 2017 official viral species. Vertebrate virus acronyms by species

Herpesvirus resource September 2017
A Herpesvirus page have been developed to describe the specific molecular biology of herpesviridae. This includes a deeper description of the virion, the virus life-cycle, a list of herpesviridae host-virus interactions

Taxonomy update September 2017
The International Committee on Taxonomy of Viruses (ICTV) has ratified in january 2017 the creation of 11 new families and 126 new genera. ViralZone has been updated accordingly, and in taxonomy pages these new nodes are tagged as .

Circular ssRNA virus/viroid March 2017
Viroids are plant selfish circular complementary RNA entities that behave like viruses but are not classified as such because they do not encode for proteins. Viroids can replicate either by symmetrical or assymmetrical rolling circle. Surprisingly the human hepatitis Delta virus genome and it's replication are similar to those of plant avsunviroidae, suggesting a common ancestor. Hepatitis D is the only known virus of its kind, and was discovered because it does have an impact on human health. We can expect to discover more of those virus/viroid in the future

Communication between viruses guides lysis-lysogeny decisions March 2017
In phi3T bacteriophage, the decision between latency and replication depends on the concentration of a small peptide that is secreted by infecting viruses and an intracellular receptor that acts as a transcriptional regulator. When a virus infects an as-yet-uninfected bacteria in which the peptide has accumulated, latency will be promoted.

Virus complete genomes October 2016 A list of curated virus complete genomes has been gathered and cleaned up from several resources. The list for vertebrate viruses covers 78,725 viruses comprising 333,953 sequences. Strain names with accession numbers are available for download.

Zika virus update February 2016 A dedicated ViralZone page has been created to describe the emerging pathogen Zika virus. This page includes basic information on the epidemiology of the Zika virus and links to its proteome and genome.

ICTV taxonomy update November 2015 The International Committee on Taxonomy of Viruses has updated Virus Taxonomy in 2014, voted and accepted it in 2015 . 1 new Family, and 52 new Genera. Viralzone taxonomy has been updated accordingly, new taxonomic pages are marked by the logo.

HIV resource October 2015
A HIV home page have been developed to describe the molecular biology of HIV and the effect of antiretroviral drugs on it. This resource is supported by the Swiss South Africa Joint Research Programme.

New hidden genes in RNA viruses October 2015
New hidden genes have been discovered in RNA viruses.

Alphavirus TF ,
Orbivirus NS4 , Luteovirus and Polerovirus P3a .
Interestingly, Potyvirus P3N-PIPO would be expressed by polymerase slippage,
a process not observed in ss+RNA viruses before .

Reference sequences: September 2015
In the swarm of sequence data and databases, how choosing a dedicated set of reference sequences for a given study? The page Reference sequence helps answering the question.

Virus entry and exit updated: September 2015
Virus entry and virus exit have been updated.
Several new pages have been created:
Apoptotic mimicry
ESCRT budding,
Viral latency,
ESCRT independent budding,
Actin transport,
Budding by cellular exocytosis,
Budding at plasma membrane

New Archaea virus families September 2015
The Sphaerolipoviridae and Spiraviridae are noteworthy by many aspects: the first is family whose viruses are infecting archaea and bacterias, the last is family of single-stranded DNA virus infecting archaea.

Electron microscopy images of phages
April 2015
Electron microscopy (EM) images from the virions are now available in most fact sheet pages of tailed phages. They have been inserted into a slider that allows to navigate from the virion drawing to the EM image. We are very grateful to Prof. H.-W. Ackermann who kindly provided us with the electronic microscopy images of most reference phages.

Human virus size February 2015
The picture of most common human viruses has been combined to show virion's relative size. This comparison highlights the big size of ebolavirus virion, and the small size of hepatitis viruses

Virology web links updated February 2015
A recent paper: Unraveling the Web of Viroinformatics"describes more than 100 Web servers and databases embracing all or specific viruses. With permission we have used all this information to expand ViralZone links page and stored it in a searchable table.

ICTV taxonomy update September 2014 The International Committee on Taxonomy of Viruses has released Virus Taxonomy: 2013, voted and accepted in 2014. 7 new Families, and 47 new Genera. Viralzone taxonomy has been updated accordingly, new taxonomic pages are marked by the logo.

Ebolavirus and measles updated August 2014

The structure of filoviruses nucleocapsid have been refined in 2012("PubMed":http://www.ncbi.nlm.nih.gov/pubmed/22247782), and morbiliviruses nucleocapsid as well (PubMed), and the ViralZone figures have been updated accordingly. Moreover an ebola virus cycle is available.

Bacterial viruses biology pages June 2014

The bacteriophages (Bacterial viruses) unique molecular biology is now described in 34 molecular virology pages. The content can be accessed by bacterial viruses homepage. One can discover the way M13 uses to enter cell cytoplasm by pilus retraction, the replicative transposition of Mu phage or the evasion of host toxin-antitoxin mechanisms of bacteriophages. Two replication cycles have been added: T7 phage and Mu phage.
The ViralZone team is thankful to Ariane Toussaint for her help.

30,000 years old and still infectious March 2014

A new virus has been isolated in a 30,000-year-old ice core harvested from permafrost in Siberia, Russia. The Pithovirus infects amoeba's and has a unique virion structure.

Amoeba's giant viruses March 2014

A recent discovered amoeba's Pandora virus has a huge genome compared to other known viruses. This fact may be related to amoebas having the biggest genome of all living cells. Their genome size would reach up to 670,000,000,000bp, that is more than 200 times the human genome size. In this context it is not surprising that amoeba's nucleo cytoplasmic large DNA viruses like pandora virus can reach 2,470,000bp, which is about six times more than the biggest vertebrate virus, canarypoxvirus 359,000bp. A new page describes the Pandoravirus.

ViralZone update January 2014
- Viral molecular biology section has been completed, for example with: leaky scanning, subgenomic transcription, viroid and hepatitis delta replication, virus genome evolution, fungal virus cell to cell movement ...
- A user pointed out the ICTV code of Virus Classification rules for orthography, and we are updating the 640 pages of ViralZone to follow the rule:

3.36 In formal taxonomic usage, the accepted names of virus Orders, Families, Subfamilies, and Genera are printed in italics and the first letters of the names are capitalized.

poliovirus replication cycle June 2013
The replication cycle of poliovirus is annotated and linked to virus ontology.

ICTV February 2013 The International Committee on Taxonomy of Viruses has released many updates to the viral taxonomy in 2012: 9 new Families, 3 new Subfamilies, and 34 new Genera. Viralzone taxonomy has been updated accordingly, new taxonomic pages are marked by the logo.

A new family of ssDNA virus infecting archaea has been discovered by Pietila et al in 2009. The family comprises now seven species and is tentatively named Pleolipoviridae. They are the first enveloped ssDNA virus described so far.

E-learning course(1) October 2012

A self-learning module for students has been developed in collaboration with FAO and IAEA about viral phylogenetic tree. The module comprises four chapters: Basics, Building Phylogenetic Trees, Interpreting Trees, and Exercices.

Hepatitis B virus replication cycle September 2012
In partnership with Hoffmann-La Roche, an interactive HBV life cycle resource has been created with 28 new pages linking to 180 publications from PubMed. The entry point to the HBV resource is an illustration depicting the virus replication cycle in a hepatocyte. The cycle has been divided into 27 molecular events that gives access to specific description pages.

Viral molecular ontology September 2012
An ontology that covers both virus structure and viral molecular events has been set up and can be accessed through the Viral molecular biology page. This viral ontology has been cross-linked in ViralZone pages to allow a better understanding of specific processes and characteristics of virus families. For viruses known to hijack or inhibit their host's functions, complex relationships with the host are detailed in a new host-virus interaction section of ViralZone description pages.

Virus inducing host gene shutoff May 2012
A new section describes the shutoff of host proteins induced by viruses, with subsection for the shutoff of cellular transcription, host mRNA suppression and host translation shutoff. More often than not viruses inducing a host gene expression shutoff are able to express their own proteins through specific mechanisms. For example many viruses inducing a shutoff of host translation have their mRNA translated through an IRES.

Fundamentals of Molecular Virology, 2nd edition January 2012
The second edition of Fundamentals of Molecular Virology written by Nicholas H. Acheson is now available. It includes five new chapters and upgraded full-color graphics. We want to thank Pr. Acheson for having worked with us on few of these graphics, which helped us to improve virion representation in ViralZone.

New NCBI Genome database released January 2012
The entrez genome database hosted in NCBI has been redesigned with new data model, views and formats in November 2011. See the official news. Here is an example of the new view of the genome of human herpesvirus-1 RefSeq. The changes in genome adress resulted in several broken or misdirected links in ViralZone reference strains, This is fixed now.

Endogenous Bornavirus gene in Human genome!
A survey of mammalian genomes has unexpectedly unearthed DNA derived from ssRNA Bornaviruses, leading to speculation about the role of these viruses in causing mutations with evolutionary and medical consequences.
Nature 463, 39-40, 7 January 2010

XMRV
Xenotropic murine leukemia virus-related virus (XMRV) is the first gammaretrovirus known to infect humans.It may be related to prostate cancer () and Chronic Fatigue Syndrome ()
ICTV
International Committee on Taxonomy of Viruses has released many updates to the viral taxonomy in August 2009: a new Order, 8 new Families, 7 new Subfamilies, and 39 new Genera. Viralzone taxonomy has been updated accordingly, new taxonomic pages are marked by a logo