Which Came First: The Virus or the Host?

They existed 3.5 billion years before humans evolved on Earth. They’re neither dead nor alive. Their genetic material is embedded in our own DNA, constituting close to 10% of the human genome. They can attack most forms of life on our planet, from bacteria to plants to animals. And yet, if it wasn’t for them, humans might never have existed.

3D structure of a coronavirus, viral evolution
A depiction of the shape of coronavirus as well as the cross-sectional view. The image shows the major elements including glycoproteins, viral envelope and helical RNA. This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license.

No, that’s not the blurb for a new Hollywood blockbuster, although recent developments have proven, once again, that truth is decidedly more bizarre than fiction. Now that “coronavirus” has become a household word, the level of interest in all things virus-related is growing at an unprecedented rate. At the time of writing, coronavirus and COVID-19 topics dominated search traffic on Google, as well as trends on social media. A recent FAQ on this blog addresses many of the questions we hear on these topics.

Continue reading “Which Came First: The Virus or the Host?”

Moving Towards Zero Hunger, One Genome at a Time

Farmer and a pile of cassava bulbs.

Have you ever thought about plant viruses? Unless you’re a farmer or avid gardener, probably not. And yet, for many people the battle against agricultural viruses never ends. Plant viruses cause billions of dollars in damage every year and leave millions of people food insecure (1–2), making viruses a major barrier to meeting the United Nations’ global sustainable development goal of Zero Hunger by 2030.

At the University of Western Australia, Senior Research Fellow Dr. Laura Boykin is using genomics and supercomputing to tackle the problem of viral plant diseases. In a recent study, Dr. Boykin and her colleagues used genome sequencing to inform disease management in cassava crops. For this work, they used the MinION, a miniature, portable sequencer made by Oxford Nanopore Technologies, to fully sequence the genomes of viruses infecting cassava plants.

Cassava (Manihot esculenta) is one of the 5 most important calorie sources worldwide (3). Over 800 million people rely on cassava for food and/or income (4). Cassava is susceptible to a group of viruses called begomoviruses, which are transmitted by whiteflies. Resistant cassava varieties are available. However, these resistant plants are usually only protected against a small number of begomoviruses, so proper deployment of these plants means farmers must know both whether their plants are infected and, if so, the strain of virus that’s causing the infection.

Continue reading “Moving Towards Zero Hunger, One Genome at a Time”

Will Warmer Weather Wake the Sleeping Giant (Viruses)?

Artist's conception of Mimivirus structure, the first of the giant viruses identified.
Artist’s conception of Mimivirus structure, the first of the giant viruses identified.

Following the discovery of Mimivirus (1) the first virus with a particles large enough to be visible under the light microscope, two additional “giant” viruses infecting Acanthamoeba have been discovered Pandoravirus (2) and Pithovirus sibericum (3), the latter from a 30,000 year old Siberian permafrost. A fourth type was recently isolated from the same sample of permafrost by Legendre et al, and named Mollivirus sibericum (4).

Mollivirus sibericum has an approximately spherical virion (0.6 µm diameter) with a 651kb GC-rich genome that encodes 523 proteins. To further characterize the virus the researchers performed transcromic- and proteomic-based time course experiments.

For the particle proteome and infectious cycle analysis, proteins were extracted and then run a 4–12% polyacrylamide gel, and trypsin digests were performed in-gel before nano LC-MS/MS analysis of the resulting peptides. Proteomic studies of the particle showed that it lacked an embarked transcription apparatus, but revealed an unusual presence of many ribosomal and ribosome-related proteins.

When the researchers explored the proteome during the course of an entire infectious cycle, the relative proportions of Mollivirus-, mitochondrion-, and Acanthamoeba encoded proteins were found to vary consistently with an infectious pattern that preserved the cellular host integrity as long as possible and with the release of newly formed virus particles through exocytosis.

In an interesting footnote, the authors of this study point out the fact that two different viruses retain their infectivity in prehistorical permafrost layers should be a concern in the context of global warming and the potential to expose humans to primeval viruses.


1. La Scola, B. et al.   (2003) A giant virus in amoebae. Science  299, 2033.
2. Philippe, N. et al. (2013) Pandoraviruses. Amoeba virus with genomes up to 2.5Mb reaching that of parasitic eukaryotes. Science 341,281–6.
3. Legendre, M. et al. (2014) Thirty thousand year old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc.Natl. Acad. Sci. 111, 4274–9.
4. Legendre, M. et al. (2015)  In depth study of Mollivirus sibercum, a new 30,000 year old giant virus infecting Acanthamoeba.  Proc. Natl. Acad. Sci. 112, E5327–35 (online).

Virophages: The Enemy of My Enemy is My Friend

Algae and, quite possibly, some virophages
Algae and, quite possibly, some virophages

Viruses are small DNA- or RNA-based infectious agents that can replicate only inside living cells of a host organism. Most people know what a virus is, and many of us harbor at least one or two of them at some point during the cold and flu season. However, I would guess that many of us do not know what a virophage is, even though they seem to be more common than previously thought.

Virophages were first discovered and characterized by LaScola et al. in 2008 (1) during studies with Acanthamoeba polyphaga mimivirus (APMV), the largest known virus—so large that it is visible by optical microscopy. Continue reading “Virophages: The Enemy of My Enemy is My Friend”