Viruses in nature: contagious, destructive, and yet still useful

During the corona pandemic, most people probably see viruses as dangerous pathogens. However, the tiny infectious particles play an important part in very different ecosystems and regulate global cycles. In this interview, bioinformatician Prof. Dr Manja Marz and chemist Prof. Dr Georg Pohnert shed light on the roles of viruses in nature.

Where in nature are viruses found?

Marz: Wherever there are organisms, there are viruses; they need host organisms in order to replicate. This means that we also have viruses inside our bodies—in our intestines, for example. Viruses are found in the air, in waters, but also on our keyboards, and in our beds.

Are there reliable numbers or estimates of how many species of viruses exist?

Marz: There are approximately 3,500 known species of viruses—although, biologically speaking, viruses are no “species”, because they are not classified as living organisms. They only consist of wrapped-up genetic material: DNA or RNA. In order to duplicate, they have to enter the cells of a host organism and hijack their machinery (see infobox 1). However, more than 99 percent of all virus species are still unknown. Our body contains ten times as many bacteria as human cells; and there are also ten times as many viruses.

Which viruses do you study in your work as scientists?

Marz: In 2017, we founded the European Virus Bioinformatics Center, which has since had its seat at the University of Jena (see infobox 2). The centre deals with bacteriophages—viruses that replicate within bacteria—but also with other DNA and RNA viruses. Our working group mainly investigates RNA viruses, which include SARS, MERS and other coronaviruses; but we also research Zika, Dengue, yellow fever, hepatitis C, influenza and Ebola viruses.

Pohnert: We study viruses in oceans that infect unicellular algae like the coccolithophore Emiliania huxleyi. In open ocean waters, microalgae form the base of the marine food web and account for almost half of the global photosynthesis. They absorb carbon dioxide and release oxygen. This means that the global climate and our nutrition depend on these algae. Specialized viruses such as the Emiliania huxleyi virus 86 can infect these algae and destroy them. In our research, we deal with the mechanisms of this viral infection and look for mechanisms of resistance.

What happens if viruses infect algae in oceans?

Pohnert: When viruses infect algae, they enter their cells and completely reprogramme their metabolism. Biochemical metabolic pathways that the algae usually use at a very low rate are activated; and the algae then produce components for the viruses’ capsids. Once the number of viruses reproduced in the algae’s cells is high enough, lysis is induced; the algae burst, releasing a huge number of viruses ready to infect algae themselves and thus extinguishing entire populations.

This sounds like a rather one-sided partnership.

Pohnert: The virus infection obviously kills the individual algae cells. As a result, however, the viruses fulfil a vital function in the ecosystem. We have to bear in mind that a complex community of microorganisms is coexisting in the ocean, one that is constantly changing. When these specialized viruses reduce one algae species in the ecosystem, they create space for another species of algae to proliferate. In addition, viruses do not kill all individuals of a species; some cells are always more resistant and will be able to proliferate later in the year or in the next season. Viruses play the role of regulators, making sure that there is a healthy mix of species.

Viruses are also found in groundwater. Should we worry about that?

Marz: No, I don’t think so. Only a very small fraction of viruses is pathogenic for humans. Most viruses—more than 99 percent or so—are not virulent, but necessary for marine ecosystems for example, as we have just heard. It is believed that viruses regulate not only unicellular algae, but also bacteria living in water—in the groundwater, for example. The exact composition of the viruses in the groundwater is still unknown, but one thing is already clear now: Without viruses, the bacterial composition of groundwater would be entirely different.

Can we say that viral infections are a common way in nature to regulate the growth of microorganisms?

Pohnert: Yes, and not only of microalgae. Numerous bacteriophages—viruses that attack bacteria—have a regulatory effect on microbial communities; but viruses can be found in all multicellular organisms. Many plants are infected by viruses such as the tobacco mosaic virus, which causes the leaves to change colour and leads to a poor harvest. Livestock are also affected by viruses. They are closely monitored in order to contain possible outbreaks.

Marz: Viruses also play a very big role in human gut microbiome. Researchers at Jena University Hospital investigate the causes of gastrointestinal diseases and the role played by viruses. For this purpose, Prof. Dr Andreas Stallmach’s working group carries out fecal transplants. Together with his group, we are trying to gain a better understanding of the role viruses play in stool.

Are there results from your virus research that can be transferred to the current corona pandemic?

Marz: Coronaviruses, similar to other respiratory viruses (e.g. influenza), spread in small airborne droplets. The higher the humidity during a season, the longer the viruses circulate before they stop replicating. If the climate now becomes warmer and dryer, it might have a rather adverse effect on the viruses. In a joint project with virologists from the University Hospital, we are trying to determine the half-life of RNA viruses in liquids.

Infobox 1

Viruses—inanimate survivalists

Although they aren’t even organisms, viruses are true survivalists: they have been around for millions of years. Some of the most dangerous human diseases are caused by viruses—AIDS, smallpox, Ebola, or Covid-19. With a size of no more than a few hundred nanometres, the small particles only consist of genetic material—DNA or RNA—surrounded by a protein shell. They have no organelles such as mitochondria or ribosomes, which means that they have no metabolism and cannot reproduce on their own. In order to do so, they need the cells of their host organisms. Their small size and simple nature makes them so dangerous. The fact that viruses do not live makes them harder to “kill”. In order to spread, they infiltrate their host’s cells with their own genetic material and have the host replicate it; in the process, new protein components for new viruses are produced, too. Once a certain virus concentration in the host’s cell is reached, the latter disintegrates and releases a new generation of viruses. Other viruses incorporate their own genetic material into the host cell’s genetic material and are thus duplicated with each cell division. They continue to “live” on in their host organisms as stowaways.

  • Fun fact: Approximately eight percent of the human genome comes from viruses and has been incorporated in our genome throughout evolution.
Elektronenmikroskopische Aufnahme eines SARS-Coronavirus-2. Maßstab: 100 nm. Abbildung: Tobias Hoffmann, Michael Laue/RKI
Electron microscope image of a SARS corona virus 2. Scale: 100 nm.
Image: Tobias Hoffmann, Michael Laue/RKI

Infobox 2

The European Virus Bioinformatics Center

The European Virus Bioinformatics Center (EVBC) was founded in 2017 at the Friedrich Schiller University Jena. Prof. Dr Manja Marz is the head of the centre. Researchers from the fields of bioinformatics and virology analyse genome sequencing data in order to find new approaches for antiviral therapies, accelerate the development of vaccines, and make reliable prognoses regarding the potential risk of viruses. Currently, the emphasis is on the novel coronavirus SARS-CoV-2. Coronavirus experts such as virologist Prof. Dr Christian Drosten from the Charité hospital try to understand infection processes in order to provide potential therapies and vaccines as soon as possible. Bioinformaticians, on the other hand, develop specific analytics software for coronaviruses, which helps to detect changes in the virus during the pandemic or to provide a better understanding of the human-virus interaction, among others.

Das Genom von RNA-Viren (zu denen auch die Coronaviren zählen) zu entschlüsseln, wird durch jüngste Fortschritte in der Biotechnologie immer einfacher. Dank der neuartigen Nanoporen-Sequenzierung (Oxford Nanopore) sind die notwenigen Arbeitsschritte schneller und einfacher, so dass die Sequenzierung auch außerhalb eines Labors erfolgen kann. Die Geräte sind in etwa so groß wie ein USB-Stick und können direkt mit dem Computer verbunden werden. Die Arbeitsgruppe von Prof. Marz hat gezeigt, dass Dank dieser Technologie komplette Virengenome direkt am Stück entschlüsselt werden können. Foto: Lisa-Marie Barf
Recent advancements in biotechnology make it increasingly easier to decipher the genome of RNA viruses (which includes coronaviruses). Thanks to the innovative approach of nanopore sequencing (Oxford Nanopore), the necessary steps become faster and simpler, allowing researchers to perform sequencing outside of the lab. The devices are about the size of a USB flash drive and can be directly connected to a computer. The working group of Prof. Marz has shown that using this technology, complete viruses’ genomes can be decoded directly at a stretch.
Image: Lisa-Marie Barf

Infobox 3

What do viruses have to do with the White Cliffs of Dover?

Unicellular coccolithophores are very abundant in the oceans. During the algal bloom, their huge populations can even be seen from the orbit, as the picture of the sea between England and France depicted below shows. If viruses infect such an algal bloom, the algae die within a short period of time and sink to the bottom of the ocean. The biological material is broken down; however, the algaes’ scales—the coccoliths—remain intact and form the characteristic white sediment, the main component of the White Cliffs of Dover or the Rügen White Chalk formation.

Satellitenbild einer Algenblüte vor der Bretagne. Foto: NASA
Satellite image of an algal bloom off the coast of Bretagne.
Image: NASA