Facts About Giant Viruses: Fascinating and Mysterious Entities
Giant viruses are fascinating entities that are much bigger than other viruses and larger than some bacteria. Researchers have discovered that they have a huge genome consisting of many genes. They often infect amoebas and bacteria, which are one-celled creatures. Some types have been found in the our mouth and digestive tract, where their effects are unknown. Their nature is intriguing. New discoveries are causing scientists to reassess their origin.
Not all biologists consider viruses to be living organisms, even though they have genes. This is why I refer to them as "entities". They lack the structures found in cells and must hijack a cell's machinery in order to reproduce. Nevertheless, their genes contain instructions for a cell to follow, as ours do, and they reproduce once they are inside a cell. For these reasons, some researchers classify viruses as living things.
A specific type of virus is vaguely equivalent to a "species" in reference to cellular organisms. Examples of viruses are the Epstein-Barr virus, the hepatitis A virus, and the COVID-19 virus. Individual particles of a particular virus are sometimes referred to as virions.
A DNA molecule is a double helix. Each strand of the molecule contains a "backbone" made of alternating deoxyribose and phosphate molecules. Nitrogenous bases extend from the deoxyribose. The order of nitrogenous bases on a DNA strand forms the genetic code.
DNA and Genes in Cellular Life Forms
The activities of a giant virus or of a smaller one depend on the genes in its nucleic acid, which is either DNA (deoxyribonucleic acid) or RNA (ribonucleic acid). Cellular life forms contain both of these chemicals, but the genes are located in the DNA. Since viruses infect cellular organisms and make use of their internal biology, it's helpful to know a little about how DNA functions in cells.
A DNA molecule consists of two strands twisted around each other to form a double helix. The two strands are held together by chemical bonds between the nitrogenous bases in each strand, as shown in the illustration above. The bases are named adenine, thymine, cytosine, and guanine. The double helix has been flattened in the illustration to show the structure of the molecule more clearly. The bond between a base on one strand and a base on the other one forms a structure known as a base pair. Adenine always joins to thymine on the opposite strand (and vice versa) and cytosine always joins to guanine.
A gene is a segment of a DNA strand that contains the code for making a particular protein. Only one strand of a DNA molecule is read when proteins are being made. The code is created by the order of the bases on the strand, somewhat like the order of letters makes words and sentences in English. Some segments of a DNA strand don't code for protein, although they do contain bases. Researchers are gradually learning what these segments do.
The complete set of genes in an organism is called its genome. The proteins produced from the genes have vital functions in our body (and in the life of other cellular organisms and of viruses). Without them, we couldn't exist.
The chromatin in the nucleus of a cell consists of DNA molecules mixed with protein.
Protein Synthesis in Cellular Life Forms
Viruses stimulate cells to make viral proteins. Protein synthesis includes the same steps whether a cell is making its own proteins or viral ones.
Protein synthesis is a multistep process. DNA contains the instructions for making proteins and is located in the nucleus of a cell. Proteins are made on the surface of ribosomes, which are located outside the nucleus. The membrane around the nucleus contains pores, but DNA doesn't travel through them. Another molecule is needed to take the DNA code to the ribosomes. This molecule is known as messenger RNA, or mRNA. The mRNA copies the DNA code in a process known as transcription.
The Genetic Code
Messenger RNA travels to a ribosome so that the protein can be created. Proteins are made of amino acids joined together. Twenty kinds of amino acids exist. The sequence of bases in a segment of a nucleic acid strand codes for the sequence of amino acids needed to make a particular protein. This code is said to be universal. It's the same in humans, other cellular organisms, and viruses.
When the messenger RNA arrives at a ribosome, transfer or tRNA molecules bring amino acids to the ribosome in the correct order according to the copied code. The amino acids then join together to make the protein. The manufacture of proteins on the surface of ribosomes is known as translation.
There are more types of RNA than just the messenger and transfer forms. In humans, DNA is double stranded and RNA is generally (but not always) single stranded. Viruses have single or double-stranded DNA or single or double-stranded RNA.
On the left in the illustration above, messenger RNA is being made from the DNA template in the nucleus. The mRNA meets a ribosome outside the nucleus. Transfer RNA molecules are bringing the correct amino acids into position. Amino acids have joined and the resulting protein (the pink structure) is forming its final shape. The large blue ball in the nucleus is the nucleolus.
Life Cycle of a Virus
Structure and Behavior of a Virus
A virus consists of nucleic acid (DNA or RNA) surrounded by a protein coat, or capsid. In some viruses, a lipid envelope surrounds the coat. Despite the seemingly simple structure of viruses compared to that of cellular organisms, they are very capable entities when they have contact with a cell. The presence of a cell is required in order for them to become active, however.
In order to infect a cell, a virus attaches to the outer membrane of the cell. Some viruses then enter the cell. Others inject their nucleic acid into the cell, leaving the capsid outside. In either case, the viral nucleic acid uses the cell's equipment to make copies of the nucleic acid and new capsids. These are assembled to make virions. The virions break out of the cell, often killing it in the process. They then infect new cells. In essence, the virus reprograms the cell to do its bidding. It's an impressive feat.
In general, the term “giant virus” is now commonly used to refer to viruses that have a large genome (>200,000 base pairs) and/or particle size (>0.2 μm).— Steven W Wilhelm et al, PLOS Pathogens
What Is a Giant Virus?
Though giant viruses are noticeable for their large and distinctive size, a more precise definition of what makes a virus a giant varies. They are often defined as viruses that can be seen under a light microscope. A more powerful electron microscope is required to see most viruses and to see details of the giant viruses.
Since even giant viruses are small entities by human standards, their dimensions are measured in micrometers and nanometers. A micrometer or μm is a millionth of a meter or a thousandth of a millimeter. A nanometer is a billionth of a meter or a millionth of a millimeter.
Some scientists have tried to create a numerical definition for the term "giant virus". The definition above was created by some University of Tennessee scientists. In their paper (referenced below), the scientists say that "a variety of arguments can be made for altering these metrics" with respect to the quote. They also say that whatever definition is used, the number of potentially active genes inside giant viruses is in the range found in cellular organisms.
Scientists often refer to the total length of giant virus nucleic acid molecules in terms of number of base pairs. The abbreviation kb stands for kilobase pair, or a thousand base pairs. The abbreviation Mb stands for megabase pair (a million base pairs) and Gb for a billion base pairs. Sometimes the abbreviations kbp, Mbp, and Gbp are used to avoid confusion with computer terminology. The "k" in kb or kbp isn't capitalized.
The number of proteins coded for by the genome is lower than the number of base pairs, as shown in the quote below, since a sequence of multiple bases codes for a single protein.
To date, the largest genomes belong to pandoravirus isolates, and the largest one, P. salinus, has 2,473,870 bp and encodes 2,556 putative proteins.— Abrahao et al, via Nature Communications (with respect to giant viruses)
A mimivirus is a type of giant virus. In the photo above, VF represents the viral factory. The factory is the center for virion production in a cell. Cyt is the cytoplasm of the host cell. The arrows show virions at different stages of assembly.
The Discovery of Giant Viruses
The first giant virus to be discovered was found in 1992 and described in 1993. The virus was found inside a one-celled organism called an amoeba. The amoeba was discovered in biofilm (slime made by microbes) scraped from a cooling tower in England. Since then, numerous other giant viruses have been found and named. The name of the first giant virus to be found is Acanthamoeba polyphaga mimivirus, or APMV. Acanthamoeba polyphaga is the scientific name of the host.
It might be wondered why giant viruses weren't discovered until 1992. Researchers say that they are so big that they have sometimes been wrongly classified as bacteria. In fact, the virus described above was thought to be a bacterium at first. As microscopes, laboratory techniques, and genetic analysis methods improve, it's becoming easier for scientists to detect that the entities that they have discovered are viruses, not bacteria.
Two theories exist for the creation of giant viruses. One says that they evolved from earlier cellular organisms. These ancestors lost some of their genes, became simpler in structure, and became parasites. The second theory says that giant viruses were created over time by the collection of genes from multiple hosts.
The Reactivation of an Ancient Virus
In 2014, some French scientists found a giant virus in Siberian permafrost. The virus was named Pithovirus sibericum and was estimated to be 30,000 years old. Although it had the size of a giant virus, it contained only 500 genes. When the permafrost sample thawed, the virus became active and was able to attack amoebas. (It doesn't attack human cells.)
Modern viruses can survive harsh conditions in an inactive state and then reactivate under favorable conditions. The huge inactivation time of the Siberian virus is amazing, however. The reactivation is a worrying reminder that there could be pathogenic (disease-causing) viruses in the permafrost that may be released as the temperature rises.
Tupanvirus Photos (No Sound)
Their genomes are 1.44–1.51 Mb linear double-strand DNA coding for 1276–1425 predicted proteins.— Abrahao et al, via Nature Communications (with respect to Tupanviruses)
The discovery of Tupanviruses in Brazil was reported in 2018. They are named after Tupã (or Tupan), a thunder god of the local people where the viruses were found. One strain is known as Tupanvirus soda lake because it was discovered in a soda (alkaline) lake. The other is known as Tupanvirus deep ocean because it was discovered in in the Atlantic Ocean at a depth of 3000m. The viruses are significant for more than their size. Though they don't have the largest number of genes in the giant virus group, their genome is interesting. They have the largest collection of genes involved in translation of any virus so far discovered.
Tupanviruses belong to a family called the Mimiviridae, like the first giant virus that was found. They have double-stranded DNA and are found as parasites in amoebas and their relatives. The viruses have an unusual appearance. They have a long tail-like structure and are covered with fibers, which makes them look like they're coated with fuzz when they're viewed under an electron microscope.
Regular viruses contain a few to as many as 100 or sometimes 200 genes. Based on the analysis performed so far, giant viruses appear to have from 900 genes to over two thousand. As the quote from the researchers states, Tupanviruses are thought to have from 1276 to 1425 genes. In the quote below, aaRS stands for enzymes called aminoacyl tRNA synthetases. Enzymes are proteins that control chemical reactions.
These giant viruses (Tupanviruses) present the largest translational apparatus within the known virosphere, with up to 70 tRNA, 20 aaRS, 11 factors for all translation steps, and factors related to tRNA/mRNA maturation and ribosome protein modification.— Abrahao et al, via Nature Communications
In 2019, Japanese scientists described some features of the Medusavirus. The virus was found in a hot spring in Japan. It gets its name because it stimulates Acanthamoeba castellanii to develop a stony covering when it infects the organism. In Ancient Greek mythology, Medusa was a monstrous creature with snakes instead of hair. People who looked at her were turned to stone.
Though the feature described above is interesting, the virus has an even more interesting characteristic. The researchers have found that it has genes that code for complex proteins found in animals (including humans) and plants. This could have an important evolutionary significance. More research is needed to understand the meaning of the discovery.
Features of the Medusavirus
Giant Viruses in Humans
A team of scientists from multiple countries has found giant viruses of a type known as bacteriophages, or simply phages. Phages infect bacteria. The ones recently discovered by researchers are around ten times larger that "normal" phages. They carry from 540,000 to 735,000 base pairs as opposed to up to 52,000 in regular phages.
According to researchers at the University of California, Berkeley, giant phages have been found in the human digestive tract. They are almost certainly influencing our bacteria. It's unknown whether the influence is positive or negative. Many of the numerous bacteria that live in our digestive tract appear to benefit us in some way, but some may be harmful.
Exploring the phages and their behavior is important. An estimate of the percentage of people that contain the entities could be helpful. It's possible that some of the numerous genes that they carry may be useful for us.
Fascinating and Still Mysterious Entities
The description of protein synthesis given in this article is a basic overview. Many enzymes and processes are involved in the production of proteins and many genes are required. So far, there is no evidence that giant viruses can make proteins by themselves. Like their relatives, they need to enter a cell and control the structures and processes involved in protein synthesis. How they do this is a topic of great importance. Understanding the behavior of giant viruses might help us to understand how some of their relatives behave.
Tupanviruses are impressive because they contain so many of the genes involved in translation. The Medusavirus is interesting because it contains genes found in advanced organisms. Giant viruses in the human body are intriguing. Future discoveries about the nature of the entities could be surprising and very interesting.
- Biology of viruses from the Khan Academy
- Standing on the Shoulders of Giant Viruses from PLOS Pathogens
- Ideas about the origin of giant viruses from NPR (National Public Radio)
- Tupanvirus discovery and facts from the Nature Journal
- Information from the BBC about a giant virus found in permafrost that was reactivated
- Facts about the giant Medusavirus from the phys.org news service
- More discoveries about giant viruses including ones in humans from The Atlantic
© 2018 Linda Crampton