A Tour of Virus Characteristics

In our first four posts, we learned about three key components of viruses: the genome, capsid, and lipid envelope with associated glycoproteins. Here, we will dig into the variety of viruses by taking a quick tour of three viruses you may have heard of, and describing the genome, capsid, and lipid envelope of each. You will see that even though these are by some measures similar viruses (all have helical capsids and RNA genomes), each virus has unique biological characteristics that explain some of the differences we see in the diseases they cause.

Tobacco Mosaic Virus

The Tobacco Mosaic Virus (TMV) is a plant virus that causes discoloration of leaves in tobacco and related plants. Experiments using TMV and tobacco leaves led to the discovery of viruses as non-bacterial infectious agents in the 1890s, and later on in the 1930s, TMV was the first virus to be crystallized and imaged using protein crystallography. As a result, though you have likely never heard of TMV and it’s not a particularly important virus in terms of human disease, it has been instrumental in our ability to study viruses and their characteristics in general.
  • Genome: TMV is an RNA virus. It has a single strand of RNA about 6,400 bases long. The RNA encodes four genes, two of which help copy the genome during the replication process, one of which is a movement protein that helps the virus transit between cells, and one of which is the capsid protein that forms the shell of the virus.
  • Capsid: TMV is a helical virus. The rod-like capsid surrounds the 6,400 nucleotides of RNA, using 2,130 copies of the capsid protein to do so. The final virion (capsid plus genome) is about 300 nanometers (nm) long and about 18nm wide.
  • Envelope: Like most plant viruses, TMV has no lipid envelope, and cannot simply exit the cell wall. It therefore relies on special channels called plasmodesmata that allow for passage between the cells of infected plants.

Influenza

The influenza virus is the culprit behind the annual flu, and it causes around half a million deaths a year globally. There are four families of influenza virus (A through D), all of which are similar in structure and characteristics, but Influenza A is the one most commonly associated with human infections, including the 1918 Spanish Flu and the seasonal flu we all know and love.
  • Genome: Influenza is also a single-stranded RNA virus, but instead of a single long strand of RNA, it produces eight independent segments of RNA, ranging in length from 800 to 2,300 nucleotides. Each segment contains one or two genes, and all eight are necessary to produce an effective viral particle. One side effect of this segmentation is that the Influenza genome is frequently shuffled as it is being packed into the capsid, and this proves to be a robust source of genetic variation in the virus. If multiple strains of the virus infect a single host, segments from both viruses can mix within single viral particles. This process is called recombination, and it contributes to the rapid evolution of the influenza virus, which in turn makes Influenza a hard virus to target.
  • Capsid: Influenza has a helical capsid that is 80 - 120nm in diameter. The length of the capsid is variable, as the virus extends the capsid with as many proteins as required to encapsulate its particular assortment of the eight genomic segments.
  • Envelope: Influenza exits cells through budding, resulting in a lipid envelope that wraps the helical capsid. The envelope presents two types of glycoproteins on the surface of the viral particle: hemagglutinin and neuraminidase. The hemagglutinin binds to sialic acid, which is a molecule that is attached to many cell surface proteins. Because the binding does not require a specific cellular receptor, and instead operates on a common chemical modification of proteins, Influenza can bind to and often enter a wide variety of host tissues and cells. Neuraminidase, on the other hand, does the opposite: it cleaves sialic acid from the cell surface, allowing the viral particles to detach from cells. It’s not clear exactly how and why this ability to detach from cells is useful to Influenza, but it is theorized that it allows viral particles to retry entering cells if they happen to bind to one that it cannot enter effectively.


SARS-CoV-2

SARS-CoV-2 is the virus du jour-- the culprit behind COVID-19. It belongs to a group of viruses known as coronaviruses that cause certain seasonal colds as well as SARS (or Severe Acute Respiratory Syndrome, the 2003 version) and MERS (or Middle East Respiratory Syndrome). We currently suspect SARS-CoV-2 evolved from earlier coronaviruses in bats, though it is not yet clear how the virus was introduced into human circulation.
  • Genome: SARS-CoV-2 is a single-stranded RNA virus, and, at nearly 30K nucleotides long, it is among the longest RNA viruses. The genome is similar to its SARS predecessor, but several key mutations result in increased binding to human receptors and may account for the increased virulence that we have seen. The long genome allows the virus to encode a dozen proteins, including a polymerase for replication of the RNA genome and several different capsid and envelope proteins.
  • Capsid: SARS-CoV-2 has a helical capsid made up of the Nucleocapsid protein and tethered to the lipid envelope with the Matrix protein.
  • Envelope: The characteristic image of SARS-CoV-2 that we have all grown familiar with is a spiky ball. The ball is actually the lipid envelope, 50 - 200 nanometers in diameter, with the helical capsid inside. The spikes are glycoproteins, rather descriptively called Spike proteins, that allow the viral particle to bind to a receptor called ACE2 in humans and related animals. This receptor is present in lung cells and many other cells throughout the body, allowing SARS-CoV-2 to spread and replicate across many tissues. Once the Spike protein binds to the host cell’s receptor, a second protein on the surface of the host cell cleaves the spike, resulting in a change in the shape of the viral particle. The change in shape exposes a viral fusion protein that allows the virus to fuse with the host cell membrane and dump its payload inside. 


Now we have a sense for some of the ways in which viruses might differ from each other, and some of the ways that scientists study and describe these differences. In the next post, we’ll dig into the other side of the equation: how immune systems see and respond to viruses.

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