My last post was written to introduce the concept of quasispecies in an RNA virus population.
This article will further expand on the topic and show how the quasispecies concept was used with powerful genetic sequencing technology to figure out a specific question: How many hepatitis C virus particles does it take to start an infection in humans?
Hepatitis C virus (HCV) is a member of the Flaviviridae family of RNA viruses. Genetically, HCV is one of the most diverse viral species on the planet, having even more variability than the well-known viral chameleon HIV.
Before we get into the virology of the article today I want to take a moment to describe the ethical considerations that guided the human samples. All of the blood samples that they used came from humans who had been recently infected with HCV. Nobody was purposefully infected for these studies.
So how did researchers get this blood without infecting people? They used donations from a blood bank where donors were given anonymous identification numbers and allowed to donate frequently at the same location. Since the early 1990s all blood products in the US have been screened for HCV to make sure that people getting donated blood don’t contract hepatitis A, B, or C. During the course of their donations some individuals went from being HCV negative to HCV positive, indicating that they had become infected between donations.
These consecutive samples from very early in infection provide a unique glimpse into what HCV looks like when it is first establishing an infection. Normally scientists don’t get to see this part of the viral life cycle, let alone sequence it because many people do not learn that they are infected with HCV until they become sick weeks to years later. With HCV many people do not know that they are infected and the serious symptoms of the disease often take decades to materialize.
By using a new sequencing techniques, these researchers were able to look at the quasispecies composition in people at different times by sequencing the same short sequence from single genome copies. What researchers found were distinct genetic profiles that could be used to determine the number of viral particles that started in infection. See the figure below.
Each line represents a sequenced genome, and each colored symbol represents a single mutation. When many single genomes were sequenced (this was done one-at-a-time to be able see the individual point mutations) distinct groupings of mutations indicated that those genomes were descended from a single viral genome and therefore particle. In this figure you can see how some of these different mutations seem to group together, indicating that they all came from the same founder. In A and B the observed mutations (or relative lack of them) indicate that all of these came from a single founder virus. Figures C and D show distinct genomes that indicate that an infection was started with three virions.
By looking at different patient profiles they were able to show that as even one viral particle was enough to start an infection. At the other end, as many as 37 genetically distinct particles start an infection, while the average was 4.
This is really impressive as it shows that even just one virion of HCV is needed to start an infection, although the average of this study was 4 particles to start an infection. These particles are only 55-65 nanometers (that’s 55 billionths of a meter). When you stop to think that a single particle this small can lead to serious diseases like cirrhosis of the liver it’s rather incredible.
If you want to read the source article and see the other figures this article is available for free on PubMed.
1. Li, H. et al. Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing. PLoS pathogens 8, e1002880 (2012).