February 2010

(Example: Influenza virus)

There is a major molecular requirement that must be met by any negative sense RNA genome virus. Specifically, if just the viral genome enters the cell, there is no way for it to be copied or expressed, because there is no cellular machinery for using negative sense RNA as a template for either replication or gene expression. So, all of these viruses must bring a virion RNA polymerase enzyme into the cell along with the RNA genome, because only in this way will it be possible to produce a positive sense RNA that can function as a mRNA and get viral gene expression started.

As we have seen already for picornaviruses, another problem for all RNA genome viruses is how to be able to make a protein from each of its genes, given that the translation mechanism in the host cell results generally in one polypeptide produced from one mRNA. As we saw last time, the "solution" used by the picornaviruses is that the mRNA is one long molecule of about 8Kb (the entire viral genome) which gets translated as one long product (the "polyprotein"), which gets self-cleaved into the individual proteins. Some of the negative sense ss RNA genome viruses use a similar apporach, but the orthomyxoviruses (such as influenza ) use a different approach. As we saw in Table 1 several classes ago, these viruses have their genome in pieces, and thus mRNAs coding for single individual proteins are produced from the separate genome segments.

1. How does influenza virus, with an 8-piece negative sense RNA genome, replicate?

The influenza virus genome segments have common terminal sequences, and the 5' and 3' ends are partially complementary, allowing for hydrogen bonding in the virion and perhaps during replication. The mRNAs synthesized from the virion (negative sense) RNAs are modified to contain a cellular-like 5' cap.

An overview of the influenza replication cycle is shown in the Figure below. The figure as drawn does not present all the details on where and how certain things happen. Viral nucleic acid synthesis occurs in the nucleus, as does at least part of new virion core assembly (viral RNA segments and lots of protein NP). These cores then leave the nucleus and get transported somehow to the cell surface, to patches consisting of a layer of matrix protein M1 underneath a region of plasma membrane containing HA, NA, and M2. The cores bud through these patches, producing enveloped virions in the extracellular space.

Figure: Overview of Replication Cycle of Influenza Virus


The diagram above is very general, and needs significant editing to specify the locations of various events (nucleus or cytoplasm) and the roles of the various proteins. We will do this in class, and you should construct an accurate and comprehensive diagram of the influenza virus replication cycle.


2. What is an update on the assembly of the influenza core in the nucleus?

In the very last issue of 2006, Nature has a research article by Ye et al .titled "The mechanism by which influenza A virus nucleoprotein forms oligomers and binds RNA."

3. What is an early 2010 update on the replication of pandemic H1N1 influenza and seasonal influenza strains?

Here is a January 2010 article by Steel et al. in the Journal of Virology titled "Transmission of Pandemic H1N1 Influenza Virus and Impact of Prior Exposure to Seasonal Strains or Interferon Treatment".