I would like to know if there is a published work studying the within-host mutation rate of a virus versus the between-hosts mutation rate, when a direct transmission event occurred between those hosts.
Perhaps, when the virus is transmitted, the selective pressures of adjusting to a new host promote fixation of different nucleotides in a sequence; which will not happen if the virus remains within the first host. So, for repeated sequence samples in different time points, the within-host genetic difference is lower (from time to time) than the between-hosts genetic difference?
It depends on the virus and the host. Hundreds of factors go into the mutation rate and the evolution rate (mutation rate plus selection pressures). Viral load, or number of replication cycles per day in the host would be one factor. If the virus has a very small population in one host it has less chance to evolve, than in a host where it can reach a huge population size quickly.
Also, in a new host, the new host does not have any sort of herd immunity to the virus, so it does not need to change to avoid that immunity. Many viruses are driven by host immune selection pressure to keep changing. But this is different for the dominant human influenza A virus that goes around the world each year, than it is for HIV-1 viruses which are still spreading into naive human individuals slowly over time.
Selection pressures for and against change are important, but there is no way to generalize to say the same thing happens for all viruses. Even within a single virus, some genes are important for immune escape, others for regulating viral load, others for transmissibility, etc...
It depends on the virus and the host. Hundreds of factors go into the mutation rate and the evolution rate (mutation rate plus selection pressures). Viral load, or number of replication cycles per day in the host would be one factor. If the virus has a very small population in one host it has less chance to evolve, than in a host where it can reach a huge population size quickly.
Also, in a new host, the new host does not have any sort of herd immunity to the virus, so it does not need to change to avoid that immunity. Many viruses are driven by host immune selection pressure to keep changing. But this is different for the dominant human influenza A virus that goes around the world each year, than it is for HIV-1 viruses which are still spreading into naive human individuals slowly over time.
Selection pressures for and against change are important, but there is no way to generalize to say the same thing happens for all viruses. Even within a single virus, some genes are important for immune escape, others for regulating viral load, others for transmissibility, etc...
R. Carrasco Hernandez Look at Tan Z, Gibbs AJ, Tomitaka Y, Sanchez F, Ponz F, Ohshima K. Mutations in Turnip mosaic virus genomes that have adapted to Raphanus sativus. Journal of General Virology. 2005 Feb 1;86(2):501-10.
Your question is not as simple as it seems as different viruses have different biology characteristics and life span in their host.
RNA viruses have generally a greater mutation rate than DNA viruses due to the poor fidelity of their RNA dependent RNA polymerase.
A second factor contributing to virus evolution between host is the level of antiviral immune response present in the host population and its genetic diversity.
A third parameter is the duration of the infection intra-host. Short term infection like influenza virus infection in immunocompetent host allows the virus to replicated for only a couple of weeks, limiting the time frame for the mutation to emerge and to be selected. In contrast, chronic infections, like HIV or HCV, will last for a longer time, allowing viruses to accumulated mutations and escape immune responses. As a consequence, these chronic viruses harbor signature of the immune pressure under which the viruses were able to maintain in the host.
You probably need to rephrase your question and consider limiting it to a virus or a family of virus.
There are so many factors causing mutations (from cosmic radiation through ... [thousands of different factors] to pollution of the environment) that mutations are carried out permanently to a significant extent regardless of the current environmental conditions. But on the other hand, the current environmental conditions (living organisms) in which virys function and grow, multiply their genetic code, they also affect the direction of mutation processes, i.e. what new strains of viruses will arise. My thesis is confirmed by the results of current observations, conducted research (early April 2020), which shows that the SARS-CoV-2 coronavirus causing Covid-19 disease with a high level of probability has already created different types of strains that in different regions, continents of the world can cause slightly different disease effects in humans.
Regards
Dariusz Prokopowicz
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