Brain tropism acquisition: The spatial dynamics and evolution of a measles virus collective infectious unit that drove lethal subacute sclerosing panencephalitis.

It is increasingly appreciated that pathogens can spread as infectious units constituted by multiple, genetically diverse genomes, also called collective infectious units or genome collectives. However, genetic characterization of the spatial dynamics of collective infectious units in animal hosts is demanding, and it is rarely feasible in humans. Measles virus (MeV), whose spread in lymphatic tissues and airway epithelia relies on collective infectious units, can, in rare cases, cause subacute sclerosing panencephalitis (SSPE), a lethal human brain disease. In different SSPE cases, MeV acquisition of brain tropism has been attributed to mutations affecting either the fusion or the matrix protein, or both, but the overarching mechanism driving brain adaptation is not understood. Here we analyzed MeV RNA from several spatially distinct brain regions of an individual who succumbed to SSPE. Surprisingly, we identified two major MeV genome subpopulations present at variable frequencies in all 15 brain specimens examined. Both genome types accumulated mutations like those shown to favor receptor-independent cell-cell spread in other SSPE cases. Most infected cells carried both genome types, suggesting the possibility of genetic complementation. We cannot definitively chart the history of the spread of this virus in the brain, but several observations suggest that mutant genomes generated in the frontal cortex moved outwards as a collective and diversified. During diversification, mutations affecting the cytoplasmic tails of both viral envelope proteins emerged and fluctuated in frequency across genetic backgrounds, suggesting convergent and potentially frequency-dependent evolution for modulation of fusogenicity. We propose that a collective infectious unit drove MeV pathogenesis in this brain. Re-examination of published data suggests that similar processes may have occurred in other SSPE cases. Our studies provide a primer for analyses of the evolution of collective infectious units of other pathogens that cause lethal disease in humans. Author summary: Autopsy material from the brain of a patient who succumbed to subacute sclerosing panencephalitis (SSPE), a lethal brain infection caused by measles virus (MeV) persistence, provided a unique opportunity to characterize the spatial dynamics of a collective infectious unit in a human host. We discovered that brain colonization was driven by multiple distinct genome lineages that co-replicated even at the level of single cells. Brain adaptation yielded a genetically diverse and widely dispersed viral genome population at patient death. We identified mutations affecting the matrix and fusion proteins similar or identical to those previously shown to drive brain spread in other SSPE cases. Mutations affecting the cytoplasmic tails of both envelope proteins–fusion and hemagglutinin–appeared to be constrained to intermediate prevalence by frequency-dependent selection, which may permit the virus to achieve optimal fusogenicity for brain spread. These observations are best interpreted by postulating the spread of an evolving collective infectious unit constituted by multiple genetically diverse genomes. Our results raise profound questions about the importance of collective infectious units in human disease. [ABSTRACT FROM AUTHOR]