[Source: PLoS Pathogens, full page: (LINK). Abstract, edited.]
OPEN ACCESS / PEER-REVIEWED / RESEARCH ARTICLE
Cyclical adaptation of measles virus quasispecies to epithelial and lymphocytic cells: To V, or not to V
Ryan C. Donohue, Christian K. Pfaller, Roberto Cattaneo
Published: February 15, 2019 / DOI: https://doi.org/10.1371/journal.ppat.1007605 / This is an uncorrected proof.
Measles virus (MeV) is dual-tropic: it replicates first in lymphatic tissues and then in epithelial cells. This switch in tropism raises the question of whether, and how, intra-host evolution occurs. Towards addressing this question, we adapted MeV either to lymphocytic (Granta-519) or epithelial (H358) cells. We also passaged it consecutively in both human cell lines. Since passaged MeV had different replication kinetics, we sought to investigate the underlying genetic mechanisms of growth differences by performing deep-sequencing analyses. Lymphocytic adaptation reproducibly resulted in accumulation of variants mapping within an 11-nucleotide sequence located in the middle of the phosphoprotein (P) gene. This sequence mediates polymerase slippage and addition of a pseudo-templated guanosine to the P mRNA. This form of co-transcriptional RNA editing results in expression of an interferon antagonist, named V, in place of a polymerase co-factor, named P. We show that lymphocytic-adapted MeV indeed produce minimal amounts of edited transcripts and V protein. In contrast, parental and epithelial-adapted MeV produce similar levels of edited and non-edited transcripts, and of V and P proteins. Raji, another lymphocytic cell line, also positively selects V-deficient MeV genomes. On the other hand, in epithelial cells V-competent MeV genomes rapidly out-compete the V-deficient variants. To characterize the mechanisms of genome re-equilibration we rescued four recombinant MeV carrying individual editing site-proximal mutations. Three mutations interfered with RNA editing, resulting in almost exclusive P protein expression. The fourth preserved RNA editing and a standard P-to-V protein expression ratio. However, it altered a histidine involved in Zn2+ binding, inactivating V function. Thus, the lymphocytic environment favors replication of V-deficient MeV, while the epithelial environment has the opposite effect, resulting in rapid and thorough cyclical quasispecies re-equilibration. Analogous processes may occur in natural infections with other dual-tropic RNA viruses.
Key questions in infectious disease are how pathogens adapt to different cells of their hosts, and how the interplay between the virus and host factors controls the outcome of infection. Human measles virus (MeV) and related animal morbilliviruses provide important models of pathogenesis because they are dual-tropic: they replicate first in immune cells for spread through the body, and then in epithelial cells for transmission. We sought here to define the underlying molecular and evolutionary processes that allow MeV to spread rapidly in either lymphocytic or epithelial cells. We discovered unexpectedly rapid and thorough genome adaptation to these two tissues. Genome variants that cannot express functional V protein, an innate immunity control protein, are rapidly selected in lymphocytic cells. These variants express only the P protein, a polymerase co-factor, instead of expressing P and V at similar levels. Upon passaging in epithelial cells, V-competent MeV genome variants rapidly re-gain dominance. These results suggest that cyclical quasispecies re-equilibration may occur in acute MeV infections of humans, and that suboptimal variants in one environment constitute a low frequency reservoir for adaptation to the other, where they become dominant.
Citation: Donohue RC, Pfaller CK, Cattaneo R (2019) Cyclical adaptation of measles virus quasispecies to epithelial and lymphocytic cells: To V, or not to V. PLoS Pathog 15(2): e1007605. https://doi.org/10.1371/journal.ppat.1007605
Editor: Diane E. Griffin, Johns Hopkins Bloomberg School of Public Health, UNITED STATES
Received: November 26, 2018; Accepted: January 29, 2019; Published: February 15, 2019
Copyright: © 2019 Donohue et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: RNAseq data, selected analyses, and reference sequences were deposited in the GEO database under accession number GSE126126.
Funding: RC received the award, 5R21AI128037-02, from National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID) https://projectreporter.nih.gov/project_info_description.cfm?aid=9406235&icde=39429219. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Keywords: Morbillivirus; Measles; Viral pathogenesis.