Stronger together: Multi-genome transmission of measles virus

Abstract

Measles virus (MeV) is an immunosuppressive, extremely contagious RNA virus that remains a leading cause of death among children. MeV is dual-tropic: it replicates first in lymphatic tissue, causing immunosuppression, and then in epithelial cells of the upper airways, accounting for extremely efficient contagion. Efficient contagion is counter-intuitive because the enveloped MeV particles are large and relatively unstable. However, MeV particles can contain multiple genomes, which can code for proteins with different functional characteristics. These proteins can cooperate to promote virus spread in tissue culture, prompting the question of whether multi-genome MeV transmission may promote efficient MeV spread also in vivo. Consistent with this hypothesis, in well-differentiated primary human airway epithelia large genome populations spread rapidly through intercellular pores. In another line of research, it was shown that distinct lymphocytic-adapted and epithelial-adapted genome populations exist; cyclical adaptation studies indicate that suboptimal variants in one environment may constitute a low frequency reservoir for adaptation to the other environment. Altogether, these observations suggest that, in humans, MeV spread relies on en bloc genome transmission, and that genomic diversity is instrumental for rapid MeV dissemination within hosts.

Keywords: Cyclical adaptation; Epithelial spread; Measles virus; Quasispecies; Tissue adaptation; Virus transmission.

Figure 1.. Diagram of a MeV particle (top) and of the viral RNA genome (bottom).

The particle is drawn with its six main components: the nucleocapsid (N) that covers the genomic RNA and interacts with the phosphoprotein (P), and polymerase (large, L), forming the ribonucleocapsid complex; the fusion (F) and hemagglutinin (H) proteins forming the membrane fusion apparatus; and the matrix (M) protein controlling particle assembly as well as transcription and membrane fusion. Particles contain multiple encapsidated genomes, of which three are drawn schematically. On the genome (shown here as positive strand, bottom), the coding regions of the proteins are color-coded, non-coding regions are black. The P gene codes also for the V and C proteins (see Fig. 3 for details).

Figure 2.. The MeV infectious cycle (Muehlebach et al., 2011).

The lymphatic phase of infection is shown in (a and b); the epithelial phase is shown in (c and inset). Infectious viral particles are shown as red spheres; viral glycoproteins as small spikes on extracellular viruses and infected immune cells (inset). Infected cells and organs are red at the peak of infection, or pink after the peak. a, MeV enters the airways and infects macrophages and dendritic cells, which ferry the infection to the regional lymph nodes. b, MeV infects the local lymph nodes and the infection spreads rapidly to the primary lymphatic organs (red). c, infection spreads to epithelia. Inset: MeV enters the airway epithelium carried from an infected immune cell that expresses the viral glycoproteins on its plasma membrane. The viral hemagglutinin binds to nectin-4 (orange) in the adherens junction (AJ, blue rectangle), which is located basolateral to the tight junction (TJ, green rectangle). Infection spreads laterally via AJ (red arrows). Epithelial cells express viral glycoproteins in their membranes (not shown).

Figure 3.. Cyclical quasispecies re-equilibration.

(A) Strategy for adaptation of MeV to two cell types. The original inoculum (p1) was passaged 14 times on lymphoid cells (L1 to L14) or epithelial cells (E1 to E14). L7 was also passaged on epithelial cells seven times to generate S14. (B) P gene variants selected by adaptation to lymphoid cells. (Top) The MeV genome. Coding regions are shown as white boxes, non-coding regions are in black. Four nearby P gene variant positions are shown by colored arrows. (Center) Schematic of P gene coding regions. The P protein is translated from the first AUG start codon. The C protein is translated from the second AUG, on a different reading frame. V is generated from transcripts with an additional G inserted after the AAAAAGGG sequence AUG start codon (see bottom). V shares the first 231 amino acids with P (V_N), but has a different C-terminal domain (V_C). (Bottom) Sequence and position of the lymphoid variants. Variants are indicated by colored arrowheads, and their positions relative to the G insertion site (circled) are shown above the arrowheads. Amino acid sequences are shown below the nucleotide sequences. (C) Analysis of editing site-proximal variants across passage history. The y-axis shows the percentage reads with the indicated alleles. Alleles are colored as in panel B: wild type (WT, grey), −10 (yellow), −9 (blue), −7 (orange), +1(G) (dark green), and +1(A) (light green). The passage numbers analyzed are indicated on the horizontal axis, and the passage history is drawn schematically on the bottom.