Abstract
ABSTRACTRhinoviruses (RVs) cause recurrent infections of the nasal and pulmonary tracts, life-threatening conditions in chronic respiratory illness patients, predisposition of children to asthmatic exacerbation, and large economic cost. RVs are difficult to treat. They rapidly evolve resistance and are genetically diverse. Here, we provide insight into RV drug resistance mechanisms against chemical compounds neutralizing low pH in endolysosomes. Serial passaging of RV-A16 in the presence of the vacuolar proton ATPase inhibitor bafilomycin A1 (BafA1) or the endolysosomotropic agent ammonium chloride (NH4Cl) promoted the emergence of resistant virus populations. We found two reproducible point mutations in viral proteins 1 and 3 (VP1 and VP3), A2526G (serine 66 to asparagine [S66N]), and G2274U (cysteine 220 to phenylalanine [C220F]), respectively. Both mutations conferred cross-resistance to BafA1, NH4Cl, and the protonophore niclosamide, as identified by massive parallel sequencing and reverse genetics, but not the double mutation, which we could not rescue. Both VP1-S66 and VP3-C220 locate at the interprotomeric face, and their mutations increase the sensitivity of virions to low pH, elevated temperature, and soluble intercellular adhesion molecule 1 receptor. These results indicate that the ability of RV to uncoat at low endosomal pH confers virion resistance to extracellular stress. The data endorse endosomal acidification inhibitors as a viable strategy against RVs, especially if inhibitors are directly applied to the airways.IMPORTANCE Rhinoviruses (RVs) are the predominant agents causing the common cold. Anti-RV drugs and vaccines are not available, largely due to rapid evolutionary adaptation of RVs giving rise to resistant mutants and an immense diversity of antigens in more than 160 different RV types. In this study, we obtained insight into the cell biology of RVs by harnessing the ability of RVs to evolve resistance against host-targeting small chemical compounds neutralizing endosomal pH, an important cue for uncoating of normal RVs. We show that RVs grown in cells treated with inhibitors of endolysosomal acidification evolved capsid mutations yielding reduced virion stability against elevated temperature, low pH, and incubation with recombinant soluble receptor fragments. This fitness cost makes it unlikely that RV mutants adapted to neutral pH become prevalent in nature. The data support the concept of host-directed drug development against respiratory viruses in general, notably at low risk of gain-of-function mutations.
Highlights
Rhinoviruses (RVs) cause a majority of the common cold incidences worldwide [1]
low-density lipoprotein receptor (LDLR) binds to minor group RVs on the ring-shaped mesa around the fivefold axis, whereas intercellular adhesion molecule 1 (ICAM-1) penetrates into the canyon reaching into the hydrophobic pocket at the floor of the canyon, where a lipophilic pocket factor is located [8, 9]
RV-A16 was passaged on HeLa-Ohio cells in presence of permissive concentrations of either bafilomycin A1 (BafA1) or NH4Cl, where the inhibitor concentrations were increased every 2-3 passages (Fig. 1A)
Summary
Rhinoviruses (RVs) cause a majority of the common cold incidences worldwide [1]. In the United States alone, lost workdays were estimated to be dozens of millions per year, with almost $3 billion USD of over-the-counter remedy cost, and an annual economic burden of 40 billion USD [2, 3]. Upon ICAM-1 binding or incubation of virus with desaturated albumin the pocket factor is released, and gives rise to a metastable virion conformation, the activated (A) particle. This transition can be blocked by stabilizing compounds binding to the capsid pocket, for example the WIN-compound pleconaril, a broad A- and B-type RV inhibitor [10,11,12,13]. Binding of capsid-stabilizing agents increases the energy barrier, and stiffens the capsid [19, 23] This coincides with decreased particle breathing and reduced externalization of VP4 and VP1 N-termini [24]. Repeated passage of low pH-exposed RV-B14 gives rise to point mutations in VP1 that render the virus low pH-resistant, showing that native virus particles can evolve to increase stability [25]
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