VP1 Sequencing of All Human Rhinovirus Serotypes:Insights into Genus Phylogeny and Susceptibility to AntiviralCapsid-BindingCompounds

Abstract

Rhinoviruses are the most common infectious agents of humans. They are the principal etiologic agents of afebrile viral upper-respiratory-tract infections (the common cold). Human rhinoviruses (HRVs) comprise a genus within the family Picornaviridae. There are >100 serotypically distinct members of this genus. In order to better understand their phylogenetic relationship, the nucleotide sequence for the major surface protein of the virus capsid, VP1, was determined for all known HRV serotypes and one untyped isolate (HRV-Hanks). Phylogenetic analysis of deduced amino acid sequence data support previous studies subdividing the genus into two species containing all but one HRV serotype (HRV-87). Seventy-five HRV serotypes and HRV-Hanks belong to species HRV-A, and twenty-five HRV serotypes belong to species HRV-B. Located within VP1 is a hydrophobic pocket into which small-molecule antiviral compounds such as pleconaril bind and inhibit functions associated with the virus capsid. Analyses of the amino acids that constitute this pocket indicate that the sequence correlates strongly with virus susceptibility to pleconaril inhibition. Further, amino acid changes observed in reduced susceptibility variant viruses recovered from patients enrolled in clinical trials with pleconaril were distinct from those that confer natural phenotypic resistance to the drug. These observations suggest that it is possible to differentiate rhinoviruses naturally resistant to capsid function inhibitors from those that emerge from susceptible virus populations as a result of antiviral drug selection pressure based on sequence analysis of the drug-binding pocket.Human rhinoviruses are the most common viral infectious agents in humans (9). In the United States, rhinoviruses account for more than one billion cases annually of viral respiratory tract infections (VRTI; i.e., the common cold) (34). The National Center for Health Statistics estimated that in 1996, 62 million cases of the common cold required medical attention or resulted in restricted activity in the United States (33). During this period, colds caused 45 million days of restricted activities and 22 million days lost from school. Roughly one in six colds results in a doctor's office visit, and up to 50% of these visits result in an antibiotic prescription (15,29,35,47). In 1998, more antibiotic prescriptions were written for presumed VRTIs than for bacterial infections, at a cost of approximately $726 million (14). Such inappropriate antibiotic prescribing is a major contributing factor to the development of drug-resistant bacterial pathogens (4,28,35,48). The total economic impact of non-influenza-related VRTI in terms of both direct (health care resource use) and indirect (productivity loss) costs approaches $40 billion annually (11).HRVs comprise a genus within the family Picornaviridae. Picornaviruses are small, nonenveloped viruses containing a single strand of message sense RNA. The RNA is protected by a protein coat or capsid composed of 60 copies of each of four structur...

Molecular mechanism of a specific capsid binder resistance caused by mutations outside the binding pocket

“…Substitutions of amino acids in the center of the pocket that confer high-level resistance have also been reported for rhinoviruses Heinz et al, 1989;Ledford et al, 2005;Ledford et al, 2004;Zhang et al, 2004) and echovirus 11 (Benschop et al, 2015). The activity of pleconaril derivatives lacking one or both of the methyl groups of the central phenyl ring of pleconaril (Schmidtke et al, 2009) is less affected by the substitution of I1092.…”

“…I1092 is situated in the center of the pocket and interacts with one of the two methyl groups of pleconaril's phenyl ring. Substitutions of amino acids in the center of the pocket that confer high-level resistance have also been reported for rhinoviruses Heinz et al, 1989;Ledford et al, 2005;Ledford et al, 2004;Zhang et al, 2004) Ledford et al, 2005;Ledford et al, 2004;Zhang et al, 2004) and echovirus 11 (Benschop et al, 2015) (Benschop et al, 2015). The activity of pleconaril derivatives lacking one or both of the methyl groups of the central phenyl ring of pleconaril (Schmidtke et al, 2009) (Schmidtke et al, 2009) is less affected by the substitution of I1092.…”

“…All high-level resistance (HR) ) to CIs reported to date involve residues forming the hydrophobic pocket of EVEVs Benschop et al, 2015;Groarke and Pevear, 1999;Ledford et al, 2005;Ledford et al, 2004;Schmidtke et al, 2005) Benschop et al, 2015;Groarke and Pevear, 1999;Ledford et al, 2005;Ledford et al, 2004;Schmidtke et al, 2005), hence directly interfering with the binding of CIs. Because of similarities in the binding mode of CIs, cross-resistance may be observed, as reported for pleconaril and vapendavir (Feil et al, 2012) (Feil et al, 2012).…”

“…All high-level resistance to CIs reported to date involve residues forming the hydrophobic pocket of EVs Benschop et al, 2015;Groarke and Pevear, 1999;Ledford et al, 2005;Ledford et al, 2004;Schmidtke et al, 2005), hence directly interfering with the binding of CIs. Because 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 of similarities in the binding mode of CIs, cross-resistance may be observed, as reported for pleconaril and vapendavir (Feil et al, 2012).…”

The Minor Receptor Group of Human Rhinovirus (HRV) Includes HRV23 and HRV25, but the Presence of a Lysine in the VP1 HI Loop Is Not Sufficient for Receptor Binding

“…As seen in Fig. 1, out of the 99 HRV serotypes (16), all minor group viruses but also HRV8, -18, -23, -24, -25, -40, -54, -56, -58, -85, -95, and -98 possess a lysine at the equivalent position. However, no obvious conservation of the other residues shown for HRV2 to be in contact with the receptor is apparent within the minor group.…”