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US-20260124291-A1 - RHINOVIRUS MRNA VACCINE

US20260124291A1US 20260124291 A1US20260124291 A1US 20260124291A1US-20260124291-A1

Abstract

The present invention provides a method for identifying the amino acid sequence of a naturally occurring polyprotein from a group A or C rhinovirus that can be used as an immunogen capable of eliciting an immune response against rhinoviruses from multiple serotypes within the same group. The invention also provides immunogenic compositions that comprise at least one mRNA comprising a non-naturally occurring optimized nucleic acid encoding a polyprotein identified by this method.

Inventors

  • Catherine BERRY
  • Cyril CHAVAGNAC
  • Nicholas Clark
  • Yves Girerd-Chambaz
  • Valerie Lecouturier
  • Nathalie Mantel
  • Vincent PAVOT
  • Khang Anh TRAN

Assignees

  • SANOFI PASTEUR

Dates

Publication Date
20260507
Application Date
20250618
Priority Date
20221220

Claims (20)

  1. 1 . A method of identifying a rhinovirus polyprotein for use as an immunogen that is capable of eliciting an immune response against rhinoviruses from multiple serotypes within a group, said method comprising: (a) retrieving a plurality of amino acid sequences from a database comprising amino acid sequences from naturally occurring rhinovirus isolates; (b) removing from the plurality of amino acid sequences retrieved in step (a) amino acid sequences shorter than 800 amino acids; (c) assigning the amino acid sequences remaining after step (b) into different phylogenetic clusters; (d) aligning the amino acid sequences to determine a consensus amino acid sequence for a complete rhinovirus polyprotein for one or more phylogenetic clusters identified in step (c); (e) aligning the consensus amino acid sequence obtained in step (d) with complete polyproteins of naturally occurring rhinovirus isolates; and (f) selecting a rhinovirus polyprotein as an immunogen that has an average identity of at least 80% to the corresponding amino acid sequences of rhinoviruses from at least two phylogenetic clusters identified in step (c).
  2. 2 . The method of claim 1 , wherein: (i) the rhinovirus polyprotein selected in step (f) is a VP0 polyprotein or a P2 polyprotein; and/or (ii) the group is rhinovirus group A or rhinovirus group C; and/or (iii) the one or more phylogenetic clusters each comprises at least 5 different serotypes or at least 10, 15, 20, or 25 different serotypes.
  3. 3 - 8 . (canceled)
  4. 9 . The method of claim 1 , wherein (i) determining the consensus sequence in step (d) comprises: (i) selecting the most frequent amino acid at each position; and/or (ii) creating a gap when the sum of amino acids for a given position is lower than 50% of the number of retrieved sequences, or selecting the most frequent amino acid when the sum of amino acids for a given position is equal to or greater than 50% of the number of retrieved sequences.
  5. 10 - 11 . (canceled)
  6. 12 . The method of claim 1 , further comprising a step of generating an optimized nucleic acid sequence encoding the rhinovirus polyprotein selected in step (f).
  7. 13 . An immunogenic composition comprising at least one messenger RNA (mRNA) comprising a first non-naturally occurring optimized nucleic acid sequence encoding a first polyprotein from a group A or C rhinovirus, wherein said first polyprotein has an amino acid sequence that: (a) has an average identity of at least 80% to the amino acid sequences of corresponding polyproteins from at least two, at least three, or at least four phylogenetic clusters of rhinoviruses of the same group; and (b) is naturally occurring aside from an optional single amino acid substitution.
  8. 14 . (canceled)
  9. 15 . The immunogenic composition of claim 13 , wherein the first polyprotein is: (i) a VP0 polyprotein comprising proteins VP2 and VP4; or (ii) a P2 polyprotein comprising proteins 2A, 2B, and 2C.
  10. 16 - 25 . (canceled)
  11. 26 . The immunogenic composition of claim 15 , wherein the first polyprotein is a P2 polyprotein and the single amino acid substitution is in the 2A protein and reduces or abolishes the proteolytic activity of the P2 polyprotein, optionally wherein the single amino acid substitution is C>A substitution or C>S in the catalytic triad of the active site of the 2A protein.
  12. 27 . (canceled)
  13. 28 . The immunogenic composition of claim 15 , wherein: (i) the VP0 polyprotein is from a group C rhinovirus or a group A rhinovirus; or (ii) the P2 polyprotein is from a group A rhinovirus or a group C rhinovirus.
  14. 29 . The immunogenic composition of claim 28 , wherein: (i) the VP0 polyprotein from the group C rhinovirus is of serotype 11, 17, or 34; or (ii) the VP0 polyprotein from the group A rhinovirus is of serotype 21 or 90; or (iii) the P2 polyprotein from the group A rhinovirus is of serotype 21 or 57; or (iv) the P2 polyprotein from the group C rhinovirus is of serotype 11 or 17.
  15. 30 - 39 . (canceled)
  16. 40 . The immunogenic composition of claim 13 , further comprising (ii) a second non-naturally occurring optimized nucleic acid sequence encoding a second polyprotein from a group A or C rhinovirus, wherein said second polyprotein is different from the first polyprotein and the second polyprotein has an amino acid sequence that: (a) has an average identity of at least 80% to the amino acid sequences of corresponding polyproteins from at least two, at least three, or at least four phylogenetic clusters of rhinoviruses of the same group; and (b) is naturally occurring aside from an optional single amino acid substitution.
  17. 41 . (canceled)
  18. 42 . The immunogenic composition of claim 40 , wherein the first polyprotein is a VP0 polyprotein comprising proteins VP2 and VP4, optionally wherein VP0 polyprotein is from a group A rhinovirus, optionally wherein the group A rhinovirus is of serotype 21 or 90.
  19. 43 - 46 . (canceled)
  20. 47 . The immunogenic composition of claim 40 , wherein: (i) the second polyprotein is a P2 polyprotein comprising proteins 2A, 2B and 2C, optionally wherein the single amino acid substitution is in the 2A protein and reduces or abolishes the proteolytic activity of the P2 polyprotein, optionally wherein the single amino acid substitution is C>A substitution or C>S in the catalytic triad of the active site of the 2A protein; and/or (ii) the P2 polyprotein is from a group A rhinovirus, optionally wherein the group A rhinovirus is of serotype 21 or 57; or wherein the second polyprotein is a VP0 polyprotein from a group C rhinovirus, optionally wherein the group C rhinovirus is of serotype 11, 17, or 34.

Description

RELATED APPLICATIONS This application is a continuation of International Application PCT/EP2023/087041 filed 20 Dec. 2025, which claims priority from European patent application no. 22315341.2, filed Dec. 20, 2022, and European patent application no. 23306405.4, filed Aug. 22, 2023; the contents of which are herein incorporated by reference in their entirety. SEQUENCE LISTING The present specification makes reference to a Sequence Listing submitted electronically as a .xml file named “pat22129_sequence_listing” on 20 Dec. 2023. The .xml file was generated on 18 Dec. 2023 and is 147,456 bytes in size. The entire contents of the sequence listing are herein incorporated by reference. FIELD OF THE INVENTION The present invention relates to a messenger RNA (mRNA)-based rhinovirus vaccine. The vaccine is specifically designed to elicit an immune response that is effective against multiple rhinovirus serotypes of the same group, in particular rhinovirus group A or group C. The selected immunogens encoded by the mRNA are naturally occurring rhinovirus polyproteins that comprise highly conserved and likely T-cell epitope-rich regions. BACKGROUND OF THE INVENTION Rhinoviruses are small, non-enveloped, positive-stranded RNA viruses that belong to the Picornaviridae family. They are characterized into three groups, A, B, and C, for which 81, 33, and 56 serotypes, respectively, have been described to date. The large number of serotypes accounts for the huge genetic and antigenic variability observed among rhinoviruses. The rhinovirus genome encodes for a single polyprotein comprising both structural and non-structural proteins. The polyprotein is cleaved in a protease-dependent manner to produce the precursor proteins P1, P2, and P3. These are in turn further cleaved into four structural (capsid) proteins, VP1, VP2, VP3, and VP4, and seven non-structural proteins, 2A, 2B, 2C, 3A, 3B, 3C, and 3D, respectively. VP2 and VP4 result from the cleavage of intermediate polyprotein, VP0. FIG. 1 provides a schematic illustration of the domain structure of the rhinovirus mRNA. Human rhinoviruses (HRV) are the principal cause of the common cold, accounting for two thirds of cases annually. Transmission occurs through direct contact with respiratory secretions and is associated with upper and lower respiratory tract infections. There is currently no approved antiviral therapy for the prevention or treatment of rhinovirus infection. Human challenge studies have indicated that pre-challenge antibodies reduce viral load and disease expression (Barclay et al., Epidemiol Infect. 1989 December; 103(3): 659-669; Alper et al., Clin Infect Dis. 1998 July; 27(1): 119-128; Touabi et al., Viruses. 2021 February; 13(3): 360). Symptom severity has also been reported to inversely correlate with T helper type 1 (TH1) and interferon-gamma (IFNγ) responses to experimental rhinovirus infection (Parry et al., J Allergy Clin Immunol. 2000 April; 105(4): 692-698; Gem et al., Am J Respir Crit Care Med. 2000 December; 162(6): 2226-2231; Message et al., Proc Natl Acad Sci USA. 2008 September; 105(36): 13562-13567). In healthy individuals, an effective TH1 response is induced, which may minimize viral infection, thereby typically avoiding severe illness. In contrast, individuals that suffer from respiratory conditions, such as chronic obstructive pulmonary disease (COPD) and asthma, may experience viral-related exacerbations as a consequence of HRV infection due to an increased likelihood of initiating a T helper type 2 (TH2) response. The induction of a TH2 response, combined with a delayed IFN response, may contribute to asthma exacerbation through mucus hypersecretions and allergic inflammation. The absence of cross-protection from natural infection represents a clinical challenge highlighting the need for a suitable vaccine strategy. Although rhinovirus infections are typically mild in healthy individuals, repeat infections causing severe symptoms of the common cold can place a considerable economic burden on society in terms of lost working days. Various approaches to rhinovirus vaccine development exist. One approach is the induction of broadly neutralizing antibodies (Katpally et al., J Virol. 2009 July; 83(14): 7040-7048). Clinical data supports the notion that T-cells can protect against development of symptomatic respiratory disease when antibody-mediated protection against rhinovirus infection is circumvented, e.g., because a patient's immune system has not previously been exposed to a particular serotype (Parry et al., J Allergy Clin Immunol. 2000 April; 105(4): 692-698; Gem et al., Am J Respir Crit Care Med. 2000 December; 162(6): 2226-2231; Message et al., Proc Natl Acad Sci USA. 2008 September; 105(36): 13562-13567). Prior research indicates that the structural protein VP4 comprises conserved T-cell epitopes across rhinovirus A and C subtypes, and it has been proposed to target these conserved T-cell epitopes through a peptide-based approach (