US 12,454,555 B2
Engineered influenza antigenic polypeptides and immunogenic compositions thereof
Tod Strugnell, Cambridge, MA (US); and Eliud Oloo, Cambridge, MA (US)
Assigned to SANOFI PASTEUR INC., Swiftwater, PA (US)
Filed by Sanofi Pasteur Inc., Swiftwater, PA (US)
Filed on Oct. 21, 2020, as Appl. No. 17/075,985.
Application 17/075,985 is a division of application No. 16/306,346, granted, now 10,844,097, previously published as PCT/US2017/035747, filed on Jun. 2, 2017.
Claims priority of provisional application 62/344,862, filed on Jun. 2, 2016.
Prior Publication US 2021/0147488 A1, May 20, 2021
Int. Cl. C07K 14/11 (2006.01); A61K 39/145 (2006.01); A61P 31/16 (2006.01); C07K 14/005 (2006.01); G16B 15/20 (2019.01); G16B 15/30 (2019.01)
CPC C07K 14/11 (2013.01) [A61P 31/16 (2018.01); C07K 14/005 (2013.01); G16B 15/20 (2019.02); G16B 15/30 (2019.02); A61K 39/145 (2013.01); C12N 2760/16022 (2013.01); C12N 2760/16034 (2013.01); C12N 2760/16062 (2013.01)] 19 Claims
 
1. A method of producing an engineered mosaic influenza B hemagglutinin (HA) polypeptide, comprising:
a) aligning influenza B HA amino acid sequences from multiple circulating strains of influenza B virus to generate an alignment;
b) identifying the positions of amino acids corresponding to known B cell epitopes and antigenic regions;
c) compiling amino acid residues across the alignment at the identified positions for each B cell epitope and antigenic region, thereby generating an antigenic repertoire for each B cell epitope and antigenic region;
d) defining a set of amino acid sequence patterns within the antigenic repertoire for each B cell epitope and antigenic region, wherein each amino acid sequence pattern in the set is represented only once;
e) i) selecting a sequence from the set of amino acid sequence patterns for each B cell epitope or antigenic region, thereby resulting in a combination of selected sequences, each selected sequence corresponding to a different B cell epitope or antigenic region, or ii) generating a consensus sequence from each set for each B cell epitope or antigenic region, thereby resulting in a combination of consensus sequences, each consensus sequence corresponding to a different B cell epitope or antigenic region;
f) inserting the combination of selected sequences or the combination of consensus sequences into corresponding locations in a structural backbone of influenza B HA, thereby generating a mosaic influenza B HA polypeptide sequence;
g) repeating steps e) and f) to generate a population of mosaic influenza B HA polypeptide sequences, wherein each mosaic influenza B HA polypeptide sequence in the population is different from one another;
h) calculating folding energy of each mosaic influenza B HA polypeptide sequence in the population and selecting one with a negative total energy score as the engineered mosaic influenza B HA polypeptide, wherein the engineered mosaic influenza B HA polypeptide is distinct from naturally circulating strains; and
i) expressing the engineered mosaic influenza B HA polypeptide in a host cell transformed with an expression vector comprising a nucleic acid molecule encoding the engineered mosaic influenza B HA polypeptide.