Structure and Function Analysis of an Antibody Recognizing All Influenza A Subtypes

Kallewaard, Nicole L.; Corti, Davide; Collins, Patrick J.; Neu, Ursula; McAuliffe, Josephine M.; Benjamin, Ebony; Wachter-Rosati, Leslie; Palmer-Hill, Frances J.; Yuan, Andy Q.; Walker, Philip A.; Vorlaender, Matthias K.; Bianchi, Siro; Guarino, Barbara; De Marco, Anna; Vanzetta, Fabrizia; Agatic, Gloria; Foglierini, Mathilde; Pinna, Debora; Fernandez-Rodriguez, Blanca; Fruehwirth, Alexander; Silacci, Chiara; Ogrodowicz, Roksana W.; Martin, Stephen R.; Sallusto, Federica; Suzich, JoAnn A.; Lanzavecchia, Antonio; Zhu, Qing; Gamblin, Steven J.; Skehel, John J.

Hemagglutinin (HA) full-length gene sequences for all subtypes (H1 to H18) were obtained from NCBI Influenza Virus Resource (IVR) database (Bao et al., 2008) and the Global Initiative on Sharing Avian Influenza Database (GISAID) EpiFlu™ database as of July 20, 2015. For each HA subtype, after purging sequences that were identical or contained ambiguous nucleotide identities, the protein coding sequences were pairwise aligned with their respective HA subtype reference protein sequence. Sequences with different length than the reference were removed. In total, 12'472 H1, 404 H2, 12'263 H3, 1'005 H4, 694 H5, 1'152 H6, 119 H7, 119 H8, 1'838 H9, 590 H10, 487 H11, 153 H12, 67 H13, 16 H14 , 10 H15, 7 H16, 2 H17 and 1 H18 isolates were analyzed respectively. The resulting protein datasets from IVR and GISAID were merged for each HA subtype and only the sequences not in IVR were added from GISAID. Finally, the occurrence of different amino acid identities was analyzed at HA residues 8 (HA1), 15, 16, 18, 19, 20, 21, 38, 42, 45, 48, 49 and 52 (HA2) . The HA subtype reference protein sequences for HA subtypes 1 to 16 were aligned with Clustal Ω (Sievers et al., 2011 ) and a phylogenic tree was derived by neighbor-joining method (bootstrapped 1,000 times) using MEGA 7 software (Kumar et al., 2016) (Figure 2A ).