In the past decade, a number of broadly neutralizing human immunodeficiency virus (HIV) antibodies have been identified; however, tools for assessing antibody cross-reactivity are still relatively low throughput. Ultradense linear peptide arrays enable the determination of antibody reactivity to as many as six million peptides in a single assay. Identification of antibodies capable of binding a wide variety of HIV strains has potential to help guide the development of vaccines and therapeutics. Here we prototyped the use of an ultradense peptide microarray to assess antibody cross-reactivity from cynomolgus macaques infected with SIVmac239 against a panel of simian immunodeficiency virus (SIV) species used to infect macaques.
Proteins represented on the array included the complete Env proteins of 21 strains of SIV and the complete proteome of SIVmac239, tiled in peptides 16 amino acids in length which overlapped by 12 amino acids. We assessed serum and plasma samples taken prior to infection and 125 days to 1 year after infection with SIVmac239 and compared pre-infection and post-infection antibody binding to proteins represented on the array. Fluorescence intensity from the application of a secondary antibody indicated regions in which primary antibodies had bound peptides representing the SIV proteins.
No or minimal binding against SIV viral peptides was observed prior to infection. Following infection, evidence of antibody binding was consistently observed in peptides representing the Gag, Pol, and Env proteins of SIVmac239, with the highest levels of binding in Env. Antibody binding against other SIVmac239 proteins was also observed, though these results were less consistent between animals. We observed variable levels of antibody binding to peptides from other SIV strains, though all animals assessed showed some degree of cross-reactive binding to some number of SIV strains other than the infecting strain.
Serum profiling of antibody binding throughout the proteome of SIVmac239 and throughout the the Env proteins of multiple strains of SIV reveals cross-reactive antibody binding and highlights the potential of ultradense peptide arrays for high-throughput assessment of antibody binding specificity to diverse viruses.