Two-dimensional antigenic dendrogram and phylogenetic tree of avian influenza virus H5N1

Abstract

The hemagglutination-inhibition (HI) titers of a panel of twenty-five mouse monoclonal antibodies (MAbs) against forty-four isolates of highly pathogenic avian influenza virus H5N1 were determined. A two-dimensional antigenic dendrogram was constructed by hierarchical clustering of HI titers. Viruses with similar reactivity patterns were clustered horizontally, whereas MAbs were clustered vertically. In this 2-D dendrogram, with 40% similarity as a cut-off, four virus clusters and four MAbs clusters were identified. A phylogenetic tree based on the deduced amino acid sequence of the hemagglutinin (HA) gene of tested viruses was constructed and its topology was compared to the antigenic dendrogram. Interestingly, viruses with high genetic homology in the phylogenetic tree also had high similarity in their reactivity patterns, as indicated by their relatedness in the tree and close clustering in the dendrogram, respectively. However, the reverse and the converse were also true. Of the five pairs of viruses in the dendrogram with bootstrap values higher than 75, four pairs were in concordance with their genetic relatedness. However, one pair contained viruses belong to two distinct genetic clades. These results were discussed in the context of antigenic variation, genetic polymorphism, and the potential application of MAbs in antigenic analysis.

Cross-neutralizing antibodies elicited by the Cervarix® human papillomavirus vaccine display a range of Alpha-9 inter-type specificities

“…To examine the discrepancy between cross-reactive antibody profiles, both sets of serological data were subjected to hierarchical clustering. This approach has been used for the evaluation of HIV [27–30] , foot and mouth disease virus [31] and H5N1 avian Influenza virus [32] antibody specificities, but we believe this is the first time that this approach has been used to examine HPV vaccine antibody specificity. Differences between pseudovirus neutralizing and VLP binding antibody profiles were stark.…”

Expanded Cocirculation of Stable Subtypes, Emerging Lineages, and New Sporadic Reassortants of Porcine Influenza Viruses in Swine Populations in Northwest Germany

“…HI procedures followed the method described by Lange et al (18), including treatment with bacterial neuraminidases. HI results were analyzed by hierarchical agglomerative clustering using the HCE3.5 software package (26,27) to produce a gridded heat map of normalized titers and a 2-dimensional (2D) dendrogram representing antigenic relationships. Two-dimensional hierarchical clustering for rows and columns by the complete linkage method was based on a Euclidian distance matrix.…”

Enhanced ethanol production from sugarcane molasses by industrially engineered Saccharomyces cerevisiae via replacement of the PHO4 gene

“…Sequences of Pho4 protein were subjected to multiple alignment using CLUSTALW, and the phylogenetic tree was generated by NJ with a bootstrap set at 1000 replicates. 26 …”

“…Sequences of Pho4 protein were subjected to multiple alignment using CLUSTALW, and the phylogenetic tree was generated by NJ with a bootstrap set at 1000 replicates. 26 Sporulation and haploid protoplast formation. High-yield strain MF01, used as the control strain for gene recombination, was cultivated in YPD overnight at 30 C, shaking at Electroporation and regeneration of haploid protoplast, and recovery of diploid cells.…”