Certain pathways showed remarkably low diversity in all subtypes indicating a tight transcriptional coordination of genes involved in biological processes that are vital for all cells (e.g. ribosome metabolism, protein export, glyoxylate/dicarboxylate metabolism; Figure 3A, B).
Two sources of divergence between training and validation samples exist: clinical differences such as diversity in cancer subtype, drug response, or prognosis, and genomic differences, or differences between gene expression patterns observed in the training and validation samples.
Although the isolates from Haiti show diversity in their PFGE subtyping patterns, the constancy of the main pattern coupled with virulence genotyping results indicate a high clonality of the outbreak strains, which is consistent with a point-source introduction.
The diversity of subtypes in G2 was confirmed by phylogenetic analysis by Neighbor Joining method (data not shown) and Maximum Likelihood inference (Figure 2).
Sequences belonging to subtypes B, C, and 01_AE were individually aligned to HxB2 (using pairwise alignment functions from SeqAn (Döring et al., 2008)) to construct a summary of diversity within subtypes in HxB2 coordinates.
However, at 4 loci (C6 830′, C6 1000′, gp60, C6 1420) around gp60, an absence of genetic diversity was observed in subtype IbA10G2 compared with non-IbA10G2 subtypes.
Recent analysis of avian influenza virus subtype diversity and richness suggests that 75% of HA and NA subtype diversity in wild birds could be captured through targeted surveillance efforts in the Northern Hemisphere over a 4-year period (24 ).
The difference in transcriptional diversity between subtypes appears to concern the entire transcriptome with the exception of a few biological processes that are critical for cell survival, suggesting that basal-like and luminal A cancers differ in fundamental ways in how tightly gene co-expression is regulated within cells.
Those subtypes showing the high reassortment rates in our study, especially H1N1, H3N8 and H4N6 represent the most common subtype combinations that are found in wild ducks during periods of peak prevalence and have a maximum detectable subtype diversity in the late summer and fall [ 32, 50].
We measured HIV-1 subtype diversity in a multiethnic cohort of pregnant, HIV-infected women to determine whether nonclade B HIV-1 is emerging in Canada after population movement, and whether antenatal cohorts are suitable sentinel sites to monitor the introduction of nonclade B viruses into Canada.
