Figure 1.
Phylogenetic trees of Indonesian H5N1 influenza viruses.
ML phylogenies reconstructed from (A) HA gene; (B) M1 gene; (C) M2 gene. Topological supports (>90) summarized from 1,000 ML bootstrap replications are shown. For major lineages, NJ bootstrap support (1,000 replications) and posterior probability from BMCMC analyses (5,000 tree samples) are also shown inside parentheses (ML/NJ/BMCMC). Putative human and cat reassortant viruses are in red. Reassortant subgroups (R1, R2, and R3) are further indicated with dashed lines in (A). Putative avian reassortant viruses are in blue. The pre-emergence lineage (refer to main text) is highlighted in gray in M1 phylogeny (B). Arrows indicate the roots. The distance unit is substitutions/site.
Figure 2.
Recombination analyses on concatenated influenza virus genomes.
(A) Schematic diagram of concatenated influenza virus genomes. (B) Similarity plot. (C) Bootscan analysis. (D) GARD analysis. (E) Individual phylogenies reconstructed from non-recombinant fragments identified by GARD. Consensus sequences representing viral groups, window size of 600 bp and step size of 10 bp, were used for the similarity plot and bootscan analysis. The distance bar for the trees in (D) is 0.004 substitutions/site. Taxa of putative reassortant viruses are in red.
Figure 3.
Estimation of tMRCA and relative genetic diversity for reassortant viruses and its genetic parent (group 2).
(A) and (B) show the plots of the genetic distance from MRCA to each reassortant taxa, and the linear regression line depicting the tMRCA for HA and NA genes, respectively. 95% confidence intervals are shown by dashed lines. Red dots and regression line indicate the removal of two sequences from the NA dataset. (C) and (D) show the tMRCAs estimated respectively from HA and NA genes using the BMCMC method. 95% higher probability density (HPD) is shown by the error bar. (E) and (F) show the Bayesian Skyline plots (BSP) illustrating the change of relative genetic diversity of reassortant viruses through time estimated from the HA and NA gene datasets, respectively. (G) and (H) show the BSP for group 2 viruses estimated from HA and NA gene datasets, respectively.
Figure 4.
Map of mainland Java in Indonesia.
Locations for the putative reassortant viruses focused in this study are indicated with green triangles. Numbers inside the triangles refer to the locations of the reassortant viruses described in Table 1. Locations of group 2 and 3 viruses are indicated with orange circles and squares, respectively. Red circles and squares denote the locations of putative avian reassortant viruses in 2007. Only those parental strains genetically close to the reassortant viruses are shown in the map. A zoom-in of Greater Jakarta (G. Jakarta) and surroundings is illustrated separately in a dashed-line bounded box in the centre of the figure.
Table 1.
Cases of human infections caused by Indonesian reassortant H5N1 HPAI viruses.