Fig 1.
Maximum likelihood (ML) tree of HIV-1 CRF01_AE gag gene sequences.
ML tree was used to infer the phylogenetic relationship among the 3105 HIV-1 CRF01_AE gag sequences submitted to the LANL HIV Sequence Database, representing the years 1990 to 2017. The tree was color-coded based on the years groups. The color key for the tree is given within the figure.
Fig 2.
Maximum likelihood (ML) tree of HIV-1 CRF01_AE gag gene sequences.
ML tree was used to infer the phylogenetic relationship among the 3105 HIV-1 CRF01_AE gag sequences submitted to the LANL HIV Sequence Database, representing the years 1990 to 2017. The tree was color-coded based on the countries. The color key for the tree is given within the figure.
Fig 3.
HIV-1 CRF01_AE gag gene effective population size and time to the most recent common ancestor.
Bayesian Skyline plot, based on a ‘relaxed clock’ coalescent framework analysis, was constructed using 286 sequences (representing all years and countries). The X-axis represents time in years, while Y-axis shows an effective population size. The thick black line represents the median, while the blue band represents 95% highest posterior density (HPD) intervals. The tMRCA of the HIV-1 subtype AE gag gene is indicated by a black dotted line and a black box. Grey, red, blue, green, yellow, and purple shaded areas represent the period of the plateau phase, increase in viral effective population size, plateau phase, decline, increase, and plateau, respectively.
Fig 4.
Time-dependent changes in HIV-1 CRF01_AE gag genomic variability.
The mean entropy score for each year group was calculated and plotted using GraphPad software. The Redline over bars represents a statistically significant difference between the groups (p<0.05). Error bars represent the standard error of the mean.
Fig 5.
Proteasomal degradation sites in HIV-1 CRF01_AE gag protein.
Proteasomal degradation sites gag protein sequences from 1990–1994 (blue), 1995–1999 (light green), 2000–2004 (grey), 2005–2009 (yellow), 2010–2014 (dark green), and 2015–2017 (red) year groups were predicted using NetChop software. Below the sequence, the numbers indicating the position of each amino acid with reference to the HXB2 reference strain are shown. Only proteasomal degradation sites with a cut-off value >0.5 are shown. The black box indicates the position at which the mutation occurred.
Table 1.
HIV-1 CRF01_AE gag CTL mutated and novel epitopes.
The epitopes are divided into three categories: Novel epitopes (epitopes unique to one year group), intermittently recurring epitopes and mutated epitopes. Mutation(s) in epitope are underlined, while ‘-‘ in the table represents the absence of epitope in a particular year group.
Fig 6.
Divergence and evolution of HIV-1 CRF01_AE gag CTL epitopes.
Bar chart summarizing epitope data for each year group. Black bars show the total number of gag epitopes observed for each year group, white bars represent epitope variability (total number of mutations in all epitope sequences in the year group/total number of epitopes in a year group), dark grey bars indicate intermittently recurring epitopes, and light grey bars indicate novel epitopes that were observed in one year group only.
Fig 7.
Divergence and evolution of HIV-1 CRF01_AE envelope CTL epitopes.
Bar chart summarizing epitope data for each year group. Black bars show the total number of envelope epitopes observed for each year group, white bars represent epitope variability (total number of mutations in all epitope sequences in the year group/total number of epitopes in a year group), dark grey bars indicate intermittently recurring epitopes, and light grey bars indicate novel epitopes that were observed in one year group only.