Article Figures & Data
Figures
- FIG 1
Rotavirus strains, genetic constellations, and phylogenetic networks of G1P[8] rotaviruses detected in Malawian children at QECH from 1997 to 2015. (a) Schematic representation of the proportions of all genotypes detected in rotavirus-positive stool samples. The size of the circle is directly proportional to the frequency of detection of G and P genotypes. There were no rotavirus surveillance activities in 2010; hence, samples were not collected at this time. (b) Bayesian maximum clade credibility tree for concatenated whole-rotavirus-genome sequences illustrating the genetic constellation and reassortment patterns for 32 pre- and 18 postvaccine G1P[8] strains from Malawi as well as the prototype Wa and DS-1 strains for comparison. Genotype and genogroup assignments for each segment were based on nucleotide sequence identities, assigned by using RotaC. Genome segments that were assigned the same genotype are shown with the same color and genotype numbers. (C) Phylogenetic network of complete concatenated whole-genome sequences of G1P[8] rotavirus strains detected in Malawi from 1998 to 2014. Branches are drawn to scale, and splits in the network indicate reassortments. Network clusters are color-coded and named in accordance with their phylogenic lineages (L1 to L3) that correlated with the time of strain isolation before or after rotavirus vaccine introduction. Clusters L1 (green) and L2 (blue) contain prevaccine G1P[8] strains, whereas L3 (red) contains postvaccine strains. Network subclusters within each main cluster are shaded in blue (L1), red (L2), or orange (L3).
- FIG 2
Bayesian maximum clade credibility (MCC) time tree based on complete nucleotide sequences illustrating lineage replacement within the genome segments encoding structural proteins of the G1P[8] strains that circulated in Malawi from 1998 to 2014. With the exception of VP4 and VP7 genes that had L2 and L3 genes sharing close ancestry, the rest had three distinct G1P[8] lineages. L1, L2, and L3 represent lineages 1, 2, and 3, respectively.
- FIG 3
Bayesian MCC time tree based on complete nucleotide sequences of the structural proteins for G1P[8] strains from Malawi. Only DS-1-like genome segments for typical DS-1-like strains that were assigned G2P[4], G2P[6], G8P[4], G8P[6], and G12P[6] outer capsid genotypes from Malawi were included to calculate evolutionary dynamics for VP1- to VP4-, VP6-, and VP7-encoding genome segments for the atypical DS-1-like G1P[8] strains (L3 cluster).
- FIG 4
Time to the most recent common ancestor (tMRCA), evolutionary rates for each genome segment of Malawian G1P[8] strains, and comparative population dynamics of G1P[8] rotavirus strains circulating in Malawi, 1998 to 2014. (a) Evolutionary rates and tMRCAs for each genome segment of the atypical Malawian G1P[8] strains shown together with their 95% highest posterior density (HPD) intervals. (b) Absolute values for the means and ranges of evolutionary rates and tMRCA at 95% HPD intervals. (c) Phylogenies and relative genetic diversities estimated by using the Gaussian Markov random field (GMRF) model represent Bayesian Skygrid plots for VP1- to VP4-, VP6-, and NSP1- to NSP5-encoding genome segments. Lines in the GMRF plot represent the mean relative genetic diversity through time.
- FIG 5
Amino acid substitutions and structural conformation of the outer capsid glycoprotein of Malawian G1P[8] strains. (a) Complete VP7 sequences of representative pre- and postvaccine G1P[8] strains aligned to that of RV1 exhibiting amino acid substitutions that occurred within the variable regions (VR) and mapped antigenic regions (AR) over time. Lineage-defining amino acid amino acid substitutions are highlighted in green, blue, and yellow for the L1, L2, and L3 lineages, respectively. Pre- and postvaccine strains are shown with vertical green and red bars on the right, respectively. Strains belonging to the L1, L2, and L3 phylogenetic clusters are shown with green, blue, and red bars, respectively, on the right. (b) Perfect alignment of superimposed VP7 structures exhibiting few differences between RV1 and L1 to L3 strains. Antigenic regions A, B, and C are shown in white. L1 to L3 and RV1 strains are shown in yellow, green, blue, and red, respectively. (c to e) Surface visualization of VP7 from outside the virion on the 3-fold axis displaying amino acid differences when structures for L1 (c), L2 (d), and L3 (e) G1P[8] strains were superimposed on the structure of the outer capsid glycoprotein of RV1. Numbers correspond to the positions where mutations occurred.
Tables
- TABLE 1
Evolutionary selective forces and recombination in all 11 proteins of the Malawian G1P[8] rotavirus strainsa
Protein dN/dS by SLAC ω (β/α) by FUBAR VP1 0.0502 2.22 VP2 0.0538 2.67 VP3 0.0965 2.47 VP4 0.1052 3.15 VP6 0.0310 4.66 VP7 0.2033 6.01 NSP1 0.2239 4.21 NSP2 0.0920 5.62 NSP3 0.0870 5.44 NSP4 0.1097 7.10 NSP5 0.1097 7.47 ↵a Shown are posterior distributions of synonymous (α) and nonsynonymous (β) substitution rates over sites as well as mean posterior probabilities for a ω (β/α) value of <1 at a site. The consensus selective force in all cases was purifying selection, and there was no recombination determined by GARD or SBP.
Supplemental material
- Supplemental file 1 -
Table S1 (Whole-genotype constellations of pre- and postvaccine Malawian G1P[8] strains and reference rotaviruses.)
XLS, 72K
- Supplemental file 2 -
Fig. S1 (G1P[8] rotavirus strains characterized from stool samples collected from Malawian infants at QECH from 1997 to 2015.)
Fig. S2 (Phylogenetic analysis of complete ORFs for individual 11 genome segments of Malawian G1P[8] strains compared to reference strains from elsewhere using the maximum-likelihood method.)
Fig. S3. Bayesian maximum clade credibility (MCC) time tree based on complete nucleotide sequences illustrating lineage replacement within the genome segments encoding nonstructural proteins of the G1P[8] strains that circulated in Malawi from 1998 to 2014.) Fig. S4 (Bayesian MCC time tree based on complete nucleotide sequences of nonstructural proteins for G1P[8] strains from Malawi.)
PDF, 3.9M
- Supplemental file 1 -
