A
Com5
B
B
C
L2
S7
Fig. S1 Plaque phenotypes of the parent CHIKV isolate (Com5), the large (L2) and small (S7) plaque variants, 4
days post infection in Vero cells. Plaque variants were isolated from Com5 using a standard plaque assay. Plaques of
different sizes were observed, selected using a glass capillary pipette and re-analysed by plaque assay to obtain the
two purified plaque isolates. The figure represents the parent strain (A), the large plaque variant (L2) measuring 1.5
± 0.3 mm (B) and the small plaque variant (S7) measuring 0.5 ± 0.3 mm (C). The two variants retained their sizes
after several passages confirming a stable phenotype.
Comoros/L2/KF283987/05
84
50
Comoros/S7/KF283986/05
Comoros/ComJ/HQ456252.1/05
Comoros/Com25/HQ456251.1/05
94
Kenya/KPA15/HQ456254.1/04
62 Comoros/Com125/HQ456253.1/05
100
Reunion/LR2006_OPY1/DQ443544.2/06
ECSA
Kenya/Lamu33/HQ456255.1/04
79
100
Sri-Lanka/SL-CK1/HM045801.1/07
99
India/DRDE-06/EF210157.2/06
69
India/DRDE-07/EU372006.1/07
Tanzania/Ross/HM045811.1/53
100
Tanzania/S27/AF369024.2/52
100 Tanzania/Ross/AF490259.3/53
India/IND-63-WB1/EF027140.1/63
100
Senegal/PM2951/HM045785.1/66
100
Asian
India/_IND-73-MH5/EF027141.1/73
Senegal/HD_180760/HM045817.1/05
West
African
0.02
Fig. S2a Neighbour joining phylogenetic tree of nucleotide sequences of L2 and S7 genome sequences. Sequences
of plaque variants obtained in this study indicated by () were compared with selected CHIKV strains from the
Genbank. Sequences of plaque variants and reference sequences were aligned using clustalW and the phylogenetic
tree constructed using MEGA v 6.0. Bootstrap values are indicated on branches. Scale bar indicates nucleotide
substitutions per site. The plaque variants clustered closely with CHIKV Comoros Island isolates and other Indian
Ocean isolates in the East, Central South African genotype (ECSA) cluster[1]. The isolates are named in this order:
country of origin/strain name/accession number/year of sample collection
.
42
84
Comoros/L2/KF283987/05
Comoros/S7/KF283986/05
50
Comoros/ComJ/HQ456252.1/05
Comoros/Com25/HQ456251.1/05
38
Kenya/KPA15/HQ456254.1/04
94
62
Comoros/Com125/HQ456253.1/05
100
Reunion/LR2006_OPY1/DQ443544.2/06
Kenya/Lamu33/HQ456255.1/04
Sri-Lanka/SL-CK1/HM045801.1/07
79
India/DRDE-06/EF210157.2/06
99
69
India/DRDE-07/EU372006.1/07
0.0002
Fig. S2b A magnified phylogenetic sub-tree of nucleotide sequences of whole genome of the isolates highlighted in
Fig Sa. Sequences of plaque variants under study indicated by () were compared with selected CHIKV strains
from the Genbank. Bootstrap values are indicated on branches. Scale bar indicates nucleotide substitutions per site.
The plaque variants clustered closely with CHIKV isolates from Comoros Island, Kenya and Re-union Island,
indicating evolutionary relationship between these isolates. The isolates are named in this order: country of origin
/strain name/accession number /year of sample collection.