doi:10.1007/s12250-017-4077-5

Lineage	NS1	NS2	NS3	NS4	C	E3	E2	K	E1
Asia.reemerge	P/S₃ K/M₂₅₃ S/G₄₅₄	P/L₁₆ Q/L₂₇₃ K/M₃₃₈ N/S₇₆₈	Del:380-382	M/T₅₈ T/V₁₀₁ Q/R₂₃₅ E/D₂₈₀ V/A₅₈₂	P/S₂₃ Q/K₃₇ A/V₅₅ Q/R₇₈ A/V₉₃	Q/R₁₉ K/S₄₄ S/R₆₀	T/I₂ N/H₃ V/A₁₅₇ G/S₁₉₄ G/D₂₀₅ N/S₂₀₇ V/A₃₆₈	T/M₄₅ A/T₄₇	A/T₉₈ P/S₃₀₄
Asia.old	P/S₃ K/M₂₅₃ S/G₄₅₄	P/L₁₆K/M₃₃₈		M/T₅₈ T/V₁₀₁ E/D₂₈₀ V/A₅₈₂	Q/K₃₇ A/V₅₅ Q/R₇₈ A/V₉₃	K/S₄₄ S/R₆₀	T/I₂ V/A₁₅₇ G/S₁₉₄ G/D₂₀₅	A/T₄₇	A/T₉₈ P/S₃₀₄
ECSA.IOL	T/K₁₂₈	S/N₅₄ H/Y₃₇₄ L/S₅₃₉		L/A₄₃ R/S₈₂ T/A₂₅₄ A/T₃₆₆ Q/L₅₀₀			K/Q₂₅₂ V/A₃₈₆		S/A₇₂ E/K₂₁₁ A/V₂₂₆ D/E₂₈₄
ECSA.Africa		H/Y₃₇₄		L/A₄₃A/T₃₆₆			A/T₁₆₄		S/N₇₂
WA	T/A₁₂₈	G/N₂₂₆					A/T₁₆₄

Table 1. Lineage-specific mutations of CHIKV. The different mutations in sites of CHIKV from Pakistan comparing to most other IOL strains were indicated in bold characters

Lineage	Evolutionary rate (subs/nt/year)	Transmission pattern
Asia.old	4.078E-4	epidemic
Asia.reemerge	2.596E-4	epidemic
ECSA.Africa	2.27E-4	enzootic
ECSA.IOL	7.43E-4	epidemic
West Africa	2.203E-4	enzootic
Total	2.978E-4	--

Table 2. Evolutionary rate of each lineage

Primer pairs	Sequence	Length of PCR products
CHIKV-F-1 CHIKV-R-1347	ATGGCTGCGTGAGACACACGTAG TTGAATGCCCATAGACARCAGC	1374 bp
CHIKV-F-1308 CHIKV-R-2866	GAGAAAGAACACTGACCTGCTG TTGTCTAACTGCGTAAACTCCT	1559 bp
CHIKV-F-2705 CHIKV-R-4151	GTGGACACTACAGGCTCAACAA GAGGGTTAGCGGCGTTGACT	1447 bp
CHIKV-F-3751 CHIKV-R-5302	TCGCATACACCATTAYCAACAG GTTTCTCCCTCGCCTTCTTC	1552 bp
CHIKV-F-5281 CHIKV-R-6813	CAGAAGAAGGCGAGGGAGAAAC AGTGAATCATCTTGGCTCTTATC	1533 bp
CHIKV-F-6786 CHIKV-R-8191	CCTTTGATAAGAGCCAAGATGA TGCCAGCACCTGTAGGGATG	1406 bp
CHIKV-F-7920 CHIKV-R-9270	GCACGAAGGTAAGGTAACAGGT CGGGACCAGAGGGGAGTTAT	1350 bp
CHIKV-F-9032 CHIKV-R-10430	CCGAAGAGATAGAGGTACACAT GCAGTTACAGTGATGTTATTTCC	1399 bp
CHIKV-F-10286 CHIKV-R-11812	CTGAAAACACGCAGTTGAGC GAAATATTAAAAACAAAATAACATCTCC	1527 bp

Table S1. Primers used for CHIKV genome assembly

Geographic division	Country	No. sequence	Total
WA (West Africa)	Nigeria	2	14
	Senegal	9
	Cote dIvoire	2
	Cameroon	1
SEA (South east Asia)	Indonesia	4	92
	Thailand	28
	Philippine	7
	Malaysia	11
	China	17
	Myanmar	5
	Bangladesh	1
	Cambodia	7
	Singapore	12
Oceania	New Caledonia	1	1
CA (Central America)	Nicaragua	50	50
NA (North America)	USA	45	46
NA (North America)	Mexico	1	46
CI (Caribbean Island)	Dominican Republic	9	10
	Country	1
	Saint Martin
SA (South America)	Brazil	6	7
SA (South America)	French Guiana	1	7
ESCA (East/South/Central Africa)	Congo	2	16
	South Africa	3
	Central African	4
	Tanzania	1
	Gabon	1
	Uganda	1
	Angola	1
	Yemen	1
	Kenya	2
IOL (India and Indian Ocean island)	India	30	58
	Sri Lanka	20
	Reunion	2
	Mauritius	2
	Madagascar	1
	Mayotte	1
	Comoros	2
Pakistan_2016	Pakistan	8	8
Europe	Italy	5	6
Europe	France	1	6

Table S2. Geographic classification of CHIKV