Table 3.

Evidence of positive selection on the IOL CHIKV ORFs inferred using individual site models.

Codon Site	MEME p < 0.1	FUBAR pp > 0.9	FEL p < 0.1	SLAC p < 0.1	Amino Acid Substitution	Sequences with Derived Amino Acid State
Nonstructural proteins
171	0.00	0.999	0.002	0.006	nsP1-R171Q	Comoros 2005: HQ456252 Italy 2007: MK120202, KX262993 Sri Lanka 2006: AB455493 India 2016: MW321606, MG137428; 2017: MK286893 Kenya 2016: MH423803; 2017: MT380161
665	0.12	0.946	0.095	0.131	nsP2-H130Y	Singapore 2009: MH647212; 2010: MH647214 2012: MH647182, MH647184; 2013: MH647187 India 2014: MW042254; 2015: MK370031 IE clade virus *, IS clade virus *
Structural proteins
24	0.09	0.893	0.069	0.296	C-T24A	Laos 2013: MF076569 Djibouti 2019: MT023791 Thailand 2019: LC580269; 2020: BHTD20-WM14, BHTD20-WM19
471	0.03	0.995	0.022	0.079	E2-Q146R	Seychelles 2005: AM258991 Bangladesh 2017: MG912993 Kenya 2018: MT526797 Thailand 2019: MN075150; 2020: BHTD20-WM05
546	0.12	0.965	0.097	0.237	E2-K221R	India 2012: MW581867 Bangladesh 2017: LC580241, LC580244 Thailand 2019: MN075150; 2020: BHTD20-WM27
795	0.07	0.902	0.061	0.296	6K-A47V 6K-A47G	India 2016: MK473625 Pakistan 2016: MF774613 Singapore 2013: MH647192; 2014: MH647202
813	0.12	0.946	0.093	0.198	E1-V4A	India 2007: EU372006; 2008: GQ428215; 2009: KT336777 2015: KX619425, KX619424 2016: MK518340, MK551552, MK551553, MK473628 Bangladesh 2008: FJ807898; 2011: KU365371 Singapore 2013: MH647192; 2014: MH647202 Thailand 2020: BHTD20-WM44, BHTD20-WM27, BHTD20-WM48

Positive selection site is highlighted in boldface, p = p-value, pp = posterior probability, * Virus clades correspond to those in Figure 3.