Table 2.

Pairwise nucleotide identity of the RT-RNase H sequence for cacao-infecting badnavirus isolates

CSSTAV	TG_AJ781003	100
CSSCDV	CI_JN606110	76	100
	GH67	75	73	100
CRVV	CI286	75	72	82	100
	CI275	75	73	82	83	100
	GH64	75	73	82	84	86	100
	TG_L14546	75	75	76	75	76	76	100
	TG_AJ534983	75	75	76	76	76	76	98	100
	CI44	75	75	75	76	76	77	88	88	100
	CI134	75	75	75	76	76	76	90	90	93	100
	CI215	75	75	75	76	76	76	90	91	93	99	100
	GH_AJ608931	75	75	75	76	75	76	90	90	92	98	98	100
CSSV	GH75	75	75	75	76	75	76	90	90	92	98	98	99	100
	GH_AJ609020	75	75	75	76	75	76	89	90	92	98	98	98	97	100
	GH_AJ609019	75	75	75	76	76	76	90	90	92	98	98	98	98	98	100
	CIS3	75	75	74	75	74	75	88	88	90	96	96	95	95	96	96	100
	CI135	75	75	76	77	76	77	90	91	93	98	99	98	98	98	99	97	100
	CI301	75	75	75	76	76	76	90	90	92	98	98	98	98	97	98	96	98	100
	CI311	75	75	75	77	75	76	90	90	93	98	99	98	98	98	98	96	99	99	100
	CIT5	75	75	76	77	76	77	90	90	93	98	99	98	98	98	98	96	99	98	99	100
	CIS2	75	76	76	77	76	77	90	91	92	98	98	98	98	98	98	96	99	98	99	100	100

Legend: The sequences downloaded from GenBank are indicated by Accession number, and for each isolate, the country of origin is indicated by the country code. Each badnavirus genome sequence determined in this study is indicated by country code and sample number. The sequence alignment was carried out using MUSCLE, implemented in Standard Demarcation Tool v1.2 software, using ≥80% as the species cutoff. The abbreviations indicating the country origin of each isolate are as follows: CI-Cote d’Ivoire, GH-Ghana, and TG-Togo. Virus species abbreviations are indicated as: CSSV-Cacao swollen shoot virus; CSSTAV-Cacao swollen shoot Togo A virus; CSSCDV-Cacao swollen shoot CD virus; and CRVV-Cacao red vein virus