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Table 2 Pairwise nucleotide identity of the RT-RNase H sequence for cacao-infecting badnavirus isolates

From: The proposed new species, cacao red vein virus, and three previously recognized badnavirus species are associated with cacao swollen shoot disease

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

  1. 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