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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