Figure 2. Phylogenetic analysis of the relationship between sequences of 21 Ugandan measles virus isolates obtained during 2006–2009 and 22 other recently described clade B nucleoprotein (N) gene sequences, including the World Health Organization reference strains for the B clade (13). Boldface indicates different genotypes. Analyses are based on sequences of the 450 nt encoding the COOH-terminal 150 nt of the N gene. The unrooted neighbor-joining consensus tree was generated by bootstrap analysis of 500 replicates by using MEGA4 software (www.megasoftware.net). Bootstrap percentages are shown when >75%. Only names of the isolates from Uganda (UGA) start with “MVi,” and all comparison strains have their GenBank accession numbers indicated in parentheses. Genotypes of the World Health Organization reference sequences are indicated after the accession number. Comparison sequences were from viruses isolated in Benin (BEN), Cameroon (CAE), Côte d’Ivoire (CIV), Gabon (GAB), the Gambia, Germany (DEU), Great Britain (GBR), Kenya (KEN), Niger (NIG), Nigeria (NIE/NGA), Spain (ESP), Sudan (SUD), the Netherlands (NLD), and the United States (USA). Sequences from Uganda were most closely related to the B3.1 viruses of the September–December 2005 measles outbreak in Kenya (8). Scale bar indicates nucleotide substitutions per site.