Phylogenetic tree of the hemagglutinin (HA) gene segment of Ugandan influenza B isolates (in bold font) at the nucleotide level. The HA sequences of our Ugandan influenza B isolates were compared with relevant virus sequences available in GenBank and GISAID databases: the reference strains for each lineage and group (for the Victorian lineage: B/Brisbane/60/2008, B/Victoria/304/2006, B/Uruguay/12/2008, B/Fujian-Gulou/1272/2008, B/Singapore/19/2009, and B/Argentina/R158/2010 as representatives of group 1, 2, 3, 4, 5, and 6, respectively; for the Yamagata lineage: B/Florida/04/2006, B/Brisbane/03/2007, and B/Bangladesh/3333/2007 as representatives of group 1, 2, and 3, respectively; all represented in italic underlined font), as well as all the African influenza B viruses from 2008 to 2010 available in the databases (a single representative virus was selected for strains with identical amino acid (aa) sequences). B/Uganda/MUWRP-81/2009 was identical to B/Uganda/0514/2009, B/Uganda/MUWRP-54/2009, B/Uganda/MUWRP-55/2009, B/Uganda/MUWRP-57/2009, B/Uganda/MUWRP-60/2009, B/Uganda/MUWRP-63/2009, B/Uganda/MUWRP-64/2009, B/Uganda/MUWRP-68/2009, B/Uganda/MUWRP-76/2009, B/Uganda/MUWRP-77/2009, B/Uganda/MUWRP-78/2009, B/Uganda/MUWRP-80/2009, B/Uganda/MUWRP-84/2009, B/Uganda/MUWRP-115/2009, B/Uganda/MUWRP-122/2009, B/Uganda/MUWRP-136/2009, B/Uganda/MUWRP-158/2010, and B/Uganda/MUWRP-237/2010; B/Uganda/MUWRP-73/2009 to B/Uganda/MUWRP-88/2009 and B/Uganda/MUWRP-89/2009. The number of identical Ugandan isolates is indicated in parenthesis when necessary. Aa substitutions characteristics of the main groups are indicated on the tree nodes. Bootstrap values (1000 replicates) >50 are indicated on the nodes. * indicate partial sequence data.