Phylogenetic analyses
In the phylogenetic tree constructed using 39 full-length gene sequences of P[9] strains, five lineages could be identified (Fig. 1). Lineage I consisted of G3P[9], G1P[9], G3G4P[9], and G12P[9] strain from Paraguay, Japan, China, Thailand and Korea. Paraguayan strains were of genotypes G1P[9], G3P[9], G3G4P[9], and G12P[9]. Strains from other countries were of genotype G3P[9] (Additional file 3). Lineage II consisted of strains from Italy, Australia, and Japan. All these strains were of genotype G3P[9]. Lineage III consisted of G3P[9] and G6P[9] strains from Russia, Japan, Italy, Korea, and Tunisia. Among these, strains from Russia, Korea, and Italy were G3P[9], while strains from Tunisia and Japan were G6P[9]. Lineage IV consisted of strains from the USA, Italy, and Russia; all were G3P[9]. Lineage V consisted of strains from Paraguay, Brazil, Italy and Thailand. All of the strains in lineage V were of the G12P[9] combination.
A total of 11 phylogenetic trees were constructed using different partial-length nucleotide sequences (Additional file 2) of P[9] strains. All of these could be classified into five lineages. The distribution of strains in each lineage was consistent with the phylogenetic tree constructed using full- and partial-length gene sequences.
Overall, five lineages of P[9] strains could be identified in the phylogenetic tree constructed using 88 partial gene sequences (187–741 nt) of P[9] strains (Fig. 2). Lineage I consisted of G3P[9], G1P[9], G9P[9], GxP[9], G12P[9], and G3G4P[9] strain from Brazil, Japan, Paraguay, Thailand, China, the USA, and Korea. The strains from Brazil, were of the G3P[9], G1P[9], and G9P[9] combination (Additional file 3). G3P[9] and GxP[9] combination were from Japan. Strains from Paraguay were G3P[9], G1P[9], G12P[9], and G3G4P[9]. All strains from Thailand, China, the USA, and Korea were G3P[9]. Lineage II consisted of G3P[9] and G6P[9] strains from Italy, Australia and Japan. Genotype G3P[9] and G6P[9] were from Italy. The strains from Australia and Japan were G3P[9]. Lineage III consisted of genotype G3P[9], G6P[9], and G9P[9] from Bulgaria, Russia, Hungary, Italy, Tunisia, France, Japan, and Korea. The strains from Bulgaria were of genotype G6P[9], and G3P[9]. Russian strains were of the G3P[9] combination. The strains from Hungary were of genotype G6P[9] and G9P[9]. Italian strains were of genotype G3P[9] and G6P[9]. The strains from Tunisia and Japan were G6P[9], and from France and Korea were G3P[9]. Lineage IV consisted of genotypes G3P[9] and GxP[9] from Hungary, the USA, Italy, Russia and Israel. The strains from Hungary, the USA, Italy, and Russia were G3P[9], while the strain from Israel was GxP[9]. Lineage V consisted of strains from Paraguay, Brazil, Argentina, Japan, Thailand and Italy. All strains were of the G12P[9] combination.
Timeline of evolution
The phylogenetic tree constructed using the Bayesian method also showed five lineages of P[9] strains (Fig. 3), which corresponded with the lineages as determined using the neighborur-joining method. Approximately 168 years ago the current P[9] strains of rotavirus emerged (95% highest posterior density [HPD] years) and evolved into different lineages (Fig. 3). Lineage I derived from lineages II, III, and IV approximately 79 years ago (95% HPD 56.07–99.69 years) and different strains of lineage I evolved approximately 48 years ago (95% HPD 37.00–54.96 years). Lineage II diverged from lineage III approximately 70 years ago (95% HPD 49.45–87.93 years), and the strains in lineage II started evolving around 47 years ago (95% HPD 35.61–55.07 years). Lineage III diverged from lineage II approximately 70 years ago (95% HPD 49.45–87.93yrs) ago, and the strains in lineage III started evolving around 40 years ago (95% HPD 26.65–50.03 years). Lineage IV diverged from lineages II and III approximately 74 years ago (95% HPD 52.49–83.44 years), and the strains in lineage IV evolved around 47 years ago (95% HPD 43.09–83.44 years). Lineage V diverged from lineages I, II, III, and IV around 168 years ago, at the very beginning of the emergence of the P[9] strain.