To investigate the molecular evolution of the HuNoV VP1 and RdRp genes, 950 stool specimens were collected from various areas (13 prefectures) of Japan during the 2004–2015 seasons. These samples were obtained from patients with acute gastroenteritis due to HuNoV infections, in compliance with the Food Sanitation Law and the Law Concerning the Prevention of Infections and Medical Care for Patients of Infections of Japan. The personal data related to these samples were anonymized. RNA was extracted from 10% PBS suspensions of the specimens, and the HuNoV genomes were comprehensively analyzed by next-generation sequencing as described (Matsushima et al., 2015). Of 950 samples, the complete genome sequences of 538 strains were obtained (a success rate of 57%). Next, HuNoV genotypes were confirmed with the Norovirus Typing Tool (Version1.0), based on the nucleotide sequences of RdRp and VP1 genes as described by Kroneman et al. (2011). GII.2 strains were selected from these all genotyped strains, and then a few of strains having the undetermined base sequences (e.g., N, Y, R, and V) were omitted. Finally, 51 GII.2 strains were used for evolutionary analyses for the present study (Supplementary Table 1). The obtained nucleotide sequences for the GII.2 strains were deposited in GenBank under the accession numbers LC209431 to LC209481.