Surveillance of human norovirus in oysters collected from production area in Shandong Province, China during 2017-2018
Sequencing data were processed using Usearch v11 (Edgar, 2010). Search was run to find matches of nucleotide sequences to a database containing primer. The n and m bases were removed at the start and end of sequence (for GI, n=19, m=20; for GII, n=23, m=19). The reads were filtered in FASTQ file by default parameter with discard sequences < 250 letters and identify unique sequences. Sequences were sorted in FASTA files by decreasing length and cluster sequences using UCLUST with identity threshold set to 0.97. Operational Taxonomic Units (OTUs) table was generated to determine the number of reads contained in each OTU. All OTUs were confirmed by a web-based genotyping tool (http://www.rivm.nl/mpf/norovirus/typingtool Version2.0) (Kroneman, et al., 2011).