Global Trends in Norovirus Genotype Distribution Among Children With Acute Gastroenteritis

Jennifer L. Cannon; Joseph Bonifacio; Filemon Bucardo; Javier Buesa; Leesa Bruggink; Martin Chi-Wai Chan; Tulio M. Fumian; Sidhartha Giri; Mark D. Gonzalez; Joanne Hewitt; Jih-Hui Lin; Janet Mans; Christian Muñoz; Chao-Yang Pan; Xiao-Li Pang; Corinna Pietsch; Mustafiz Rahman; Naomi Sakon; Rangaraj Selvarangan; Hannah Browne; Leslie Barclay; Jan Vinjé

Disclosures

Emerging Infectious Diseases. 2021;27(5):1438-1445. 

In This Article

Methods

NoroSurv

All but 2 participating hospitals and medical centers collected norovirus–positive stool samples from children with AGE; 2 sites in Nicaragua and Australia obtained only samples from symptomatic children in community-based studies. Staff at hospitals, medical centers, universities, and reference laboratories processed and typed the samples. Each laboratory uploaded norovirus sequences; patient demographic data (e.g., deidentified patient age and sex); and information on sample type, collection date, and setting to the password-protected NoroSurv web portal. All laboratories used a standardized protocol for norovirus dual typing that comprised screening by genotype-specific real-time reverse transcription PCR (RT-PCR), conventional RT-PCR, and Sanger sequencing of RT-PCR products.[20] Raw DNA chromatogram files or nucleotide sequences were automatically typed by NoroSurv using the most recent reference sequences and classification for noroviruses.[16] Ethics approval for the New Zealand component of this study was granted by the Health and Disability Ethics Committee, New Zealand (approval no. 19/CEN/96).

Data Analysis

We analyzed NoroSurv data associated with samples collected during September 1, 2016–August 31, 2020. We excluded samples from children ≥5 years of age, from asymptomatic patients, or that had missing or low-quality dual typing information. We downloaded sequences and associated data from NoroSurv; we then aggregated, cleaned, analyzed, and visualized the data using R software (The R Project, https://www.r-project.org). After downloading the sequences from NoroSurv as fasta files, we checked the quality of the submitted sequences using Bioconductor (http://bioconductor.org) packages in R. When discrepancies existed between the manually entered and autotyped information, we conducted phylogenetic analysis to confirm the correct type; we updated NoroSurv records accordingly.

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