Genetic diversity of human sapovirus across the Americas

• Published in: Journal of clinical virology Vol. 104; no. C; pp. 65 - 72
• Main Authors: Diez-Valcarce, Marta, Castro, Christina J., Marine, Rachel L., Halasa, Natasha, Mayta, Holger, Saito, Mayuko, Tsaknaridis, Laura, Pan, Chao-Yang, Bucardo, Filemon, Becker-Dreps, Sylvia, Lopez, Maria Renee, Magaña, Laura Cristal, Ng, Terry Fei Fan, Vinjé, Jan
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.07.2018; Elsevier
• Subjects: Adolescent; Adult; Aged; Aged, 80 and over; Americas - epidemiology; Caliciviridae Infections - epidemiology; Caliciviridae Infections - virology; Child; Child, Preschool; Female; Gastroenteritis - epidemiology; Gastroenteritis - virology; Genetic Variation; Genome, Viral; Genotype; Genotypes; High-Throughput Nucleotide Sequencing; Humans; Infant; Infant, Newborn; Male; Metagenomics; Middle Aged; Molecular Epidemiology; Next generation sequencing; Sapovirus; Sapovirus - classification; Sapovirus - genetics; Sapovirus - isolation & purification; Sequence Analysis, DNA; Viral gastroenteritis; Young Adult; Americas; Viral gastroenteritis; Next generation sequencing; Sapovirus; Genotypes
• ISSN: 1386-6532; 1873-5967
• DOI: 10.1016/j.jcv.2018.05.003

•Human sapoviruses cause epidemic and sporadic acute gastroenteritis globally (n = 79).•Typing methods were designed based on a limited number of sapovirus sequences (n = 80).•Success rate typing is suboptimal due to viral evolution (n = 59).•We report 68 new near-complete genome sequences of all human sapovirus genogroups (n = 84).•New sequences show several discrepancies with primer binding sites (n = 69). Sapoviruses are responsible for sporadic and epidemic acute gastroenteritis worldwide. Sapovirus typing protocols have a success rate as low as 43% and relatively few complete sapovirus genome sequences are available to improve current typing protocols. To increase the number of complete sapovirus genomes to better understand the molecular epidemiology of human sapovirus and to improve the success rate of current sapovirus typing methods, we used deep metagenomics shotgun sequencing to obtain the complete genomes of 68 sapovirus samples from four different countries across the Americas (Guatemala, Nicaragua, Peru and the US). VP1 genotyping showed that all sapovirus sequences could be grouped in the four established genogroups (GI (n = 13), GII (n = 30), GIV (n = 23), GV (n = 2)) that infect humans. They include the near-complete genome of a GI.6 virus and a recently reported novel GII.8 virus. Sequences of the complete RNA-dependent RNA polymerase gene could be grouped into three major genetic clusters or polymerase (P) types (GI.P, GII.P and GV.P) with all GIV viruses harboring a GII polymerase. One (GII.P-GII.4) of the new 68 sequences was a recombinant virus with the hotspot between the NS7 and VP1 regions. Analyses of this expanded database of near-complete sapovirus sequences showed several mismatches in the genotyping primers, suggesting opportunities to revisit and update current sapovirus typing methods.