Genetic Diversity of Sapoviruses among Inpatients in Germany, 2008−2018

Abstract

Sapovirus enteric disease affects people of all ages across the globe, in both sporadic cases and outbreak settings. Sapovirus is seldom assessed in Germany and its epidemiology in the country is essentially unknown. Thus, sapovirus occurrence and genetic diversity were studied by real-time reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of major viral structural protein (VP1) gene in two different sets of stool samples: 1) a selection of 342 diarrheal stools collected from inpatient children during 2008−2009, and 2) 5555 stool samples collected during 2010–2018 from inpatients of all age groups with gastrointestinal complaints. Results showed year-round circulation of sapoviruses, with peaks during cooler months. In total, 30 samples (8.8%) of the first and 112 samples of the second set of samples (2.0%) were sapovirus positive. Capsid gene sequencing was successful in 134/142 samples (94.4%) and showed circulation of all known human pathogenic genogroups. Genotype GI.1 predominated (31.8%), followed by GII.1 (16.7%), GII.3 (14.5%), GI.2 (13.8%) and GV.1 (12.3%). Additionally, minor circulation of GI.3, GI.6, GII.2, GII.4, GII.6 and GIV.1 was shown. Consequently, sapovirus diagnostics need broadly reactive RT-PCR protocols and should particularly be considered in infants and young children. Further studies from other sampling sites are essential to extend our knowledge on sapovirus epidemiology in Germany.

Tracing the fate of wastewater viruses reveals catchment-scale virome diversity and connectivity

“…PCR-based detection of sapoviruses in older studies show that among cases of gastro-intestinal disease, sapoviruses accounted for only 4% of cases (vs 36% for noroviruses) 33 , however, the primers used in that study (SR80 34 , JV33 35 ) did not match the two sapovirus genomes reconstructed in this study (data not shown). The detection of this complete genome sequence from two different wastewater treatment plants is another indication that sapoviruses are more common in the UK than previously reported, similar to its incidence reported in other countries [36][37][38] .…”

Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

“…Their taxonomic classification is based on the capsid (VP1) sequence, with GI, GII, GIV and GV being the genogroups responsible for human gastroenteritis. Additionally, genogroups are further classified into genotypes, a classification system that keeps growing due to their high genetic diversity, with GI.1, GII.1, and GI.2 being the genotypes most commonly associated with clinical cases [ 48 , 50 , 51 ].…”

Occurrence of Human Enteric Viruses in Water Sources and Shellfish: A Focus on Africa

“…SaVs are phylogenetically clustered into 19 genogroups, of which GI, GII, GIV and GV contain human SaVs and are further subdivided into genotypes GI.1-GI.7, GII.1-GII.8, GIV.1 and GV.1-GV.2 (Oka et al 2015 ; Diez-Valcarce et al 2018 ; Makhaola et al 2020 ). Globally, strains belonging to genogroups GI and GII are more prevalent than SaVs belonging to genogroups GIV and GV (Fioretti et al 2016 ; Yoneda et al 2017 ; Mann et al 2019 ; Supadej et al 2019 ; Varela et al 2019 ). Recently, GI was confirmed as the most prevalent genogroup detected in people and the environment within African countries (Makhaola et al 2020 ).…”