Human sapovirus classification based on complete capsid nucleotide sequences

Propagating and banking genetically diverse human sapovirus strains using a human duodenal cell line: investigating antigenic differences between strains

There are four genogroups and 18 genotypes of human sapoviruses (HuSaVs) responsible for acute gastroenteritis. To comprehend their antigenic and virological differences, it is crucial to obtain viral stocks of the different strains. Previously, we utilized the human duodenum-derived cell line HuTu80, and glycocholate, a conjugated bile acid, to replicate and propagate GI.1, GI.2, and GII.3 HuSaVs (H. Takagi et al., Proc Natl Acad Sci U S A 117:32078-32085, 2020, https://10.1073/pnas.2007310117). First, we investigated the impact of HuTu80 passage number on HuSaV propagation. Second, we demonstrated that taurocholate improved the initial replication success rate and viral RNA levels in fecal specimens relative to glycocholate. By propagating 15 HuSaV genotypes (GI.1-7, GII.1-5, -8, and GV.1-2) and accomplishing preparation of viral stocks containing 1.0 × 109 to 3.4 × 1011 viral genomic copies/mL, we found that all strains required bile acids for replication, with GII.4 showing strict requirements for taurocholate. The deduced VP1 sequences of the viruses during the scale-up of serial passaged virus cultures were either identical or differed by only two amino acids from the original sequences in feces. In addition, we purified virions from nine strains of different genotypes and used them as immunogens for antiserum production. Enzyme-linked immunosorbent assays (ELISAs) using rabbit and guinea pig antisera for each of the 15 strains of different genotypes revealed distinct antigenicity among the propagating viruses across genogroups and differences between genotypes. Acquisition of biobanked viral resources and determination of key culture conditions will be valuable to gain insights into the common mechanisms of HuSaV infection.

IMPORTANCE

The control of human sapovirus, which causes acute gastroenteritis in individuals of all ages, is challenging because of its association with outbreaks similar to those caused by human norovirus. The establishment of conditions for efficient viral propagation of various viral strains is essential for understanding the infection mechanism and identifying potential control methods. In this study, two critical factors for human sapovirus propagation in a conventional human duodenal cell line were identified, and 15 strains of different genotypes that differed at the genetic and antigenic levels were isolated and used to prepare virus stocks. The preparation of virus stocks has not been successful for noroviruses, which belong to the same family as sapoviruses. Securing virus stocks of multiple human sapovirus strains represents a significant advance toward establishing a reliable experimental system that does not depend on limited virus-positive fecal material.

Epidemiology and molecular evolution of GI.1 sapovirus in the recent era

Sapovirus (SaV) infection is increasing worldwide. Herein, we provided evidence of a significant increase in SaV infection in Japan during 2010-2022, primarily due to the considerable (p = 0.0003) rise of the GI.1 genotype. Furthermore, we found that all major and minor SaV outbreaks in Japan, including the largest SaV outbreak in 2021-2022, were caused by the GI.1 genotype. Therefore, to get insight into the underlying molecular mechanism behind this rising trend of the SaV GI.1 type, we selected 15 SaV GI.1 outbreak strains for complete genome analysis through next-generation sequencing. Phylogenetically, our strains remained clustered in different branches in lineages I and II among the GI.1 genotype. We showed all amino acid (aa) substitutions in different open reading frames (ORFs) in these strains. Importantly, we have demonstrated that the strains involved in the largest SaV outbreak in Japan in 2021-2022 belonged to lineage II and possessed the third ORF. We have identified some unique aa mutations in these major outbreak strains in the NS1 and NS6-NS7 regions that are thought to be associated with viral pathogenicity, cell tropism, and epidemiological competence. Thus, in addition to enriching the database of SaV's complete sequences, this study provides insights into its important mutations.

Genomic Characterization and Molecular Evolution of Sapovirus in Children under 5 Years of Age

Sapovirus (SaV) is a type of gastroenteric virus that can cause acute gastroenteritis. It is highly contagious, particularly among children under the age of 5. In this study, a total of 712 stool samples from children under the age of 5 with acute gastroenteritis were collected. Out of these samples, 28 tested positive for SaV, resulting in a detection rate of 3.93% (28/712). Samples with Ct < 30 were collected for library construction and high-throughput sequencing, resulting in the acquisition of nine complete genomes. According to Blast, eight of them were identified as GI.1, while the remaining one was GI.6. The GI.6 strain sequence reported in our study represents the first submission of the GI.6 strain complete genome sequence from mainland China to the Genbank database, thus filling the data gap in our country. Sequence identity analysis revealed significant nucleotide variations between the two genotypes of SaV and their corresponding prototype strains. Phylogenetic and genetic evolution analyses showed no evidence of recombination events in the obtained sequences. Population dynamics analysis demonstrated potential competitive inhibition between two lineages of GI.1. Our study provides insights into the molecular epidemiological and genetic evolution characteristics of SaV prevalent in the Nantong region of China, laying the foundation for disease prevention and control, as well as pathogen tracing related to SaV in this area.

Human Sapovirus Replication in Human Intestinal Enteroids

Human sapoviruses (HuSaVs), like human noroviruses (HuNoV), belong to the Caliciviridae family and cause acute gastroenteritis in humans. Since their discovery in 1976, numerous attempts to grow HuSaVs in vitro were unsuccessful until 2020, when these viruses were reported to replicate in a duodenal cancer cell-derived line. Physiological cellular models allowing viral replication are essential to investigate HuSaV biology and replication mechanisms such as genetic susceptibility, restriction factors, and immune responses to infection. In this study, we demonstrate replication of two HuSaV strains in human intestinal enteroids (HIEs) known to support the replication of HuNoV and other human enteric viruses. HuSaVs replicated in differentiated HIEs originating from jejunum, duodenum and ileum, but not from the colon, and bile acids were required. Between 2h and 3 to 6 days postinfection, viral RNA levels increased up from 0.5 to 1.8 log10-fold. Importantly, HuSaVs were able to replicate in HIEs independent of their secretor status and histo-blood group antigen expression. The HIE model supports HuSaV replication and allows a better understanding of host-pathogen mechanisms such as cellular tropism and mechanisms of viral replication. IMPORTANCE Human sapoviruses (HuSaVs) are a frequent but overlooked cause of acute gastroenteritis, especially in children. Little is known about this pathogen, whose successful in vitro cultivation was reported only recently, in a cancer cell-derived line. Here, we assessed the replication of HuSaV in human intestinal enteroids (HIEs), which are nontransformed cultures originally derived from human intestinal stem cells that can be grown in vitro and are known to allow the replication of other enteric viruses. Successful infection of HIEs with two strains belonging to different genotypes of the virus allowed discovery that the tropism of these HuSaVs is restricted to the small intestine, does not occur in the colon, and replication requires bile acid but is independent of the expression of histo-blood group antigens. Thus, HIEs represent a physiologically relevant model to further investigate HuSaV biology and a suitable platform for the future development of vaccines and antivirals.

Distribution of Human Sapovirus Strain Genotypes over the last four Decades in Japan: a Global Perspective

Sapovirus (SaV) infections are a public health problem because they cause acute gastroenteritis in humans of all ages both as outbreaks and in sporadic cases. However, publicly-available SaV sequence information, especially whole genome sequences for all the SaV genotypes, is still limited. Therefore, in this study, we determined the full/near-full-length genomic sequences of 138 SaVs from the 2001-2015 seasons in 13 prefectures across Japan. The GI genogroup was predominant (67%, n = 92), followed by GII (18%, n = 25), GIV (9%, n = 12), and GV (6%, n = 9). Within the GI genogroup, four different genotypes were identified, as follows: GI.1 (n=44), GI.2 (n=40), GI.3 (n=7), and GI.5 (n=1). We then compared these Japanese SaV sequences with a total of 3119 public human SaV sequences from 49 countries over the last 46 years. The results indicated that GI.1 and GI.2 have been the predominant genotypes in Japan as well as in other countries over at least four decades. Together with public SaV sequences, the 138 newly determined Japanese SaV sequences could facilitate a better understanding of the evolutionary patterns of SaV genotypes.

High Genetic Diversity of Porcine Sapovirus From Diarrheic Piglets in Yunnan Province, China

As one of the most important enteric viruses, sapovirus (SaV) can infect humans and a variety of animals. Until now, 19 SaV genogroups have been identified, among which 4 from human (GI, GII, GIV, and GV) and 8 from swine (GIII, GV–GXI). Porcine sapovirus (PoSaV) GIII has been prevalent in China; however, the status of PoSaV infection in Yunnan province remains unknown. In this study, 202 fecal samples were collected from piglets associated with outbreaks of acute diarrhea in Yunnan between January and May 2020. PoSaV detection revealed that the total PoSaV infection rate in Yunnan was 35.2%, with 21 PoSaV strains determined and phylogenetically analyzed. The phylogenetic tree analyses demonstrated that twenty PoSaV strains belonged to GIII and fell into five genotypes, whereas one PoSaV strain (YNQB) belonged to GV. Sequence alignments revealed deletions in VP2 region in 10 of the 20 GIII strains, as well as deletions and insertions in VP1 region of the GV strain (YNQB). Furthermore, genomic recombination analyses showed that two GIII strains (YNAN and YNJD) were recombinants, closely related to reference sequences MK965898 and LC215880, MK965898 and FJ387164, respectively. In summary, PoSaV-GIII strains were identified in Yunnan in 2020, and for the first time, a PoSaV-GV strain was identified from China, whereas the comprehensive analyses illustrated high genetic diversity of Yunnan PoSaV strains. This study may shed new light on the current PoSaV infections in Yunnan and pave the way toward further control of the PoSaV infections in China.

High Prevalence and Diversity of Caliciviruses in a Community Setting Determined by a Metagenomic Approach

We recently carried out a metagenomic study to determine the fecal virome of infants during their first year of life in a semirural community in Mexico. A total of 97 stool samples from nine children were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In this work, we describe the prevalence and incidence of caliciviruses in this birth cohort. We found that 54 (56%) and 24 (25%) of the samples were positive for norovirus and sapovirus sequence reads detected by next-generation sequencing, respectively. Potential infections were arbitrarily considered when at least 20% of the complete virus genome was determined. Considering only these samples, there were 3 cases per child/year for norovirus and 0.33 cases per child/year for sapovirus. All nine children had sequence reads related to norovirus in at least 2 and up to 10 samples, and 8 children excreted sapovirus sequence reads in 1 and up to 5 samples during the study. The virus in 35 samples could be genotyped. The results showed a high diversity of both norovirus (GI.3[P13], GI.5, GII.4, GII.4[P16], GII.7[P7], and GII.17[P17]) and sapovirus (GI.1, GI.7, and GII.4) in the community. Of interest, despite the frequent detection of caliciviruses in the stools, all children remained asymptomatic during the study. Our results clearly show that metagenomic studies in stools may reveal a detailed picture of the prevalence and diversity of gastrointestinal viruses in the human gut during the first year of life.

IMPORTANCE Human caliciviruses are important etiological agents of acute gastroenteritis in children under 5 years of age. Several studies have characterized their association with childhood diarrhea and their presence in nondiarrheal stool samples. In this work, we used a next-generation sequencing approach to determine, in a longitudinal study, the fecal virome of infants during their first year of life. Using this method, we found that caliciviruses can be detected significantly more frequently than previously reported, providing a more detailed picture of the prevalence and genetic diversity of these viruses in the human gut during early life.

Molecular Epidemiology of Sapovirus in Children Living in the Northwest Amazon Region

Sapovirus is an important etiological agent of acute gastroenteritis (AGE), mainly in children under 5 years old living in lower-income communities. Eighteen identified sapovirus genotypes have been observed to infect humans. The aim of this study was to identify sapovirus genotypes circulating in the Amazon region. Twenty-eight samples were successfully genotyped using partial sequencing of the capsid gene. The genotypes identified were GI.1 (n = 3), GI.2 (n = 7), GII.1 (n = 1), GII.2 (n = 1), GII.3 (n = 5), GII.5 (n = 1), and GIV.1 (n = 10). The GIV genotype was the most detected genotype (35.7%, 10/28). The phylogenetic analysis identified sapovirus genotypes that had no similarity with other strains reported from Brazil, indicating that these genotypes may have entered the Amazon region via intense tourism in the Amazon rainforest. No association between histo-blood group antigen expression and sapovirus infection was observed.

Molecular Epidemiology of Human Sapovirus Among Children with Acute Gastroenteritis in Western Canada

Objectives: Sapovirus is increasingly recognized as an important cause of acute gastroenteritis (AGE) worldwide, however studies of prevalence, genetic diversity and strain-specific clinical implications have been scarce. Methods: To fill this knowledge gap, we used reverse transcription real-time PCR and sequencing of the partial major capsid protein VP1 gene to analyze stool specimens and rectal swabs obtained from 3347 children with AGE and 1355 asymptomatic controls (all <18 years old) collected between December 2014 and August 2018 in Alberta, Canada. Results: Sapovirus was identified in 9.5% (317/3347) of the children with AGE and 2.9% of controls. GI.1 (36%) was the predominant genotype identified, followed by GI.2 (18%), GII.5 (8%) and GII.3 (6%). Rare genotypes GII.1, GII.2, GV.1, GII.4, GIV.1, GI.3 and GI.7 were also seen. Sapovirus was detected year-round, peaking during the winter months of November to January. The exception was the 2016-2017 season when GI.2 overtook GI.1 as the predominant strain with a high detection rate persisting into April. We did not observe significant difference in the severity of gastroenteritis by genogroup or genotype. Repeated infection by sapovirus of different genogroups occurred in three controls who developed AGE later. Conclusions: Our data suggests that sapovirus is a common cause of AGE in children with high genetic diversity.

Diversity of human sapovirus genotypes detected in Japanese pediatric patients with acute gastroenteritis, 2014-2017

Sapovirus (SaV) is one of the pathogens related to acute gastroenteritis (AGE) in adults and children worldwide. This study reported the diversity of SaV genotypes in children with AGE in Japan from July 2014 to June 2017. Of a total of 2259 stool samples tested by using reverse transcription-PCR method and further analyzed by nucleotide sequencing, 114 (5.0%) were positive for SaV and GI.1 (83.3%) was the most predominant genotype, followed by GII.1, GIV.1, GI.2, GI.3, and GII.3 genotypes. Monthly distribution analysis demonstrated two epidemic peaks from July to December 2015 and February to May 2017. However, no detection peak was observed in 2014 and 2016. Phylogenetic analysis of the complete VP1 nucleotide sequences of these GI.1 strains revealed two major clusters of GI.1 and each of which contained GI.1 strains of both 2015 and 2017. This study suggests that the continuous surveillance of SaV is needed to monitor high genetic diversity in Japanese children with AGE.

Protection From Natural Immunity Against Enteric Infections and Etiology-Specific Diarrhea in a Longitudinal Birth Cohort

BACKGROUND

The degree of protection conferred by natural immunity is unknown for many enteropathogens, but it is important to support the development of enteric vaccines.

METHODS

We used the Andersen-Gill extension of the Cox model to estimate the effects of previous infections on the incidence of subsequent subclinical infections and diarrhea in children under 2 using quantitative molecular diagnostics in the MAL-ED cohort. We used cross-pathogen negative control associations to correct bias due to confounding by unmeasured heterogeneity of exposure and susceptibility.

RESULTS

Prior rotavirus infection was associated with a 50% lower hazard (calibrated hazard ratio [cHR], 0.50; 95% confidence interval [CI], 0.41-0.62) of subsequent rotavirus diarrhea. Strong protection was evident against Cryptosporidium diarrhea (cHR, 0.32; 95% CI, 0.20-0.51). There was also protection due to prior infections for norovirus GII (cHR against diarrhea, 0.67; 95% CI, 0.49-0.91), astrovirus (cHR, 0.62; 95% CI, 0.48-0.81), and Shigella (cHR, 0.79; 95% CI, 0.65-0.95). Minimal protection was observed for other bacteria, adenovirus 40/41, and sapovirus.

CONCLUSIONS

Natural immunity was generally stronger for the enteric viruses than bacteria, potentially due to less antigenic diversity. Vaccines against major causes of diarrhea may be feasible but likely need to be more immunogenic than natural infection.

Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery. Viral metagenomics in routine clinical settings has the potential to identify unexpected or novel variants of viral pathogens that cause gastroenteritis. In this study, 124 samples from acute gastroenteritis patients from 2012–2014 previously tested negative for common gastroenteritis pathogens were pooled by age and analyzed by next generation sequencing (NGS) to elucidate unidentified viral infections. The most abundant sequences detected potentially associated to acute gastroenteritis were from Astroviridae and Caliciviridae families, with the detection of norovirus GIV and sapoviruses. Lower number of contigs associated to rotaviruses were detected. As expected, other viruses that may be associated to gastroenteritis but also produce persistent infections in the gut were identified including several Picornaviridae members (EV, parechoviruses, cardioviruses) and adenoviruses. According to the sequencing data, astroviruses, sapoviruses and NoV GIV should be added to the list of viral pathogens screened in routine clinical analysis.

An outbreak of gastroenteritis associated with a novel GII.8 sapovirus variant-transmitted by vomit in Shenzhen, China, 2019

Background

Human Sapoviruses (SaVs) has been reported as one of the causative agents of acute gastroenteritis (AGE) worldwide. An outbreak of SaVs affected 482 primary school students during spring activities from February 24 to March 11, 2019 in Shenzhen City, China. Our study was aimed at determining the epidemiology of the outbreak, investigating its origins, and making a clear identification of the SaVs genetic diversity.

Methods

Epidemiological investigation was conducted for this AGE outbreak. Stool samples were collected for laboratory tests of causative agents. Real-time reverse-transcription polymerase chain reaction (rRT-PCR) and conventional RT-PCR were used for detecting and genotyping of SaVs. The nearly complete genome of GII.8 SaV strains were amplified and sequenced by using several primer sets designed in this study. Phylogenetic analysis was performed to characterize the genome of GII.8 SaV strains.

Results

The single factor analysis showed that the students who were less than 1.5 m away from the vomitus in classroom or playgroundwere susceptible (P < 0.05). Seven of 11 fecal samples from patients were positive for GII.8 SaV genotype. In this study, we obtained the genome sequence of a SaV GII.8 strain Hu/SaV/2019008Shenzhen/2019 /CHN (SZ08) and comprehensively analyzed the genetic diversity. The phylogenetic analysis showed that the GII.8 strain SZ08 formed an independent branch and became a novel variant of GII.8 genotype. Strain SZ08 harbored 11 specific amino acid variations compared with cluster A-D in full-length VP1.

Conclusions

This study identified SaVs as the causative agents for the AGE outbreak. Strain Hu SZ08 was clustered as independent branch and there was no recombination occurred in this strain SZ08. Further, it might become the predominant strain in diarrhea cases in the near future. Constant surveillance is required to monitor the emerging variants which will improve our knowledge of the evolution of SaVs among humans.

Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses

Sapoviruses are increasingly being recognized as pathogens associated with gastroenteritis in humans. Human sapoviruses are currently assigned to 18 genotypes (GI.1-7, GII.1-8, GIV.1, and GV.1-2) based on the sequence of the region encoding the major structural protein. In this study, we evaluated 11 polymerase chain reaction (PCR) assays using published and newly designed/modified primers and showed that four PCR assays with different primer combinations amplified all of the tested human sapovirus genotypes using either synthetic DNA or cDNA prepared from human sapovirus-positive fecal specimens. These assays can be used as improved broadly reactive screening tests or as tools for molecular characterization of human sapoviruses.

Porcine sapoviruses: Pathogenesis, epidemiology, genetic diversity, and diagnosis

The first porcine Sapovirus (SaV) Cowden strain was discovered in 1980. To date, eight genogroups (GIII, V-IX) and three genogroups (GIII, GV, and GVI) of porcine SaVs have been detected from domestic pigs worldwide and wild boars in Japan, respectively based on the capsid sequences. Although GIII Cowden strain replicated in the villous epithelial cells and caused intestinal lesions in the proximal small intestines (mainly in duodenal and less in jejunum), leading to mild to severe diarrhea, in the orally inoculated neonatal gnotobiotic pigs, the significance of porcine SaVs in different ages of pigs with diarrhea in the field is still undetermined. This is due to two reasons: 1) similar prevalence of porcine SaVs was detected in diarrheic and non-diarrheic pigs; and 2) co-infection of porcine SaVs with other enteric pathogens is common in pigs. Diagnosis of porcine SaV infection is mainly based on the detection of viral nucleic acids using reverse transcription (RT)-PCR and sequencing. Much is unknown about these genetically diverse viruses to understand their role in pig health and to evaluate whether vaccines are needed to prevent SaV infection.

Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions

Human sapovirus is a causative agent of acute gastroenteritis in all age groups. The use of full-length viral genomes has proven beneficial to investigate evolutionary dynamics and transmission chains. In this study, we developed a full-length genome sequencing platform for human sapovirus and sequenced the oldest available strains (collected in the 1970s) to analyse diversification of sapoviruses. Sequence analyses from five major genotypes (GI.1, GI.2, GII.1, GII.3, and GIV.1) showed limited intra-genotypic diversification for over 20–40 years. The accumulation of amino acid mutations in VP1 was detected for GI.2 and GIV.1 viruses, while having a similar rate of nucleotide evolution to the other genotypes. Differences in the phylogenetic clustering were detected between RdRp and VP1 sequences of our archival strains as well as other reported putative recombinants. However, the lack of the parental strains and differences in diversification among genomic regions suggest that discrepancies in the phylogenetic clustering of sapoviruses could be explained, not only by recombination, but also by disparate nucleotide substitution patterns between RdRp and VP1 sequences. Together, this study shows that, contrary to noroviruses, sapoviruses present limited diversification by means of intra-genotype variation and recombination.

Molecular detection and characterisation of sapoviruses and noroviruses in outpatient children with diarrhoea in Northwest Ethiopia

Childhood morbidity and mortality of diarrhoeal diseases are high, particularly in low-income countries and noroviruses and sapoviruses are among the most frequent causes worldwide. Their epidemiology and diversity remain not well studied in many African countries. To assess the positivity rate and the diversity of sapoviruses and noroviruses in Northwest Ethiopia, during November 2015 and April 2016, a total of 450 faecal samples were collected from outpatient children aged &lt;5 years who presented with diarrhoea. Samples were screened for noroviruses and sapoviruses by real-time RT-PCR. Partial VP1 genes were sequenced, genotyped and phylogenetically analysed. Norovirus and sapovirus stool positivity rate was 13.3% and 10.0%, respectively. Noroviruses included GII.4 (35%), GII.6 (20%), GII.17 (13.3%), GII.10 (10%), GII.2 (6.7%), GII.16 (5%), GII.7 (3.3%), GII.9, GII.13, GII.20 and GI.3 (1.7% each) strains. For sapoviruses, GI.1, GII.1 (20.0% each), GII.6 (13.3%), GI.2 (8.9%), GII.2 (11.1%), GV.1 (8.9%), GIV.1 (6.7%), GI.3 and GII.4 (2.2% each) genotypes were detected. This study demonstrates a high genetic diversity of noroviruses and sapoviruses in Northwest Ethiopia. The positivity rate in stool samples from young children with diarrhoea was high for both caliciviruses. Continued monitoring is recommended to identify trends in genetic diversity and seasonal variations.

Genetic recombination and diversity of sapovirus in pediatric patients with acute gastroenteritis in Thailand, 2010-2018

Background

Human sapovirus (SaV) is an etiologic agent of acute gastroenteritis (AGE) in all age groups worldwide. Genetic recombination of SaV has been reported from many countries. So far, none of SaV recombinant strain has been reported from Thailand. This study examined the genetic recombination and genotype diversity of SaV in children hospitalized with AGE in Chiang Mai, Thailand.

Methods

Stool samples were collected from children suffering from diarrhea who admitted to the hospitals in Chiang Mai, Thailand between 2010 and 2018. SaV was detected by RT-PCR and the polymerase and capsid gene sequences were analysed.

Results

From a total of 3,057 samples tested, 50 (1.6%) were positive for SaV. Among positive samples, SaV genotype GI.1 was the most predominant genotype (40%; 20/50), followed by GII.1 and GII.5 (each of 16%; 8/50), GI.2 (14%; 7/50), GIV.1 (4%; 2/50), and GI.5 (2%; 1/50). In addition, 4 SaV recombinant strains of GII.1/GII.4 were identified in this study (8%; 4/50).

Conclusions

The data revealed the genetic diversity of SaV circulating in children with AGE in Chiang Mai, Thailand during 2010 to 2018 and the intragenogroup SaV recombinant strains were reported for the first time in Thailand.

First identification of Sapoviruses in wild boar

Sapoviruses (SaVs) are enteric viruses that have been detected in human and animals previously; however, SaVs have not been identified in wild boar yet. Using a metagenomics approach, we identified SaVs in fecal samples of free-living wild boars in Japan for the first time. Six of the 48 specimens identified belonged to one genogroup (G)III, one GV and four GVI SaV sequence reads. We successfully determined complete genome of GV and GVI SaV strains using the long reverse transcription PCR strategy and the 5' rapid amplification of cDNA end method. Phylogenetic tree analysis and pairwise distance calculation revealed that GV SaV detected from wild boar was related to recently assigned GV.5 strains from pig, while GVI SaV was assigned to a new genotype within GVI. Moreover, wild boar may act as a reservoir for transmission of SaVs to the pig population (and vice versa) because GIII, GV, and GVI SaVs were all detected in pigs previously.

Detection of Sapoviruses in two biological lines of Tunisian hospital wastewater treatment

The efficiency of rotating biodisks and natural oxidizing lagoon procedures is investigated at a Tunisian semi-industrial pilot plant, El Menzeh I, where the wastewater is mainly provided by three different neighbouring hospital clinics. Throughout 2011, 102 wastewater samples were collected from the two mentioned wastewater treatment procedures. Results showed that the Sapovirus (SaV) frequency was approximately 29.4% using the real-time reverse transcription polymerase chain reaction (RT-PCR) technique, and about 16.6% using the conventional RT-PCR. Also, the SaV genogroups and genotypes were identified and genotyping revealed that all of the four Tunisian SaV strains obtained belonged to the two genogroups GIV.1 and GGI.3. In addition, two new genotypes, D and C, were detected. A moderate decrease in the SaV frequencies was observed at the exit of the two treatment processes and the SaV removal rate was around 90% in the natural oxidizing lagoons and 94% in the rotating biodisks procedure showing the temperate sensitivity of these viruses to the implemented biological wastewater. Therefore, an urgent disinfection process should be implemented downstream of the two biological treatment procedures for safe release of treated effluent in the different natural environments. Abbreviations: NoV: Noroviruses; SaV: Sapoviruses; EC: Electrical Conductivity; COD: Chemical Oxygen Demand; BOD5: Biological Oxygen Demand; SS: Suspended Solids; NH4-N: Ammonium Nitrogen; P-PO4: Ortho-Phosphate; AlCl3: aluminum chloride.

Prevalence and genetic diversity of human sapovirus associated with sporadic acute gastroenteritis in South China from 2013 to 2017

Human sapovirus (SaV) is an important viral agent for acute diarrhea worldwide, but timely prevalence data of human SaV in South China are still lacking. In this study, a 4-year surveillance was conducted to characterize the prevalence and genetic characteristics of the circulating SaV associated with sporadic diarrhea in South China. From November 2013 to October 2017, 569 fecal samples from patients with acute diarrhea were collected. SaV was detected in 11 samples with a positive rate of 1.93%. Three human genogroups of GI, GII, and GIV were identified, including five GI.1 strains, three GI.2 strains, one GI.3 strain, one GII.8 strain, and one GIV strain. Furthermore, multiple alignments of complete capsid protein VP1 genes of five local GI.1 strains and other available GI.1 strains in GenBank were performed. Average pairwise identities were calculated at 95.33% and 99.36% at nucleotide and amino acid levels, and only six variable amino acid sites were found during its 36-years' evolution process. GI.1 strains could be further phylogenetically divided into four clusters with an approximate temporal evolution pattern, and local strains belonged to Cluster-d with other four strains from China and Japan. In summary, SaV was identified as an etiological agent responsible for sporadic gastroenteritis in Guangzhou with a low prevalence rate as in other Chinese cities, but its high genetic diversity suggested the necessity of continuous SaV surveillance in the future.

Genome characteristics and molecular evolution of the human sapovirus variant GII.8

Human sapovirus is regarded as an important viral agent for acute diarrhea worldwide. GII.8, a recently reported genotype, has been detected in a few countries and regions. In this study, we obtained the first genome sequence of a sapovirus GII.8 strain isolated in mainland China, and comprehensively analyzed the genetic diversity and evolutionary process of this genotype. The viral genome of the new GII.8 Guangzhou strain GZ2014-L231 comprised 7433 nucleotides, including two ORFs. Pairwise alignments of the new genome with representative sequences of different genotypes showed inconsistent homology between different protein-encoding regions, of which NS1 and VP2 were found as the variable proteins, and NS3, NS5, and NS6/7 were found as the conserved ones. Compared with other reported GII.8 genomes, the Guangzhou strain introduced 34 new nucleotide changes and one new amino acid change. Phylogenetic analysis based on full-length VP1 sequences demonstrated that 11 GII.8 strains could be divided into 4 clusters A-D, with 88 SNP and 10 SAP spots occurred during their evolutionary process. The Guangzhou strain has higher homology with seven GII.8 strain detected after 2014, especially the US and Peruvian strains of 2015/2016, which have the identical VP1 amino acid sequences. Using a Bayesian coalescent method based on VP1 sequences, GII.8 was predicted to emerge in 2001 with the evolution rate of 1.45 × 10^-3 nucleotide substitutions/site/year (strict clock). In summary, the data in this study not only provided reference data from mainland China for sapovirus researches in future, but also firstly described the evolutionary process of the GII.8 genotype.

Human Sapovirus among Outpatients with Acute Gastroenteritis in Spain: A One-Year Study

Viral agents of human gastroenteritis affect people of all ages across the globe. As a mainly self-limiting disease, it is difficult to evaluate the real prevalence of etiological agents circulating in each region. Many of the analyzed outbreaks are caused by viruses of the family Caliciviridae, especially the genus Norovirus (NoV). Most studies have focused on other enteric viruses, leaving sapovirus (SaV) underestimated as an important emerging human threat. This one-year study analyzed clinical samples from hospital outpatients with acute gastroenteritis in Spain, with the aim of revealing the importance of human SaV as an emerging viral pathogen. A total of 2667 stools were tested using reverse transcription (RT)-qPCR to detect and quantify SaV. Sapovirus was detected in all age groups, especially in infants, children, and the elderly. The prevalence was 15.64% (417/2667), and was slightly higher in 0–2- and 3–5-year-olds (19.53% and 17.95%, respectively) and much lower in 13–18-year-olds (9.86%). Positive samples were detected throughout the year, with peaks of detection during autumn and the late winter to early spring months. The mean value for the quantified samples was 6.5 × 10⁵ genome copies per gram of stool (GC/g) (range 2.4 × 10³–6.6 × 10¹¹ GC/g). RT-nested PCR and sequencing were used for further genotyping. Genetic characterization showed a predominance of genogroup I (GI), followed by GII and GIV. The detection of multiple genotypes suggests the circulation of different strains without any clear tendency. The results obtained suggest SaV as the second major gastroenteritis agent after NoV in the region.

Broadly reactive real-time reverse transcription-polymerase chain reaction assay for the detection of human sapovirus genotypes

Sapoviruses are associated with acute gastroenteritis. Human sapoviruses are classified into four distinct genogroups (GI, GII, GIV, and GV) based on their capsid gene sequences. A TaqMan probe-based real-time reverse transcription-polymerase chain reaction (RT-PCR) assay that detects the representative strains of these four genogroups is widely used for screening fecal specimens, shellfish, and environmental water samples. However, since the development of this test, more genetically diverse sapovirus strains have been reported, which are not detectable by the previously established assays. In this study, we report the development of a broader-range sapovirus real-time RT-PCR assay. The assay can detect 2.5 × 10⁷ and 2.5 × 10 ¹ copies of sapovirus and therefore is as sensitive as the previous test. Analysis using clinical stool specimens or synthetic DNA revealed that the new system detected strains representative of all the 18 human sapovirus genotypes: GI.1-7, GII.1-8, GIV.1, and GV.1, 2. No cross-reactivity was observed against other representative common enteric viruses (norovirus, rotavirus, astrovirus, and adenovirus). This new assay will be useful as an improved, broadly reactive, and specific screening tool for human sapoviruses.

Prevalence of Human Sapovirus in Low and Middle Income Countries

Background

Sapovirus (SV) infection is a public health concern which plays an important role in the burden of diarrhoeal diseases, causing acute gastroenteritis in people of all ages in both outbreaks and sporadic cases worldwide.

Objective/Study Design

The purpose of this report is to summarise the available data on the detection of human SV in low and middle income countries. A systematic search on PubMed and ScienceDirect database for SV studies published between 2004 and 2017 in low and middle income countries was done. Studies of SV in stool and water samples were part of the inclusion criteria.

Results

From 19 low and middle income countries, 45 published studies were identified. The prevalence rate for SV was 6.5%. A significant difference (P=0) in SV prevalent rate was observed between low income and middle income countries. Thirty-three (78.6%) of the studies reported on children and 8 (19%) studies reported on all age groups with diarrhoea. The majority (66.7%) of studies reported on hospitalised patients with acute gastroenteritis. Sapovirus GI was shown as the dominant genogroup, followed by SV-GII.

Conclusion

The detection of human SV in low and middle income countries is evident; however the reports on its prevalence are limited. There is therefore a need for systematic surveillance of the circulation of SV, and their role in diarrhoeal disease and outbreaks, especially in low and middle income countries.

Intragenogroup Recombination in the Complete Genome Sequence of Human Sapovirus Circulating in Bangladesh

Human sapovirus (SaV) is responsible for severe gastroenteritis among infants and children. Research about the genetic configuration of SaV is scarce in Bangladesh. Here, we report the complete genome sequence of an SaV strain with intragenogroup recombination, isolated from an infant with severe diarrhea in Bangladesh in 2005.

First Complete Genome Sequences of Human Sapovirus Strains Classified as GI.3, GI.4, GI.6, GI.7, and GII.7

We report here the first complete genome sequences of genotype GI.3, GI.4, GI.6, GI.7, and GII.7 sapovirus strains, detected from fecal samples of acute gastroenteritis patients. Complete or nearly complete genome sequences of all 18 genotypes of human sapoviruses are now available for phylogenetic analysis and primer design.

Attempts to grow human noroviruses, a sapovirus, and a bovine norovirus in vitro

Noroviruses (NoVs) and Sapoviruses (SaVs) are enteric caliciviruses that have been detected in multiple mammalian species, including humans. Currently, efficient cell culture systems have been established only for murine NoVs and porcine SaV Cowden strain. Establishment of an efficient in vitro cell culture system for other NoVs and SaVs remains challenging; however, human NoV (HuNoV) replication in 3D cultured Caco-2 cells and a clone of Caco-2 cells, C2BBe1, human enteroids and in human B cells has been reported. In this study, we tested various cells and culture conditions to grow HuNoVs and a human SaV (HuSaV) to test the possibility of the propagation in different cells and culture conditions. We also attempted to grow a bovine NoV (BoNoV) in ex vivo organ cultures. We did not observe significant RNA level increases for HuSaV and BoNoV under our test conditions. HuNoV RNA levels increased to a maximum of ~600-fold in long-term Caco-2 cells that were cultured for 1–2 months in multi-well plates and inoculated with HuNoV-positive and bacteria-free human stool suspensions using serum-free medium supplemented with the bile acid, GCDCA. However, this positive result was inconsistent. Our results demonstrated that HuNoVs, BoNoV and HuSaV largely failed to grow in vitro under our test conditions. Our purpose is to share our findings with other researchers with the goal to develop efficient, reproducible simplified and cost-effective culture systems for human and animal NoVs and SaVs in the future.

Novel highly divergent sapoviruses detected by metagenomics analysis in straw-colored fruit bats in Cameroon

Sapoviruses (SaVs) belong to the Sapovirus genus, in the family Caliciviridae. They have been associated with gastroenteritis in humans and in pigs but not in other animals. In addition, some strains from pigs, chimpanzees and rodents show close sequence identity with human SaVs thereby suggesting the possibility of interspecies transmissions. Bats are known to be a major reservoir of zoonotic viruses, however, very little is known about the genetic diversity of SaVs in bats. To explore the genetic diversity of bat SaVs, fecal samples of Eidolon helvum and Epomophorus gambianus were treated according to the NetoVIR protocol and sequenced by Illumina technology. Nearly complete genome sequences of six highly divergent SaVs and one partial SaV (only VP1 region) were identified in Eidolon helvum and based on sequence identities and phylogenetic analysis, they potentially represent two novel genogroups, only distantly related to known SaVs. Furthermore, comparing these sequences with currently used screening primers and probes indicated that the novel SaVs would not be detected in routine epidemiological screening studies in humans in case an interspecies transmission would occur. Therefore, we designed and validated new primers that can detect both human and bat SaVs. In this study, we identified multiple novel bat SaVs, however, further epidemiological studies in humans are needed to unravel their potential role in gastroenteritis.

Development of a quantitative real-time PCR assay for sapovirus in children under 5-years-old in Regina Margherita Hospital of Turin, Italy

Gastroenteritis is a common disease in children. It is characterized by diarrhea, vomiting, abdominal pain, and fever. Sapovirus (SaV) is a causative agent of acute gastroenteritis, but it causes milder illness than do rotavirus and norovirus. There is high variability in the analytical performance of quantitative PCR-based assays among clinical laboratories. This study developed a reverse transcription real-time PCR method to detect SaV in fecal specimens collected from children under 5-years-old with acute gastroenteritis. Of 137 episodes of acute gastroenteritis, 15 (10.9%) were associated with SaV genomic detection, with a median viral load of 6.6(log10) ± 7.1(log10) genomes/mg fecal specimens. There was a significant difference in detection rate between males and females (9.48% (13/15) vs. 1.46% (2/15), p = 0.0232). Among the 15 SaV-positive cases, 6 were also positive for rotavirus. Viral RNA recovery rate ranged from 46% to 77% in the manual RNAzol protocol and from 31% to 90% in the automated Maxwell protocol. We also studied whether human genomic DNA influences the sensitivity of the assay: its presence caused a decrease in PCR sensitivity. The development of a laboratory-designed real-time PCR TaqMan assay for quantitative detection of SaV and the optimization and standardization of this assay, using stools of children with acute gastroenteritis, are described.

Complete genome sequence of a sapovirus from a child in Zhejiang, China

Although Sapovirus (Caliciviridae) has been accepted as one of the causes of acute gastroenteritis worldwide, little is known about the genetic characteristics of the whole genome of sapoviruses in China, especially those that infect humans. Here we report the complete genome sequence of a sapovirus strain, Human/Zhejiang1/2015/China, obtained from a child with acute gastroenteritis in Hangzhou, Zhejiang Province, China. Samples were collected and delivered to the CDC laboratories and were detected by RT-PCR. Sanger sequencing was used to obtain the full genome and molecular characterization of the genome was determined. A phylogenetic analysis of the genome was also performed. The results indicated that Human/Zhejiang1/2015/China belongs to Genogroup I. No recombination events were detected. This is the first complete sequence from a child to be reported in China. The sequence information is important for surveillance of this emerging gastrointestinal infection.

The prevalence of enteric RNA viruses in stools from diarrheic and non-diarrheic people in southwestern Alberta, Canada

Southwestern Alberta is a region of Canada that has high rates of enteritis as well as high densities of livestock. The presence of enteric RNA viruses, specifically norovirus (NoV) GI, GII, GIII, GIV; sapovirus (SaV); rotavirus (RV); and astrovirus (AstV), was evaluated in stools from diarrheic (n = 2281) and non-diarrheic (n = 173) people over a 1-year period in 2008 and 2009. Diarrheic individuals lived in rural (46.6 %) and urban (53.4 %) settings and ranged in age from less than 1 month to 102 years, and the highest prevalence of infection in these individuals was in November. In all, viruses were detected in diarrheic stools from 388 individuals (17.0 %). NoV GII was the most frequently detected virus (8.0 %; n = 182) followed by SaV (4.3 %; n = 97), RV (2.0 %; n = 46), AstV (1.8 %; n = 42), NoV GI (0.9 %; n = 20), and NoV GIV (0.1 %; n = 1). Animal NoV GIII was never detected. The prevalence of mixed viral infections in diarrheic individuals was 2.8 % (n = 11). Children from 1 to 5 years of age accounted for the highest prevalence of positive stools, followed by the elderly individuals (≥70 years). Only NoV GII (1.2 %; n = 2) and SaV (1.2 %; n = 2) were detected in stools from non-diarrheic people. Sequence analysis of a subset of stools revealed homology to NoV, SaV and RV sequences from humans but not to strains from non-human animals. The results of this study do not support the hypothesis that viruses of animal origin have a significant impact on the occurrence of acute gastroenteritis caused by RNA enteric viruses in people living in southwestern Alberta.

Divergent Sapovirus Strains and Infection Prevalence in Wild Carnivores in the Serengeti Ecosystem: A Long-Term Study

The genus Sapovirus, in the family Caliciviridae, includes enteric viruses of humans and domestic animals. Information on sapovirus infection of wildlife is limited and is currently lacking for any free-ranging wildlife species in Africa. By screening a large number of predominantly fecal samples (n = 631) obtained from five carnivore species in the Serengeti ecosystem, East Africa, sapovirus RNA was detected in the spotted hyena (Crocuta crocuta, family Hyaenidae), African lion (Panthera leo, family Felidae), and bat-eared fox (Otocyon megalotis, family Canidae), but not in golden or silver-backed jackals (Canis aureus and C. mesomelas, respectively, family Canidae). A phylogenetic analysis based on partial RNA-dependent RNA polymerase (RdRp) gene sequences placed the sapovirus strains from African carnivores in a monophyletic group. Within this monophyletic group, sapovirus strains from spotted hyenas formed one independent sub-group, and those from bat-eared fox and African lion a second sub-group. The percentage nucleotide similarity between sapoviruses from African carnivores and those from other species was low (< 70.4%). Long-term monitoring of sapovirus in a population of individually known spotted hyenas from 2001 to 2012 revealed: i) a relatively high overall infection prevalence (34.8%); ii) the circulation of several genetically diverse variants; iii) large fluctuations in infection prevalence across years, indicative of outbreaks; iv) no significant difference in the likelihood of infection between animals in different age categories. The likelihood of sapovirus infection decreased with increasing hyena group size, suggesting an encounter reduction effect, but was independent of socially mediated ano-genital contact, or the extent of the area over which an individual roamed.

Epidemiological profile and genetic diversity of sapoviruses (SaVs) identified in children suffering from acute gastroenteritis in Pune, Maharashtra, Western India, 2007–2011

Sapoviruses (SaVs) are responsible for sporadic cases and outbreaks of acute gastroenteritis. Despite this, few studies in India have focused on the epidemiological investigation of SaV in cases of acute gastroenteritis. The aim of this study was to understand the molecular epidemiology, genetic diversity and clinical impact of SaV in diarrhoeic children from Pune, Western India. Between 2007 and 2011, a total of 985 faecal samples from diarrhoeic cases and non-diarrhoeic controls were collected and examined for the presence of SaV by nested RT–PCR. SaV was detected in 2·7% (21/778) of the cases and 1·9% (4/207) of the controls. We observed that the majority of SaV mono-infections caused severe gastroenteritis (67%) with clinical manifestations of diarrhoea (100%), vomiting (73%) and dehydration (80%). All known human SaV genogroups were detected in the study. At least eight genotypes were identified from cases and controls. Genogroups GIV and GV, along with genotypes GI.5, GII.4 and GII.6, were discovered for the first time in India. Two GII.4 study strains were found to be 98·5–99% identical, having a novel intra-genogroup recombinant (GII.1/GII.4) recently reported from the Philippines, suggesting probable evidence of recombination. The circulation pattern of SaV genotypes varied during the study period, with GII.1 being predominant in 2007 and 2009, GIV.1 in 2008, and GV.1 in 2011.

Human Sapovirus in Mussels from Ría do Burgo, A Coruña (Spain)

The prevalence and genetical diversity of human Sapovirus were studied during an 18-month study in Ría do Burgo, an estuary nearby the city of A Coruña in Galicia (NW Spain). Sapovirus was detected using RT-qPCR procedure in 30 out of 80 mussel samples (37.5 %). Quantifications ranged from 2.2 × 10(3) to 2.1 × 10(5) RNA copies per gram of digestive tissue. Detection occurred mainly during the cold and rainy seasons of the period studied. Sequences obtained could be distributed into 5 genotypes being the most abundant GI.1 and GI.3. Results obtained indicate that the hydrodynamic characteristics of the harvesting area and the proximity of population density clearly influence the presence of the virus in shellfish.

Human and Animal Viruses in Food (Including Taxonomy of Enteric Viruses)

In recent years, there has been an increase in the incidence of foodborne diseases worldwide, with viruses now being recognized as a major cause of these illnesses. The most common viruses implicated in foodborne disease are enteric viruses, which are found in the human gastrointestinal tract, excreted in human feces and transmitted by the fecal-oral route. Many different viruses are found in the gastrointestinal tract but not all are recognized as foodborne pathogens. The diseases caused by enteric viruses fall into three main types: gastroenteritis, enterically transmitted hepatitis, and illnesses that can affect other parts of the body such as the eye, the respiratory system and the central nervous system leading to conjunctivitis, poliomyelitis, meningitis and encephalitis. Viral pathogens excreted in human feces include noroviruses, sapoviruses, enteroviruses, adenoviruses, hepatitis A virus (HAV), hepatitis E virus (HEV), rotaviruses, and astroviruses. Most of these viruses have been associated with foodborne disease outbreaks. Noroviruses and HAV are commonly identified as foodborne causes of gastroenteritis and acute hepatitis, respectively.

First detection and molecular characterization of sapoviruses and noroviruses with zoonotic potential in swine in Ethiopia

Noroviruses (NoVs) and sapoviruses (SaVs), which belong to the family Caliciviridae, are important human and animal enteric pathogens with zoonotic potential. In Ethiopia, no study has been done on the epidemiology of animal NoVs and SaVs. The aim of this study was to detect and characterize NoVs and SaVs from swine of various ages. Swine fecal samples (n = 117) were collected from commercial farms in Ethiopia. The samples were screened for caliciviruses by reverse transcription polymerase chain reaction (RT-PCR) using universal and genogroup-specific primer pairs. Phylogenetic analysis was conducted using a portion of the RNA-dependent RNA polymerase (RdRp) region and the VP1 region of genome sequences of caliciviruses. Among 117 samples, potential caliciviruses were detected by RT-PCR in 17 samples (14.5 %). Of the RT-PCR-positive fecal samples, four were sequenced, of which two were identified as human NoV GII.1 and the other two as porcine SaV GIII. The porcine SaV strains that were detected were genetically related to the porcine enteric calicivirus Cowden strain genogroup III (GIII), which is the prototype porcine SaV strain. No porcine NoVs were detected. Our results showed the presence of NoVs in swine that are most similar to human strains. These findings have important implications for NoV epidemiology and food safety. Therefore, continued surveillance of NoVs in swine is needed to define their zoonotic potential, epidemiology and public and animal health impact. This is the first study to investigate enteric caliciviruses (noroviruses and sapoviruses) in swine in Ethiopia.

Etiological Role and Repeated Infections of Sapovirus among Children Aged Less than 2 Years in a Cohort Study in a Peri-urban Community of Peru

Human sapovirus has been shown to be one of the most important etiologies in pediatric patients with acute diarrhea. However, very limited data are available about the causative roles and epidemiology of sapovirus in community settings. A nested matched case-control study within a birth cohort study of acute diarrhea in a peri-urban community in Peru from 2007 to 2010 was conducted to investigate the attributable fraction (AF) and genetic diversity of sapovirus. By quantitative reverse transcription-real-time PCR (qPCR) sapovirus was detected in 12.4% (37/299) of diarrheal and 5.7% (17/300) of nondiarrheal stools (P = 0.004). The sapovirus AF (7.1%) was higher in the second year (13.2%) than in the first year (1.4%) of life of children. Ten known genotypes and one novel cluster (n = 5) within four genogroups (GI, GII, GIV, and GV) were identified by phylogenetic analysis of a partial VP1 gene. Further sequence analysis of the full VP1 gene revealed a possible novel genotype, tentatively named GII.8. Notably, symptomatic reinfections with different genotypes within the same (n = 3) or different (n = 5) genogroups were observed in eight children. Sapovirus exhibited a high attributable burden for acute gastroenteritis, especially in the second year of life, of children in a Peruvian community. Further large-scale studies are needed to understand better the global burden, genetic diversity, and repeated infections of sapovirus.

Diverse sapovirus genotypes identified in children hospitalised with gastroenteritis in selected regions of South Africa

BACKGROUND

Sapoviruses (SaVs) are recognised as causative agents of gastroenteritis worldwide. However, data on the genetic diversity of this virus in Africa are lacking, particularly in the form of current long-term studies.

OBJECTIVE

To determine the genetic diversity of SaVs in children hospitalised with gastroenteritis in South Africa (SA).

STUDY DESIGN

From April 2009 to December 2013, SaVs were characterised from stool specimens from children hospitalised with gastroenteritis in four provinces of SA.

RESULTS

Fourteen different SaV genotypes were identified from the 221 strains that were characterised. Genogroup (G) IV predominated overall and was detected in 24% (53/221) of specimens. The other identified genotypes included six belonging to GI (GI.1-GI.3, GI.5, GI.6, and GI.7) and seven belonging to GII (GII.1-GII.7).

CONCLUSION

This study has provided the first comprehensive data on the genetic diversity of SaVs in a clinical setting in SA, contributing to the global knowledge of this virus.

Epidemics of GI.2 sapovirus in gastroenteritis outbreaks during 2012-2013 in Osaka City, Japan

Sapovirus (SaV) is a causative agent of gastroenteritis in humans in both sporadic cases and outbreaks. During the period from January 2005 to August 2014, SaV was detected in 30 (5.9%) of 510 gastroenteritis outbreaks in Osaka City, Japan using real-time RT-PCR. Seasonal distribution of SaV-associated outbreaks revealed an increase during the 2011-2012 season and the highest frequency of outbreaks during the 2012-2013 season. Genotyping analysis based on the capsid region demonstrated that the most common genotype was GI.2 (36.7%), in which the strains were closely related. The comparison of complete capsid gene sequences with 18 GI.2 strains (7 strains in this study and 11 from GenBank) between 1990 and 2013 showed that GI.2 strains were classified into at least three genetic clusters (1990-2000, 2004-2007, and 2008-2013) with chronologically unique amino acid residues and accumulation of mutations in the predicted P domain, suggesting the one of the causes of emergence and spread of GI.2 strains. This study will also be helpful for understanding the evolutionary mechanism of the SaV genome.