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

Tohma, Kentaro; Kulka, Michael; Coughlan, Suzie; Green, Kim Y.; Parra, Gabriel I.

doi:10.3390/v12050516

Cited by 17 publications

(13 citation statements)

References 73 publications

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“…Similar observations were made previously in diarrheic cases in Southeast Asia ( 55 ), even though subgroup B and C adenoviruses are commonly associated with respiratory infections ( 59 ). Few members of the Caliciviridae (including the globally circulating SV GI.2) were detected at low prevalence in our study, which was rather unexpected, as they are frequently reported in gastroenteritis ( 15 , 60 ).…”

Section: Discussionsupporting

confidence: 41%

High Prevalence of Coinfecting Enteropathogens in Suspected Rotavirus Vaccine Breakthrough Cases

et al. 2021

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Despite the global use of rotavirus vaccines, vaccine breakthrough cases remain a pediatric health problem. In this study, we investigated suspected rotavirus vaccine breakthrough cases using next-generation sequencing (NGS) based viral metagenomics (n=102) and a panel of semi-quantitative reverse transcription PCR (RT-qPCR) (n=92) targeting known enteric pathogens. Overall, we identified co-infections in 80% of the cases. Enteropathogens such as Adenovirus (32%), Enterovirus (15%), diarrheagenic Escherichia coli (1-14%), Astrovirus (10%), Blastocystis spp. (10%), Parechovirus (9%), Norovirus (9%), Clostridium difficile (9%), Dientamoeba fragilis (9%), Sapovirus (8%), Campylobacter jejuni (4%) and Giardia lamblia (4%) were detected. Except for a few reassortant rotavirus strains, unusual genotypes or genotype combinations were not present. However, in addition to well-known enteric viruses, divergent variants of enteroviruses and non-classic astroviruses were identified using NGS. We estimated that in 31.5% of the patients, rotavirus was likely not the cause of gastroenteritis and in 14.1% of the patients, it contributed together with another pathogen(s) to disease. The remaining 54.4% of the patients likely had a ‘true vaccine breakthrough infection’. The high prevalence of alternative enteropathogens in the suspected rotavirus vaccine breakthrough cases suggests that gastroenteritis is often the result of a co-infection, and the rotavirus vaccine effectiveness might be underestimated in clinical and epidemiological studies.

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Section: Discussionsupporting

confidence: 41%

High Prevalence of Coinfecting Enteropathogens in Suspected Rotavirus Vaccine Breakthrough Cases

et al. 2021

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“…To trace the distribution of sapovirus genotypes in different settings and geographical areas is relevant, as this information is epidemiologically useful to design and develop broadly protective sapovirus vaccines [ 1 ]. Even though several sapovirus recombinant strains of both intragenogroup and intergenogroup recombinations have been reported [ 18 , 25 , 44 ], sequence analyses from five major genotypes (GI.1, GI.2, GII.1, GII.3, and GIV.1) have shown, contrary to noroviruses, limited intra-genotypic diversification for over 40 years [ 45 ]. The relationship between sapovirus genotypes and serotypes is still unknown and more studies are needed to clarify this question, but this observation gives hope to the future development of sapovirus vaccines.…”

Section: Discussionmentioning

confidence: 99%

Epidemiological and Genetic Characterization of Sapovirus in Patients with Acute Gastroenteritis in Valencia (Spain)

Oliveira-Tozetto

Santiso-Bellón

Ferrer-Chirivella

et al. 2021

Viruses

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Sapovirus is a common cause of acute gastroenteritis in all age groups. Sapovirus infections are seldom investigated in Spain, and its epidemiology in the country is not well known. The use of molecular diagnostic procedures has allowed a more frequent detection of sapoviruses in patients with diarrhea. A total of 2545 stool samples from patients with acute gastroenteritis attended from June 2018 to February 2020 at the Clinic University Hospital in Valencia, Spain, were analyzed by reverse transcription (RT) and real-time multiplex PCR (RT-PCR) to investigate the etiology of enteric infections. Sapovirus was the second enteric virus detected with a positive rate of 8%, behind norovirus (12.2%) and ahead of rotavirus (7.1%), astrovirus (4.9%) and enteric adenoviruses (2.9%). Most sapovirus infections occurred in infants and young children under 3 years of age (74%) with the highest prevalence in autumn and early winter. Coinfections were found in 25% of the patients with sapovirus diarrhea, mainly with other enteric viruses. Genotyping demonstrated the circulation of seven different genotypes during the study period, with a predominance of genotypes GI.1, GI.2, and GII.1. Phylogenetic analysis showed that genogroup GII strains form a cluster separated from genogroup GI and GV, being genotype GV.1 strains related to genotype GI.1 and GI.2 strains.

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“…The genome sequences of some GIII strains shared only 85.8% nt identities. Both intra‐ and inter‐genogroup recombinant strains have been reported for porcine SaV (Kuroda et al., 2017; Li et al., 2017; Wang et al., 2020; Wang et al., 2005) as well as human SaV (Dey et al., 2018; Kumthip et al., 2020; Lasure & Gopalkrishna, 2017; Liu et al., 2015; Tohma et al., 2020). However, most of the recombinant studies were performed with reference strains and few field strains have been investigated for recombination.…”

Section: Discussionmentioning

confidence: 99%

Genetic characterization of porcine sapoviruses identified from pigs during a diarrhoea outbreak in Iowa, 2019

Shen

Zhang

Gauger

et al. 2021

Transbounding Emerging Dis

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Porcine sapovirus (SaV) was first identified by electron microscopy in the United States in 1980 and has since been reported from both asymptomatic and diarrhoeic pigs usually in mixed infection with other enteric pathogens. SaV as the sole aetiological agent of diarrhoea in naturally infected pigs has not previously been reported in the United States. Here, we used four independent lines of evidence including metagenomics analysis, real‐time RT‐PCR (rRT‐PCR), histopathology, and in situ hybridization to confirm porcine SaV genogroup III (GIII) as the sole cause of enteritis and diarrhoea in pigs. A highly sensitive and specific rRT‐PCR was established to detect porcine SaV GIII. Examination of 184 faecal samples from an outbreak of diarrhoea on a pig farm showed that pigs with clinical diarrhoea had significantly lower Ct values (15.9 ± 0.59) compared to clinically unaffected pigs (35.8 ± 0.71). Further survey of 336 faecal samples from different states in the United States demonstrated that samples from pigs with clinical diarrhoea had a comparable positive rate (45.3%) with those from asymptomatic pigs (43.1%). However, the SaV‐positive pigs with clinical diarrhoea had significantly higher viral loads (Ct = 26.0 ± 0.5) than the SAV‐positive but clinically healthy pigs (Ct = 33.2 ± 0.9). Phylogenetic analysis of 20 field SaVs revealed that all belonged to SaV GIII and recombination analysis indicated that intragenogroup recombination had occurred within the field isolates of SaV GIII. These results suggest that porcine SaV GIII plays an important aetiologic role in swine enteritis and diarrhoea and rRT‐PCR is a reliable method to detect porcine SaV. Our findings provide significant insights to better understand the epidemiology and pathogenicity of porcine SaV infection.

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

Cited by 17 publications

References 73 publications

High Prevalence of Coinfecting Enteropathogens in Suspected Rotavirus Vaccine Breakthrough Cases

High Prevalence of Coinfecting Enteropathogens in Suspected Rotavirus Vaccine Breakthrough Cases

Epidemiological and Genetic Characterization of Sapovirus in Patients with Acute Gastroenteritis in Valencia (Spain)

Genetic characterization of porcine sapoviruses identified from pigs during a diarrhoea outbreak in Iowa, 2019

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