Salivirus type 1 and type 2 in patients with acute gastroenteritis, Germany

Human Bocavirus in children with acute gastroenteritis in Piedmont, Italy

BACKGROUND

Gastroenteritis is a common disease in children, characterized by diarrhea, vomiting, abdominal pain, and fever. Co-detection of human Bocavirus (HBoV) with other gastroenteric viruses was reported a lot in patients with acute gastroenteritis.

METHODS

This paper presents the real-time RT-PCR Taqman assay for the detection and quantification of HBoV for clinical fecal samples collected from hospitalized children with acute gastroenteritis in Piedmont.

RESULTS

All fecal specimens were tested for the presence of HBoV with specific primers and probe. A total of 17 out of 123 (13.92%) episodes of acute gastroenteritis were associated with HBoV genomic detection with median viral load 6864.75±19784.79 genomes/mg fecal specimens. Among the 17 HBoV-positive cases, 11 were also positive for other viral pathogens, including Rotavirus (N.=2), astrovirus (N.=1), norovirus GII (N.=6), norovirus GI (N.=2). Two cases were positive for more than one virus including norovirus GII and norovirus GI (N.=1) and Rotavirus, sapovirus and astrovirus (N.=1). A higher detection of HBoV infections was observed in winter, and peaking in February.

CONCLUSIONS

Although HBoV is suspected to be responsible for gastroenteritis in children, our data showed that this association was uncertain since no difference was observed in term of viral load in the group with single infection of HBoV and group of coinfections with other viral agent.

Rotavirus vaccine-derived cases in Belgium: Evidence for reversion of attenuating mutations and alternative causes of gastroenteritis

Since the introduction of live-attenuated rotavirus vaccines in Belgium in 2006, surveillance has routinely detected rotavirus vaccine-derived strains. However, their genomic landscape and potential role in gastroenteritis have not been thoroughly investigated. We compared VP7 and VP4 nucleotide sequences obtained from rotavirus surveillance with the Rotarix vaccine sequence. As a result, we identified 80 vaccine-derived strains in 5125 rotavirus-positive infants with gastroenteritis from 2007 to 2018. Using both viral metagenomics and reverse transcription qPCR, we evaluated the vaccine strains and screened for co-infecting enteropathogens. Among the 45 patients with known vaccination status, 39 were vaccinated and 87% received the vaccine less than a month before the gastroenteritis episode. Reconstruction of 30 near complete vaccine-derived genomes revealed 0-11 mutations per genome, with 88% of them being non-synonymous. This, in combination with several shared amino acid changes among strains, pointed at selection of minor variant(s) present in the vaccine. We also found that some of these substitutions were true revertants (e.g., F167L on VP4, and I45T on NSP4). Finally, co-infections with known (e.g., Clostridioides difficile and norovirus) and divergent or emerging (e.g., human parechovirus A1, salivirus A2) pathogens were detected, and we estimated that 35% of the infants likely had gastroenteritis due to a 'non-rotavirus' cause. Conversely, we could not rule out the vaccine-derived gastroenteritis in over half of the cases. Continued studies inspecting reversion to pathogenicity should monitor the long-time safety of live-attenuated rotavirus vaccines. All in all, the complementary approach with NGS and qPCR provided a better understanding of rotavirus vaccine strain evolution in the Belgian population and epidemiology of co-infecting enteropathogens in suspected rotavirus vaccine-derived gastroenteritis cases.

Viruses associated with ill health in wild chimpanzees

Viral infection is a major cause of ill health in wild chimpanzees (Pan troglodytes), but most evidence to date has come from conspicuous disease outbreaks with high morbidity and mortality. To examine the relationship between viral infection and ill health during periods not associated with disease outbreaks, we conducted a longitudinal study of wild eastern chimpanzees (P. t. schweinfurthii) in the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We collected standardized, observational health data for 4 years and then used metagenomics to characterize gastrointestinal viromes (i.e., all viruses recovered from fecal samples) in individual chimpanzees before and during episodes of clinical disease. We restricted our analyses to viruses thought to infect mammals or primarily associated with mammals, discarding viruses associated with nonmammalian hosts. We found 18 viruses (nine of which were previously identified in this population) from at least five viral families. Viral richness (number of viruses per sample) did not vary by health status. By contrast, total viral load (normalized proportion of sequences mapping to viruses) was significantly higher in ill individuals compared with healthy individuals. Furthermore, when ill, Kanyawara chimpanzees exhibited higher viral loads than Ngogo chimpanzees, and males, but not females, exhibited higher infection rates with certain viruses and higher total viral loads as they aged. Post-hoc analyses, including the use of a machine-learning classification method, indicated that one virus, salivirus (Picornaviridae), was the main contributor to health-related and community-level variation in viral loads. Another virus, chimpanzee stool-associated virus (chisavirus; unclassified Picornavirales), was associated with ill health at Ngogo but not at Kanyawara. Chisavirus, chimpanzee adenovirus (Adenoviridae), and bufavirus (Parvoviridae) were also associated with increased age in males. Associations with sex and age are consistent with the hypothesis that nonlethal viral infections cumulatively reflect or contribute to senescence in long-lived species such as chimpanzees.

Salivirus infection: Systematic review and meta-analysis of association with gastrointestinal symptoms in children

Salivirus (SaV) is a newly described member of the family Picornaviridae that has been associated with gastrointestinal (GI) symptoms, particularly in children. The aim of the present study was to evaluate the prevalence of SaV in symptomatic children and its potential association with GI complications. A systematic search was conducted from 01 December 2009 to 10 December 2020, in three major English databases, including Scopus, PubMed and Web of Science as well as Google scholar search engine. Random effect model-based overall prevalence and odds ratio (OR) were assessed in cross-sectional and case-control studies by STATA 14.1. The random effect model-based pooled prevalence of SaV was 1.6% (95% CI, 0.010-0.022%) and overall OR for all eight case-control studies indicated an association (3.19 with 95% confidence interval 1.35-7.57) that was not statistically significant, due to the small number of studies available. More comprehensive case-control studies in multiple geographies should be conducted on the prevalence of SaV in children.

Bufavirus, Cosavirus, and Salivirus in Diarrheal Italian Infants

Three newly discovered viruses have been recently described in diarrheal patients: Cosavirus (CosV) and Salivirus (SalV), 2 picornaviruses, and bufavirus (BuV), a parvovirus. The detection rate and the role of these viruses remain to be established in acute gastroenteritis (AGE) in diarrheal Italian infants. From November 2016 to November 2017, stool samples were collected from 160 children <5 years old suffering from AGE and attending the Children's Hospital in Turin, Italy. During the study period, 1 (0.5%) sample was positive for 1 of the 3 investigated viruses: 0 (0%) CosV, 1 (0.5%) SalV, and 0 (0%) BuV, whereas 42 (26.0%) children were infected with rotavirus and 2 (1%) with adenovirus. No mixed infections involving the 3 viruses were found. Although these viruses are suspected to be responsible for AGE in children, our data showed that this association was uncertain. Therefore, further studies with large cohorts of healthy and diarrheal children will be needed to evaluate their clinical role in AGE.

Molecular Detection of Human Salivirus in Italy Through Monitoring of Urban Sewages

Salivirus (SalV) is a newly discovered virus associated to acute gastroenteritis in humans. In Italy, its prevalence and genetic diversity is unknown. To reduce this knowledge gap, 124 sewage samples collected throughout the country were analyzed for SalV by two nested RT-PCRs targeting the 5'UTR and the 3D regions and by real-time RT-qPCR. Virus RNA was detected in 37 (29.8%) samples; of these, 24 could be characterized and all belonged to genotype A1. Viral concentrations ranged between 2.8 × 10³ and 1.9 × 10⁵ genome copies per liter. This is the first report of SalV occurrence in water environments in Italy, suggesting that SalV infection is not uncommon in this country.

Occurrence of Salivirus in Sewage and River Water Samples in Karaj, Iran

Salivirus is a newly discovered virus which seems to be related to acute gastroenteritis in children. Salivirus may infect susceptible children by fecal-oral route after exposure to contaminated water. The present study aims to evaluate the occurrence and quantity of Salivirus in treated and untreated sewage water and river water samples collected in the city of Karaj, Iran by reverse transcription-quantitative PCR assay. A total of 50 samples were collected from environmental waters containing 22 treated and untreated sewage water in volume of 1 l and 28 river water samples in volume of 5 l were included in this study. After viral RNA extraction, the Real-time PCR was performed to amplify the 5'UTR sequence of Salivirus genome and viral load was assessed. Out of the 50 samples tested, the Salivirus genomic RNA was identified in 5/12 (41.6%) of treated and 3/10 (30%) of untreated sewage samples and in 8/28 (28.5%) of river water samples. The maximum viral load was 4.8 × 10⁶ copies/l in treated sewage water sample in September and the lower viral load was 4 × 10⁵ copies/l related to treated sewage water taken in December. This is the first report of Salivirus occurrence in the environmental waters in Iran. The viral prevalence of Salivirus in each of the three sets of tested samples was within low to moderate in range.

Molecular Detection of Human Astrovirus in Children With Gastroenteritis, Northern Italy

BACKGROUND

Human astroviruses have increasingly been identified and are important agents of diarrheal disease, especially in infants and young children. This article presents the real-time polymerase chain reaction TaqMan assay for the detection and quantification of human astrovirus for clinical fecal samples collected from hospitalized children with acute gastroenteritis in Piedmont (northern Italy) from December 2014 to November 2015.

METHODS

A total of 159 fecal specimens from hospitalized children with acute gastroenteritis, previously screened for rotavirus, adenovirus, norovirus, human parechovirus, salivirus and sapovirus, were tested for human astrovirus.

RESULTS

The most commonly detected virus was norovirus GII (33.8%), followed by rotavirus (21.3%), sapovirus (10.9%), human parechovirus (8%), norovirus GI (6.7%), adenovirus (1%) and salivirus (0.52%). A total of 30 of 159 (18.87%) episodes of acute gastroenteritis were associated with human astrovirus genomic detection.

CONCLUSIONS

Our data showed that the detection rate of astrovirus in diarrheal children (18.87%) was higher than observed in other countries, where they were reported in diarrheal children in 10.3%-0.8% of patients and a mean incidence worldwide of 11%. Our data showed that the detection rate of astrovirus in pediatric gastroenteritis was greater than previously reported in Italy.

Salivirus infection in children with diarrhea, Thailand

A new member of the Picornaviridae family named salivirus, and also known as klassevirus, was identified recently from the feces of children with gastroenteritis. At present, it remains unclear whether salivirus is associated with gastroenteritis in humans and epidemiological data are very limited. To investigate the prevalence of salivirus in Thailand, we performed molecular screening of fecal samples from children hospitalized with acute gastroenteritis in Chiang Mai, Thailand during 2015-2016 through the application of RT-nested PCR. Salivirus was detected in 1 out of 229 (0.44%) fecal samples tested and it belonged to genotype A1, based on nucleotide sequences of the 5'UTR, VP1, and 3D regions. This is the first report of salivirus infection in young children with acute diarrhea in Thailand.

Saliviruses-the first knowledge about a newly discovered human picornavirus

The salivirus, first discovered in the year 2009, is a member of the large and growing family Picornaviridae. At present, the genus Salivirus contains 1 species Salivirus A and 2 genotypes, Salivirus A1 and Salivirus A2. Salivirus has been identified in humans and chimpanzees and may cause acute gastroenteritis in humans, having been detected in 0% to 8.7% of fecal samples collected from gastroenteritis in different human populations. Salivirus is ubiquitous in wastewater of human origin and river water specimens worldwide and represents a potential indicator human RNA virus for monitoring of environmental samples. This review summarizes the current knowledge on saliviruses including discovery, taxonomy, genome structure, and genetic diversity; covers all aspects of infection including epidemiology, molecular epidemiology, clinical feature, host species, environmental characteristics, and laboratory diagnosis; and gives a summary of possible future perspectives.

Clinico-epidemiology and genetic diversity of Salivirus in acute gastroenteritis cases from Pune, Western India: 2007-2011

Acute gastroenteritis is a leading cause of mortality in children from developing countries. Recently, Salivirus has been frequently detected in acute gastroenteritis patients, suggesting its possible aetiological role. Conflicting reports available on disease association of Salivirus have made it difficult to ascertain their causative role. The overall epidemiology and clinical features of Salivirus infections are poorly understood. The present five year study was undertaken to investigate the presence and genetic diversity of Salivirus in acute gastroenteritis cases from Pune, Western India and to determine the clinico-epidemiological features of Salivirus infections. A total of 985 faecal samples (778 acute gastroenteritis and 207 asymptomatic controls), collected from three local hospitals (Jan2007-Dec2011) were examined for the presence of Salivirus by RT-PCR. Molecular characterization was performed by PCR amplification of the 3D and VP regions. Frequency of Salivirus detection in cases (2.6%) and controls (1.93%) was not significantly different (p = 0.57). Co-infection with other enteric viruses was seen in 50% of the cases. Comparison of clinical features between Salivirus mono and mixed infections revealed that Salivirus alone did not exacerbate gastroenteritis. The frequency of diarrhoea and overall clinical severity of mixed infections was significantly greater than mono infections (p = 0.02). Based on clinical findings, our study suggests that Salivirus does not cause severe gastroenteritis. Phylogenetic analysis indicated that study strains belonged to Salivirus A1 and formed 2 distinct clusters which shared nucleotide identities of 94.1-96.2% and 88.9-93.8% between themselves in 3D and VP regions, respectively. Interestingly, the more divergent Cluster2 strains shared a low nucleotide identity with the closest reference strain in both regions (~95% in 3D and ~92% in VP) suggesting that they could represent a variant type of Salivirus A1. The genetic diversity in strains detected from study region, emphasizes the need for Salivirus surveillance from other regions of India.

A cluster of salivirus A1 (Picornaviridae) infections in newborn babies with acute gastroenteritis in a neonatal hospital unit in Hungary

Salivirus (family Picornaviridae) may be associated with acute gastroenteritis in humans, but there have been no reports of salivirus outbreaks. Salivirus A1 infection with faecal virus concentrations of 2.1-2.6 × 10(9)/g were identified retrospectively in newborn babies, between the ages of 1.5 and 5 days, with apparent clinical symptoms of diarrhea (100 %), fever (40 %), vomiting (40 %), and loss of appetite (40 %) in a neonatal hospital unit in Hungary in July 2013. The complete genome sequence of the salivirus (including the 5'-terminal end) was determined. Salivirus mono-infection may be associated with gastroenteritis in babies who are a few days old. Salivirus testing should be done in public health laboratories in gastroenteritis outbreaks with unknown etiology.

Characterization of a Salivirus (Picornaviridae) from a Diarrheal Child in Guatemala

The complete genome sequence of a salivirus was identified in a stool sample from a Guatemalan child with acute gastroenteritis during a 2009 norovirus outbreak. This genome (genotype A1 strain GUT/2009/A-1746) shares 82% to 94% genome-wide nucleotide identity with saliviruses from the United States, China, Germany, and Nigeria, representing the first salivirus sequence from Central America.