Saliviruses-the first knowledge about a newly discovered human picornavirus

Ten different viral agents infecting and co-infecting children with acute gastroenteritis in Southern Italy: Role of known pathogens and emerging viruses during and after COVID-19 pandemic

Acute gastroenteritis (AGE) represents a world public health relevant problem especially in children. Enteric viruses are the pathogens mainly involved in the episodes of AGE, causing about 70.00% of the cases. Apart from well-known rotavirus (RVA), adenovirus (AdV) and norovirus (NoV), there are various emerging viral pathogens potentially associated with AGE episodes. In this study, the presence of ten different enteric viruses was investigated in 152 fecal samples collected from children hospitalized for gastroenteritis. Real time PCR results showed that 49.3% of them were positive for viral detection with the following prevalence: norovirus GII 19.7%, AdV 15.8%, RVA 10.5%, human parechovirus (HPeV) 5.3%, enterovirus (EV) 3.3%, sapovirus (SaV) 2.6%. Salivirus (SalV), norovirus GI and astrovirus (AstV) 1.3% each, aichivirus (AiV) found in only one patient. In 38.2% of feces only one virus was detected, while co-infections were identified in 11.8% of the cases. Among young patients, 105 were ≤5 years old and 56.0% tested positive for viral detection, while 47 were >5 years old with 40.0% of them infected. Results obtained confirm a complex plethora of viruses potentially implicated in gastroenteritis in children, with some of them previously known for other etiologies but detectable in fecal samples. Subsequent studies should investigate the role of these viruses in causing gastroenteritis and explore the possibility that other symptoms may be ascribed to multiple infections.

A broad wastewater screening and clinical data surveillance for virus-related diseases in the metropolitan Detroit area in Michigan

BACKGROUND

Periodic bioinformatics-based screening of wastewater for assessing the diversity of potential human viral pathogens circulating in a given community may help to identify novel or potentially emerging infectious diseases. Any identified contigs related to novel or emerging viruses should be confirmed with targeted wastewater and clinical testing.

RESULTS

During the COVID-19 pandemic, untreated wastewater samples were collected for a 1-year period from the Great Lakes Water Authority Wastewater Treatment Facility in Detroit, MI, USA, and viral population diversity from both centralized interceptor sites and localized neighborhood sewersheds was investigated. Clinical cases of the diseases caused by human viruses were tabulated and compared with data from viral wastewater monitoring. In addition to Betacoronavirus, comparison using assembled contigs against a custom Swiss-Prot human virus database indicated the potential prevalence of other pathogenic virus genera, including: Orthopoxvirus, Rhadinovirus, Parapoxvirus, Varicellovirus, Hepatovirus, Simplexvirus, Bocaparvovirus, Molluscipoxvirus, Parechovirus, Roseolovirus, Lymphocryptovirus, Alphavirus, Spumavirus, Lentivirus, Deltaretrovirus, Enterovirus, Kobuvirus, Gammaretrovirus, Cardiovirus, Erythroparvovirus, Salivirus, Rubivirus, Orthohepevirus, Cytomegalovirus, Norovirus, and Mamastrovirus. Four nearly complete genomes were recovered from the Astrovirus, Enterovirus, Norovirus and Betapolyomavirus genera and viral species were identified.

CONCLUSIONS

The presented findings in wastewater samples are primarily at the genus level and can serve as a preliminary "screening" tool that may serve as indication to initiate further testing for the confirmation of the presence of species that may be associated with human disease. Integrating innovative environmental microbiology technologies like metagenomic sequencing with viral epidemiology offers a significant opportunity to improve the monitoring of, and predictive intelligence for, pathogenic viruses, using wastewater.

Wastewater-based epidemiology applied at the building-level reveals distinct virome profiles based on the age of the contributing individuals

BACKGROUND

Human viruses released into the environment can be detected and characterized in wastewater. The study of wastewater virome offers a consolidated perspective on the circulation of viruses within a population. Because the occurrence and severity of viral infections can vary across a person's lifetime, studying the virome in wastewater samples contributed by various demographic segments can provide valuable insights into the prevalence of viral infections within these segments. In our study, targeted enrichment sequencing was employed to characterize the human virome in wastewater at a building-level scale. This was accomplished through passive sampling of wastewater in schools, university settings, and nursing homes in two cities in Catalonia. Additionally, sewage from a large urban wastewater treatment plant was analysed to serve as a reference for examining the collective excreted human virome.

RESULTS

The virome obtained from influent wastewater treatment plant samples showcased the combined viral presence from individuals of varying ages, with astroviruses and human bocaviruses being the most prevalent, followed by human adenoviruses, polyomaviruses, and papillomaviruses. Significant variations in the viral profiles were observed among the different types of buildings studied. Mamastrovirus 1 was predominant in school samples, salivirus and human polyomaviruses JC and BK in the university settings while nursing homes showed a more balanced distribution of viral families presenting papillomavirus and picornaviruses and, interestingly, some viruses linked to immunosuppression.

CONCLUSIONS

This study shows the utility of building-level wastewater-based epidemiology as an effective tool for monitoring the presence of viruses circulating within specific age groups. It provides valuable insights for public health monitoring and epidemiological studies.

Diversity of picornaviruses detected in diarrheal samples from children in Belém, Brazilian Amazon (1982-2019)

In this investigation, fecal specimens from children with diarrhea were collected from four community studies conducted between 1982 and 2019 in Belém, Brazilian Amazon. A total of 234 samples were tested by quantitative reverse transcription polymerase chain reaction (RT-qPCR) to detect infections by picornaviruses of the Enterovirus (EV), Parechovirus (HPeV), Cosavirus (HCoSV), Kobuvirus (Aichivirus - AiV) and Salivirus (SalV) genera. The positive samples were subjected to different amplification protocols of the VP1 region of the genome, such as nested PCR or snPCR, and were subsequently genotyped by sequencing VP1 and VP3 of the viral genome. Positivity was observed in 76.5% (179/234) of the samples tested using RT-qPCR for at least one virus, and co-infection was observed in 37.4% (67/179) of the cases. EV was detected in 50.8% (119/234), HPeV in 29.9% (70/234), HCoSV in 27.3% (64/234), and AiV/SalV in 2.1% (5/234) of the specimens tested by RT-qPCR. Using nested PCR and/or snPCR techniques, the positivity rates were 94.11% (112/119) for EV, 72.85% (51/70) for HPeV, and 20.31% (13/64) for HCoSV. It was not possible to amplify the samples that were positive for AiV/SalV. Sequencing revealed 67.2% (80/119) EV, 51.4% (36/70) HPeV, and 20.31% (13/64) HCoSV. Forty-five different types of EV were found among species A, B, and C; HCoSV identified five species, including a possible recombinant strain; all HPeV were identified as belonging to species A, in two samples a possible recombination involving three different strains was verified. This study demonstrated the high circulation and diversity of different types of picornaviruses in fecal samples, including those collected more than 30 years ago. This endorsed the evaluation of important points in the epidemiology of these viruses, such as the presence of co-infection and the possibility of knowing more about these agents, considering that some were recently described; therefore, their detection in older samples can provide more data about their ancestry.

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.

Gut Susceptibility to Viral Invasion: Contributing Roles of Diet, Microbiota and Enteric Nervous System to Mucosal Barrier Preservation

The gastrointestinal lumen is a rich source of eukaryotic and prokaryotic viruses which, together with bacteria, fungi and other microorganisms comprise the gut microbiota. Pathogenic viruses inhabiting this niche have the potential to induce local as well as systemic complications; among them, the viral ability to disrupt the mucosal barrier is one mechanism associated with the promotion of diarrhea and tissue invasion. This review gathers recent evidence showing the contributing effects of diet, gut microbiota and the enteric nervous system to either support or impair the mucosal barrier in the context of viral attack.

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.

Occurrence, fates and potential treatment approaches for removal of viruses from wastewater: A review with emphasis on SARS-CoV-2

The world is combating the emergence of Coronavirus disease 2019 (COVID-19) caused by novel coronavirus; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Further, due to the presence of SARS-CoV-2 in sewage and stool samples, its transmission through water routes cannot be neglected. Thus, the efficient treatment of wastewater is a matter of utmost importance. The conventional wastewater treatment processes demonstrate a wide variability in absolute removal of viruses from wastewater, thereby posing a severe threat to human health and environment. The fate of SARS-CoV-2 in the wastewater treatment plants and its removal during various treatment stages remains unexplored and demands immediate attention; particularly, where treated effluent is utilised as reclaimed water. Consequently, understanding the prevalence of pathogenic viruses in untreated/treated waters and their removal techniques has become the topical issue of the scientific community. The key objective of the present study is to provide an insight into the distribution of viruses in wastewater, as well as the prevalence of SARS-CoV-2, and its possible transmission by the faecal-oral route. The review also gives a detailed account of the major waterborne and non-waterborne viruses, and environmental factors governing the survival of viruses. Furthermore, a comprehensive description of the potential methods (physical, chemical, and biological) for removal of viruses from wastewater has been presented. The present study also intends to analyse the research trends in microalgae-mediated virus removal and, inactivation. The review also addresses the UN SDG 'Clean Water and Sanitation' as it is aimed at providing pathogenically safe water for recycling purposes.

Metagenomics-based evaluation of groundwater microbial profiles in response to treated wastewater discharge

This study aims to demonstrate the use of metagenomics to assess groundwater quality. Metagenomics revealed a lower alpha diversity for both bacteria and virus in wastewater-exposed groundwater compared to the upstream controls. An increase in the relative abundance of Planctomycetes and Picornaviridae was also observed in wastewater-exposed groundwater. However, comparison of antibiotic resistome cannot clearly differentiate wastewater-exposed groundwater from control. Findings suggest that metagenomics can detect selected microbial signatures indicative of treated wastewater discharge.

Viruses in Vietnamese Patients Presenting with Community-Acquired Sepsis of Unknown Cause

Community-acquired (CA) sepsis is a major public health problem worldwide, yet the etiology remains unknown for >50% of the patients. Here we applied metagenomic next-generation sequencing (mNGS) to characterize the human virome in 492 clinical samples (384 sera, 92 pooled nasal and throat swabs, 10 stools, and 6 cerebrospinal fluid samples) from 386 patients (213 adults and 173 children) presenting with CA sepsis who were recruited from 6 hospitals across Vietnam between 2013 and 2015. Specific monoplex PCRs were used subsequently to confirm the presence of viral sequences detected by mNGS. We found sequences related to 47 viral species belonging to 21 families in 358 of 386 (93%) patients, including viruses known to cause human infections. After PCR confirmation, human viruses were found in 52 of 386 patients (13.4%); picornavirus (enteroviruses [n = 14], rhinovirus [n = 5], and parechovirus [n = 2]), hepatitis B virus (n = 10), cytomegalovirus (n = 9), Epstein-Barr virus (n = 5), and rotavirus A (n = 3) were the most common viruses detected. Recently discovered viruses were also found (gemycircularvirus [n = 5] and WU polyomavirus, Saffold virus, salivirus, cyclovirus-VN, and human pegivirus 2 [HPgV2] [n, 1 each]), adding to the growing literature about the geographic distribution of these novel viruses. Notably, sequences related to numerous viruses not previously reported in human tissues were also detected. To summarize, we identified 21 viral species known to be infectious to humans in 52 of 386 (13.4%) patients presenting with CA sepsis of unknown cause. The study, however, cannot directly impute sepsis causation to the viruses identified. The results highlight the fact that it remains a challenge to establish the causative agents in CA sepsis patients, especially in tropical settings such as Vietnam.

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.

A novel passerivirus (family Picornaviridae) in an outbreak of enteritis with high mortality in estrildid finches (Uraeginthus sp.)

An enteric outbreak with high mortality (34/52, 65.4%) was recorded in 2014 in home-reared estrildid finches (Estrildidae) in Hungary. A novel passerivirus was identified in a diseased violet-eared waxbill using viral metagenomics and confirmed by RT-(q)PCR. The complete genome of finch picornavirus strain waxbill/DB01/HUN/2014 (MF977321) showed the highest amino acid sequence identity of 38.9%, 61.6%, 69.6% in P1^cap, 2C^hel and 3C^proD^pol, respectively, to passerivirus A1 (GU182406). A high viral load (6.58 × 10¹⁰ genomic copies/ml) was measured in a cloacal specimen and in the tissues (spinal cord, lung, and the intestines) of two additional affected finches. In addition to intestinal symptoms (diarrhoea), the presence of extra-intestinal virus suggests a generalized infection in this fatal disease, for which the passerivirus might be a causative agent.

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.