Typing of human astroviruses from clinical isolates by enzyme immunoassay and nucleotide sequencing

Molecular characterization of human astrovirus infection in children under 5 years of age with acute gastroenteritis in Tehran, Iran, 2021-2022: co-infection with rotavirus

Human astroviruses (HAstVs) are considered important causative pathogens of acute gastroenteritis (AGE) in children under 5 years of age worldwide, along with group A rotavirus (RVA), norovirus (NoV), and enteric adenovirus (EAdV). The present study was aimed to both detect HAstV and its co-infections and investigate genetic analysis of circulating HAstV and co-infected virus in hospitalized children under 5 years of age with AGE in Iran. Accordingly, a sum of 200 stool specimens were screened by PCR for HAstV during 2021-2022. The HAstV was found in 0.5% of 200 specimens (n = 1) while was co-infected with RVA. The genetic and phylogenetic analysis indicated HAstV1 genotype, which clustered with viruses from lineage 1b, which has not been previously reported in Iran. The detected RVA strain belonged to G1 lineage II/P[8]-lineage III, which has been reported previously in Iran as the most common strain. The further genetic analysis of RVA VP6 and NSP4 demonstrated an atypical genotype pattern G1P[8]-I1-E2, as a mono-reassortant of a Wa-like genogroup, which appeared to be reassorted with the NSP4 gene of E2 genotype of the G2P[4] DS-1 genogroup. Although the clinical outcomes of the AGE-causing viruses co-infection is not yet entirely clear, it seems that future studies will be helpful to merge clinical and epidemiological data of co-infecting viruses for a more accurate medical and clinical relevance in symptomatic children.

Activated sludge and UV-C254 for Sapovirus, Aichivirus, Astrovirus, and Adenovirus processing

In this study, the detection rates of four enteric viruses, Human Astrovirus (HAstVs), Aichivirus (AiVs), Human Adenovirus (HAdVs), and Sapovirus (SaVs) are carried out to assess the virological quality of the treated wastewater. A total of 140 samples was collected from wastewater treatment plant WWTP of Tunis-City. Real-time RT-PCR and conventional RT-PCR results showed high frequencies of detection of the four enteric viruses investigated at the entry and exit of the biological activated sludge procedure and a significant reduction in viral titers after tertiary treatment with UV-C254 irradiation. These results revealed the ineffectiveness of the biological activated sludge treatment in removing viruses and the poor quality of the treated wastewater intended for recycling, agricultural reuse, and safe discharge into the natural environment. The UV-C254 irradiation, selected while considering the non-release of known disinfection by-products because of eventual reactions with the large organic and mineral load commonly present in the wastewater.

Classic human astrovirus 4, 8, MLB-3, and likely new genotype 5 sublineage in stool samples of children in Nigeria

Human astrovirus (HAstV) is a nonenveloped RNA virus and has been implicated in acute gastroenteritis among children and elderly. However, there exists a substantial dearth of information on HAstV strains circulating in Nigeria. Viral-like particles were purified from archived 254 stool samples of children with acute flaccid paralysis between January and December 2020 from five states in Nigeria, using the NetoVIR protocol. Extracted viral RNA and DNA were subjected to a reverse transcription step and subsequent random polymerase chain reaction amplification. Library preparation and Illumina sequencing were performed. Using the virome paired-end reads pipeline, raw reads were processed into genomic contigs. Phylogenetic and pairwise identity analysis of the recovered HAstV genomes was performed. Six near-complete genome sequences of HAstV were identified and classified as HAstV4 (n = 1), HAstV5 (n = 1), HAstV8 (n = 1), and MLB-3 (n = 3). The HAstV5 belonged to a yet unclassified sublineage, which we tentatively named HAstV-5d. Phylogenetic analysis of open reading frames 1a, 1b, and 2 suggested recombination events inside the MAstV1 species. Furthermore, phylogenetic analysis implied a geographic linkage between the HAstV5 strain from this study with two strains from Cameroon across all the genomic regions. We report for the first time the circulation of HAstV genotypes 4, 8, and MLB-3 in Nigeria and present data suggestive for the existence of a new sublineage of HAstV5. To further understand the burden, diversity, and evolution of HAstV, increased research interest as well as robust HAstV surveillance in Nigeria is essential.

Biological Specimen Banking as a Time Capsule to Explore the Temporal Dynamics of Norovirus Epidemiology

Norovirus is recognised as a major cause of epidemic and sporadic acute gastroenteritis (AGE) in all age groups. Information on the genetic diversity of the noroviruses circulating in the 1980s and 1990s, before the development and adoption of dedicated molecular assays, is limited compared with the last decades. Between 1986 and 2020, uninterrupted viral surveillance was conducted in symptomatic children hospitalized with AGE in Palermo, Italy, providing a unique time capsule for exploring the epidemiological and evolutionary dynamics of enteric viruses. A total of 8433 stool samples were tested using real-time RT-PCR. All samples were stored at -20 or -80 °C until processing. In this 35-year long time span, noroviruses of genogroup II (GII) were detected in 15.6% of AGE requiring hospitalization, whilst GI noroviruses were detected in 1.4% of AGE. Overall, the predominant norovirus capsid (Cap) genotype was GII.4 (60.8%), followed by GII.3 (13.3%) and GII.2 (12.4%). Temporal replacement of the GII.4 Cap variants associated with different polymerase (Pol) types were observed over the study period. The chronology of emergence and circulation of the different GII.4 variants were consistent with data available in the literature. Also, for GII.3 and GII.2 NoVs, the circulation of different lineages/strains, differing in either the Cap or Pol genes or in both, was observed. This long-term study revealed the ability of noroviruses to continuously and rapidly modify their genomic makeup and highlights the importance of surveillance activities in vaccine design.

Epidemiology of pediatric astrovirus gastroenteritis in a Nicaraguan birth cohort

Background

Astrovirus is a leading cause of acute gastroenteritis in children worldwide. However, few prospective studies have analyzed astrovirus in community-dwelling pediatric populations in low-and-middle-income countries.

Methods

We assessed the incidence, risk factors, clinical characteristics, genotypes, viral coinfections and seasonality of astrovirus gastroenteritis in 443 healthy Nicaraguan children born in 2017-2018, followed for 36 months. Children were recruited from maternity hospitals and birth records in an economically-diverse neighborhood of León, the second-largest city in Nicaragua. Astrovirus-positive episodes and genotypes were identified from diarrheal specimens with reverse transcription quantitative polymerase chain reaction and Sanger sequencing.

Results

Of 1708 total specimens tested, eighty children (18%) experienced at least 1 astrovirus episode, and 9 experienced repeat episodes, mostly during the rainy season (May-October). The incidence of astrovirus episodes was 7.8/100 child-years (95% CI: 6.2, 9.8). Genotype-specific incidence of astrovirus also exhibited seasonality. Median age of astrovirus episode onset was 16 months (IQR 9, 23). Initial astrovirus episodes were not associated with protection against future episodes during the age span studied. Astrovirus cases were exclusively breastfed for a shorter period than uninfected children, and the human milk oligosaccharide lacto-N-fucopentaose-I was more concentrated in mothers of these children. Home toilets appeared to protect against future astrovirus episodes (HR=0.19, 95% CI 0.04-0.91). Human astrovirus-5 episodes, comprising 15% of all typed episodes, were associated with longer diarrhea and more symptomatic rotavirus co-infections.

Conclusion

Astrovirus was a common cause of gastroenteritis in this cohort, and future studies should clarify the role of astrovirus genotype in clinical infection severity.

Norovirus and sapovirus infections after allogeneic hematopoietic stem cell transplantation: is it worth it to look for them?

Norovirus (NoV) and Sapovirus (SaV) are potential causative agents of diarrhea after allogeneic HSCT but little is known in this population. We performed a retrospective analysis by RT-PCR of calicivirus (NoV and SaV), Human adenovirus (HAdV), rotavirus (RV), Aichi virus (AiV), enterovirus (EV), human parechovirus (HPeV) and Human bocavirus (HBoV) in the diarrheal stools of patients after allogeneic HSCT. 49/162 patients had positive viral assays: HAdV (17%), EV (7%), NoV (4.3%), RV and HBoV (3.1% each), SaV (1.9%), AiV (1.2%), HPeV (0.6%). Seven patients were positive for NoV and 3 for SaV. Among viruses-positive samples, the frequency of caliciviruses cases was 7% in the 6 months post-HSCT compared to 40% after (p < 0.0001). The median duration of symptom was 0.7 months but 2 cases, occurring more than one year after HSCT, were chronic, undiagnosed and strongly contributed to morbidity. Systematic testing of caliciviruses appears especially useful in late chronic diarrhea.

Triple Intergenotype Recombination of Human Astrovirus 5, Human Astrovirus 8, and Human Astrovirus 1 in the Open Reading Frame 1a, Open Reading Frame 1b, and Open Reading Frame 2 Regions of the Human Astrovirus Genome

Human astrovirus (HAstV) strains exhibit high levels of genetic diversity, and many recombinant strains with different recombination patterns have been reported. The aims of the present study were to investigate the emergence of HAstV recombinant strains and to characterize the recombination patterns of the strains detected in pediatric patients admitted to the hospital with acute gastroenteritis in Chiang Mai, Thailand. A total of 92 archival HAstV strains detected in 2011 to 2020 were characterized regarding their open reading frame 1a (ORF1a) genotypes in comparison with their ORF1b genotypes to identify recombinant strains. The recombination breakpoints of the putative recombinant strains were determined by whole-genome sequencing and were analyzed by SimPlot and RDP software. Three HAstV strains (CMH-N178-12, CMH-S059-15, and CMH-S062-15) were found to be recombinant strains of three different HAstV genotypes, i.e., HAstV5, HAstV8, and HAstV1 within the ORF1a, ORF1b, and ORF2 regions, respectively. The CMH-N178-12 strain displayed recombination breakpoints at nucleotide positions 2681 and 4357 of ORF1a and ORF1b, respectively, whereas the other two recombinant strains, CMH-S059-15 and CMH-S062-15, displayed recombination breakpoints at nucleotide positions 2612 and 4357 of ORF1a and ORF1b, respectively. This is the first study to reveal nearly full-length genome sequences of HAstV recombinant strains with a novel recombination pattern of ORF1a-ORF1b-ORF2 genotypes. This finding may be useful as a guideline for identifying other recombinant HAstV strains in other geographical regions and may provide a better understanding of their genetic diversity, as well as basic knowledge regarding virus evolution. IMPORTANCE Recombination is one of the mechanisms that plays a crucial role in the genetic diversity and evolution of HAstV. We wished to investigate the emergence of HAstV recombinant strains and to analyze the whole-genome sequences of the putative HAstV recombinant strains detected in pediatric patients with acute gastroenteritis in 2011 to 2020. We reported 3 novel intergenotype recombinant strains of HAstV5-HAstV8-HAstV1 at the ORF1a-ORF1b-ORF2 regions of the HAstV genome. The hot spots of recombination occur frequently near the ORF1a-ORF1b and ORF1b-ORF2 junctions of the HAstV genome. The findings indicate that intergenotype recombination of HAstV occurs frequently in nature. The emergence of a novel recombinant strain allows the new virus to adapt and successfully escape from the host immune system, eventually emerging as the predominant genotype to infect human populations that lack herd immunity against novel recombinant strains. The virus may cause an outbreak and needs to be monitored continually.

Identification and genetic characteristics of tusavirus in fecal samples of patients with chronic diseases in Guangzhou, China

Purpose

The Tunisian stool-associated parvovirus [Tusavirus (TuV)] is a novel member of the genus Protoparvovirus, which may be linked to diarrhea. Herein, we investigated the prevalence of TuV in different populations and analyzed its genetic and bioinformatic characteristics.

Methods

This study was conducted in a tertiary hospital in Guangzhou (China) from February 2018 to July 2022. Demographic and clinical information and stool samples were collected from individuals who visited the hospital. ProtScale, SwissModel, Datamonkey, and other tools were used to analyze and predict the physicochemical parameters, tertiary structure, selection pressure, and B-cell epitopes of capsid viral protein 2 of TuV (VP2-TuV).

Results

A total of 3,837 participants were enrolled, among which two stool samples from patients with chronic illnesses were tested positive for TuV DNA. However, no positive sample was detected among patients with diarrhea. Two near-complete genome sequences were amplified. The genetic analysis revealed the presence of diversity among TuVs isolated from distinct host species. Bioinformatics analysis revealed that VP2-TuV exhibited hydrophilic properties and lacked transmembrane domains and signal peptides. The secondary structure of VP2-TuV was composed mainly of random coils and β-strands. Selective-pressure analysis of the VP2 region suggested that TuV primarily underwent negative selection during evolution. Negatively selected codon sites coincided with residues comprising of B-cell epitopes, suggesting minimal changes in the immunogenicity of TuV over time.

Conclusion

TuV was detected in patients with chronic diseases but not in patients with diarrhea. The putative roles of TuV in the pathogenicity of human diseases and zoonotic viruses must be determined by additional studies.

Clinical and Epidemiologic Features of Viral Gastroenteritis in Hospitalized Children: An 11-Year Surveillance in Palermo (Sicily)

In order to acquire information regarding viral agents and epidemiologic features of severe paediatric Viral Acute Gastroenteritis (VAGE) across multiple seasons in the pre-rotavirus-vaccine era, the epidemiologic characteristics of VAGE were investigated among paediatric patients hospitalized in a major Sicilian paediatric hospital from 2003 to 2013. Overall, 4725 children were observed and 2355 (49.8%) were diagnosed with a viral infection: 1448 (30.6%) were found positive to rotavirus, 645 (13.7%) to norovirus, 216 (4.6%) to adenovirus, and 46 (0.97%) to astrovirus. Viral infections showed different patterns of hospitalization in terms of age at risk (younger for rotavirus and adenovirus infections), seasonality (increased risk in winter for rotavirus and norovirus), trend over time (reduced risk in 2011-2013 for norovirus and rotavirus) and major diagnostic categories (digestive diseases more frequent in adenovirus and astrovirus but not in norovirus). This study increases general knowledge of VAGE epidemiology and contributes to suggest some a priori diagnostic criteria that could help clinicians to identify and treat viral agents responsible for gastroenteritis in hospital settings.

Viral pathogens of acute gastroenteritis in Egyptian children: role of the parechovirus

BACKGROUND AND AIM

Human parechovirus (HPeV) has emerged as a pathogen associated with acute gastroenteritis (AGE).

AIM

To detect the presence of HPeV in the stool samples from Egyptian children with AGE seeking care and the possibility of its co-infection with other enteric viruses.

METHODOLOGY

One hundred stool samples were collected from children attending Mansoura University Children's Hospital with AGE. HPeV and astrovirus were detected by reverse transcriptase-polymerase chain reaction (RT-PCR). At the same time, detection of rotavirus antigen and norovirus was achieved by enzyme-linked immunosorbent assay and rapid immunochromatographic method, respectively.

RESULTS

The most frequently detected virus was rotavirus (39%), followed by norovirus (27%), HPeV (19%), and astrovirus (12%). Interestingly, the single infection with HPeV was 5%. Among the 19 HPeV positive samples, the co-infection of HPeV with other enteric viruses was detected in 9(43.9%) for rotavirus, 7(36.8%) for norovirus, 2(10.5%) for astrovirus, in 3(15.8%) for rotavirus and norovirus and 1(5.3%) for norovirus and astrovirus. Regarding the clinical presentation, there was no significant difference between children infected with HPeV alone and those infected with viruses other than HPeV alone; fever (p = 0.3), vomiting (p = 0.12), abdominal pain (p = 0.12), and grades of severity (P = 0.82). HPeV alone infected children were of mild severity (60%), and their main presenting symptom was fever (60%).

CONCLUSIONS

Detection of HPeV as a single viral pathogen in the stool of some children with AGE showed that this virus could be a causative agent of AGE in Egyptian children. Therefore, HPeV could be included as one of the viruses screened for AGE diagnosis in children in Egypt.

Human Astrovirus in Symptomatic and Asymptomatic Children: A Cross-Sectional Study on Hospitalized and Outpatients from Rural Communities of South Africa between 2017-2021

Human astroviruses are considered acute gastroenteritis agents (AGE) and are largely reported in children worldwide. There are limited data on astrovirus prevalence in rural communities, especially in hospitalized and asymptomatic cases. This study was a cross-sectional survey aiming to investigate the prevalence of classic human astroviruses in symptomatic and asymptomatic cases and hospitalized and outpatient children in rural communities of the Vhembe District, South Africa. A total of 236 stool samples (166 symptomatic and 70 asymptomatic) were collected from young children under 5 years of age. Real-time RT-PCR for astrovirus detection, RT-PCR amplification of capsid and polymerase partial genes as well as Sanger sequencing were performed. The classic astrovirus prevalence in symptomatic patients (7.23%, 12/166) as compared to healthy controls (4.29%, 3/70) was not statistically different (t-value: 1.782, p = 0.141: 95% CI). We did not observe a significant difference of classic astrovirus prevalence rate between the hospitalized group (6.52%, 3/46) and outpatient group (7.5%, 9/120). Symptomatic children below 6 months old were the most affected group (18.18%, 6/33). This study characterized human astrovirus genotype 2 and a putative recombinant strain (polymerase genotype 1/capsid genotype 2). Phylogenetic analysis revealed these genotypes are closely related to the strains circulating elsewhere within the African continent. The findings suggest that astrovirus is a common enteric pathogen in the study area. The results highlight the exposure of children and the need to monitor astroviruses for their potential impact in diarrhoeal diseases.

Experimental porcine astrovirus type 3-associated polioencephalomyelitis in swine

Porcine astrovirus type 3 (PoAstV3) is an emerging virus in the family Astroviridae that has been recently associated with polioencephalomyelitis/encephalitis. Herein, we describe the experimental oral and intravenous inoculation of an infectious central nervous system (CNS) tissue homogenate containing PoAstV3 to cesarean-derived, colostrum-deprived pigs, and the subsequent development of clinical signs, histologic lesions, specific humoral immune response, and detection of viral particles by electron microscopy (EM) and viral RNA by RT-qPCR (reverse transcriptase quantitative polymerase chain reaction) and in situ hybridization (ISH). IgG against a portion of the PoAstV3 ORF2 capsid was first detected at 7 days post-inoculation (DPI) in 2 of 4 inoculated animals and in all inoculated animals by 14 DPI. At 21 and 28 DPI, 2 of 4 inoculated animals developed ataxia, tetraparesis, and/or lateral recumbency. All inoculated animals had histologic lesions in the CNS including perivascular lymphoplasmacytic cuffs, multifocal areas of gliosis with neuronal necrosis, satellitosis, and radiculoneuritis, and PoAstV3 RNA as detected by RT-qPCR within multiple anatomic regions of the CNS. Consistent viral structures were within the soma of a spinal cord neuron in the single pig examined by EM. Of note, PoAstV3 was not only detected by ISH in neurons of the cerebrum and spinal cord but also neurons of the dorsal root ganglion and nerve roots consistent with viral dissemination via axonal transport. This is the first study reproducing CNS disease with a porcine astrovirus strain consistent with natural infection, suggesting that pigs may serve as an animal model to study the pathogenesis of neurotropic astroviruses.

A potential risk assessment tool to monitor pathogens circulation in coastal waters

The present study reports data on a 20 months campaign monitoring enteric viruses (hepatitis A, norovirus, rotavirus, astrovirus, sapovirus, and aichivirus) and bacteria (Salmonella spp.) in seawater. The aim of this work was to assess the potential correlation among the presence of viruses/bacteria and different environmental factors like seasonality, water discharge sources (treated and untreated wastewater, mixed waters and raw water) as well as influence of the Italian lockdown measure against COVID-19 pandemic. Results showed different prevalence of the investigated viruses with values equal to 16 % for norovirus GI, 15.1 % for norovirus GII, followed by 13.8 % for astrovirus, and 13.3 % for sapovirus. Rotavirus was detected in the 8.4 % of samples and aichivirus was detected with the lowest prevalence of 3.5 %. Hepatitis A virus was never identified in the monitoring campaign. Salmonella spp. was detected with a prevalence of 36.6 %. Statistical analysis displayed a high correlation for the two noroviruses simultaneous detection (NGI and NGII) while a lower correlation was found for co-presence of noroviruses with astrovirus, sapovirus or Salmonella spp. A significant decrease of enteric pathogens in seawater was observed during the restrictions period. Results on seasonality highlighted a higher viral prevalence correlated to the wet season for all the pathogens but rotavirus and aichivirus, which instead showed an opposite trend and a higher incidence in the dry season. With respect to discharge typology, some viruses displayed a higher prevalence in treated waters (astrovirus, rotavirus, sapovirus and aichivirus) while the other investigated pathogens (noroviruses and Salmonella spp.) showed a higher prevalence in mixed waters. The main observations of this work were used to define a potential monitoring strategy that could be useful for sanitary Authorities to implement surveillance plans aimed at preventing possible sanitary outbreaks and/or environmental quality deterioration.

Human astrovirus types 1, 4 and 5 circulating among children with acute gastroenteritis in a rural Brazilian state, 2010-2016

This study combined conventional epidemiology of human astroviruses. From 2010 to 2016, 232 stool samples from children under 5 years of age were screened using NGS and conventional RT-PCR followed by genetic analysis in order to investigate the genotypic diversity of classical human astrovirus (HAstV) circulating in Tocantins State, Brazil. HAstV was detected in 16 cases (6.9%). Seven specimens (43.7%; 7/16) were positive according RT-PCR and next-generation sequencing (NGS) to investigate the molecular to both NGS and RT-PCR. NGS and RT-PCR individually revealed six (37.5%; 6/16) and three (18.8%; 3/16) additional positive samples, respectively. Sequencing of the HAstV-positive samples revealed HAstV-1a (9/16), HAstV-4c (3/16), and HAstV-5c (4/16) lineages.

Molecular and epidemiological characterization of human adenovirus and classic human astrovirus in children with acute diarrhea in Shanghai, 2017-2018

BACKGROUND

In addition to rotavirus and norovirus, human adenovirus (HAdV) and classic human astrovirus (classic HAstV) are important pathogens of acute diarrhea in infants and young children. Here, we present the molecular epidemiology of HAdV and classic HAstV in children with acute diarrhea in Shanghai.

METHODS

Fecal specimens were collected from 804 outpatient infants and young children diagnosed with acute diarrhea in Shanghai from January 2017 to December 2018. All of the samples were screened for the presence of HAdV and classic HAstV. HAdV and classic HAstV were detected using traditional PCR and reverse-transcription PCR, respectively. All of the HAdV and classic HAstV positive samples were genotyped by phylogenetic analysis.

RESULTS

Among the 804 fecal samples, 8.58% (69/804) of samples were infected with either HAdV or classic HAstV, and five were co-infected with two diarrhea viruses. The overall detection rates of HAdV and classic HAstV were 3.47% (28/804) and 5.22% (42/804), respectively. Four subgroups (A, B, C, and F) and seven genotypes (HAdV-C1, -C2, -B3, -C5, -A31, -F40, and -F41) of HAdV were detected. Subgroup F had the highest constituent ratio at 64.29% (18/28), followed by non-enteric HAdV of subgroup C (21.43%, 6/28) and subgroup B 10.71% (3/28). HAdV-F41 (60.71%, 17/28) was the dominant genotype, followed by HAdV-C2 (14.29%, 4/28) and HAdV-B3 (10.71%, 3/28). Two genotypes of classic HAstV (HAstV-1 and HAstV-5) were identified in 42 samples during the study period; HAstV-1 (95.24%, 40/42) was the predominant genotype, and the other two strains were genotyped as HAstV-5. No significant differences were found between boys and girls in the detection rates of HAdV (P = 0.604) and classic HAstV (P = 0.275). Over half of the HAdV infections (82.14%, 23/28) and classic HAstV infections (66.67%, 28/42) occurred in children less than 36 months. Seasonal preferences of HAdV and classic HAstV infections were summer and winter, respectively. In this study, the common clinical symptoms of children with acute diarrhea were diarrhea, vomiting, fever and abdominal pain.

CONCLUSIONS

Our findings indicate that HAdV and classic HAstV play important roles in the pathogenesis of acute diarrhea in children in Shanghai. Systematic and long-term surveillance of HAdV and classic HAstV are needed to monitor their prevalence in children and prevent major outbreak.

Evaluation of the diagnostic performances of two commercially available assays for the detection of enteric adenovirus antigens

The performance of 2 antigenic commercial assays for enteric adenovirus (AdV) infection, bioNexia Rota-Adeno ImmunoChromatographic Tests (ICT) and LIAISON® Adenovirus ChemiLuminescence Immuno Assays (CLIA), was evaluated on 321 stools from children hospitalized for acute gastroenteritis in Palermo, Italy, using a Real time-PCR (Rt-PCR) as reference method. The CLIA showed higher sensitivity (77% vs 60%), accuracy (94.4 vs 90.9) and concordance (k: 0.81 vs 0.67) with respect to ICT, despite equivalent specificity (98.8%). Using the Ct values of the Rt-PCR as a proxy of the fecal viral load, similar Ct values (mean 9.32 vs 9.89) were observed among the true positive samples, whilst a significant difference (P < 0.05) was observed in false negative samples of CLIA (mean Ct 25.68) and ICT (mean Ct 19.87). Cross-reactivity with other enteric viruses was not observed. These results indicate that both the assays tested are suitable for diagnosis of AdV gastroenteritis.

Human Astrovirus Outbreak in a Daycare Center and Propagation among Household Contacts

We investigated an outbreak of acute gastroenteritis due to human astrovirus in a daycare center, describing the transmission mechanism, the most affected age groups, conditioning factors and the extent of the outbreak among household contacts of the daycare center attenders. Data were collected from persons exposed at the daycare center and their home contacts. Fecal samples from affected and non-affected daycare center attenders were analyzed for viruses causing acute gastroenteritis by RT-PCR. The percentage of households affected and the attack rates (AR) were calculated. The attack rates were compared using the rate ratio (RR) with 95% confidence intervals. Information was obtained from 245 people (76 attenders and 169 contacts) of whom 49 were clinical cases. Five HAstV-4, two HAstV-8 and three non-typable HAstV cases were identified (six from clinical cases and four from asymptomatic infected people). The global AR was 20% (41.2% in children aged < 2 years). Data were obtained from 67 households: 20 households of affected attenders and 47 of non-affected attendees. Household contacts of affected attenders had a higher AR (74.3%) than that of non-affected attendees (2.4%). We found asymptomatic infections amongst daycare attendees. The transmission of HAstV during the outbreak was not limited to the daycare center but extended to household contacts of both affected and non-affected attenders.

Enteric viruses circulating in undiagnosed central nervous system infections at tertiary hospital in São José do Rio Preto, São Paulo, Brazil

Enterovirus (EV) is commonly associated with central nervous system (CNS) syndromes. Recently, gastroenteric viruses, including rotavirus (RVA), human astrovirus (HAstV), and norovirus (NoV), have also been associated with CNS neurological disorders. The aim of the present study was to investigate the presence of EV, RVA, HAst, and NoV associated to CNS infections with undiagnosed etiology in Northwest region of São Paulo State, Brazil, and to conduct the molecular characterization of the positive samples detected. A total of 288 cerebrospinal fluid samples collected from July to December 2017 were tested for EV and NoV by quantitative real-time polymerase chain reaction (RT-qPCR), HAstV by conventional RT-PCR, and RVA by enzyme-linked immunosorbent assay. Positive-EV samples were inoculated in cells lines, amplified by RT-PCR and sequenced. RVA, NoV, and HAstV were not detected. EV infection was detected in 5.5% (16/288), and five samples successful genotyped: echovirus 3 (E3) (1/5), coxsackie virus A6 (CVA6) (1/5), and coxsackie virus B4 (CVB4) (3/5). Meningitis was the main syndrome observed (12/16; 75%). CVA6, CVB4, and E3 were identified associated with aseptic meningitis. Reports of CVA6 associated with aseptic meningitis are rare, E3 had not been previously reported in Brazil, and epidemiological data on CVB4 in the country is virtually unknown. The present investigation illustrates the circulation of diverse EV types in a small regional sample set and in a short period of time, highlighting the importance of an active EV surveillance system in CNS infections. Enhanced understanding of undiagnosed CNS infections will assist in public health and health care planning.

Murine astrovirus tropism for goblet cells and enterocytes facilitates an IFN-λ response in vivo and in enteroid cultures

Although they globally cause viral gastroenteritis in children, astroviruses are understudied due to the lack of well-defined animal models. While murine astroviruses (muAstVs) chronically infect immunodeficient mice, a culture system and understanding of their pathogenesis is lacking. Here, we describe a platform to cultivate muAstV using air-liquid interface (ALI) cultures derived from mouse enteroids, which support apical infection and release. Chronic muAstV infection occurs predominantly in the small intestine and correlates with higher interferon-lambda (IFN-λ) expression. MuAstV stimulates IFN-λ production in ALI, recapitulating our in vivo findings. We demonstrate that goblet cells and enterocytes are targets for chronic muAstV infection in vivo, and that infection is enhanced by parasite co-infection or type 2 cytokine signaling. Depletion of goblet cells from ALI limits muAstV infection in vitro. During chronic infection, muAstV stimulates IFN-λ production in infected cells and induces ISGs throughout the intestinal epithelium in an IFN-λ-receptor-dependent manner. Collectively, our study provides insights into the cellular tropism and innate immune responses to muAstV and establishes an enteroid-based culture system to propagate muAstV in vitro.

Trends in acute viral gastroenteritis among children aged ≤5 years through the national surveillance system in South Korea, 2013-2019

Acute gastroenteritis is a global public health concern. This study aimed to analyze the trend and characteristics of acute viral gastroenteritis through a national surveillance network. Enteric viruses were detected in 9510 of 31,750 (30.1%) cases assessed from 2013 to 2019 by EnterNet. The most prevalent pathogens were norovirus (15.2%) and group A rotavirus (9.7%); most infections were reported in 2017 (34.0%). Norovirus and rotavirus coinfections were the most common. Norovirus infections were prevalent among 1‐year‐old children (1835 out of 9510 cases) during winter, and group A rotavirus infections were common during spring. Seasonality was not observed among enteric adenovirus, astrovirus, and sapovirus. The prevalent viral genotypes detected included norovirus GII.4, enteric adenovirus F41, astrovirus genotype 1, and sapovirus GI.1. However, changes in enteric virus trends were noted during the study period. Norovirus prevalence extended into spring, and new genotypes of enteric adenovirus, astrovirus, and sapovirus were identified. These surveillance data elucidate enteric virus epidemiological characteristics.

Genetic Diversity of Astrovirus in Children From a Birth Cohort in Nepal

Objective: This study describes the types of Human astroviruses detected in stool samples collected from a birth cohort of children in Nepal.

Methods: Using a commercial kit (ProSpecT), a total of 5,224 diarrheal and non-diarrheal stool samples were screened for Human astrovirus by ELISA. RT-PCR was performed on ELISA positive samples (2.8%) for further confirmation. The primary RT-PCR assay used targets the ORF2 region and detects human astrovirus type 1–8. Samples that were negative in this assay were further analyzed using primers that target the ORF1b region of human astrovirus which detect both classical type (HAstV 1–8) and novel types (MLB1–5, VA 1–5). PCR positive samples were analyzed by Sanger sequencing to determine the genotype.

Results: A total of 148 available ELISA positive stool samples were analyzed by RT-PCR and further genotyped. RT-PCR analysis of these samples using the ORF2 and ORF1b assay revealed that 124 (84%) were positive for classical human types (HAstV 1–8). Seven different classical HAstV genotypes based on ORF2 and ORF1a were identified (HAstV 1- HAstV 8) with the greatest prevalence of HAstV 5 genotype (42.2%), followed by HAstV 1 (34.7%), HAstV 2 and HAstV 8 (7.4%), HAstV 4 (4.1%), HAstV 3 (3.3%), and HAstV 6 (0.8%). Non-classical types were not detected in our study.

Conclusion: A high diversity of circulating Astrovirus strains were detected in young children, both with and without symptoms of gastroenteritis. HAstV 5 and HAstV 1 were the most common genotypes in young children in Nepal.

First report of human astrovirus MLB2 in Brazil detected in feces of children with acute gastroenteritis living in the state of Roraima, Northern Brazil

Human astrovirus (HAstV) 1–8 and highly divergent HAstVMLB1−3 genotypes have been detected in children both with and without acute gastroenteritis (AGE). One hundred and seventy fecal samples from children (≤5 years old) living in the Amazon region were evaluated for the presence of HAstV1–8, HAstV MLB1−3 and HAstVVA1−3, using an usual RT-PCR protocol and a new protocol with specific primers designed to detect HAstVMLB1−3. HAstVMLB1 and HAstV MLB2, as well as the HAstV3 and 5 genotypes were detected. HAstVMLB1−2 genotype was detected for the first time in Brazil at a frequency of 3.5% (6/170).

Molecular study of human astrovirus in Egyptian children with acute gastroenteritis

Introduction

Human astrovirus (HAstV) has been increasingly identified as an important cause of acute gastroenteritis in young children. Limited information is available about the prevalence and genotype distribution of classic HAstV causing acute gastroenteritis in Egyptian children.

Methods

Stool samples were collected from 100 infants and children attending the gastroenterology outpatient clinic in Mansoura University Children Hospital and suffering from acute gastroenteritis during the period extending from January 2018 to January 2019. Samples were tested for HAstV using reverse transcription PCR. Genotyping was performed using type-specific reverse transcription nested PCR.

Results

Among 100 children included in this study, the detection rate of HAstV was 11% (11 patients). There was a significant difference regarding age between cases positive and negative for HAstV (p=0.005). There was a higher prevalence of HAstV in children aged one year or younger. Significant association was detected between HAstV positive cases and rural residence (p=0.002), summer season (p=0.025) and fever (p=0.017). The HAstV genotypes detected were HAstV-8 (8/11, 72.7%), HAstV-3 (2/11, 18.2%) and HAstV-2 (1/11, 9.1%).

Conclusions

This study suggests that HAstV is a common pathogen causing gastroenteritis in Egyptian children especially in rural areas. The most frequent HAstV genotype in our study was HAstV-8.

Molecular epidemiology of astrovirus in children with gastroenteritis in southwestern Nigeria

Human astrovirus (HAstV) is recognized as one of the major causative agents of acute gastroenteritis in children worldwide. Data on the genetic diversity of HAstV in Nigeria are limited. The aim of this study was to determine the prevalence and molecular epidemiology of classical HAstV in children under 5 years of age with acute gastroenteritis in Ogun State, Nigeria. Fecal samples (331) as well as socio-demographic and clinical data were collected across the three senatorial districts of the state from February 2015 to April 2017. One hundred seventy-five samples were randomly selected and analyzed for the presence of HAstV using RT-PCR. PCR amplicons from positive samples were sequenced, and phylogenetic analysis was done to determine genotypes and lineages. The overall prevalence rate was 19.4% (34), with the highest occurrence observed in 2015 (41.4%). Viral coinfections were detected in 13 cases (38.2%). HAstV infection occurred throughout the year and in all age groups, mainly in the age group of 0-12 months. There was significant association between prevalence rate and collection year; however, no association was observed with gender, age, symptoms or risk factors. HAstV-5 was the predominant genotype (76.5%) circulating throughout the study period, followed by HAstV-1 (23.5%), which circulated only in the first 2 years of the study. Phylogenetic analysis showed that all HAstV-5 strains detected belonged to the 5a lineage, while HAstV-1 strains were grouped into lineage 1b. This study, to the best of our knowledge, is the first comprehensive report on molecular characterization of classical HAstV among children with gastroenteritis in the country, and this will serve as baseline information for implementing appropriate infection control practices.

Prevalence of astrovirus and parvovirus in Japanese domestic cats

Feces obtained from 204 domestic cats with gastrointestinal symptoms were genetically examined for feline astrovirus (FeAstV) and feline parvovirus (FPV), both of which are known feline gastroenteric viruses. FeAstV detection rates were significantly higher in winter (44.4%) than in other seasons, and in cats under a year old (27.8%) than in a year or older ones (12.4%) (P<0.05). In contrast, no significant seasonal and age differences were obtained in FPV detection rates. Upon FeAstV ORF2 sequence analysis, the 23 present isolates were classified into the same clade (Mamastrovirus 2) as the 18 reference strains from other countries. Our findings suggest that FeAstV is already circulating in Japan, and it is more prevalent in juvenile cats in winter, unlike FPV.

Viral gastroenteritis in hospitalized patients: Evaluation of immunochromatographic methods for rapid detection in stool samples

BACKGROUND

. Viral infections are recognized as the most common cause of acute gastroenteritis (AGE). Virus detection by immune analytical methods is recommended for diagnosis because of its simplicity and low cost.

OBJECTIVES

. Two commercial immunochromatographic (ICG) techniques (Materlab) for rapid detection of rotavirus/adenovirus and norovirus respectively, were evaluated by comparison to the results obtained using PCR methods. In addition, clinical and epidemiologic characteristics of AGE infections have been described.

STUDY DESIGN

. A total of 100 faecal samples collected from patients with AGE (84% children) admitted into a Spanish Hospital between February and July 2018, were studied for rotavirus-A, adenovirus and norovirus GI/GII by the ICG tests as well as by PCR and sequencing. Other enteric viruses (enterovirus and astrovirus) were investigated by PCR methods. Gastrointestinal bacteria and parasites were also tested.

RESULTS

. Evaluated ICG tests yielded high specificity (>97%). Sensitivity values were high for rotavirus/adenovirus (>80%) but lower for norovirus (57%). Overall, and taking into account coinfections, viruses (32%), bacteria (14%) and parasites (1%) could be detected. Rotavirus-A were the most frequently identified viruses (16%), followed by enterovirus (12%), norovirus (4%), adenovirus 41 (4%) and astrovirus (1%). In five vaccinated children, a rotavirus was detected.

CONCLUSIONS

. ICG technique is a useful tool for the routine diagnosis of AGE infections at hospital, but for surveillance and epidemiological studies, it is needed the use of amplification and sequencing methods, which also allow monitoring of new strains or variants emergence. In this study, an etiological pathogen was determined only in 44% of samples.

Assessing the burden of viral co-infections in acute gastroenteritis in children: An eleven-year-long investigation

BACKGROUND

Acute gastroenteritis is an important cause of childhood morbidity and mortality worldwide. A number of pathogens are responsible for human acute gastroenteritis. The recent introduction of syndromic assays for the diagnosis of enteric infections, including a wide panel of enteric pathogens, has unveiled the frequency of mixed infections. This study was carried out to assess the burden of viral co-infections and the genetic diversity of the viruses detected in children hospitalized with acute gastroenteritis in Italy.

METHODS

A total of 4161 stool samples collected from diarrheic children over 11 years, from January 2008 to December 2018, were investigated for the presence of four enteric viruses, i.e. group A rotavirus, norovirus, astrovirus and adenovirus. The samples were initially screened by either molecular or immunochromatographic assays and subsequently confirmed by Real-time PCR and sequence analyses.

RESULTS

At least one viral agent was detected in 48.6 %of specimens. Rotavirus was the most prevalent virus (24.7 %) followed by norovirus (19.6 %), adenovirus (5.3 %) and astrovirus (3%). Co-infections were detected in 8.3 % of virus-positive patients, with common viral combination being rotavirus with norovirus (70.6 % of co-infections) or with astrovirus (9.6 %). A variety of viral genotypes was detected in co-infections and in single infections. Using Real-time PCR cycle thresholds as a proxy measure of fecal viral load, rotavirus was generally detected at higher levels in co-infected patients.

CONCLUSIONS

Combining and deciphering measurable indicators of viral load and epidemiological information could be useful for an accurate interpretation of viral co-infections.

Occurrence of human astrovirus associated with gastroenteritis among Congolese children in Brazzaville, Republic of Congo

INTRODUCTION

Acute viral gastroenteritis is a major public health concern, especially among children younger than 5 years of age. The aim of this study was to determine the occurrence of human astrovirus infection in children with acute gastroenteritis.

METHODS

Stool specimens were collected from 506 children under 5 years of age hospitalized with acute diarrhoea (289 male and 208 female), and human astrovirus was investigated by RT-PCR. Associations of socio-demographic, clinical, and behavioural conditions with infection were analysed.

RESULTS

The overall prevalence of human astrovirus was found to be 10.3%. The mean age of positive cases was 12.41 ± 6.21 months and this was associated with infection (p = 0.013). Children >18 months of age were at three times the risk of infection when compared to those aged 0-6 months (odds ratio (OR) 3.19, 95% confidence interval (CI) 1.15-8.88; p = 0.026). Children living in houses with more than one room (OR 0.60, 95% CI 0.28-0.96; p = 0.036) and mothers using treated water (OR 0.47, 95% CI 0.25-0.86; p = 0.015) were associated with reduced infection.

CONCLUSIONS

In this study, infection with astrovirus was common in acute gastroenteritis cases among children younger than 5 years of age. Drinking treated water and living in non-crowded environments protected the children from infection.

Investigation of a large waterborne acute gastroenteritis outbreak caused by group B rotavirus in Maharashtra state, India

An acute gastroenteritis outbreak at Devli Karad village, Maharashtra, India with an attack rate of 22.6% affected mainly adolescent and adult population. The viral investigations conducted on fecal specimens of patients hospitalized indicated the presence of rotavirus B (RVB) using RNA polyacrylamide gel electrophoresis and reverse transcription polymerase chain reaction. The samples collected from the source of drinking water also showed the presence of the only RVB. Absence of other viral agents and identification of RVB of genotype G2 as the etiological agent of the acute gastroenteritis outbreak highlights, the necessity of monitoring RVB, the viral agent known for its large outbreak potential.

Effectiveness of Lanzhou lamb rotavirus vaccine in preventing gastroenteritis among children younger than 5 years of age

BACKGROUND

Lanzhou Lamb rotavirus (LLR) vaccine was licensed in China in 2000. It was the only vaccine available in private market before 2018. However, the data about the post-marketing effectiveness is very limited. To assess the vaccine effectiveness (VE), we conducted a case-control study based on the hospital surveillance system in Beijing from 2015 to 2017.

METHODS

Seven hospitals located in seven districts in Beijing, from October 1, 2015, to March 31, 2017, were included. The VE of LLR vaccine was assessed in laboratory-confirmed rotavirus infection among children younger than five years old through a case-control design, using rotavirus-negative cases as controls. LLR vaccination was documented from a vaccination registry. VE was estimated adjusting for age group, gender, study site, the month of illness onset and interval days between illness onset to sampling through a logistic regression model.

RESULTS

A total of 598 cases and 1766 controls were included in this study. The vaccine average coverage rate during 2015-2017 among children younger than five years old was 10.8% in Beijing. The adjusted VE for LLR vaccine of 1 dose versus 0 dose was 34.9% (95%CI, 5.3-55.3). We also obtained the adjusted VE of 87.7% (95%CI, 32.7-97.8) for patients with the severity score ≥11, 36.2% (95%CI, 4.7-57.3) for children of 2-35 months age group and 40.8% (95%CI, 7.8-61.9) against G9 rotavirus infection. Vaccinated cases were less likely to have watery stool (OR = 0.42) and have diarrhea longer than 5 days (OR = 0.47) than unvaccinated cases.

DISCUSSION

LLR vaccine conferred protection against rotavirus disease. Children who were vaccinated presented with less severe clinical manifestations. An immunization schedule of receiving all three doses in the first year should be preferred.

Epidemiology of enteric viruses in children with gastroenteritis in Ogun State, Nigeria

Acute gastroenteritis (AGE) remains a global public health concern and Nigeria is one of the two countries accounting for 42% of global under-5 deaths attributable to gastroenteritis. This study aimed to determine the prevalence, seasonality, and risk factors of enteric viruses (EVs) in children with AGE in Ogun State, Nigeria. Stool samples collected from children under-5 from three different hospitals between February 2015 and April 2017 were analyzed using molecular methods for the presence of four EVs (group A rotavirus [RVA], norovirus [NoV], human astrovirus [HAstV], and human adenovirus [HAdV]). Among the 175 samples analyzed, 63 (36%) were positive for at least one EV. The most prevalent was HAstV (19.4%), followed by RVA (16.6%), NoV (5.1%), and HAdV (5.1%). Mixed infections were found in 17 cases. No significant association was observed with age, sex, and risk factors. Though not significant, EV prevalence was higher in the dry season. Positive cases (asides HAdV) had no correlation with temperature and/or humidity. This study provides information on the prevalence and seasonal fluctuations of EVs, which will be of value in the effective management of patients and control strategies for viral gastroenteritis in the country.

Epidemiological and molecular investigation of norovirus and astrovirus infections in Rio Branco, Acre, Northern Brazil: A retrospective study

Norovirus (NoV) is a major cause of nonbacterial acute gastroenteritis (AGE) outbreaks worldwide, with infections reported in semiclosed environments, particularly in hospitals and nursing homes. Astrovirus (HAstV) is prevalent worldwide, especially in developing countries. We aimed to determine the prevalence, spatial distribution, and genetic diversity of NoV and HAstV in children under 5 years of age in Rio Branco city, Acre State, Amazon Region, Brazil. Stool samples from children with (n = 240) and without (n = 248) AGE were collected from January to December 2012 from seven neighborhoods. The overall NoV prevalence was 12.3% (60 of 488); representing 15.8% (38 of 240) of the symptomatic samples and 8.9% (22 of 248) of the controls. HAstVs infection was observed in 4.7% (23 of 488) of the samples tested, 6.2% (15 of 240) of AGE cases, and 2.4% (6 of 248) of the controls (plus two without information about feces consistency). Infections were found in all age groups with higher frequency in children less than two years of age, for both viruses. NoV was detected in all neighborhoods, with a higher concentration in the fourth (30%; 18 of 60). NoV nucleotide sequencing performed in 86.7% (52 of 60) of the positive samples showed the circulation of the strains GII.4 (57.7%; 30 of 52), GIIPe/GII.4 (19.2%; 10 of 52), GII.7, GII.Pg/GII.1, and GII.Pc (3.8%; 2 of 52 for each), GII.6 and GII.Pg (1.9%; 1 of 52 for each), and GI.3 (7.7%; 4 of 52). Three GII.4 variants were detected: Den Haag_2006b (n = 1), New Orleans_2009 (n = 1), and Sydney_2012 (n = 14). HAstV types HAstV-1a (81.8%; 9 of 11) and HAstV-2c (18.2%; 2 of 11) were observed in the 47.8% (11 of 23) of characterized samples. This is the first data obtained in Acre State regarding the prevalence of these viruses and provides epidemiological and molecular information for a better understanding of their role among children with and without AGE.

Changing pattern of prevalence and genetic diversity of rotavirus, norovirus, astrovirus, and bocavirus associated with childhood diarrhea in Asian Russia, 2009-2012

This hospital-based surveillance study was carried out in Novosibirsk, Asian Russia from September 2009 to December 2012. Stool samples from 5486 children with diarrhea and from 339 healthy controls were screened for rotavirus, norovirus, astrovirus, and bocavirus by RT-PCR. At least one enteric virus was found in 2075 (37.8%) cases with diarrhea and 8 (2.4%) controls. In the diarrhea cases, rotavirus was the most commonly detected virus (24.9%), followed by norovirus (13.4%), astrovirus (2.8%) and bocavirus (1.1%). Mixed viral infections were identified in 4.3% cases. The prevalence of enteric viruses varied every season. Rotavirus infection was distributed in a typical seasonal pattern with a significant annual increase from November to May, while infections caused by other viruses showed no apparent seasonality. The most common rotavirus was G4P[8] (56%), followed by G1P[8] (20.1%), G3P[8] (5.5%), G9P[8], G2P[4] (each 1.3%), six unusual (1.2%), and five mixed strains (0.5%). Norovirus GII.3 (66.5%) was predominant, followed by GII.4 (27.3%), GII.6 (3.7%), GII.1 (1.6%), and four rare genotypes (totally, 0.9%). Re-infection with noroviruses of different genotypes was observed in four children. The classic human astrovirus belonged to HAstV-1 (82%), HAstV-5 (8%), HAstV-4 (4.7%), HAstV-3 (4%) and HAstV-2 (1.3%). Consecutive episodes of HAstV-1 and HAstV-4 infections were detected in one child with an 8-month interval. Bocavirus strains were genotyped as HBoV2 (56.5%), HBoV1 (38.7%), HBoV4 (3.2%) and HBoV3 (1.6%). In the controls, norovirus strains belonged to GII.4 (n = 4), GII.1, GII.3, and GII.6, and HBoV2 strain were detected. Most of the detected virus isolates were characterized by a partial sequencing of the genomes. The genotype distribution of most common enteric viruses found in the Asian part of Russia did not differ considerably from their distribution in European Russia in 2009-2012.

PCR assays for detection of human astroviruses: In silico evaluation and design, and in vitro application to samples collected from patients in the Netherlands

BACKGROUND

Human astroviruses (HAstV) comprise three phylogenetically compact and non-adjacent groups of species including classical HAstV (HAstV-C) and the novel ones (HAstV-VA/HMO and HAstV-MLB). Of these, HAstV-C is known to be responsible for gastroenteritis while the novel HAstV are associated with cases of neurological disorders. Accurate detection of all known variants by (real-time) PCR is challenging because of the high intra- and intergroup genetic divergence of HAstV.

OBJECTIVES

To evaluate published HAstV PCR assays in silico, design de novo real-time PCR assays that can detect and discriminate three groups of HAstV, and apply those to patient samples to analyse the prevalence of HAstV in stool and cerebrospinal fluid (CSF) specimens.

STUDY DESIGN

In silico evaluation of published PCR assays and design of real-time PCR assays for detection of different subsets of HAstV was conducted within a common computational framework that used all astrovirus full genome sequences from GenBank. The newly designed real-time PCR assays were evaluated in vitro and applied to faecal samples (collected in January-May 2016) and cerebrospinal fluid specimens (2010-2016) from patients in the Netherlands.

RESULTS

Quantitative in silico evaluation of published PCRs is provided. The newly designed real-time PCR assays can reliably assign all available HAstV genome sequences to one of the three phylogenetic groups in silico, and differentiate among HAstV-specific controls in vitro. A total of 556 samples were tested using these PCR assays. Fourteen fecal samples (2.5%) tested positive for HAstV, 3 of which could be identified as the novel HAstV-MLB variants. No novel HAstV were found in CSF specimens.

CONCLUSION

Newly designed real-time PCR assays with improved detection of all known HAstV allowed the first-time identification of novel astroviruses from stool samples in the Netherlands.

Performance evaluation of a newly developed molecular assay for the accurate diagnosis of gastroenteritis associated with norovirus of genogroup II

The performance of a newly proposed fully automated cassette-based sample-to-results solution for norovirus (NoV) detection, InGenius Norovirus ELITe MGB®, was evaluated. A total of 120 selected archival stool samples from children hospitalized for acute gastroenteritis were used to compare the results to a reference real-time RT-PCR. The InGenius NoV assay showed optimal diagnostic accuracy (sensitivity, 100%; specificity, 95.7%) and was able to correctly detect the entire wide panel of epidemiologically relevant genotypes tested. These preliminary results suggest that the InGenius NoV assay can be recommended as a valuable method for accurate diagnosis of NoV GII infection in epidemic and sporadic gastroenteritis.

Next-generation amplicon sequencing identifies genetically diverse human astroviruses, including recombinant strains, in environmental waters

Human astroviruses are associated with gastroenteritis and known to contaminate water environments. Three different genetic clades of astroviruses are known to infect humans and each clade consists of diverse strains. This study aimed to determine the occurrence and genetic diversity of astrovirus strains in water samples in different geographical locations, i.e., influent and effluent wastewater samples (n = 24 each) in Arizona, U.S., and groundwater (n = 37) and river water (n = 14) samples collected in the Kathmandu Valley, Nepal, using next-generation amplicon sequencing. Astrovirus strains including rare types (types 6 and 7 classical human astroviruses), emerging type (type 5 VA-astroviruses), and putative recombinants were identified. Feline astrovirus strains were collaterally identified and recombination between human and feline astroviruses was suggested. Classical- and VA-astroviruses seemed to be prevalent during cooler months, while MLB-astroviruses were identified only during warmer months. This study demonstrated the effectiveness of next-generation amplicon sequencing for identification and characterization of genetically diverse astrovirus strains in environmental water.

Enteric Infections Circulating during Hajj Seasons, 2011-2013

Foodborne-associated bacteria with increased incidence of antimicrobial drug resistance were the most common cause.

Hajj, the annual Muslim pilgrimage to Mecca, Saudi Arabia, is a unique mass gathering event that raises public health concerns in the host country and globally. Although gastroenteritis and diarrhea are common among Hajj pilgrims, the microbial etiologies of these infections are unknown. We collected 544 fecal samples from pilgrims with medically attended diarrheal illness from 40 countries during the 2011–2013 Hajj seasons and screened the samples for 16 pathogens commonly associated with diarrheal infections. Bacteria were the main agents detected, in 82.9% of the 228 positive samples, followed by viral (6.1%) and parasitic (5.3%) agents. Salmonella spp., Shigella/enteroinvasive Escherichia coli, and enterotoxigenic E. coli were the main pathogens associated with severe symptoms. We identified genes associated with resistance to third-generation cephalosporins ≈40% of Salmonella- and E. coli–positive samples. Hajj-associated foodborne infections pose a major public health risk through the emergence and transmission of antimicrobial drug–resistant bacteria.

Persistent Infections with Diverse Co-Circulating Astroviruses in Pediatric Oncology Patients, Memphis, Tennessee, USA

Human astroviruses are a major cause of pediatric gastroenteritis, especially in immunocompromised children. We conducted a retrospective study to demonstrate that diverse astrovirus genotypes can co-circulate in pediatric oncology patients. A subset of cases is associated with long-term virus shedding (range 17–183 days).

Detection and Molecular Characterization of Human Adenovirus Infections among Hospitalized Children with Acute Diarrhea in Shanghai, China, 2006-2011

Background: Human adenovirus (HAdV) is considered a significant enteropathogen associated with sporadic diarrhea in children. However, limited data are available regarding the epidemiology of HAdV in hospitalized children with viral diarrhea in Shanghai. The aim of this study was to characterize the epidemiology of HAdVs and describe their association with acute diarrhea in hospitalized children. Methods: A total of 674 fecal samples were subjected to PCR or RT-PCR to detect RVA, HuCV, HAstV, and HAdV. Results: HAdV infections were detected in 4.7% (32/674) of specimens, with detection rates of 13.4% (11/82), 4.6% (8/174), 3.2% (4/124), 4.1% (3/74), 2.0% (2/100), and 3.3% (4/120) from 2006 to 2011, respectively. Comprehensive detection of the four viruses revealed the presence of a high percentage (90.6%) of coinfections among HAdV-positive samples, where HAdV+RVA was the most prevalent coinfection. Of the 32 HAdV-positive samples, 50.0% (16/32) were classified as HAdV-41, and 18.8% (6/32) were classified as HAdV-3. Almost 94.0% of children infected with HAdV were less than 24 months of age. Conclusions: These results clearly indicated diversity across the HAdV genotypes detected in inpatient children with acute diarrhea in Shanghai and suggested that HAdVs play a role in children with acute diarrhea.

Molecular evolutionary analysis of type-1 human astroviruses identifies putative sites under selection pressure on the capsid protein

Human astroviruses (HAstV) are important enteric pathogens that can be classified into eight sero/genotypes (HAstV-1 to -8). Although the various HAstV types show global spread, type-1 strains tend to be predominant. Molecular analysis of the genomic region encoding the capsid protein (ORF2) has revealed discrete sequence variation, with different lineages within each HAstV type and at least three major lineages have been identified within HAstV-1. Longitudinal epidemiological surveillance has revealed temporal shift of the various HAstV-1 lineages. Metadata analysis of HAstV-1 sequences available in the databases also revealed temporal shifts of the circulation of HAstV-1 lineages, suggesting possible antigenic-related mechanisms of selection at the sub-genotype level. By comparison of HAstV-1 capsid sequences, lineage-defining residues under positive selection were identified. Structural analysis of HAstV-1 capsid allowed identifying at least six residues exposed on the virion surface. Two residues were located in the VP34 (shell region) whilst four residues were mapped in the VP25/27 (protruding region) of HAstV capsid protein, in proximity of the putative receptor binding S site. These findings suggest that mechanisms similar to those observed and/or hypothesized for other enteric viruses are also shaping the evolution of HAstVs, with intra-typic diversification being a possible mechanism to decrease the antigenic pressure to which these viruses are exposed.

The Expanding Field of Mammalian Astroviruses: Opportunities and Challenges in Clinical Virology

Astroviruses are best known as being one of the leading causes of diarrhea in infants and were first described in this context in 1975. In its first years, astrovirus research was mainly restricted to electron microscopy and serology studies. The ability to culture some of these viruses in vitro allowed a first consequent step forward, especially at the molecular level. Since the emergence of more powerful genetic methods, though, the face of this research field has dramatically changed and evolved. From the exponential number of discoveries of new astrovirus strains in the most varied of animal species to their association with atypical diseases, these viruses revealed a lot of surprises, and many more are probably still waiting to be uncovered. This chapter summarizes the most important knowledge about astroviruses and discusses the implication of the latest findings in this area of research.

Novel and classical human astroviruses in stool and cerebrospinal fluid: comprehensive screening in a tertiary care hospital, Switzerland

Classical human astroviruses (HAstV) are the third most common cause of non-bacterial acute gastroenteritis. Due to the lack of routine molecular assays, novel HAstV are underdiagnosed and the magnitude of their contribution to clinical disease remains unknown. To better understand their prevalence and the susceptible patient profile, we conducted a comprehensive screening of novel and classical HAstV in stool and cerebrospinal fluid (CSF) samples collected for clinical care in a tertiary care hospital using a specially designed rRT-PCR panel for the detection of novel (MLB1-3 and VA1-4) and classical HAstV. Of the 654 stool samples, 20 were positive for HAstV, and the novel (n=10; 3 MLB1, 4 MLB2; 3 VA2) and classical (n=10) serotypes were equally prevalent. None of the 105 CSF samples were positive. Investigating the patient profile, we found a higher prevalence (P=0.0002) of both novel and classical HAstV in pediatric stool samples (3.4% and 3%, respectively) compared with adult stool samples (0.5% and 0.7%, respectively). Furthermore, all novel and classical HAstV-positive pediatric subjects were ≤four years old, demonstrating similar susceptible populations. Forty-five percent of positive patients were immunocompromised (novel: 40%, classical: 50%). A comparison of novel and classical HAstV-positive cases showed a lower viral load for novel HAstV (P=0.0007) with significantly more upper respiratory symptoms (70% of subjects; P=0.02); this observation may suggest a unique pathogenic pathway. This study confirms the clinical and epidemiological relevance of novel HAstV and identifies a target population in which routine screening may yield clinically valuable information.

Comparison of three multiplex gastrointestinal platforms for the detection of gastroenteritis viruses

BACKGROUND

Viruses are major etiological agents of childhood gastroenteritis. In recent years, several molecular platforms for the detection of viral enteric pathogens have become available.

OBJECTIVE/STUDY DESIGN

We evaluated the performance of three multiplex platforms including Biofire's Gastrointestinal Panel (FilmArray), Luminex xTAG^® Gastrointestinal Pathogen Panel (GPP), and the TaqMan Array Card (TAC) for the detection of five gastroenteritis viruses using a coded panel of 300 archived stool samples.

RESULTS

The FilmArray detected a virus in 199 (96.1%) and the TAC in 172 (83.1%) of the 207 samples (187 samples positive for a single virus and 20 samples positive for more than one virus) whereas the GPP detected a virus in 100 (78.7%) of the 127 (97 positive for one virus and three positive for more than one virus) samples. Overall the clinical accuracy was highest for the FilmArray (98%) followed by TAC (97.2%) and GPP (96.9%). The sensitivity of the FilmArray, GPP and TAC platforms was highest for rotavirus (100%, 95.8%, and 89.6%, respectively) and lowest for adenovirus type 40/41 (97.4%, 57.9% and 68.4%). The specificity of the three platforms ranged from 95.6% (rotavirus) to 99.6% (norovirus/sapovirus) for the FilmArray, 99.6% (norovirus) to 100% (rotavirus/adenovirus) for GPP, and 98.9% (astrovirus) to 100% (rotavirus/sapovirus) for TAC.

CONCLUSION

The FilmArray demonstrated the best analytical performance followed by TAC. In recent years, the availability of multi-enteric molecular testing platforms has increased significantly and our data highlight the strengths and weaknesses of these platforms.