Detection of a novel species A, DS-1-like, G4P[6] rotavirus strain from a Brazilian child with gastroenteritis.

Rotaviruses belonging to species A (RVA) remain among the most common causes of severe gastroenteritis in children aged <5 years, leading to substantial morbidity and mortality worldwide. Genome reassortment events between two human strains or human and animal strains represent one of the mechanisms which appear to generate the broad genetic variability of circulating. According to a nucleotide, sequence-based classification system, RVA strains are currently classified into three genotype constellations including Wa-like (genogroup I), DS-1-like (genogroup II), and AU-like (genogroup III). The present study reports the detection of an unusual RVA G4P[6] strain (coded as strain HSE005), which might have originated from a natural reassortment event between human and animal RVA strains. Molecular characterization of this isolate showed that it belonged to genogroup II, genotype G4P[6]. In addition, two genes (VP3 and NSP4) of this strain denoted evidence of reassortment events involving strains of distinct zoonotic evolutionary origins. Therefore, we propose that a new G4P[6] strain was identified, highlighting a possible first zoonotic transmission including a reassortment event that involved the VP3 gene.

Genomic stratification and differential natural selection signatures among human norovirus genogroup II isolates.

Noroviruses (NoVs), which are members of the family Caliciviridae, are the most common cause of gastroenteritis in humans. Ten NoV genogroups have been reported so far. Of these, genogroup II (GII) is the most prevalent, and it causes serious infections worldwide. The complete genome sequences of NoV GII isolates from different geographical regions were retrieved from the public database. The model-based clustering approach, implemented in the STRUCTURE resource, was employed for assessment of genetic composition. The MEGA X and IQ Tree tools were used for phylogenetic analysis. Genome-wide natural selection analysis was performed using maximum-likelihood-based methods. The demographic features of NoV GII genome sequences were assessed using the BEAST package. All of the NoV GII sequences initially clustered into two main subpopulations at significant K = 2, where the genotype GII.4 samples clearly split from the rest of the genotypes. This indicates a marked genetic distinction between norovirus GII.4 and non-GII.4 samples. Phylogenetic analysis showed the presence of five distinct subclades for genotype GII.2 and seven subclades for GII.4 samples. Several isolates with admixed ancestry were identified that constituted distinct subclusters in the phylogenetic tree. No continental-specific genetic distinctions were observed among the NoV GII samples. Significant genomic signatures of both positive and negative natural selection were identified across the NoV GII genes. A differential pattern of positive selection signals was inferred between the GII.4 and non-GII.4 genotypes. The demographic analysis revealed an increase in the effective population size of NoV GII during 2009-2010, followed by a rapid fall in 2015.

Epitope mapping of histo blood group antigens bound to norovirus VLPs using STD NMR experiments reveals fine details of molecular recognition.

Attachment of human noroviruses to histo blood group antigens (HBGAs) is thought to be critical for the infection process. Therefore, we have determined binding epitopes of synthetic type 1 to 6 blood group A- and B-tetrasaccharides binding to GII.4 human Norovirus virus like particles (VLPs) using STD NMR experiments. So far, little information is available from crystal structure analysis studies on the interactions of the reducing-end sugars with the protruding domain (P-domain) of the viral coat protein VP1. Here, we show that the reducing-end sugars make notable contacts with the protein surface. The type of glycosidic linkage, and the identity of the sugar at the reducing end modulate HBGA recognition. Most strikingly, type 2 structures yield only very poor saturation transfer indicating impeded binding. This observation is in accordance with previous mass spectrometry based affinity measurements, and can be understood based on recent crystal structure data of a complex of highly homologous GII.4 P-dimers with H-type 2 trisaccharide where the N-acetyl group of the reducing N-acetyl glucosamine residue points towards a loop comprising amino acids Q390 to H395. We suggest that in our case, binding of type 2 A- and B-tetrasaccharides leads to steric conflicts with this loop. In order to identify factors determining L-Fuc recognition, we also synthesized GII.4 VLPs with point mutations D391A and H395A. Prior studies had suggested that these residues, located in a second shell around the L-Fuc binding site, assist L-Fuc binding. STD NMR experiments with L-Fuc and B-trisaccharide in the presence of wild type and mutant VLPs yield virtually identical binding epitopes suggesting that these two mutations do not significantly alter HBGA recognition. Our study emphasizes that recognition of α-(1→2)-linked L-Fuc residues is a conserved feature of GII.4 noroviruses. However, structural variation of the HBGA core structures clearly modulates molecular recognition depending on the genotype.

Molecular epidemiology of genogroup II norovirus infection among hospitalized children with acute gastroenteritis in Suzhou (Jiangsu, China) from 2010 to 2013.

Noroviruses (NoVs) are the most common cause of acute gastroenteritis in both sporadic and outbreak cases. Genotyping and recombination analyses were performed in order to help getting more knowledge of the distribution and genetic diversity of NoVs in Suzhou, located in Jiangsu province of China. All stool samples were collected from hospitalized children younger than 5 years old with acute gastroenteritis. For genotyping, the open reading frame (ORF) 1 and ORF2 were partially amplified and sequenced. 26.9% of stool samples were positive for genogroup II NoVs. The most common genotype was GII.4 and its variants included Den Haag-2006b, New Orleans-2009, and Sydney-2012. The Den Haag-2006b variants predominated during 2010-2012. In 2013, it was replaced by the Sydney-2012 variant. The second most common genotype was GII.12/GII.3. NoVs could be detected throughout the year, with GII.4 and GII.12/GII.3 coexisting during the cold months, and GII.4 was the main genotype during the warm months. The highest prevalence of NoV was detected in young children aged <24 months. Patients infected with GII.4 had a higher chance of getting moderate fever than other NoV-positive patients, while those infected with GII.12/GII.3 tended to have a mild degree of fever. NoV is an important pathogen responsible for viral gastroenteritis among children in Suzhou. Analyses of NoV circulating between 2010 and 2013 revealed a change of predominant variant of NoV GII.4 in each epidemic season and intergenotype recombinant strains represented an important part.

Epidemiological investigation of norovirus infections in Punjab, Pakistan, through the One Health approach.

Introduction: Norovirus, mainly associated with acute gastroenteritis, is very contagious and can affect a vast range of species ranging from cattle, pigs, dogs, mice, cats, sheep, and lions to humans. It is a foodborne pathogen that mainly transmits through the fecal-oral route. Methods: This is the first-ever study conducted in Lahore and Sheikhupura districts of Punjab, Pakistan, to investigate noroviruses through the One Health approach. From January 2020 to September 2021, 200 fecal samples were collected from clinical cases of hospitalized patients and 200 fecal samples from sick animals at veterinary hospitals and local farms. In addition, 500 food and beverage samples were collected from street vendors and retail stores. A predesigned questionnaire was used to assess the risk factors and clinical characteristics of sick people and animals. Results and discussion: Overall, 14% of the human clinical samples were positive by RT-PCR for genogroup GII. All bovine samples were negative. Food and beverage samples were tested in pools, resulting in sugarcane juice samples positive for genogroup GII. Previous contact with acute gastroenteritis patients, sex, and presence of vomiting were found to be significant risk factors (p ≤ 0.05). The substantial number of diarrhea cases associated with noroviruses calls for additional studies to investigate the epidemiology and transmission and to improve surveillance.

High Prevalence of Genogroup I and Genogroup II Picobirnaviruses in Dromedary Camels.

Picobirnaviruses (PBVs) are small non-enveloped bisegmented double-stranded RNA viruses found in humans, mammals, and birds. Increasing molecular epidemiology studies suggest a high sequence diversity of PBVs in numerous hosts and the environment. In this study, using 229 fecal samples from dromedary camels in Dubai, 52.8% were positive for PBVs, of which 77.7% and 41.3% were positive for genogroup I and II, respectively, and 19.0% were positive for both genotypes. Phylogenetic analysis showed high diversity among the sequences of genogroup I and II dromedary PBVs. Marked nucleotide polymorphisms were observed in 75.5% and 46.0% of genogroup I and II RNA-dependent RNA polymerase (RdRp) sequences, respectively, suggesting the co-existence of multiple strains in the same specimen. Both high genetic diversity and prevalence of genogroup I and II PBV in dromedaries were observed. In fact, the prevalence of genogroup II PBV in dromedaries is the highest among all animals to date. The complete/near-complete core genomes of five genogroup I and one genogroup II dromedary PBVs and partial segment 1 and 2 of both genotypes were also sequenced. The dromedary PBV genome organizations were similar to those of other animals. Genetic reassortment and mutation are both important in the ecology and evolution of PBVs.

Emergence of multiple norovirus strains in Thailand, 2015-2017.

Norovirus is a major cause of non-bacterial acute gastroenteritis worldwide. Infection can be sporadic or result in widespread outbreaks. The surveillance of norovirus samples (n = 1591) obtained from patients with diarrhea in Thailand from January 2015 to February 2017 suggested that the predominance of norovirus GII.4 often seen in sporadic infection had been superseded by the emergence of GII.17. More recently, a sharp increase in acute gastroenteritis associated with norovirus GII·P16-GII.2 recombinant strain was observed at the end of 2016. Thus, previously rare norovirus strains and their recombinant derivatives may be more frequently responsible for future outbreaks.

Emergence of Norovirus GII.17-associated Outbreak and Sporadic Cases in Korea from 2014 to 2015.

Human norovirus are major causative agent of nonbacterial acute gastroenteritis. In general, genogroup (G) II.4 is the most prominent major genotype that circulate in human population and the environment. However, a shift in genotypic trends was observed in Korea in December 2014. In this study, we investigated the trend of norovirus genotype in detail using the database of Acute Diarrhea Laboratory Surveillance (K-EnterNet) in Korea. GII.17 has since become a major contributor to outbreaks of norovirus-related infections and sporadic cases in Korea, although the reason for this shift remain unknown.

Clinical and epidemiological characteristics of norovirus gastroenteritis among hospitalized children in Lebanon.

AIM: To assess the burden of norovirus (NoV) and to determine the diversity of circulating strains among hospitalized children in Lebanon. METHODS: Stool samples were collected from children presenting with acute gastroenteritis to six major hospitals in Lebanon. A total of 739 eligible stool samples, testing negative for diarrhea caused by rotavirus as a possible viral pathogen, were collected between January 2011 and June 2013. A standardized questionnaire including demographic, epidemiological and clinical observations was used at the time of hospitalization of children presenting with diarrhea. Viral RNA was extracted from stool samples followed by reverse transcription polymerase chain reaction and nucleotide sequencing of a fragment of the viral protein 1 capsid gene. Multiple sequence alignments were carried out and phylogenetic trees were constructed using the MEGA 6 software. RESULTS: Overall, 11.2% of stool samples collected from children aged < 5 years tested positive for NoV genogroups I (GI) and II (GII). GII accounted for 10.6% of the gastroenteritis cases with only five samples being positive for GI (0.7%). The majority of hospitalized children showed symptoms of diarrhea, dehydration, vomiting and fever. Upon sequencing of positive samples and based on their clustering in the phylogenetic tree, 4/5 of GI gastroenteritis cases were designated GI.3 and one case as GI.4. GII.4 was predominantly detected in stool of our study participants (68%). We report a JB-15/KOR/2008 GII.4 Apeldoorn 2008-like variant strain circulating in 2011; this strain was replaced between 2012 and 2013 by a variant sharing homology with the Sydney/NSW0514/2012/AUS GII.4 Sydney 2012 and Sydney 2012/FRA GII.4 strains. We also report the co-circulation of non-GII.4 genotypes among hospitalized children. Our data show that NoV gastroenteritis can occur throughout the year with the highest number of cases detected during the hot months. CONCLUSION: The majority of NoV-associated viral gastroenteritis cases among our participants are attributable to GII.4, which is compatible with results reported worldwide.

Burden of norovirus in healthcare facilities and strategies for outbreak control.

Norovirus is the most frequently occurring cause of community-acquired acute gastroenteritis in people of all ages. It is also one of the most frequent causes of outbreaks in healthcare settings, affecting both long-term care facilities and acute care hospitals. Whereas norovirus gastroenteritis is typically mild and resolves without medical attention, healthcare-associated infections often affect vulnerable populations, resulting in severe infections and disruption of healthcare services. Globally, most norovirus outbreaks in hospitals and residential care institutions are associated with genogroup II type 4 (GII.4) strains. Recent data demonstrate that excess mortality occurs during outbreak periods in healthcare facilities. Nosocomial outbreaks can result in large economic and societal costs. Current control measures for norovirus are largely based on general infection control principles, and treatment is mainly supportive and non-specific. While neither vaccines nor antiviral agents are currently available, both are being developed with encouraging results.

Animal picobirnavirus.

Picobirnavirus (PBV) is a small, non-enveloped, bisegmented double-stranded RNA (dsRNA) virus of vertebrate hosts. The name 'Picobirnavirus' derives from the prefix 'pico' (latin for 'small') in reference to the small virion size, plus the prefix 'bi' (latin for 'two') and the word 'RNA' to indicate the nature of the viral genome. The serendipitous discovery of PBV dates back to 1988 from Brazil, when human fecal samples collected during the acute gastroenteritis outbreaks were subjected for routine rotavirus surveillance by polyacrylamide gel electrophoresis (PAGE) and silver straining (S/S). The PAGE gels after silver staining showed a typical 'two RNA band' pattern, and it was identified as Picobirnavirus. Likewise, the feces of wild black-footed pigmy rice rats (Oryzomys nigripes) subjected for PAGE assay by the same research group in Brazil reported the presence of PBV (Pereira et al., J Gen Virol 69:2749-2754, 1988). PBVs have been detected in faeces of humans and wide range of animal species with or without diarrhoea, worldwide. The probable role of PBV as either a 'primary diarrhoeal agent' in 'immunocompetent children'; or a 'potential pathogen' in 'immunocompromised individuals' or an 'innocuous virus' in the intestine remains elusive and needs to be investigated despite the numerous reports of the presence of PBV in fecal samples of various species of domestic mammals, wild animals, birds and snakes; our current knowledge of their biology, etiology, pathogenicity or their transmission characteristics remains subtle. This review aims to analyse the veterinary and zoonotic aspects of animal Picobirnavirus infections since its discovery.

A gastroenteritis outbreak caused by noroviruses in Greece.

In June 2006, an outbreak alert regarding cases of acute gastroenteritis in a region in North Eastern Greece (population 100,882 inhabitants), triggered investigations to guide control measures. The outbreak started the first days of June, and peaked in July. A descriptive epidemiological study, a virological characterization of the viral agent identified from cases as well as a phylogenetic analysis was performed. From June 5 to September 3, 2006 (weeks 23-44), 1,640 cases of gastroenteritis (45.2% male and 54.8% female, aged 3 months to 89 years) were reported. The overall attack rate for the period was 16.3 cases/1,000 inhabitants. About 57% of cases observed were under the age of 15 years. Analysis of faecal samples identified Norovirus GII strains. Fifteen different Norovirus GII strains were recorded, presenting a homology of 94.8% (86-97%) to GII strains obtained from GenBank. The long duration of the outbreak suggests an important role of person-to-person transmission, while the emergence of the outbreak was possibly due to contaminated potable water, although no viruses were detected in any tested water samples. This outbreak underscores the need for a national surveillance system for acute non-bacterial gastroenteritis outbreaks.