Evidence of the etiological predominance of norovirus in gastroenteritis outbreaks—emerging new-variant and recombinant noroviruses in Hungary

Genetic Diversity and Phylogenetic Relationship of Human Norovirus Sequences Derived from Municipalities within the Sverdlovsk Region of Russia

Human noroviruses (HuNoVs) are highly contagious pathogens responsible of norovirus-associated acute gastroenteritis (AGE). GII.4 is the prevailing HuNoV genotype worldwide. Currently there are no studies on the molecular monitoring and phylogenetic analysis of HuNoVs in the territory of the Sverdlovsk region; therefore, it is not possible to objectively assess their genetic diversity. The aim of the study is to carry out genotyping and phylogenetic analysis of HuNoVs in the Sverdlovsk region from 2022 to 2023. Fecal samples (n = 510) were collected from children suffering from HuNoV-AGE in municipalities of the Sverdlovsk region and the capsid genotype was determined by amplifying the ORF1/ORF2 junction. Of the 196 HuNoVs typed, which represent 38% of the studied samples, the largest share of HuNoV genotypes belong to the GII genogroup-86%, followed by the GI genogroup-14%. Noroviruses GII.4 and GII.17 were the co-dominant capsid genotypes (33.2% each). Phylogenetic analysis demonstrates that the identified sequences on the territory of the Sverdlovsk region have the smallest genetic distance, which gives grounds for their unification into a common cluster. Routine monitoring and phylogenetic analysis of circulating norovirus pathogens spectrum will enable timely tracking of HuNoVs genetic diversity and evolutionary events. This will lead to the development of more effective anti-epidemic measures, ultimately reducing the burden of infectious diseases.

Swine Norovirus: Past, Present, and Future

Norovirus, an ssRNA + virus of the family Caliciviridae, is a leading disease burden in humans worldwide, causing an estimated 600 million cases of acute gastroenteritis every year. Since the discovery of norovirus in the faeces of swine in Japan in the 1990s, swine norovirus has been reported in several countries on several continents. The identification of the human-associated GII.4 genotype in swine has raised questions about this animal species as a reservoir of norovirus with zoonotic potential, even if species-specific P-types are usually detected in swine. This review summarises the available data regarding the geographic distribution of norovirus in swine, the years of detection, the genotype characterisation, and the prevalence in specific production groups. Furthermore, we discuss the major bottlenecks for the detection and characterisation of swine noroviruses.

Surveillance of Adenovirus and Norovirus Contaminants in the Water and Shellfish of Major Oyster Breeding Farms and Fishing Ports in Taiwan

The enteric viruses, including adenovirus (AdVs) and norovirus (NoVs), in shellfish is a significant food safety risk. This study investigated the prevalence, seasonal occurrence, genetic diversity, and quantification of AdVs and NoVs in the water and cultured shellfish samples at the four major coastal oyster breeding farms (COBF), five major fishing ports (FP), and their markets in Taiwan. The AdVs/NoVs in the water and shellfish samples were isolated by the membrane filtration and direct elution methods. The RNA of NoVs was reverse-transcribed into complementary DNA through reverse transcription reaction. Further NoVs and AdVs were detected using nested PCR. A higher detection rate was recorded in the low-temperature period than high-temperature. Detection difference was noted between nested PCR and qPCR outcomes for AdVs. The total detection rate of AdVs was higher in the water samples (COBF-40.6%, FP 20%) than the shellfish samples (COBF-11.7% and FP 6.3%). The AdVs load in the water and shellfish samples ranged from 1.23 × 103 to 1.00 × 106 copies/L and 3.57 × 103 to 4.27 × 104 copies/100g, respectively. The total detection of NoVs was highest in the water samples of the FP and their market shellfish samples (11.1% and 3.2%, respectively). Genotyping and phylogenetic analysis were identified as the prevalent AdVs and NoVs genotypes in the water and shellfish samples: A species HAdVs serotype 12; F species HAdVs serotype 41; and C species PAdVs serotype 5 (NoVs GI.2, GI.3 and GII.2). No significant differences were observed between the presence of AdVs, and all of the water quality parameters evaluated (heterotrophic plate count, water temperature, turbidity, pH, salinity, and dissolved oxygen). The virus contamination occurs mainly due to the direct discharge of domestic sewage, livestock farm, and fishing market wastewater into the coastal environment. Thus, this study suggested framing better estuarine management to prevent AdVs/NoVs transmission in water and cultured/distributed shellfish.

Frequency and molecular characterization of human norovirus in Erzurum, Turkey

BACKGROUND/AIM

There are limited studies on genotyping and phylogenetic analysis of norovirus in Turkey, and this has not previously been studied in the Eastern Anatolia region. The aim of the present study was to determine the norovirus profile in this region with genotyping and phylogenetic analysis.

MATERIALS AND METHODS

Included in the study were stool samples obtained from 427 people from different age groups in Eastern Anatolia. The nucleic acid samples isolated by the automatic system and nucleic acid sequence reactions and phylogenetic analyses were performed on RNA samples.

RESULTS

The presence of norovirus was detected in 86 (20.1%) of the 427 stool samples by RT-PCR analysis. Twenty-six samples selected randomly from norovirus-RNA positive samples were subjected to the sequence reaction. In 24 of the 26 samples, genogroup GII was determined, as well as one each from GI and GIV in sequence reactions. Four different genotypes were detected in genogroup GII, which were determined to be the dominant types. These were GII.1, GII.4, GII.16, and GII.21. The GI.6 and GIV.1 genotypes were determined in genogroups GI and GIV, respectively.

CONCLUSION

The high frequency and genetic diversity of these infections are risk factors for disease and so vaccine studies should be undertaken in consideration of this situation.

Evolutionary Constraints on the Norovirus Pandemic Variant GII.4_2006b over the Five-Year Persistence in Japan

Norovirus GII.4 is a major cause of global outbreaks of viral gastroenteritis in humans, and has evolved by antigenic changes under the constantly changing human herd immunity. Major shift in the pandemic GII.4 strain periodically occurs concomitant with changes in the antigenic capsid protein VP1. However, how the newly emerged strain evolves after the onset of pandemic remains unclear. To address this issue, we examined molecular evolution of a pandemic lineage, termed the GII.4_2006b, by using the full-length viral genome and VP1 sequences (n = 317) from stools collected at 20 sites in Japan between 2006 and 2011. Phylogenetic tree showed a radial diversification of the genome sequences of GII.4_2006b, suggesting a rapid genetic diversification of the GII.4_2006b population from a few ancestral variants. Impressively, amino acid sequences of the variable VP1 in given seasons remained as homogeneous as those of viral enzymes under annual increase in the nucleotide diversity in the VP1 coding region. The Hamming distances between the earliest and subsequent variants indicate strong constraints on amino acid changes even for the highly variable P2 subdomain. These results show the presence of evolutionary constraints on the VP1 protein and viral enzymes, and suggest that these proteins gain near maximal levels of fitness benefits in humans around the onset of the outbreaks. These findings have implications for our understanding of molecular evolution, mechanisms of the periodic shifts in the pandemic NoV GII.4 strains, and control of the NoV GII.4 pandemic strain.

Influence of School Year on Seasonality of Norovirus Outbreaks in Developed Countries

Factors affecting the seasonal distribution of norovirus outbreaks are not well understood. This study examined whether grade school settings at the start of the school year may be a factor. We searched Ovid Medline from January 2002 to June 2014 for studies that provided all reported norovirus outbreaks in a developed country by month for a minimum of three years. Historical school years were obtained from verifiable sources. The start of the norovirus seasonal outbreak peak and peak outbreak month were determined for each study and compared to the start month of school. Northern hemisphere and southern hemisphere countries had a different norovirus seasonality and different school year structures (traditional compared to year round). In the two studies that provided outbreaks by age, outbreaks among children started several months before outbreaks in the adult population. The median number of months between school start and start of the seasonal outbreak peak was two months (interquartile range [IQR] = 2.0-3.0), while the median number of months between school start and peak outbreak month was four months (IQR = 3.0-4.0). These findings suggest the possibility the school setting at the start of the school year may be a factor in the seasonality of norovirus.

Human Norovirus prevalence in Africa: a review of studies from 1990 to 2013

OBJECTIVES

To assess the contribution of Human Norovirus to diarrhoeal diseases in Africa.

METHODS

We conducted a systematic review of the PubMed and EMBASE databases for published articles of Human Norovirus in Africa between 1990 and 2013. Data were extracted from selected studies and analysed.

RESULTS

A total of 208 eligible studies were identified, of which 55 (from 19 countries) met the inclusion criteria. Many cases were of sporadic gastroenteritis (70.9%) in children (82%), 65.4% of which were seen in an outpatient setting. Over half (59.4%) of the affected children were under 5 years of age. The pooled prevalence rate of Human NoV was 11% (95% CI 8-14%), and the meta-analysis indicated significant heterogeneity between the studies. However, the conditional negative binomial regression could not clearly find the factors affecting the Human NoV prevalence rates reported. A close relationship was found between Human Norovirus strains from environmental and clinical samples.

CONCLUSION

Unreported sporadic gastroenteritis cases of Human Norovirus are common in Africa. Most are community-associated infections. Possible environmental transmission routes have been documented. Combined environmental and clinical studies are required for targeted actions to control transmission of Human Norovirus in Africa. Systematic surveillance of Human Norovirus is needed to measure the burden of Norovirus-induced gastroenteritis in Africa and support any requirements for vaccine development.

Adenovirus and Norovirus Contaminants in Commercially Distributed Shellfish

Shellfish complying with European Regulations based on quantification of fecal bacterial indicators (FIB) are introduced into markets; however, information on viruses, more stable than FIB, is not available in the literature. To assess the presence of noroviruses (NoVs) GI and GII and human adenoviruses (HAdV) in domestic and imported mussels and clams (n = 151) their presence was analyzed during winter seasons (2004-2008) in north-west Spanish markets through a routine surveillance system. All samples tested negative for NoV GI and 13 % were positive for NoV GII. The role of HAdV as viral indicator was evaluated in 20 negative and 10 positive NoV GII samples showing an estimated sensitivity and specificity of HAdV to predict the presence of NoV GII of 100 and 74 % (cut-off 0.5). The levels of HAdV and NoVs and the efficiency of decontamination in shellfish depuration plants (SDP) were evaluated analyzing pre- and post-depurated mussels collected in May-June 2010 from three different SDP. There were no statistically significant differences in the prevalence and quantification of HAdV between pre- and post-depurated shellfish and between seawater entering and leaving the depuration systems. Moreover, infectious HAdV were detected in depurated mussels. These results confirm previous studies showing that current controls and depuration treatments limiting the number of FIB do not guarantee the absence of viruses in shellfish.

Rapid emergence of novel GII.4 sub-lineages noroviruses associated with outbreaks in Huzhou, China, 2008-2012

Infection caused by noroviruses (NoVs) is one of the most important causes of acute gastroenteritis in humans worldwide. To gain insight into the epidemiology of and genetic variation in NoV strains, stool samples collected from 18 outbreaks of acute gastroenteritis in Huzhou, China, between January 2008 and December 2012 were analyzed. Samples were tested for NoVs by real-time RT-PCR. Partial sequences of the RNA- dependent RNA polymerase (RdRp) and capsid gene of the positive samples were amplified by RT-PCR, and the PCR products were sequenced and used for phylogenetic analysis. NoVs were found to be responsible of 88.8% of all nonbacterial acute gastroenteritis outbreaks in Huzhou over the last 5 years. Genogroup II outbreaks largely predominated and represented 93% of all outbreaks. A variety of genotypes were found among genogroups I and II, including GI.4, GI.8, GII.4, and GII.b. Moreover, phylogenetic analyses identified two recombinant genotypes (polymerase/capsid): GI.2/GI.6 and GII.e/GII.4 2012 Sydney. GII.4 was predominant and involved in 8/10 typed outbreaks. During the study period, GII.4 NoV variants 2006b, New Orleans 2009, and Sydney 2012 were identified. This is the first report of the detection of GII.4 New Orleans 2009 variant, GII.e/GII.4 Sydney 2012 recombinant in outbreaks of acute gastroenteritis in China.

Monitoring of Calicivirus among day-care children: evidence of asymptomatic viral excretion and first report of GI.7 Norovirus and GI.3 Sapovirus in Brazil

Caliciviruses (Norovirus and Sapovirus) are important causes of acute gastroenteritis, with Norovirus (NoV) considered the leading cause of epidemic non-bacterial acute gastroenteritis; however, molecular and epidemiological data of the circulating Calicivirus (CV) strains among day-care children are still considered scarce. The role of asymptomatic CV excretion on viral transmission also remains poorly understood. The aim of the present study was to monitor the occurrence of NoV and Sapovirus (SaV) in a day-care center and to describe the molecular epidemiology of the circulating strains. Genomic sequencing and phylogenetic analysis of the capsid region were carried out in CV positive samples obtained from children younger than 5 years, with or without diarrhea, between October 2009 and October 2011. A total of 539 fecal samples were screened for CV. Forty-three (8%) were positive for NoV and 25 (4.6%) for SaV. Surprisingly, positivity rates for CV were significant in asymptomatic children, and virus circulation was detected in every month of the study. Great genomic diversity of CV was observed, and the circulating NoV strains were: GII.6, GII.2, GII.1, GI.7, GII.4, and GI.1. The SaV genotypes GI.1 and GI.3 were also detected. Five CV outbreaks caused by distinct viral strains were documented. This study provides an insight on the genetic diversity of CV in a day-care in Central West Brazil, highlighting the probable role of asymptomatic viral excretion and the significance of semi-closed settings in the dissemination of these agents.

Novel intergenotype human norovirus recombinant GII.16/GII.3 in Bangladesh

Noroviruses (NoVs) are one of the major etiological agents of acute gastroenteritis in all age groups. In this study, we identified an intergenotype NoV recombinant strain in the fecal specimens of two male infants with acute diarrhea in Bangladesh. Phylogenetic analysis showed that the identified strains were recombinant NoV strains with a GII.3 capsid and a GII.16 polymerase gene. The recombination breakpoint was located in the ORF1/ORF2 overlap region. To the best of our knowledge this is the first report of a NoV recombinant GII.16/GII.3 strain worldwide.

Molecular epidemiology of norovirus gastroenteritis outbreaks in New Zealand from 2002-2009

Noroviruses are the most common cause of acute non-bacterial gastroenteritis outbreaks worldwide, including New Zealand. New Zealand has a population of 4.4 million, which allows for centralized outbreak surveillance and a Norovirus Reference Laboratory, which facilitates efficient diagnosis, surveillance, and tracking of norovirus outbreaks. Norovirus outbreak strains are identified, sequenced, and compared with international reference strains. Between January 2002 and December 2009, 1,206 laboratory-confirmed norovirus outbreaks were recorded. The predominant outbreak settings were healthcare institutions for the elderly and acute care patients. Other outbreak settings included catering establishments, cruise ships, homes, community events, school camps, child-related settings, and consumption of contaminated shellfish. Of the 1,206 outbreaks, 105 (8.7%) were caused by norovirus genogroup I (GI) strains, 1,085 (89.9%) were caused by genogroup II (GII) strains, and both GI and GII strains were detected in 9 (0.8%) outbreaks. The genogroup was not identified in 7 (0.6%) outbreaks. A range of norovirus genotypes, including GI genotypes 1-6, GII genotypes 2-8, and GII.12, were associated with these outbreaks. The predominant genotype was GII.4, which was identified in 825 (68.4%) outbreaks. Norovirus GII.4 variant strains, including 2002 (Farmington Hills), 2004 (Hunter), 2006a (Laurens, Yerseke), 2006b (Minerva), and 2010 (New Orleans) implicated in overseas outbreaks also occurred in New Zealand, providing evidence of global spread.

Clinical and molecular epidemiologic analyses of norovirus-associated sporadic gastroenteritis in adults from Beijing, China

Noroviruses (NoVs) are a major cause of nonbacterial acute gastroenteritis. The molecular epidemiology of NoV infections in China has not been well characterized. To study the incidence of NoV infections and the nature of the circulating NoV genotypes, 403 specimens were collected from adult outpatients with acute gastroenteritis in Beijing, China, between October 2007 and September 2008. Samples were examined for NoV by reverse transcriptase-polymerase chain reaction (RT-PCR) and sequences corresponding to both the NoV polymerase and capsid regions were characterized. Among the 403 specimens, 48 (11.9%) were positive for NoV and 1/3 NoV-associated gastroenteritis cases occurred during the colder months (November and December). Based on polymerase region sequences, 6 NoV genotypes (GII-4, GII-b, GII-6, GI-2, GI-3, and GI-4) were identified with GII-4 2006b being the most predominant genotype (37/48, 77.1%). Eleven distinct genotype sequences in polymerase and capsid regions were identified, indicating a genetic diversity among NoV isolates. This study suggested NoVs were an important pathogen responsible for sporadic acute gastroenteritis in adults in Beijing, China.

Genomic organization and recombination analysis of human norovirus identified from China

Noroviruses (NoVs) are one of the major causal agents of acute gastroenteritis in both industrial and developing countries including China. Recent studies have revealed that NoV genome is highly prone to mutation and recombination which may lead to emergence of new strains. In the present study, three full-length genomes of human NoV from China were determined and the genomic organization and recombination were analyzed. They had similar genome organization and contained three predicted ORFs, though the 5'UTR of those three strains were 2, 4 and 8 nucleotides, respectively. Phylogenetic analysis showed that the HU/GII/SHANGHAI/SH312/2008/CHN strain may be a recombinant of GII-3 capsid and GII-4 polymerase. To confirm the finding and detect the breakpoints where the recombination event occurred, we performed recombination analysis based on the genomic sequences of HU/GII/SHANGHAI/SH312/2008/CHN as the query sequence, and AB220921/NOV/JP/GII-4 and AB365435/NOV/US/GII-3 as the background sequences, using RPD software. Results indicated that the two parental strains were AB220921/NOV/JP/GII-4 and AB365435/NOV/US/GII-3. The breakpoint for this recombination event located at position 5,107 nt of the genome (in the ORF1 and ORF2 overlap).

Characterization of a novel porcine enterovirus in domestic pig in Hungary

Porcine enteroviruses (PEVs) of genus Enterovirus are small, non-enveloped viruses with single-stranded, positive sense genomic RNA, belonging to the family Picornaviridae. The discovery of two distinct serotypes (PEV9 and 10) was first reported in 1979. Despite the sporadic detection and partial genome sequences of these viruses our knowledge about the prevalence and molecular epidemiology of PEV types in domestic pigs is very deficient. In this study, we identified a novel PEV from fecal samples of clinically healthy pigs (Sus scrofa domestica) in Hungary by RT-PCR using human enterovirus generic primer pairs for 5'UTR region, with subsequent partial VP1 and complete genome sequencing and phylogenetic analysis. Among 45 fecal and blood sample pairs collected at the same farm from domestic pigs divided into three age groups (10 days, 4 weeks, and 3 months of age, N = 15 each group) six (40%) of the 15 fecal samples of 10-day-old pigs were enterovirus-positive. PEV was not detected in serum samples. Sequence- and phylogenetic analysis of the complete genome of swine/K23/2008/HUN (HQ702854) show relationship to PEV strains but it is separated from the PEV9 and 10, especially in structural regions. Swine/K23/2008/HUN has average of 77 and 75% amino acid identity in the P1 region, and only 61% in VP1 region to PEV9 and 10, respectively. The partial VP1 sequences of the Hungarian PEV strains show 99% nucleotide identity compared to each other. PEVs could be capable of at least local endemic spread among newborn piglets and cause no clinical symptoms or viraemia. Sequence data indicates that the Hungarian PEV strain belongs to a novel PEV. To clarify the taxonomic confusion related to PEV--as a consequence of recent extensive taxonomic changes among porcine enteric picornaviruses--we propose that PEV9 and PEV10 should be reclassified as PEV1 and PEV2. In this classification swine/K23/2008/HUN represents PEV3.

[First detection of human astrovirus in gastroenteritis outbreak in Hungary]

Human astroviruses are one of the known pathogens of gastroenteritis in infants, children and rarely in elderly. It causes 4.2-7.3% of the sporadic gastroenteritis cases with diarrhea and vomiting in children. The etiological role of astrovirus has not been confirmed yet in outbreaks of gastroenteritis in Hungary.

AIMS

The first description of the detection and molecular epidemiology of astrovirus in outbreaks of gastroenteritis in Hungary.

MATERIALS AND METHODS

Stool samples originated from Komárom-Esztergom County, from a day-care center (nursery) where a gastroenteritis outbreak occurred in June, 2010. Astrovirus was detected by RT-PCR methods. The nucleotide sequence of the nearly complete genome was sequenced. Clinical and epidemiological data were collected by epidemiological investigation.

RESULTS

Out of the 29 exposed persons (24 children and 5 adults) 7 (24.1%) children had gastroenteritis with diarrhea, and vomiting in one case, in the period of June 4-15, 2010. Bacterial pathogens, rotavirus, adenovirus and norovirus were not detected, but genotype 1 astrovirus could be identified in 3 (42.8%) stool samples (HQ398856). The nucleotide sequence of the astrovirus ORF1a/ORF1b/ORF2/3'UTR regions was determined. The source of the outbreak was presumably the firstly recognized ill child and the virus was spread by fecal-oral route with direct contact in the children community.

CONCLUSIONS

Epidemiologic and clinical characteristics of the astrovirus outbreak in the nursery are described in details to prove that the possible etiological role of astroviruses in viral gastroenteritis which should not forget in order after rotaviruses, caliciviruses (norovirus and sapovirus) and enteric adenoviruses.

Identification of a novel astrovirus in a domestic pig in Hungary

The family Astroviridae consists of two genera, Avastrovirus and Mamastrovirus, whose members are associated with gastroenteritis in avian and mammalian hosts, respectively. We serendipitously identified a novel porcine astrovirus in a fecal specimen from a domestic pig (Sus scrofa domestica) in Hungary. Sequencing of a fragment indicated that it was an ORF1b/ORF2/3′UTR sequence, and it has been submitted to the database as porcine astrovirus type 2 (PAstV-2/Hungary/2007) with accession number GU562296. Its unique sequence characteristics and its phylogenetic position suggest that PAstV-2 could be an important link between previously reported astroviruses and that a genetically divergent lineage of astroviruses exist in piglets.

Divergent evolution of norovirus GII/4 by genome recombination from May 2006 to February 2009 in Japan

Norovirus GII/4 is a leading cause of acute viral gastroenteritis in humans. We examined here how the GII/4 virus evolves to generate and sustain new epidemics in humans, using 199 near-full-length GII/4 genome sequences and 11 genome segment clones from human stool specimens collected at 19 sites in Japan between May 2006 and February 2009. Phylogenetic studies demonstrated outbreaks of 7 monophyletic GII/4 subtypes, among which a single subtype, termed 2006b, had continually predominated. Phylogenetic-tree, bootscanning-plot, and informative-site analyses revealed that 4 of the 7 GII/4 subtypes were mosaics of recently prevalent GII/4 subtypes and 1 was made up of the GII/4 and GII/12 genotypes. Notably, single putative recombination breakpoints with the highest statistical significance were constantly located around the border of open reading frame 1 (ORF1) and ORF2 (P <or= 0.000001), suggesting outgrowth of specific recombinant viruses in the outbreaks. The GII/4 subtypes had many unique amino acids at the time of their outbreaks, especially in the N-term, 3A-like, and capsid proteins. Unique amino acids in the capsids were preferentially positioned on the outer surface loops of the protruding P2 domain and more abundant in the dominant subtypes. These findings suggest that intersubtype genome recombination at the ORF1/2 boundary region is a common mechanism that realizes independent and concurrent changes on the virion surface and in viral replication proteins for the persistence of norovirus GII/4 in human populations.

Vomiting calls to NHS Direct provide an early warning of norovirus outbreaks in hospitals

A wintertime peak of norovirus activity occurs each year, affecting institutions including schools and hospitals. Traditional laboratory and outbreak surveillance systems for norovirus are too vulnerable to reporting delay to act as a timely signal of activity in the community. Calls to the National Health Service (NHS) telephone service NHS Direct have the potential to be an early warning tool for public health purposes. We investigated whether NHS Direct vomiting calls can be used as a reliable indicator of norovirus activity and, if so, whether the increase in calls precedes the epidemic of hospital outbreaks. Laboratory reports were used as the reference standard to define the norovirus season. From 2004 to 2008, four series of NHS Direct call data were compared with laboratory data held at the Health Protection Agency Centre for Infections in order to identify the best predictor of the season start. The four series included: (1) modelled and extracted the proportion of calls likely to be for 'non-rotavirus' gastroenteritis; (2) the mean proportion of weekly vomiting calls in children aged <5 years; (3) the mean proportion of weekly vomiting calls for all ages; (4) the slope of the vomiting call data. Issuing an alert when 4% or more of NHS Direct vomiting calls in all age groups for two weeks in a row should provide up to four weeks' advance warning of forthcoming norovirus pressures on the health service.

Detection and characterization of human parechoviruses in archived cell cultures, in Hungary

BACKGROUND

Human parechoviruses (HPeV) belonging to the family Picornaviridae are widespread enteric pathogens and associated with various clinical symptoms in humans.

OBJECTIVES

There is no report for detection of the circulating parechoviruses in Central Europe. The aim of this retrospective study was to detect and characterize human parechoviruses in cell cultures with "enterovirus"-like cytophatic effect (CPE) archived between 1990 and 2000, in Hungary.

STUDY DESIGN

Fecal samples from children with symptoms of gastroenteritis under age of 10 were cultured as a previous routine diagnostic laboratory protocol for "enterovirus". Cell cultures indicating CPE were archived and deeply chilled (-80 degrees C) from minimum 2 individuals (2-12 patients) in each year. Specimens were tested retrospectively, in 2009, for HPeV by reverse transcription-PCR (RT-PCR) method using 5'UTR conserved primers. Specific primer pairs were designed to determine the complete nucleotide sequence of the structural region (VP0-VP3-VP1) of HPeV.

RESULTS

Nine (9.1%) of 66 archived samples were found to be HPeV-positive. Six (67%) samples were identified as HPeV1, 2 (22%) were HPeV4 and 1 could not be determined. Three HPeV1 clusters were identified according to the isolation date originated from years 1990/1991, 1992/1995 and 1998.

CONCLUSIONS

This is the first detection of human parechoviruses in Central Europe. Detection and genetic characterization of HPeV in available historical samples infected with previously unidentifiable agents with "enterovirus-like" cytopathogenic effect help to understand the genetic diversity and evolution of these viruses.

Characterization of ozone disinfection of murine norovirus

Despite the importance of human noroviruses (NoVs) in public health, little information concerning the effectiveness of ozone against NoVs is available. We determined the efficacy of ozone disinfection using murine norovirus (MNV) as a surrogate of human NoV. MNV in ozone demand-free buffer was exposed to a predetermined dose of ozone at two different pHs and temperatures. The virus remaining in the solution was analyzed by plaque assay, real-time TaqMan reverse transcriptase PCR (RT-PCR) (short template), and long-template conventional RT-PCR. Under all conditions, more than 99% of the MNV was inactivated by ozone at 1 mg/liter within 2 min. Both RT-PCR assays significantly underestimated the inactivation of MNV, compared with that measured by plaque assay. Our results indicate that NoV may be more resistant to ozone than has been previously reported. Nevertheless, proper ozone disinfection practices can be used to easily control its transmission in water.

Molecular and epidemiological features of GIIb norovirus outbreaks in Victoria, Australia, 2002-2005

The epidemiology of GIIb norovirus outbreaks and the characteristics of GIIb open reading frame (ORF) 2 recombinant forms are poorly understood and this study examined these questions using norovirus-associated gastroenteritis outbreaks in Victoria, Australia, during 2002-2005. Twenty-one GIIb outbreaks were detected and were the second most common ORF 1 norovirus outbreak genotype (5%) after GII.4 (90%). Both GIIb and GII.4 outbreaks peaked in warmer months of the year but their periodicity was different. ORF 2 sequencing analysis was carried out in the two regions previously designated C and D. RT-PCR region D primers were less sensitive than region C primers. No evidence of recombination between regions C and D was found. ORF 2 genotypes for the 21 GIIb outbreaks were: GII.1 (10 outbreaks), GII.3 (10 outbreaks) and, apparently for the first time, GII.13 (1 outbreak). GIIb outbreaks could occur in a broad range of settings and there was no correlation between ORF 2 genotype and setting except that all 5 outbreaks involving mainly young children were associated with GIIb/GII.3.

[First gastroenteritis outbreak caused by sapovirus (GI2) in Hungary - part of an international epidemic?]

Sapovirus belonging to Caliciviridae is one of the known pathogen of sporadic gastroenteritis infections in infants, children and rarely in elderly. Since the beginning of molecular monitoring of caliciviruses (mid 1990's) sapovirus was described rarely, once in approx. 5 years, as source of an outbreak. Circulation of caliciviruses has been monitored with molecular epidemiological methods by authors for 10 years in Hungary. Sapovirus has not been detected yet in the approximately 800 examined non-bacterial gastroenteritis outbreak. Based on the informal data supported by the international calicivirus surveillance study group, the number of outbreaks caused by sapovirus was increasing in Europe in 2008. Supposedly these outbreaks can be linked to genotype GI2 sapovirus.

AIMS

To describe the first verified detection and molecular epidemiological description of a gastroenteritis outbreak caused by sapovirus in Hungary.

MATERIALS AND METHODS

Stool samples originated from Bács-Kiskun County, from a mental deficiency day care center, where a gastroenteritis outbreak occurred in September, 2008. Amplification of the RNA polymerase gene of sapovirus was performed by RT-PCR method and the product was directly sequenced and phylogenetically analyzed. Clinical and epidemiological data were collected by epidemiological investigation.

RESULTS

17 of the 135 exposed people (12.6%) had gastroenteritis with vomiting and diarrhea in the period of September 11-22, 2008. Bacterial pathogens, rotavirus, adenovirus and norovirus were not detected, but sapovirus could be identified in 1 out of the 4 (25%) stool samples. The source of the outbreak was presumably the ill nurse and the virus spread with direct contact among the mentally deficient patients. Based on the RNA polymerase gene region the virus belongs to genotype GI2 sapovirus.

CONCLUSIONS

This study reports on the first detection of sapovirus from gastroenteritis outbreak in Hungary. Epidemiologic and clinical characteristics of the outbreak in the mental deficiency day care center are described in details to prove that not every case is "calicivirus" infection and epidemic is caused by the norovirus, which is another calicivirus examined by diagnostic methods. The outbreak caused by genotype GI2 sapovirus might be the part of an international epidemic, extended into a larger geographic area.

Norovirus in retail shellfish

Norovirus is a common cause of gastroenteritis outbreaks associated with consumption of raw shellfish. The majority of norovirus infections worldwide are due to genogroup II noroviruses. Bivalve molluscs (mussels, clams and oysters) at the end of the commercial chain, the points of purchase, were sampled between 2005 and 2008 in several retail points in Apulia, Italy, and screened by a semi-nested RT-PCR specific for genogroup II noroviruses. Noroviral RNA was detected in 12.1% of the samples, with lower frequency being observed in samples obtained from hypermarkets (8.1%) rather than in samples from open-air markets and fish shops (17.6% and 16.2%, respectively). By sequence analysis, the strains were characterized as norovirus variants GII.4/2004 and GII.b/Hilversum, which were both circulating in Italy in the same time-span.

Multiplex real-time RT-PCR for simultaneous detection of GI/GII noroviruses and murine norovirus 1

A quantitative two-step multiplex real-time reverse transcriptase (RT-) PCR assay for the simultaneous detection of genogroup I (GI) and genogroup II (GII) noroviruses (NoVs) is described below. A murine norovirus 1 (MNV-1) real-time PCR detection assay described recently was integrated successfully into the multiplex assay, making it possible to detect GI and GII NoVs and MNV-1 in one reaction tube with MNV-1 plasmid DNA as real-time PCR internal amplification control (IAC). The results showed a nearly complete concordance between the multiplex assay and the corresponding single-target PCRs. Analysis of competition between the individual reactions within the multiplex real-time PCR assay showed that GI and GII NoV plasmid DNAs mixed at equimolar concentrations were detected reproducibly and quantitatively, while a 4 log excess between GI and GII plasmid DNAs hindered amplification of the target with the lowest concentration. High concentrations of the real-time PCR IAC (MNV-1 plasmid DNA) also interfered with the possibility of the developed multiplex real-time RT-PCR assay to detect quantitatively and simultaneously the presence of GI and GII NoVs within one sample. The specificity of the multiplex assay was evaluated by testing a NoV RNA reference panel containing nine GI, eight GII, and one GIV in vitro synthesized RNA fragment, plus 16 clinical samples found positive for GI and GII NoVs previously. In addition, a collection of bovine NoVs and other (non-NoV) enteric viruses were found to be negative, and no cross-amplification between genogroups was observed.

Molecular epidemiology of norovirus gastroenteritis investigated using samples collected from children in Tunisia during a four-year period: detection of the norovirus variant GGII.4 Hunter as early as January 2003

Human noroviruses (NoVs) cause epidemic and endemic acute gastroenteritis in children and adults. To study the prevalence and genetic diversity of NoV in children in Tunisia, a total of 788 fecal samples were collected during a 4-year period in the region of Monastir, from children 12 years of age or younger, hospitalized or presenting in dispensaries with symptoms of acute gastroenteritis. NoV was detected by reverse transcription-PCR and confirmed by sequence analysis. This is the first report that describes the molecular epidemiology of NoV in Tunisian children: NoVs were characterized as the causative agent in 128 (16.2%) of the samples. Fourteen samples contained a mixture of two NoVs, and 33 samples were coinfected with additional enteric viruses. Eight distinct NoV genotypes were detected (GGI.2, GGI.4, GGII.1, GGII.4, GGII.8, GGII.14, GGIIb/GGII.2, and GGIIb/GGII.3). GGII.4 was the most prevalent genotype, accounting for 83 (64.8%) cases. Interestingly the GGII.4 variant Hunter, described as spreading all over the world in 2004, was found in Tunisia as early as January 2003. The delay of 1 year between the isolation in Tunisia and the worldwide emergence is somewhat surprising, considering the importance of the contacts between North Africa and Europe particularly. Nevertheless, this illustrates the idea that sporadic gastroenteritis cases may be a reservoir for emerging epidemic NoV strains.

Complete nucleotide and amino acid sequences and genetic organization of porcine kobuvirus, a member of a new species in the genus Kobuvirus, family Picornaviridae

Kobuvirus is a new genus in the family Picornaviridae. Two species are currently known: Aichi virus (human kobuvirus) and Bovine kobuvirus (U-1). In this study, the complete nucleotide and amino acid sequences and genetic organization of porcine kobuvirus (Kobuvirus/swine/S-1-HUN/2007/Hungary, EU787450) were determined. The structure of the S-1-HUN genome, VPg-5'UTR-leader protein-structural proteins (VP0, VP3, VP1)-non-structural proteins (2A-2C, 3A-3D)-3'UTR-poly(A) tail, was found to be typical of picornavirus. The 8210-nucleotide (nt)-long RNA genome contains a large open reading frame (7467 nt) encoding a potential polyprotein precursor of 2488 amino acids (aa) that has 57/56% and 63/64% nt/aa identity with Aichi virus and U-1, respectively. The 5'UTR contains a hepacivirus/pestivirus-like internal ribosomal entry site (IRES type IV group-B-like) with conserved pseudoknot, II and IIIa-f domains. A tandem repeat (a 30-amino-acid-long motif) was detected in 2B. Thirty-nine (65%) of the 60 fecal samples from pigs under the age of 6 months at the tested farm were positive (the incidence was 90% under the age of 3 weeks). Porcine kobuvirus belongs to a potential new species-the third-in the genus Kobuvirus.

Sequential evolution of genotype GII.4 norovirus variants causing gastroenteritis outbreaks from 2001 to 2006 in Eastern Spain

Noroviruses are the most common cause of outbreaks of viral gastroenteritis worldwide. Norovirus outbreaks were surveyed in Catalonia and the region of Valencia (Eastern Spain) between January 2001 and December 2006 as part of the European Union funded network "Food-borne viruses in Europe". During this time the etiology and epidemiological features of 194 outbreaks of acute non-bacterial gastroenteritis were investigated and norovirus was identified as causing 169 (87.1%) of them. Molecular epidemiology of viral strains was studied by RT-PCR and sequencing part of the RNA polymerase gene in ORF1 from 153 outbreak strains. The most commonly identified norovirus genotype was GII.4 (71.9% of the characterized outbreak strains), which is also the predominant genotype worldwide. During this survey five genetic variants of GII.4 genotype have been sequentially detected and identified as 1996, 2002, 2004, 2006a, and 2006b variants. The transition from one variant to a new one always took place over a short period of time, and thereafter the replacement of strains circulating previously was observed. These new GII.4 variants may have arisen as a consequence of viral evasion from the host immune responses, although apparently there is a lack of long-term immunity after norovirus infections.

Analysis of integrated virological and epidemiological reports of norovirus outbreaks collected within the Foodborne Viruses in Europe network from 1 July 2001 to 30 June 2006

The Foodborne Viruses in Europe network has developed integrated epidemiological and virological outbreak reporting with aggregation and sharing of data through a joint database. We analyzed data from reported outbreaks of norovirus (NoV)-caused gastroenteritis from 13 European countries (July 2001 to July 2006) for trends in time and indications of different epidemiology of genotypes and variants. Of the 13 countries participating in this surveillance network, 11 were capable of collecting integrated epidemiological and virological surveillance data and 10 countries reported outbreaks throughout the entire period. Large differences in the numbers and rates of reported outbreaks per country were observed, reflecting the differences in the focus and coverage of national surveillance systems. GII.4 strains predominated throughout the 5-year surveillance period, but the proportion of outbreaks associated with GII.4 rose remarkably during years in which NoV activity was particularly high. Spring and summer peaks indicated the emergence of genetically distinct variants within GII.4 across Europe and were followed by increased NoV activity during the 2002-2003 and 2004-2005 winter seasons. GII.4 viruses predominated in health care settings and in person-to-person transmission. The consecutive emergence of new GII.4 variants is highly indicative of immune-driven selection. Their predominance in health care settings suggests properties that facilitate transmission in settings with a high concentration of people such as higher virus loads in excreta or a higher incidence of vomiting. Understanding the mechanisms driving the changes in epidemiology and clinical impact of these rapidly evolving RNA viruses is essential to design effective intervention and prevention measures.

Genetic diversity of noroviruses and sapoviruses in children with acute sporadic gastroenteritis in New Delhi, India

BACKGROUND

Human caliciviruses (HuCVs) cause gastroenteritis throughout the world. Limited information is available on molecular epidemiology of caliciviruses from developing countries including India.

OBJECTIVES

Standardization and evaluation of a two-step multiplex RT-PCR assay for HuCVs and characterization of strains.

STUDY DESIGN

Two hundred and twenty-six stool samples were collected from children with acute gastroenteritis (AGE) over a one and half year to study the prevalence and diversity of HuCVs in children with AGE in New Delhi, India. A multiplex two-step RT-PCR using 3 sets of external and 4 sets of internal primers from the RdRp gene was standardized for detection of NoVs and SaVs. Molecular characterization of some HuCV strains was done by sequencing followed by phylogenetic analysis.

RESULTS

Fifty-nine HuCVs strains were detected in 54 (24%) of the samples; 5 samples had mixed infections. Of these 59 HuCVs, 36 (61%) were norovirus (34 were GGII; 2 were GGI) and 23 (39%) were sapovirus (22 were GGI; 1 was GGII). Phylogenetic analysis of partial RdRp gene of 12 HuCV strains identified three genotypes (GGI/4, GGII/3 and a newly identified GIIb/Hilversum cluster) in NoVs and one genotype (GGI/1) in SaVs.

CONCLUSION

This is one of the few reports from India on detection and characterization of HuCVs by multiplex RT-PCR assay. This assay can be a useful tool for epidemiological studies of HuCV infections.

Identification of a porcine calicivirus related genetically to human sapoviruses

Whether animals may act as reservoirs for human caliciviruses is unclear. By sequence analysis of a short fragment of the RNA-dependent RNA polymerase (RdRp) region, porcine sapovirus (SaV) strains that genetically resemble human SaVs have been detected in piglets, but more-informative sequences (capsid gene) were not available for a precise characterization. In this study, the 3' terminus (the 3' end of open reading frame 1 [ORF1], including the polymerase complex and the complete capsid; ORF2; and the 3' untranslated region) of one such human SaV-like strain, 43/06-18p3/2006/It, was determined, revealing that these viruses are more related genetically to human (47.4 to 54.9% amino acid identity) than to animal (35.2 to 44.7% amino acid identity) SaVs in the capsid gene. In addition, the recombination-prone RdRp-capsid junction region was highly conserved with those of human SaVs of genogroup GI. The presence of porcine viruses similar to human SaVs is a significant finding because of the potential for zoonotic infections or generation of porcine/human recombinants.

Genetic drift of norovirus genotype GII-4 in seven consecutive epidemic seasons in Hungary

BACKGROUND

Noroviruses are common pathogens in human gastroenteritis outbreaks worldwide. They belong to a genetically diverse group of RNA viruses with multiple genogroups (G) and genotypes. Genotype GII-4 norovirus (Lordsdale) is the predominant agent in epidemics.

OBJECTIVES

To investigate the genetic variation in GII-4 strains isolated during seven epidemic seasons in Hungary from November 2000 to June 2007.

STUDY DESIGN

Using the prospective epidemiological surveillance of norovirus outbreaks in Hungary, GII-4 strains were selected for further genetic analysis. After phylogenetic analysis, RNA-polymerase (open reading frame 1; ORF1), capsid (ORF2) and the ORF1/ORF2 junction were analysed by RT-PCR and sequencing.

RESULTS

Three hundred and seventy-seven (76.8%) of 491 confirmed norovirus outbreaks were caused by genotype GII-4. GII-4 was the predominant genotype in six of the seven epidemic seasons. Four main GII-4 variants--epidemic point mutants--(GII-4-2000, GII-4-2002, GII-4-2004 and GII-4-2006b) were detected, with each variant predominating in two consecutive epidemic seasons.

CONCLUSIONS

Genotype GII-4 was confirmed as the predominant genetic type in epidemic norovirus seasons in Hungary. Genetic drift successfully promotes the re-emergence of GII-4 variants in the population. The elevated number of norovirus outbreaks in the population predicts the emergence of new GII-4 genetic variants as part of an international epidemic.

Emergence of new norovirus variants on spring cruise ships and prediction of winter epidemics

A reporting system could provide early warning.

In June 2006, reported outbreaks of norovirus on cruise ships suddenly increased; 43 outbreaks occurred on 13 vessels. All outbreaks investigated manifested person-to-person transmission. Detection of a point source was impossible because of limited investigation of initial outbreaks and data sharing. The most probable explanation for these outbreaks is increased norovirus activity in the community, which coincided with the emergence of 2 new GGII.4 variant strains in Europe and the Pacific. As in 2002, a new GGII.4 variant detected in the spring and summer corresponded with high norovirus activity in the subsequent winter. Because outbreaks on cruise ships are likely to occur when new variants circulate, an active reporting system could function as an early warning system. Internationally accepted guidelines are needed for reporting, investigating, and controlling norovirus illness on cruise ships in Europe.

Epidemics of gastroenteritis during 2006 were associated with the spread of norovirus GII.4 variants 2006a and 2006b

BACKGROUND

Acute gastroenteritis is commonly associated with norovirus genogroup II (GII) infection. Norovirus GII has 17 classified genotypes (GII.1-GII.17), but only 1 norovirus genotype (GII.4) is associated with global epidemics of gastroenteritis. In 2006, an increase in global norovirus activity was observed.

METHODS

During the period from December 2005 through August 2006, a total of 231 fecal samples were obtained from patients with acute gastroenteritis from Australia and New Zealand. Norovirus RNA was amplified and sequenced to determine norovirus genotype and relatedness to known epidemic norovirus GII.4 variants.

RESULTS

Two GII.4 variants, designated 2006a and 2006b, were identified in 61.8% and 11.3%, respectively, of the 186 cases investigated. Norovirus 2006a and 2006b have also been implicated as the predominant causes of norovirus-associated gastroenteritis across Europe in 2006.

CONCLUSIONS

The global increase in norovirus-associated gastroenteritis in 2006 was linked to the emergence of 2 novel GII.4 variants, 2006a and 2006b.