Nationwide surveillance study of human astrovirus infections in an Italian paediatric population

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.

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.

Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols

Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on epidemiology. In this study, we collected 10 stool samples from a diarrhea outbreak from a diarrhea sentinel surveillance hospital in Beijing. Samples were evaluated immediately using parallel multiplex RT-qPCR and nanopore sequencing, and were then amplified by designed primers and Sanger sequencing to obtain whole genome sequences. Six isolates were categorized as HAstV-5 and subjected to whole genome analysis to characterize their genetic variation and evolution. Full genome analysis revealed low genetic variation (99.38-100% identity) among isolates. Phylogenetic analysis showed that all isolates were closely related to domestic strains Yu/1-CHN and 2013/Fuzhou/85. The recombination breakpoint of the six isolates was located at 2741 bp in the overlap region of ORF1a and ORF1b, similar to those of Yu/1-CHN and 2013/Fuzhou/85. Overall, our study highlights the combined use of RT-qPCR and sequencing as an important tool in rapid diagnosis and acquisition of whole genome sequences of HAstV.

Worldwide prevalence and genotype distribution of human astrovirus in gastroenteritis patients: A systematic review and meta-analysis

AIM

Human astrovirus (HAstV) is an important causative agent of gastroenteritis in humans, which mainly infects young children and the elderly. The goal of this study was to conduct a meta-analytic review of the prevalence of HAstV amongst patients with gastroenteritis, and to shed light on the connection between HAstV infection and gastroenteritis.

METHODS

Systematic literature searches were conducted to identify all potentially relevant studies recorded up to April 8th, 2022. For study weighting, the inverse variance method was employed and the random-effects model was applied to evaluate data. For case-control studies, the pooled odds ratio (OR) and 95% confidence interval (CI) were calculated to establish the relationship between HAstV infection and gastroenteritis.

RESULTS

Among 302423 gastroenteritis patients from 69 different countries, the overall pooled prevalence of HAstV infection was 3.48% (95% CI: 3.11%-3.89%). Case-control approach was used in 39 investigations, and the overall prevalence of HAstV infection among the 11342 healthy controls was 2.01% (95% CI: 1.40%-2.89%). Gastroenteritis and HAstV infection were associated with a pooled OR of 2.16 (95% CI: 1.72-2.71; P < 0.0001; I² = 33.7%). The most commonly found HAstV genotypes in gastroenteritis patients were HAstV1 (62.18%), HAstV7 (33.33%), and HAstV-MLB1 (17.43%).

CONCLUSION

The frequency of HAstV infection was the highest in children under the age of five, and in developing countries. The prevalence rate of HAstV was not influenced by gender. Semi-nested and nested RT-PCR were highly sensitive assays for detecting HAstV infections.

Circulation of classic and recombinant human astroviruses detected in South Africa: 2009 to 2014

BACKGROUND

Astroviruses (AstVs) are associated with diarrhoeal and extra-intestinal infections in human, animal and avian species. A prevalence of 7% was reported in selected regions in SA while AstVs detected from clinical stool specimens were almost identical phylogenetically to strains identified in environmental and water samples. This study investigated the molecular diversity of astroviruses circulating between 2009 and 2014 in South Africa (SA).

METHODS

Astroviruses detected in stool specimens collected from hospitalised children were investigated retrospectively. Astroviruses were characterised using type-specific RT-PCR, partial nucleotide sequence analyses in ORF1 and ORF2 and whole genome sequencing. Different genotypes were compared with clinical features to investigate genotype-related associations. The Vesikari severity scale (VSS) was evaluated for scoring astrovirus diarrhoeal infections.

RESULTS

Of 405 astroviruses detected, 49.9 % (202/405) were characterised into 32 genotypes comprising 66.3 % (134/202) putative-recombinants and 33.7 % (68/202) classic strains. No trends by year of collection, age or site were observed. Whole genome analysis in eight strains revealed that genotypes assigned by partial nucleotide sequence analyses to five astroviruses were incorrect. Bivariate analyses showed there were no significant associations between genotypes and clinical symptoms or severity of infection. A comparison of Vesikari parameters with astrovirus-positive proxy values demonstrated that Vesikari scores for duration of diarrhoea and admission temperatures would result in a milder infection rating in astrovirus-positive cases.

CONCLUSIONS

Diverse genotypes co-circulated with putative-recombinants predominating. Astrovirus classification was complicated by the lack of a consistent characterisation system and reliable reference database. The VSS should be used cautiously to rate astrovirus diarrhoea. While surveillance in communities and out-patient clinics must be continued, screening for human astroviruses in alternate hosts is needed to determine the reservoir species.

Analysis of GII.P7 and GII.6 noroviruses circulating in Italy during 2011-2016 reveals a replacement of lineages and complex recombination history

Noroviruses are important human enteric pathogens and monitoring their genetic diversity is important for epidemiological surveillance, vaccine development, and understanding of RNA viruses evolution. Epidemiological investigations have revealed that genogroup II, genotype 6 noroviruses (GII.6) are common agents of gastroenteritis. Upon sequencing of the ORF2 (encoding the viral capsid), GII.6 viruses have been distinguished into three variants. Sentinel hospital-based surveillance in Italy revealed that GII.6 noroviruses were the second most common capsid genotype in 2015, mostly in association with a GII.P7 ORF1 (encoding the viral polymerase). Upon molecular characterization of the ORF1 and ORF2, the GII.P7_GII.6 epidemic viruses circulating in 2014-2015 (variant GII.6b) were different from those that circulated sporadically in 2011-2013 (variant GII.6a). Analysis of the ORF1 (GII.P7) and ORF2 (GII.6) sequences available in the databases unveiled marked genetic diversity and peculiarities in the phylogenetic segregation patterns, suggesting multiple recombination events. Phylogenetic analyses suggest that recent GII.P7_GII.6b viruses were circulating as early as 2008, and formed a genetically homogenous group that emerged globally.

Co-circulation of classic and novel astrovirus strains in patients with acute gastroenteritis in Germany

OBJECTIVES

In order to analyze the molecular epidemiology of human astroviruses (HAstV) in Germany, a retrospective long-term study was performed to characterize circulating human astrovirus in patients with acute gastroenteritis in Germany.

METHODS

A total of 2877 stool samples, collected between January 2010 and December 2015 from sporadic cases and outbreaks of acute gastroenteritis were retrospectively analyzed for astrovirus. A two-step PCR algorithm was developed and used to identify and characterize human astrovirus infections.

RESULTS

Overall, 143 samples were astrovirus-positive (5.0%). Astrovirus infection was most frequently detectable in samples from children of 3-4 years (15%) followed by children of 1-2 years (8.6%), detection rates in adults were lower (1%-3.6%). A high number (71.3%) of co-infections, mainly with noro- or rotaviruses, were identified. Genotyping revealed that at least ten genotypes from all four human MAstV species were circulating in the study population. HAstV-1 was predominant in different age groups. Novel HAstV (MLB and VA genotypes) were also circulating in Germany.

CONCLUSION

Our findings give new insights into the circulation and genetic diversity of human astroviruses in patients with acute gastroenteritis. The novel HAstV-MLB and -VA genotypes could be characterized firstly in Germany while the analysis showed that these viruses have been dispersed in Germany since 2011 as a causative agent of acute gastroenteritis.

Astrovirus Biology and Pathogenesis

Astroviruses are nonenveloped, positive-sense single-stranded RNA viruses that cause gastrointestinal illness. Although a leading cause of pediatric diarrhea, human astroviruses are among the least characterized enteric RNA viruses. However, by using in vitro methods and animal models to characterize virus-host interactions, researchers have discovered several important properties of astroviruses, including the ability of the astrovirus capsid to act as an enterotoxin, disrupting the gut epithelial barrier. Improved animal models are needed to study this phenomenon, along with the pathogenesis of astroviruses, particularly in those strains that can cause extraintestinal disease. Much like for other enteric viruses, the current dogma states that astroviruses infect in a species-specific manner; however, this assumption is being challenged by growing evidence that these viruses have potential to cross species barriers. This review summarizes these remarkable facets of astrovirus biology, highlighting critical steps toward increasing our understanding of this unique enteric pathogen.

Epidemiology and genetic diversity of classic human astrovirus among hospitalized children with acute gastroenteritis in Uruguay

Classic Human Astrovirus (Classic HAstV) are one of the most important causes of pediatric acute gastroenteritis (AGE), after rotaviruses and arguably caliciviruses. The aim of this study was to determine the molecular epidemiology of Classic HAstV from 175 clinical samples, being 153 stools and 22 vomits, collected from pediatric hospitalized patients with AGE in Salto city, Uruguay, from January 2011 to December 2012. Classic HAstV were detected and genotyped by using a qualitative Retro Transcription-Polimerase Chain Reaction (RT-PCR) directed to the Open Reading Frame-2 (ORF2) region C. Amplicons were sequenced and phylogenetic analyses were carried out in order to determine genotypes and lineages. Classic HAstV were detected in 18 out of 175 analyzed samples (10.3%) and 14 of them (78.0%) were successfully sequenced being 6 (42.8%) classified as HAstV-1 (1a lineage), 4 (28.6%) as HAstV-2 (2c lineage), and 4 (28.6%) as HAstV-3 (3c lineage). A higher detection of Classic HAstV infections was observed in autumn for both years of surveillance, and the majority of the positive cases were observed in 2011. The group of children between 2 and 5 years old presented the higher percentage of infections. To our knowledge, the present study represents the first report of astrovirus from acute gastroenteritis cases in Uruguay, evidencing its role as a relevant etiologic agent in severe cases of this disease.

The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses

Astroviruses are a diverse family of viruses that infect a wide range of mammalian and avian hosts. Here we describe the phylogenetic diversity and current classification methodology of astroviruses based on the ORF1b and ORF2 genes, highlighting the propensity of astroviruses to undergo interspecies transmission and genetic recombination which greatly increase diversity and complicate attempts at a unified and comprehensive classification strategy.

Astrovirus Pathogenesis

Astroviruses are a major cause of diarrhea in the young, elderly, and the immunocompromised. Since the discovery of human astrovirus type 1 (HAstV-1) in 1975, the family Astroviridae has expanded to include two more human clades and numerous mammalian and avian-specific genotypes. Despite this, there is still little known about pathogenesis. The following review highlights the current knowledge of astrovirus pathogenesis, and outlines the critical steps needed to further astrovirus research, including the development of animal models of cell culture systems.

Complete genome sequencing of a recombinant strain between human astrovirus antigen types 2 and 8 isolated from South Korea

Human astroviruses (HAstVs) occur worldwide and are known to the causative agents of diarrhea in infants and elderly patients with immune dysfunction. This study aimed to identify recombinant HAstV strains and characterize rare genotypes. The full-length genome of a recombinant HAstV strain isolated from the stool sample of a patient with acute gastroenteritis from South Korea was amplified using three pairs of previously designed primers and seven newly designed primers. The recombinant HAstV was 6757-bp long and contained three sequential open reading frames (ORFs), designated as ORF1a (2781 bp), ORF1b (1548 bp), and ORF2 (2349 bp). Our findings suggested that a recombination event had occurred between ORF1b and ORF2 of the isolated strain, with a recombination breakpoint at 4081 bp. To our knowledge, this is the first study to reveal the complete nucleotide sequence of a recombinant HAstV strain from South Korea. Our study findings might be useful for identifying other recombinant HAstV strains and for developing vaccines against this pathogenic virus.

Clinical surveillance for human astrovirus in Monastir region, Tunisia

Background/aims

Astroviruses (AstVs) are enteric viruses that can cause gastroenteritis in children. This study is part of monitoring the circulation of astroviruses in children hospitalized and/or outpatients for acute gastroenteritis at the primary care center of Ouerdanine or at the Pediatric Department of the University Hospital Fattouma-Bourguiba (Monastir, Tunisia). The aims of our study were to know the prevalence of human astrovirus in clinical samples of children, characterize the strains and evaluate the infectivity of isolated strains on cell culture.

Methods

Fifty stool samples were collected from children under five years old in the region of Monastir (Tunisia) from October 2010 to June 2011. All specimens were subjected to RT-PCR amplification followed by sequencing and phylogenetic analysis.

Results

The study shows a low prevalence of astrovirus (4 %) in children. The two positive samples obtained were HAstV type 3. Samples that were RT-PCR positive were cultured in CaCO-2 cells and the presence of infectious viral particles was confirmed. The phylogenetic analysis shows that the different HAstV-3 strains isolated in Tunisia are grouped into two clusters. The first cluster includes strains obtained in 2004, which belong to lineage HAstV-3a, while strains isolated in 2010 belong to lineage HAstV-3c.

Conclusions

This study is part of monitoring the circulation of astroviruses in children younger than five years old from Monastir region, Tunisia. The results show low prevalence (4 %). All genotyped samples belonged to lineage HAstV-3c, which could be presently emerging. Two different lineages have been isolated in Tunisia: HAstV-3a in 2004 and HAstV-3c in 2010.

First report of an astrovirus type 5 gastroenteritis outbreak in a residential elderly care home identified by sequencing

BACKGROUND

This is the report of an outbreak of human astrovirus type 5 gastroenteritis that occurred in a residential care home for older people in June 2013 in Tayside, Scotland, and which involved seven staff members and thirteen residents. This type of astrovirus has not been found in Scotland before and is rarely described in the literature.

OBJECTIVES

Using molecular methods such as PCR and sequencing to detect the cause of this gastroenteritis outbreak and to contain the outbreak using Public Health measures.

STUDY DESIGN

Following an epidemiological investigation, stool samples were sent for routine virology and microbiology testing at the local microbiology and virology laboratory and were found to be negative. Further testing with real-time PCR and gene sequencing at the West of Scotland Specialist Virology Centre was performed. Data on the epidemiology and the response to the outbreak was collected.

RESULTS

All samples had a 99% match to human astrovirus type 5. The use of standard infection control precautions with the addition of transmission-based precautions most likely contained the spread of the virus in this situation.

CONCLUSIONS

This report illustrates the importance of using PCR and sequencing to identify pathogens such as astrovirus in outbreaks of vomiting and diarrhoea in older people particularly if routine virology and microbiology tests are negative.

Epidemiological dynamics of norovirus GII.4 variant New Orleans 2009

Norovirus (NoV) is one of the major causes of diarrhoeal disease with epidemic, outbreak and sporadic patterns in humans of all ages worldwide. NoVs of genotype GII.4 cause nearly 80-90 % of all NoV infections in humans. Periodically, some GII.4 strains become predominant, generating major pandemic variants. Retrospective analysis of the GII.4 NoV strains detected in Italy between 2007 and 2013 indicated that the pandemic variant New Orleans 2009 emerged in Italy in the late 2009, became predominant in 2010-2011 and continued to circulate in a sporadic fashion until April 2013. Upon phylogenetic analysis based on the small diagnostic regions A and C, the late New Orleans 2009 NoVs circulating during 2011-2013 appeared to be genetically different from the early New Orleans 2009 strains that circulated in 2010. For a selection of strains, a 3.2 kb genome portion at the 3' end was sequenced. In the partial ORF1 and in the full-length ORF2 and ORF3, the 2011-2013 New Orleans NoVs comprised at least three distinct genetic subclusters. By comparison with sequences retrieved from the databases, these subclusters were also found to circulate globally, suggesting that the local circulation reflected repeated introductions of different strains, rather than local selection of novel viruses. Phylogenetic subclustering did not correlate with changes in residues located in predicted putative capsid epitopes, although several changes affected the P2 domain in epitopes A, C, D and E.

Wastewater Analysis Indicates that Genetically Diverse Astroviruses, Including Strains Belonging to Novel Clades MLB and VA, Are Circulating within Japanese Populations

Human astroviruses (HAstVs) are a common etiological agent of infantile gastroenteritis. Recent studies revealed that novel astrovirus (AstV) strains of the MLB clade (MLB-AstVs) and VA clade (VA-AstVs), which are genetically distinct from the classic HAstVs, are circulating in the human population. In the present study, we quantified classic HAstVs as well as carried out a genetic analysis of classic and novel HAstVs in wastewater in Japan. The concentration of classic HAstVs in the influent water samples ranged from 10(4) to 10(5) copies per liter, and the amount removed by wastewater treatment was determined to be 2.4 ± 0.3 log10. Four types of classic HAstV strains (HAstV types 1, 2, 5, and 4/8) as well as novel AstV strains belonging to the MLB-2, VA-1, and VA-2 clades were identified using reverse transcription-PCR (RT-PCR) assays, including assays newly developed for the detection of strains of the MLB and VA clades, followed by cloning and nucleotide sequencing. Our results suggest that genetically diverse AstV strains are circulating among the human population in Japan. The newly developed (semi)nested RT-PCR assays for these novel AstV clades are useful to identify and characterize the novel AstVs in environmental waters.

Genetic heterogeneity and recombination in type-3 human astroviruses

Human astroviruses (HAstVs) are important enteric pathogens and can be classified genetically and antigenically into eight types. During molecular surveillance for HAstVs in Italy, sequence analysis of the diagnostic region C (about 400 nucleotide in length), located on the capsid (ORF2) gene, identified a novel type-3 strain. Upon sequencing of the full-length ORF2, the type-3 HAstV strain was characterized as a novel ORF2 genetic lineage, designated as 3c. By converse, in the ORF1b the virus was more similar to type-1 HAstVs, rather than to type-3 strains, suggesting a recombination nature, with the crossover site being mapped to the ORF1b/ORF2 junction region. Region C sequences of similar type-3 HAstV identified from European and extra-European countries were retrieved in the databases, suggesting the global distribution of this novel type-3 lineage.

Environmental Assessment of Classical Human Astrovirus in Uruguay

The aim of this study was to determine the molecular epidemiology of classical human astrovirus (HAstV) strains in sewage samples from four Uruguayan cities: Bella Unión, Salto, Paysandú, and Fray Bentos, located in the Northwestern region of the country. Overall, 96 sewage samples were collected biweekly between March 2011 and February 2012 and were subject to ultracentrifugation methodology in order to concentrate the viruses. RT-PCR directed to the ORF2 genome region was performed followed by sequencing and phylogenetic analysis. Forty-three (45 %) out of 96 analyzed samples were positive for HAstV (Mamastrovirus 1) and 31 of them were successfully sequenced being 21 (49 %) of them classified as HAstV-1 genotype (1a lineage) and 10 (23 %) as HAstV-2 genotype (eight strains belonging to the 2d lineage and two strains to the 2c lineage). The 1a lineage circulated throughout the year, while the 2d lineage only in the coldest months (June to October). Strikingly, the 2c lineage was detected only in Salto city during March 2011. In this city it was observed the highest frequency of HAstV and the greatest genetic diversity, probably due to its role as high touristic spot with an important influx of visitants from others regions of Uruguay and also from other countries. This study constitutes the first report in Uruguay that describes the phylogenetic diversity and genotype distribution of HAstV strains circulating in the Northwestern region evidencing a high frequency and also the presence of several different lineages.

Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system

Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5' or 3' end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established. Three main lineages could be defined in HAstV-1, four in HAstV-2, two in HAstV-3, three in HAstV-4, three in HAstV-5 and two in HAstV-6. Intratypic (inter-lineages) ORF2 recombinant strains were identified in type 1 (1b/1d) and type 2 (2c/2b) with distinct crossover points. Other potential intratypic recombinant strains were identified in type 3, type 5 and type 6. In addition, a type-1b strain with a large insertion (~600 bp) of heterologous RNA in the N-terminal region and a type-6 strain with a large RNA rearrangement in the hypervariable region were identified. The classification scheme was integrated in a novel nomenclature system suitable for designation of HAstV strains.

Development of a high resolution melting analysis for detection and differentiation of human astroviruses

Human astroviruses (AstVs), the common causes of viral gastroenteritis, consist of 8 different sero- or genotypes in which a variety of subtypes have been found. In the present study, a rapid and high-throughput method for detection and sequence-discrimination of AstVs by high resolution melting (HRM) analysis was developed. A newly designed primer set for the assay targeting ORF1b-ORF2 junction region of AstVs successfully reacted with all 8 serotypes of AstVs and allowed genotyping using their amplicons. The HRM assay consists of intercalating dye based real time quantitative PCR (qPCR) and melting curve analysis. The qPCR assay was sensitive enough to detect 1.0×10(1) copies/reaction of AstV serotypes. However, 1.0×10(3) copies/reaction of AstVs gene was required to obtain a sequence-specific difference curve, indicating that pre-amplification is necessary to apply the assay to samples containing low numbers of AstVs. AstVs in clinical specimens were subjected to the HRM assay after pre-amplification. The strains possessing same nucleotide sequences at the target region showed an identical difference curve and those possessing different nucleotide sequences showed a distinguishable difference curve. The newly developed HRM assay is an effective technique for screening of AstVs to quantify and discriminate the strains.

Analysis of early strains of the norovirus pandemic variant GII.4 Sydney 2012 identifies mutations in adaptive sites of the capsid protein

Global surveillance for norovirus identified in 2012 the emergence of a novel pandemic GII.4 variant, termed Sydney 2012. In Italy, the novel pandemic variant was identified as early as November 2011 but became predominant only in the winter season 2012-2013. Upon sequencing and comparison with strains of global origin, the early Sydney 2012 strains were found to differ from those spreading in 2012-2013 in the capsid (ORF2) putative epitopes B, C and D, segregating into a distinct phylogenetic clade. At least three residues (333, 340 and 393, in epitopes B, C and D, respectively) of the VP1 varied among Sydney 2012 strains of different clades. These findings suggest that the spread of the pandemic variant in Italy during the winter season 2012-2013 was due to the introduction of strains distinct from those circulating at low frequency in the former winter season and that similar strains were also circulating elsewhere worldwide.

Evidence for recombination between pandemic GII.4 norovirus strains New Orleans 2009 and Sydney 2012

During 2012, a novel pandemic GII.4 norovirus variant, Sydney 2012, emerged worldwide. A signature of the variant was a GII.Pe ORF1, in association with GII.4 Apeldoorn 2008-like ORF2-ORF3 genes. We report the detection of recombinant GII.4 Sydney 2012 strains, possessing the ORF1 gene of the former pandemic variant New Orleans 2009.

Genetic heterogeneity and recombination in human type 2 astroviruses

Novel lineages of human astrovirus (HAstV) types 2, 2c, and 2d have been identified. Upon sequencing of the 3' end of the genome, the type 2c and 2d HAstVs were found to be open reading frame 1b (ORF1b)-ORF2 recombinant, with ORF1b being derived from type 3 and type 1 HAstVs, respectively. An ORF2 interlineage recombinant strain, 2c/2b, was also identified.