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1.
Article in English | MEDLINE | ID: mdl-38926653

ABSTRACT

Abstract: This report from the Australian Rotavirus Surveillance Program describes the circulating rotavirus genotypes identified in children and adults during the period 1 January to 31 December 2022. After two years of a lower number of stool samples received as a result of the coronavirus disease 2019 (COVID-19) pandemic, this reporting period saw the highest number of samples received since the 2017 surveillance period, with samples received from all states and territories. During this period, 1,379 faecal specimens had been referred for rotavirus G- and P- genotype analysis, of which 1,276 were confirmed as rotavirus positive. In total, 1,119/1,276 were identified as wildtype rotavirus, 155/1,276 identified as the Rotarix vaccine strain and 2/1,276 that could not be confirmed as vaccine or wildtype due to sequencing failure. Whilst G12P[8] was the dominant genotype nationally among wildtype samples (28.2%; 315/1,119), multiple genotypes were identified at similar frequencies including G9P[4] (22.3%; 249/1,119) and G2P[4] (20.3%; 227/1,119). Geographical differences in genotype distribution were observed, largely driven by outbreaks reported in some jurisdictions. Outbreaks and increased reports of rotavirus disease were reported in the Northern Territory, Queensland, and New South Wales. A small number of unusual genotypes, potentially zoonotic in nature, were identified, including: G8P[14]; G10[14]; caninelike G3P[3]; G6P[9]; and G11P[25]. Ongoing rotavirus surveillance is crucial to identify changes in genotypic patterns and to provide diagnostic laboratories with quality assurance by reporting incidences of wildtype, vaccine-like, or false positive rotavirus results.


Subject(s)
Feces , Genotype , Rotavirus Infections , Rotavirus Vaccines , Rotavirus , Humans , Rotavirus Infections/epidemiology , Rotavirus Infections/virology , Rotavirus/genetics , Australia/epidemiology , Feces/virology , Child, Preschool , Infant , Child , Adult , COVID-19/epidemiology , COVID-19/virology , SARS-CoV-2/genetics , Adolescent , Female , Male , Disease Outbreaks , Vaccines, Attenuated , Infant, Newborn , Annual Reports as Topic , Epidemiological Monitoring , Middle Aged
2.
Article in English | MEDLINE | ID: mdl-36529132

ABSTRACT

Abstract: This report from the Australian Rotavirus Surveillance Program describes the circulating rotavirus genotypes identified in children and adults during the period 1 January to 31 December 2021. During this period, 521 faecal specimens had been referred for rotavirus G- and P- genotype analysis, of which 474 were confirmed as rotavirus positive. Of these, 336/474 were wildtype rotavirus strains and 138/474 were identified as vaccine-like. Of the 336 wildtype samples, 87.5% (n = 294/336) were identified as G8P[8], and were detected in five of the six jurisdictions that provided samples for the reporting period. Two rotavirus outbreaks, located in the Northern Territory and Western Australia, were also attributed to G8P[8]. As with the 2020 reporting period, a low number of stool samples were received for this reporting period as a result of the COVID-19 pandemic. However, an unexpectedly high proportion of samples with unusual genotypes were identified which were potentially zoonotic in nature, including feline G3, P[9], bovine-like G8, P[14], and porcine-like G4, G6, P[1], and P[6]. Ongoing rotavirus surveillance is crucial to identify changes in genotypic patterns and to provide diagnostic laboratories with quality assurance by reporting incidences of wildtype, vaccine-like, or false positive rotavirus results.


Subject(s)
COVID-19 , Gastroenteritis , Rotavirus Infections , Rotavirus , Animals , Cattle , Cats , Humans , Swine , Rotavirus/genetics , Rotavirus Infections/epidemiology , Pandemics , Gastroenteritis/epidemiology , COVID-19/epidemiology , Northern Territory/epidemiology
3.
J Infect Dis ; 225(12): 2116-2126, 2022 06 15.
Article in English | MEDLINE | ID: mdl-32692812

ABSTRACT

BACKGROUND: Rotavirus is a major cause of gastroenteritis in children <5 years of age. The disease burden in older children, adults, and the elderly is underappreciated. This study describes rotavirus disease and genotypic diversity in the Australian population comprising children ≥5 years of age and adults. METHODS: Rotavirus positive fecal samples were collected from laboratories Australia-wide participating in the Australian Rotavirus Surveillance Program between 2010 and 2018. Rotavirus samples were genotyped using a heminested multiplex reverse-transcription polymerase chain reaction. Notification data from the National Notifiable Diseases Surveillance System were also analyzed. RESULTS: Rotavirus disease was highest in children aged 5-9 years and adults ≥85 years. G2P[4] was the dominant genotype in the population ≥5 years of age. Genotype distribution fluctuated annually and genotypic diversity varied among different age groups. Geographical differences in genotype distribution were observed based on the rotavirus vaccine administered to infants <1 year of age. CONCLUSIONS: This study revealed a substantial burden of rotavirus disease in the population ≥5 years of age, particularly in children 5-9 years and the elderly. This study highlights the continued need for rotavirus surveillance across the population, despite the implementation of efficacious vaccines.


Subject(s)
Rotavirus Infections , Rotavirus Vaccines , Rotavirus , Adult , Aged , Australia/epidemiology , Child , Child, Preschool , Feces , Genotype , Humans , Infant , Rotavirus/genetics , Rotavirus Infections/prevention & control
4.
Article in English | MEDLINE | ID: mdl-34847338

ABSTRACT

ABSTRACT: This report from the Australian Rotavirus Surveillance Network describes the circulating rotavirus genotypes identified in children and adults during the period 1 January - 31 December 2020. During this period, 229 faecal specimens were referred for rotavirus G- and P- genotype analysis, including 189 samples that were confirmed as rotavirus positive. Of these, 98/189 were wildtype rotavirus strains and 86/189 were identified as vaccine-like. A further five samples could not be determined as wildtype or vaccine-like due to poor sequence reads. Genotype analysis of the 98 wildtype rotavirus samples from both children and adults demonstrated that G3P[8] was the dominant genotype identified for the third consecutive year, identified in 27.6% of samples, followed by G2P[4] in 20.4% of samples. Forty-six percent of rotavirus positive samples received were identified as vaccine-like, highlighting the need to add caution in interpreting rotavirus positive results in children aged 0-8 months. This surveillance period was significantly impacted by the coronavirus disease 2019 ( COVID-19 ) pandemic. The reduction in rotavirus notifications reflected reduced healthcare-seeking behaviour and a decrease in community spread, with 'community lockdowns', school and day-care centre closure and improved compliance with hand hygiene. Fewer stool samples were collected throughout Australia during this period. There was a reluctance to store samples at collaborating laboratories and uncertainties regarding the safety and feasibility of the transport of samples to the central laboratory during the closure of state and territory borders. Systems have now been adapted to manage and send biological samples safely and confidently. Ongoing rotavirus surveillance is crucial to identify changes in genotypic patterns and to provide diagnostic laboratories quality assurance by reporting incidences of wildtype, vaccine-like, or false positive rotavirus results.


Subject(s)
COVID-19 , Gastroenteritis , Rotavirus Infections , Rotavirus Vaccines , Rotavirus , Adult , Australia/epidemiology , Child , Communicable Disease Control , Humans , Population Surveillance , Rotavirus/genetics , Rotavirus Infections/epidemiology , Rotavirus Infections/prevention & control , SARS-CoV-2
5.
Pathogens ; 10(3)2021 Mar 16.
Article in English | MEDLINE | ID: mdl-33809709

ABSTRACT

In May, 2017, an outbreak of rotavirus gastroenteritis was reported that predominantly impacted Aboriginal children ≤4 years of age in the Kimberley region of Western Australia. G2P[4] was identified as the dominant genotype circulating during this period and polyacrylamide gel electrophoresis revealed the majority of samples exhibited a conserved electropherotype. Full genome sequencing was performed on representative samples that exhibited the archetypal DS-1-like genome constellation: G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and phylogenetic analysis revealed all genes of the outbreak samples were closely related to contemporary Japanese G2P[4] samples. The outbreak samples consistently fell within conserved sub-clades comprised of Hungarian and Australian G2P[4] samples from 2010. The 2017 outbreak variant was not closely related to G2P[4] variants associated with prior outbreaks in Aboriginal communities in the Northern Territory. When compared to the G2 component of the RotaTeq vaccine, the outbreak variant exhibited mutations in known antigenic regions; however, these mutations are frequently observed in contemporary G2P[4] strains. Despite the level of vaccine coverage achieved in Australia, outbreaks continue to occur in vaccinated populations, which pose challenges to regional areas and remote communities. Continued surveillance and characterisation of emerging variants are imperative to ensure the ongoing success of the rotavirus vaccination program in Australia.

6.
Vet Rec ; 188(12): e296, 2021 Jun.
Article in English | MEDLINE | ID: mdl-33870517

ABSTRACT

BACKGROUND: Rotavirus infections of neonatal and older pigs are widely reported. Analysis of rotavirus group C prevalence and diversity has not previously been reported for Australian pig farms. METHODS: Twenty-seven farms with or without diarrhoea present among neonatal or older pigs were enrolled across eastern Australia. Fresh faecal samples were analysed by ELISA for rotavirus and RNA extractions by polyacrylamide gel electrophoresis and RT-PCR for rotavirus. Rotavirus group C samples were genotyped via sequencing. RESULTS AND CONCLUSIONS: Rotavirus infection was diagnosed in pigs on 10 of 19 farms investigated for neonatal diarrhoea, four with group A and six with group C; also among post-weaned (5- to 11-week-old) diarrhoeic pigs on two farms. Neonatal rotavirus group C infections were exclusively noted in piglets less than 1-week-old, consisting of farm infections with a single VP7 genotype (G5 or G6). Infections in post-weaned pigs were associated with multiple VP7 genotypes (G1, G3). This first report of rotavirus group C infections of Australian pigs suggests they may form a limited population of VP7 genotypes.


Subject(s)
Diarrhea/veterinary , Rotavirus Infections/veterinary , Rotavirus/isolation & purification , Swine Diseases/virology , Animals , Animals, Newborn/virology , Australia , Diarrhea/virology , Farms , Feces/virology , Female , Genotype , Rotavirus/genetics , Rotavirus Infections/virology , Swine
7.
Article in English | MEDLINE | ID: mdl-33573534

ABSTRACT

ABSTRACT: This report, from the Australian Rotavirus Surveillance Program and collaborating laboratories Australia-wide, describes the rotavirus genotypes identified in children and adults with acute gastroenteritis during the period 1 January to 31 December 2018. During this period, 690 faecal specimens were referred for rotavirus G- and P- genotype analysis, including 607 samples that were confirmed as rotavirus positive. Of these, 457/607 were wild-type rotavirus strains and 150/607 were identified as rotavirus vaccine-like. Genotype analysis of the 457 wild-type rotavirus samples from both children and adults demonstrated that G3P[8] was the dominant genotype nationally, identified in 52% of samples, followed by G2P[4] (17%). The Australian National Immunisation Program, which previously included both RotaTeq and Rotarix vaccines, changed to Rotarix exclusively on 1 July 2017. Continuous surveillance is needed to identify if the change in vaccination schedule could affect rotavirus genotype distribution and diversity in Australia.


Subject(s)
Rotavirus Infections/epidemiology , Rotavirus Infections/prevention & control , Rotavirus Vaccines/immunology , Australia/epidemiology , Child, Preschool , Epidemiological Monitoring , Feces/virology , Female , Gastroenteritis/epidemiology , Gastroenteritis/virology , Genotype , Humans , Immunization Programs , Infant , Infant, Newborn , Male , Population Surveillance , Rotavirus/genetics , Rotavirus/immunology , Rotavirus Infections/virology , Rotavirus Vaccines/administration & dosage , Vaccines, Attenuated
8.
Article in English | MEDLINE | ID: mdl-33573535

ABSTRACT

ABSTRACT: This report, from the Australian Rotavirus Surveillance Program and collaborating laboratories Australia-wide, describes the rotavirus genotypes identified in children and adults with acute gastroenteritis during the period 1 January to 31 December 2019. During this period, 964 faecal specimens had been referred for rotavirus G- and P- genotype analysis, including 894 samples that were confirmed as rotavirus positive. Of these, 724/894 were wild-type rotavirus strains and 169/894 were identified as vaccine-like. A single sample could not be determined as wild-type or vaccine-like due to poor sequencing. Genotype analysis of the 724 wild-type rotavirus samples from both children and adults demonstrated that G3P[8] was the dominant genotype nationally, identified in 46.7% of samples, followed by G2P[4] in 8.8% of samples. The Australian National Immunisation Program (NIP) changed to the exclusive use of Rotarix as of 1 July 2017. The NIP had previously included two live-attenuated oral vaccines: Rotarix (monovalent, human) and RotaTeq (pentavalent, human-bovine reassortant) in a state-based vaccine selection. Continuous surveillance is imperative to determine the effect of this change in rotavirus vaccine schedule on the genotype distribution and diversity in Australia.


Subject(s)
Immunization Programs/statistics & numerical data , Rotavirus Infections/epidemiology , Rotavirus Infections/prevention & control , Animals , Australia/epidemiology , Cattle , Child, Preschool , Epidemiological Monitoring , Feces/virology , Female , Gastroenteritis/epidemiology , Gastroenteritis/prevention & control , Gastroenteritis/virology , Humans , Infant , Infant, Newborn , Male , Population Surveillance , Rotavirus/genetics , Rotavirus/isolation & purification , Rotavirus Infections/virology , Rotavirus Vaccines/administration & dosage , Rotavirus Vaccines/immunology , Vaccines, Attenuated
9.
Pediatrics ; 144(4)2019 10.
Article in English | MEDLINE | ID: mdl-31530719

ABSTRACT

BACKGROUND: Rotavirus vaccine has been funded for infants under the Australian National Immunisation Program since 2007, with Rotarix vaccine used in New South Wales, Australia, from that time. In 2017, New South Wales experienced a large outbreak of rotavirus gastroenteritis. We examined epidemiology, genotypic profiles, and vaccine effectiveness (VE) among cases. METHODS: Laboratory-confirmed cases of rotavirus notified in New South Wales between January 1, 2010 and December 31, 2017 were analyzed. VE was estimated in children via a case-control analysis. Specimens from a sample of hospitalized case patients were genotyped and analyzed. RESULTS: In 2017, 2319 rotavirus cases were reported, representing a 3.1-fold increase on the 2016 notification rate. The highest rate was among children aged <2 years. For notified cases in 2017, 2-dose VE estimates were 88.4%, 83.7%, and 78.7% in those aged 6 to 11 months, 1 to 3 years, and 4 to 9 years, respectively. VE was significantly reduced from 89.5% within 1 year of vaccination to 77.0% at 5 to 10 years postvaccination. Equinelike G3P[8] (48%) and G8P[8] (23%) were identified as the most common genotypes in case patients aged ≥6 months. CONCLUSIONS: Rotarix is highly effective at preventing laboratory-confirmed rotavirus in Australia, especially in infants aged 6 to 11 months. Reduced VE in older age groups and over time suggests waning protection, possibly related to the absence of subclinical immune boosting from continuously circulating virus. G8 genotypes have not been common in Australia, and their emergence, along with equinelike G3P[8], may be related to vaccine-induced selective pressure; however, further strain-specific VE studies are needed.


Subject(s)
Disease Outbreaks , Gastroenteritis/epidemiology , Rotavirus Infections/epidemiology , Rotavirus Vaccines/therapeutic use , Rotavirus/genetics , Adolescent , Adult , Age Distribution , Age Factors , Aged , Aged, 80 and over , Case-Control Studies , Child , Child, Preschool , Disease Notification/statistics & numerical data , Female , Gastroenteritis/immunology , Gastroenteritis/prevention & control , Genotype , Humans , Immunization Programs , Immunogenicity, Vaccine , Infant , Male , Middle Aged , New South Wales/epidemiology , Rotavirus/immunology , Rotavirus Infections/immunology , Rotavirus Infections/prevention & control , Treatment Outcome , Vaccines, Attenuated/therapeutic use , Young Adult
10.
Article in English | MEDLINE | ID: mdl-31315165

ABSTRACT

This report, from the Australian Rotavirus Surveillance Program and collaborating laboratories Australia-wide, describes the rotavirus genotypes identified in children and adults with acute gastroenteritis during the period 1 January to 31 December 2017. During this period, 2,285 faecal specimens were referred for rotavirus G and P genotype analysis, including 1,103 samples that were confirmed as rotavirus positive. Of these, 1,014/1,103 were wildtype rotavirus strains and 89/1,103 were identified as rotavirus vaccine-like. Genotype analysis of the 1,014 wildtype rotavirus samples from both children and adults demonstrated that G2P[4] was the dominant genotype nationally, identified in 39% of samples, followed by equine-like G3P[8] and G8P[8] (25% and 16% respectively). Multiple outbreaks were recorded across Australia, including G2P[4] (Northern Territory, Western Australia, and South Australia), equine-like G3P[8] (New South Wales), and G8P[8] (New South Wales and Victoria). This year also marks the change in the Australian National Immunisation Program to the use of Rotarix exclusively, on 1 July 2017.


Subject(s)
Epidemiological Monitoring , Rotavirus Infections/epidemiology , Rotavirus/pathogenicity , Adolescent , Age Factors , Australia/epidemiology , Child , Child, Preschool , Disease Outbreaks , Feces/virology , Gastroenteritis/epidemiology , Gastroenteritis/virology , Genotype , Humans , Infant , Infant, Newborn , New South Wales , Northern Territory , Population Surveillance , Rotavirus/classification , Rotavirus/genetics , South Australia , Victoria , Western Australia , Young Adult
11.
J Infect Dis ; 218(4): 546-554, 2018 07 13.
Article in English | MEDLINE | ID: mdl-29790933

ABSTRACT

Background: Introduction of rotavirus vaccines into national immunization programs (NIPs) could result in strain selection due to vaccine-induced selective pressure. This study describes the distribution and diversity of rotavirus genotypes before and after rotavirus vaccine introduction into the Australian NIP. State-based vaccine selection facilitated a unique comparison of diversity in RotaTeq and Rotarix vaccine states. Methods: From 1995 to 2015, the Australian Rotavirus Surveillance Program conducted genotypic analysis on 13051 rotavirus-positive samples from children <5 years of age, hospitalized with acute gastroenteritis. Rotavirus G and P genotypes were determined using serological and heminested multiplex reverse-transcription polymerase chain reaction assays. Results: G1P[8] was the dominant genotype nationally in the prevaccine era (1995-2006). Following vaccine introduction (2007-2015), greater genotype diversity was observed with fluctuating genotype dominance. Genotype distribution varied based on the vaccine implemented, with G12P[8] dominant in states using RotaTeq, and equine-like G3P[8] and G2P[4] dominant in states and territories using Rotarix. Conclusions: The increased diversity and differences in genotype dominance observed in states using RotaTeq (G12P[8]), and in states and territories using Rotarix (equine-like G3P[8] and G2P[4]), suggest that these vaccines exert different immunological pressures that influence the diversity of rotavirus strains circulating in Australia.


Subject(s)
Genetic Variation , Rotavirus Infections/epidemiology , Rotavirus Infections/virology , Rotavirus Vaccines/administration & dosage , Rotavirus/classification , Rotavirus/isolation & purification , Australia/epidemiology , Child, Preschool , Epidemiological Monitoring , Female , Genotype , Genotyping Techniques , Humans , Infant , Infant, Newborn , Longitudinal Studies , Male , Multiplex Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Rotavirus/genetics , Rotavirus Infections/prevention & control , Rotavirus Vaccines/immunology , Serotyping , Vaccines, Attenuated/administration & dosage , Vaccines, Attenuated/immunology
12.
Commun Dis Intell Q Rep ; 41(4): E455-E471, 2017 12 01.
Article in English | MEDLINE | ID: mdl-29864391

ABSTRACT

This report from the Australian Rotavirus Surveillance Program (ARSP) and collaborating laboratories Australia-wide, describes the rotavirus genotypes identified in children and adults with acute gastroenteritis during the period 1 January to 31 December 2016. During this period, 949 faecal specimens were referred for rotavirus G and P genotype analysis, of which 230 were confirmed as positive for wildtype rotavirus, and 184 were identified as rotavirus vaccine-like. Genotype analysis of the 230 samples from both children and adults revealed that G2P[4] was the dominant genotype in this reporting period nationally, identified in 29% of samples, followed by equine-like G3P[8] and G12P[8] (19% and 15% respectively). Genotype distribution remained distinct between States using RotaTeq® and Rotarix® vaccines. In RotaTeq ® States, G12P[8] strains were more common, while G2P[4] and equine-like G3P[8] genotypes were more common in Rotarix® States and Territories. This report highlights the continued dominance of G12P[8] strains in RotaTeq® States and co-dominance of G2P[4] and equine-like G3P[8] in States and Territories using Rotarix®.


Subject(s)
National Health Programs , Population Surveillance , Rotavirus Infections/epidemiology , Rotavirus Infections/virology , Rotavirus , Australia/epidemiology , Child, Preschool , Feces/virology , Female , Genotype , History, 21st Century , Humans , Infant , Infant, Newborn , Male , Molecular Typing , Rotavirus/classification , Rotavirus/genetics , Rotavirus/isolation & purification , Rotavirus Infections/history , Rotavirus Infections/prevention & control , Rotavirus Vaccines/immunology
13.
Commun Dis Intell Q Rep ; 40(4): E527-E538, 2016 Dec 24.
Article in English | MEDLINE | ID: mdl-28043228

ABSTRACT

The Australian Rotavirus Surveillance Program, together with collaborating laboratories Australia-wide, reports the rotavirus genotypes responsible for the hospitalisation of children with acute gastroenteritis during the period 1 January to 31 December 2015. During the survey period, 1,383 faecal samples were referred for rotavirus G and P genotype analysis, and of these, 1,031 were confirmed as rotavirus positive. A total of 634 specimens had been collected from children under 5 years of age, while 397 were from older children and adults. Genotype analysis of samples from both children and adults revealed that G12P[8] was the dominant genotype in this reporting period, identified in 48.2% of strains nationally. Genotype G3P[8] was the second most common strain nationally, representing 22.8% of samples, followed by G2P[4] and G1P[8] (9% and 8% respectively). G3P[8] was further divided as equine-like G3P[8] (13.2% of all strains) and other wild-type G3P[8] (9.6%). This report highlights the continued predominance of G12P[8] strains as the major cause of disease in this population. Genotype distribution was distinct between jurisdictions using RotaTeq and Rotarix vaccines. Genotype G12P[8] was more common in states using RotaTeq, while equine-like G3P[8] and G2P[4] were more common in the states and territories using Rotarix. This survey highlights the dynamic change in rotavirus genotypes observed since vaccine introduction, including the emergence of a novel equine-like G3P[8] as a major strain. The prolonged dominance of G12P[8] for a 4th consecutive year further illustrates the unexpected trends in the wild type rotaviruses circulating in the Australian population since vaccine introduction.


Subject(s)
Population Surveillance , Rotavirus Infections/epidemiology , Rotavirus Infections/microbiology , Rotavirus/genetics , Adolescent , Adult , Age Distribution , Annual Reports as Topic , Australia/epidemiology , Child , Child, Preschool , Feces/virology , Female , Gastroenteritis/epidemiology , Gastroenteritis/virology , Genotype , History, 21st Century , Humans , Infant , Infant, Newborn , Male , Middle Aged , Rotavirus Infections/history , Rotavirus Infections/prevention & control , Rotavirus Vaccines/immunology , Young Adult
14.
J Gen Virol ; 97(2): 403-410, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26588920

ABSTRACT

During 2013, a novel equine-like G3P[8] rotavirus emerged as the dominant strain in Australian children with severe rotavirus gastroenteritis. Full genome analysis demonstrated that the strain was an inter-genogroup reassortant, containing an equine-like G3 VP7, a P[8] VP4 and a genogroup 2 backbone I2-R2-C2-M2-A2-N2-T2-E2-H2. The genome constellation of the equine-like G3P[8] was distinct to Australian and global G3P[8] strains. Phylogenetic analysis demonstrated a genetic relationship to multiple gene segments of Japanese strains RVA/JPN/S13-30/2013/G3P[4] and RVA/Human-wt/JPN/HC12016/2012/G1P[8]. The Australian equine-like G3P[8] strain displayed a distinct VP7 antigenic profile when compared with the previously circulating Australian G3P[8] strains. Identification of similar genes in strains from several geographical regions suggested the equine-like G3P[8] strain was derived by multiple reassortment events between globally co-circulating strains from both human and animal sources. This study reinforces the dynamic nature of rotavirus strains and illustrates the potential for novel human/animal reassortant strains to emerge within the human population.


Subject(s)
Gastroenteritis/virology , Genotype , Reassortant Viruses/classification , Reassortant Viruses/genetics , Rotavirus Infections/virology , Rotavirus/classification , Rotavirus/genetics , Animals , Antigens, Viral/genetics , Australia , Capsid Proteins/genetics , Child , Child, Preschool , Cluster Analysis , Genome, Viral , Humans , Molecular Sequence Data , Phylogeny , RNA, Viral/genetics , Reassortant Viruses/isolation & purification , Rotavirus/isolation & purification , Sequence Analysis, DNA , Sequence Homology
15.
J Clin Virol ; 61(4): 579-84, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25464971

ABSTRACT

BACKGROUND: Intussusception, a condition where one segment of intestine invaginates into another, occurs predominantly in infants and young children. A number of potential causes have been identified including infectious agents and rotavirus vaccination. Following the introduction of rotavirus vaccination of infants in Western Australia, a laboratory surveillance programme testing notified intussusception cases for infectious agents was commenced. This led to a PCR-based study of the association between gastrointestinal viruses and intussusception. OBJECTIVES: Conduct viral testing on stool samples from intussusception patients to determine viruses that may have an association with intussusception. STUDY DESIGN: A retrospective case-control study was conducted using stool samples collected from children with intussusception (n=74) and matched controls (n=289) between 2008 and 2011. Samples were tested for rotavirus, norovirus, adenovirus, enterovirus, rhinovirus, astrovirus, parechovirus and bocavirus. Adenovirus, enterovirus and rhinovirus species were determined by DNA sequencing. RESULTS: Human adenovirus C was detected in significantly more cases than controls with 31/74 (41.9%) cases testing positive compared to 39/289 (13.49%) controls (OR=4.38, p<0.001). A significant difference was seen in Enterovirus B detections with 11/74 (14.9%) cases testing positive compared to 21/289 (7.3%) controls (OR=2.24, p=0.04). Rotavirus was detected in 7/74 (9.46%) cases and 11/289 (3.81%) controls, which was also a significant difference (OR=2.88, p=0.045). CONCLUSIONS: Our results show that intussusception is associated with non-enteric adenovirus infections, and Enterovirus B infections. While a statistical association was seen with rotavirus and intussusception, we were not able to determine if this was related to vaccine strain or wild type rotavirus.


Subject(s)
Adenoviruses, Human/isolation & purification , Enterovirus B, Human/isolation & purification , Feces/virology , Intussusception/epidemiology , Intussusception/virology , Rotavirus Vaccines/adverse effects , Rotavirus/isolation & purification , Case-Control Studies , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Male , Polymerase Chain Reaction , Retrospective Studies , Rotavirus Vaccines/administration & dosage , Sequence Analysis, DNA , Western Australia
16.
Commun Dis Intell Q Rep ; 38(1): E, 2014 Mar 31.
Article in English | MEDLINE | ID: mdl-25409347

ABSTRACT

This report from the Australian Rotavirus Surveillance Program, together with collaborating laboratories Australia-wide, describes the rotavirus genotypes responsible for the hospitalisation of children with acute gastroenteritis during the period 1 January to 31 December 2012. During the survey period, 1,300 faecal samples were referred to the centre for rotavirus G and P genotype analysis, and of these 748 were confirmed as rotavirus positive. A total of 491 specimens were collected from children under 5 years of age, while 257 were from older children and adults. Genotype analysis revealed that G1P[8] was the dominant type in this reporting period, identified in 35% of strains nationally. Genotype G2P[4] was the second most common strain nationally, representing 28% of samples, followed by genotype G12P[8] (23%). This represents the first report where G12P[8] strains are a major cause of disease in this community. Fluctuations in genotype distribution were also observed based on the vaccine type in use. Genotype G2P[4] was more common in states and territories using Rotarix while G1P[8] was more common in states using RotaTeq. This survey of rotavirus strains circulating in 2012 highlights the continued fluctuations in rotavirus genotypes, with an annual change in dominant genotypes as well as emergence of a previously rare genotype, suggesting a dynamic wild-type population.


Subject(s)
Population Surveillance , Rotavirus Infections/epidemiology , Rotavirus Infections/virology , Rotavirus/classification , Rotavirus/genetics , Age Distribution , Annual Reports as Topic , Australia/epidemiology , Child, Preschool , Female , Gastroenteritis/epidemiology , Gastroenteritis/history , Gastroenteritis/virology , Genotype , History, 21st Century , Humans , Infant , Infant, Newborn , Male , Rotavirus Infections/history
17.
Infect Genet Evol ; 25: 97-109, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24780429

ABSTRACT

A genotype G3P[14] rotavirus strain was identified in a 12year old child presenting to the Emergency Department of the Royal Children's Hospital, Melbourne, with gastroenteritis. G3P[14] strains have been previously identified in rabbits in Japan, China, the USA and Italy and a single lapine-like strain from a child in Belgium. Full genome sequence analysis of RVA/Human-wt/AUS/RCH272/2012/G3P[14] (RCH272) revealed that the strain contained the novel genome constellation G3-P[14]-I2-R3-C3-M3-A9-N2-T6-E2-H3. The genome was genetically divergent to previously characterized lapine viruses and the genes were distantly related to a range of human bovine-like strains and animal strains of bovine, bat and canine/feline characteristics. The VP4, VP6, NSP2, NSP3, NSP4 and NSP5 genes of RCH272 clustered within bovine lineages in the phylogenetic analysis and shared moderate genetic similarity with an Australian bovine-like human strain RVA/Human-tc/AUS/MG6/1993/G6P[14]. Bayesian coalescent analysis suggested these genes of RCH272 and RVA/Human-tc/AUS/MG6/1993/G6P[14] were derived from a population of relatively homogenous bovine-like ancestral strains circulating between 1943 and 1989. The VP7, VP1, VP2 and NSP1 genes shared moderate genetic similarity with the Chinese strain RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] and the VP3 gene clustered within a lineage comprised of canine and feline strains. This strain may represent the direct transmission from an unknown host species or be derived via multiple reassortment events between strains originating from various species. The patient lived in a household containing domesticated cats and dogs and in close proximity to a colony of Gray-headed Flying-foxes. However, without screening numerous animal populations it is not possible to determine the origins of this strain.


Subject(s)
Gastroenteritis/virology , Rotavirus Infections/virology , Rotavirus/classification , Rotavirus/genetics , Adolescent , Animals , Australia , Cats , Dogs , Evolution, Molecular , Genome, Viral , Humans , Male , Phylogeny , RNA, Viral , Rotavirus Infections/transmission , Sequence Analysis, RNA
18.
Commun Dis Intell Q Rep ; 38(4): E334-42, 2014 Dec 31.
Article in English | MEDLINE | ID: mdl-25631596

ABSTRACT

This report from the Australian Rotavirus Surveillance Program, together with collaborating laboratories Australia-wide, describes the rotavirus genotypes responsible for the hospitalisation of children with acute gastroenteritis during the period 1 January to 31 December 2013. During the survey period, 1,035 faecal samples were referred for rotavirus G and P genotype analysis. Of these 828 were confirmed as rotavirus positive. A total of 503 specimens were collected from children under 5 years of age, while 325 were from older children and adults. Genotype analysis of the 828 rotavirus samples collected from both children and adults revealed that G12P[8] was the dominant genotype in this reporting period, identified in 33% of strains nationally. Genotype G3P[8] was the second most common strain nationally, representing 31% of samples, followed by genotype G2P[4] (14%). This represents the first report where G12P[8] strains are the major cause of disease in this population. The genotype distribution was slightly altered when the analysis was restricted to samples collected from children under 5 years of age, with G3P[8] being the dominant genotype (39.2%) followed by G12P[8] as the second most common genotype (31%). Fluctuations in genotype distribution were also observed based on the vaccine type in use. Genotype G12P[8] was more common in states and territories using RotaTeq, while G3P[8] was more common in the locations using Rotarix. This survey highlights the yearly fluctuations in rotavirus genotypes observed since vaccine introduction, with changes in dominant genotypes an annual event. The emergence of G12P[8] as the dominant genotype further illustrates the ongoing changes in the wild type rotavirus population evident in the Australian population since vaccine introduction.


Subject(s)
Gastroenteritis/epidemiology , Rotavirus Infections/epidemiology , Rotavirus/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Annual Reports as Topic , Australia/epidemiology , Child , Child, Preschool , Epidemiological Monitoring , Feces/virology , Female , Gastroenteritis/immunology , Gastroenteritis/prevention & control , Gastroenteritis/virology , Genotype , Humans , Incidence , Infant , Infant, Newborn , Male , Middle Aged , Molecular Typing , Rotavirus/classification , Rotavirus/growth & development , Rotavirus Infections/immunology , Rotavirus Infections/prevention & control , Rotavirus Infections/virology , Rotavirus Vaccines/administration & dosage , Rotavirus Vaccines/immunology , Vaccination , Vaccines, Attenuated/administration & dosage , Vaccines, Attenuated/immunology
19.
Emerg Infect Dis ; 19(8): 1324-7, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23876354

ABSTRACT

We identified a genotype G10P[14] rotavirus strain in 5 children and 1 adult with acute gastroenteritis from the Northern Territory, Australia. Full genome sequence analysis identified an artiodactyl-like (bovine, ovine, and camelid) G10-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3 genome constellation. This finding suggests artiodactyl-to-human transmission and strengthens the need to continue rotavirus strain surveillance.


Subject(s)
Gastroenteritis/virology , Rotavirus Infections/virology , Rotavirus/genetics , Acute Disease , Aged, 80 and over , Antigens, Viral/genetics , Capsid Proteins/genetics , Child, Preschool , Genome, Viral , Humans , Infant , Multilocus Sequence Typing , Northern Territory , Phylogeny , Rotavirus/classification
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