319 results on '"Bishop RF"'
Search Results
102. Identification of Strains of RotaTeq Rotavirus Vaccine in Infants With Gastroenteritis Following Routine Vaccination.
- Author
-
Donato CM, Ch'ng LS, Boniface KF, Crawford NW, Buttery JP, Lyon M, Bishop RF, and Kirkwood CD
- Abstract
Background. RotaTeq vaccine was introduced into the Australian National Immunisation Program in 2007. This study identified and characterised rotavirus strains excreted by infants who presented with symptoms of gastroenteritis following recent RotaTeq vaccination. Methods. Fecal samples (N = 61) from children who developed gastroenteritis following recent RotaTeq vaccination were forwarded to the Australian Rotavirus Surveillance Program (ARSP). RotaTeq-positive samples were genotyped and regions of the VP3, VP4, VP6, and VP7 genes were sequenced. Also, 460 rotavirus-positive ARSP routine surveillance samples were analyzed by dot-blot Northern hybridization to detect RotaTeq vaccine-derived strains circulating in the community. Results. Thirteen of the 61 samples collected from infants developing gastroenteritis after RotaTeq vaccination contained vaccine-derived (vd) rotavirus strains. Of these, 4 contained a vdG1P[8] strain derived by reassortment between the G1P[5] and G6P[8] parental vaccine strains. Northern hybridization analysis of 460 surveillance samples identified 3 samples that contained RotaTeq vaccine-derived strains, including 2 vdG1P[8] reassortant vaccine strains. Conclusions. During replication and excretion of RotaTeq vaccine, reassortment of parental strains can occur. Shedding of RotaTeq vaccine strains in 7 of 13 infants was associated with underlying medical conditions that may have altered their immune function. The benefits of vaccination outweigh any small risk of vaccine-associated gastroenteritis. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
103. Extended coupled cluster method:Quantum many-body theory made classical
- Author
-
Arponen, J, Bishop, RF, Pajanne, E, Vashishta, P, Kalia, Rajiv K., and Bishop, RF
- Published
- 1987
104. Extended coupled cluster method: Quantum many-body theory made classical
- Author
-
Arponen, J, Bishop, RF and Pajanne, E, Vashishta, P, and Kalia, RK and Bishop, RF
- Published
- 1987
105. Towards a coupled-cluster gauge-field approach to quantum hydrodynamics
- Author
-
Arponen, J, Bishop, RF, Pajanne, E, Robinson, NI, Arponen, Jouko S., Bishop, RF, and Manninen, Matti
- Published
- 1988
106. Correlated basis functions and all that:A tribute to John W. Clark, recipient of the second Feenberg Award
- Author
-
Bishop, RF, Kallio, AJ, Pajanne, E, and Bishop, RF
- Published
- 1988
107. On an effective gauge field description of a positron impurity in polarizable media
- Author
-
Arponen, J, Bishop, RF and Pajanne, E, Vashishta, P, and Kalia, RK and Bishop, RF
- Published
- 1987
108. Pairing correlations, coherent states, and black holes
- Author
-
Bishop, RF and Vourdas, A and Malik, FB
- Published
- 1986
109. Towards a universal coupled cluster methodology for the various phases of condensed matter systems
- Author
-
Bishop, RF, Siemens, P.J., Smith, R.A., and Siemens, PJ and Smith, RA
- Published
- 1987
110. Pairing correlations, composite pairs, coupled clusters and all that
- Author
-
Bishop, RF
- Abstract
The coupled cluster [or exp(S)] formulation of quantum many-body theory is flrst extensively reviewed. It is then applied to the general problem of pairing correlations within a many-fermion system. The method is illustrated by restricting ourselves to the exact calculations that can be performed within the various generalized ladder approximations. It is shown how the formalism provides an efficient and unified framework in which to describe all aspects of pairing at the same level of approximation. Possible extensions to deal withcomposite clusters of more than two particles and to incorporate the effectsof the collective excitations, are sketched
- Published
- 1985
111. Statistical field theory
- Author
-
Bishop, RF
- Published
- 1989
- Full Text
- View/download PDF
112. Rayleigh-Schrõdinger perturbation theory revisited and extended
- Author
-
Bishop, RF, Flynn, MF, Znojil, M, and Keller, J
- Published
- 1989
113. Path integrals and condensed matter physics
- Author
-
Bishop, RF
- Published
- 1988
114. Dynamic variational principles and extended coupled cluster techniques
- Author
-
Bishop, RF, Arponen, J and Pajanne, E, and Mukherjee, D
- Published
- 1989
115. A coupled-cluster analysis of one-component Coulomb plasmas
- Author
-
Bishop, RF and Zabolitzky, J.G.
- Published
- 1983
116. The triple problem of convergence in the perturbation expansions with non-diagonal propagators
- Author
-
Znojil, M and Flynn, MF and Bishop, RF
- Published
- 1988
117. The coupled-cluster method
- Author
-
Bishop, RF and Kummel, HG
- Published
- 1987
- Full Text
- View/download PDF
118. Quantum fluid dynamics: An extended coupled cluster treatment
- Author
-
Bishop, RF, Robinson, NI, Arponen, J and Pajanne, E, and Mukherjee, D
- Published
- 1989
119. On the Coulomb plus separable model of quarkonium
- Author
-
Adam, J and Znojil, M and Bishop, RF
- Published
- 1985
120. Some recent developments in coupled cluster theory
- Author
-
Bishop, RF, Chen, J.M.C., Clark, J.W., Suntharothok-Priesmeyer, P., Chen, JMC, and Clark, JW and Suntharothok-Priesmeyer, P
- Subjects
Many-body problem ,Condensed matter - Published
- 1982
121. Linear response and sum rules in the coupled-cluster formalism
- Author
-
Bishop, RF, Wu, S.S., Kuo, T.T.S., and Wu, SS and Kuo, TTS
- Published
- 1984
122. Quantum theory of finite systems
- Author
-
Bishop, RF
- Published
- 1986
- Full Text
- View/download PDF
123. NAMING VIRUSES
- Author
-
Bishop Rf and Holmes Ih
- Subjects
business.industry ,Medicine ,General Medicine ,business - Published
- 1975
124. The coupled cluster method applied to quantum magnetism
- Author
-
Raymond F. Bishop, Damian J. J. Farnell, Schollwock, U, Richter, J, Farnell, DJJ and Bishop, RF, Schollwöck, U, Farnell, DJJ, and Bishop, RF
- Subjects
Physics ,Quantum phase transition ,Coupled cluster ,Heisenberg model ,Quantum mechanics ,Lattice (order) ,Condensed Matter::Strongly Correlated Electrons ,Statistical physics ,Spin (physics) ,Series expansion ,Square lattice ,Quantum - Abstract
The Coupled Cluster Method (CCM) is one of the most powerful and universally applied techniques of quantum many-body theory. In particular, it has been used extensively in order to investigate many types of lattice quantum spin system at zero temperature. The ground- and excited-state properties of these systems may now be determined routinely to great accuracy. In this Chapter we present an overview of the CCM formalism and we describe how the CCM is applied in detail. We illustrate the power and versatility of the method by presenting results for four different spin models. These are, namely, the XXZ model, a Heisenberg model with bonds of differing strengths on the square lattice, a model which interpolates between the Kagomé- and triangular-lattice antiferromagnets, and a frustrated ferrimagnetic spin system on the square lattice. We consider the ground-state properties of all of these systems and we present accurate results for the excitation energies of the spin-half square-lattice XXZ model. We utilise an ldquoextendedrdquo SUB2 approximation scheme, and we demonstrate how this approximation may be solved exactly by using Fourier transform methods or, alternatively, by determining and solving the SUB2-m problem. We also present the results of ldquolocalisedrdquo approximation schemes called the LSUBm or SUBm-m schemes. We note that we must utilise computational techniques in order to solve these localised approximation schemes to ldquohigh order.rdquo We show that we are able to determine the positions of quantum phase transitions with much accuracy, and we demonstrate that we are able to determine their quantum criticality by using the CCM in conjunction with the coherent anomaly method (CAM). Also, we illustrate that the CCM may be used in order to determine the ldquonodal surfacesrdquo of lattice quantum spin systems. Finally, we show how connections to cumulant series expansions may be made by determining the perturbation series of a spin-half triangular-lattice antiferromagnet using the CCM at various levels of LSUBm approximation. References
- Published
- 2004
125. Rotavirus antigenaemia and viraemia: a common event?
- Author
-
Blutt SE, Kirkwood CD, Parreño V, Warfield KL, Ciarlet M, Estes MK, Bok K, Bishop RF, and Conner ME
- Published
- 2003
- Full Text
- View/download PDF
126. Quantum phase transitions in spin systems
- Author
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Raymond F. Bishop, Johannes Richter, Damian J. J. Farnell, Sven E. Krüger, Bishop, RF, Gernoth, KA, and Walet, NR
- Subjects
Physics ,Quantum phase transition ,Phase transition ,Strongly Correlated Electrons (cond-mat.str-el) ,Condensed matter physics ,media_common.quotation_subject ,Quantum Monte Carlo ,FOS: Physical sciences ,Frustration ,Condensed Matter - Strongly Correlated Electrons ,Coupled cluster ,Condensed Matter::Strongly Correlated Electrons ,Quantum fluctuation ,Spin-½ ,media_common - Abstract
We discuss the influence of strong quantum fluctuations on zero-temperature phase transitions in a two-dimensional spin-half Heisenberg system. Using a high-order coupled cluster treatment, we study competition of magnetic bonds with and without frustration. We find that the coupled cluster treatment is able to describe the zero-temperature transitions in a qualitatively correct way, even if frustration is present and other methods such as quantum Monte Carlo fail., Comment: 8 pages, 12 Postscipt figures; Accepted for publication in World Scientific
- Published
- 2001
127. Correlated Basis Functions and all that
- Author
-
Raymond F. Bishop, Kallio, AJ, and Pajanne, E and Bishop, RF
- Subjects
Medal ,History ,Advisory committee ,Tribute ,Classics - Abstract
Eugene Feenberg was unquestionably one of the fathers of modern quantum many-body theory. Although he died in 1977, before the first of the series of International Conferences on Recent Progress in Many-Body Theories was held, the impact of his work and his inspiration have been clearly felt both in their inception and at each meeting since. This series of meetings began in its present form in Trieste, Italy, in 1978, and the second meeting was held in Oaxtepec, Mexico in 1981. By 1983, at the third Conference held in Altenberg, W. Germany, the International Advisory Committee, confirming the debt of the many-body physics community to Feenberg, took the decision to create the Eugene Feenberg Memorial Medal in Many-Body Physics. The medal was to be awarded at each subsequent conference in the series for an important contribution or contributions to the field of many-body physics. The Fourth Conference was held in 1985 in San Francisco, and it was there that David Pines was announced to be the first Feenberg Medallist by C.E. Campbell who read the tribute to him in his capacity as Chairman of the first Selection Committee.
- Published
- 1988
128. The Impact of Rotavirus Vaccines on Genotype Diversity: A Comprehensive Analysis of 2 Decades of Australian Surveillance Data.
- Author
-
Roczo-Farkas S, Kirkwood CD, Cowley D, Barnes GL, Bishop RF, Bogdanovic-Sakran N, Boniface K, Donato CM, and Bines JE
- Subjects
- 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, Genetic Variation, Rotavirus classification, Rotavirus isolation & purification, Rotavirus Infections epidemiology, Rotavirus Infections virology, Rotavirus Vaccines administration & dosage
- 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.
- Published
- 2018
- Full Text
- View/download PDF
129. Human Neonatal Rotavirus Vaccine (RV3-BB) to Target Rotavirus from Birth.
- Author
-
Bines JE, At Thobari J, Satria CD, Handley A, Watts E, Cowley D, Nirwati H, Ackland J, Standish J, Justice F, Byars G, Lee KJ, Barnes GL, Bachtiar NS, Viska Icanervilia A, Boniface K, Bogdanovic-Sakran N, Pavlic D, Bishop RF, Kirkwood CD, Buttery JP, and Soenarto Y
- Subjects
- Administration, Oral, Double-Blind Method, Feces virology, Female, Gastroenteritis epidemiology, Gastroenteritis virology, Humans, Immunization Schedule, Indonesia, Infant, Infant, Newborn, Intention to Treat Analysis, Male, Rotavirus isolation & purification, Rotavirus Vaccines administration & dosage, Rotavirus Vaccines adverse effects, Treatment Outcome, Gastroenteritis prevention & control, Rotavirus Infections prevention & control, Rotavirus Vaccines immunology
- Abstract
Background: A strategy of administering a neonatal rotavirus vaccine at birth to target early prevention of rotavirus gastroenteritis may address some of the barriers to global implementation of a rotavirus vaccine., Methods: We conducted a randomized, double-blind, placebo-controlled trial in Indonesia to evaluate the efficacy of an oral human neonatal rotavirus vaccine (RV3-BB) in preventing rotavirus gastroenteritis. Healthy newborns received three doses of RV3-BB, administered according to a neonatal schedule (0 to 5 days, 8 weeks, and 14 weeks of age) or an infant schedule (8 weeks, 14 weeks, and 18 weeks of age), or placebo. The primary analysis was conducted in the per-protocol population, which included only participants who received all four doses of vaccine or placebo within the visit windows, with secondary analyses performed in the intention-to-treat population, which included all participants who underwent randomization., Results: Among the 1513 participants in the per-protocol population, severe rotavirus gastroenteritis occurred up to the age of 18 months in 5.6% of the participants in the placebo group (28 of 504 babies), in 1.4% in the neonatal-schedule vaccine group (7 of 498), and in 2.7% in the infant-schedule vaccine group (14 of 511). This resulted in a vaccine efficacy of 75% (95% confidence interval [CI], 44 to 91) in the neonatal-schedule group (P<0.001), 51% (95% CI, 7 to 76) in the infant-schedule group (P=0.03), and 63% (95% CI, 34 to 80) in the neonatal-schedule and infant-schedule groups combined (combined vaccine group) (P<0.001). Similar results were observed in the intention-to-treat analysis (1649 participants); the vaccine efficacy was 68% (95% CI, 35 to 86) in the neonatal-schedule group (P=0.001), 52% (95% CI, 11 to 76) in the infant-schedule group (P=0.02), and 60% (95% CI, 31 to 76) in the combined vaccine group (P<0.001). Vaccine response, as evidenced by serum immune response or shedding of RV3-BB in the stool, occurred in 78 of 83 participants (94%) in the neonatal-schedule group and in 83 of 84 participants (99%) in the infant-schedule group. The incidence of adverse events was similar across the groups. No episodes of intussusception occurred within the 21-day risk period after administration of any dose of vaccine or placebo, and one episode of intussusception occurred 114 days after the third dose of vaccine in the infant-schedule group., Conclusions: RV3-BB was efficacious in preventing severe rotavirus gastroenteritis when administered according to a neonatal or an infant schedule in Indonesia. (Funded by the Bill and Melinda Gates Foundation and others; Australian New Zealand Clinical Trials Registry number, ACTRN12612001282875 .).
- Published
- 2018
- Full Text
- View/download PDF
130. Safety and immunogenicity of RV3-BB human neonatal rotavirus vaccine administered at birth or in infancy: a randomised, double-blind, placebo-controlled trial.
- Author
-
Bines JE, Danchin M, Jackson P, Handley A, Watts E, Lee KJ, West A, Cowley D, Chen MY, Barnes GL, Justice F, Buttery JP, Carlin JB, Bishop RF, Taylor B, and Kirkwood CD
- Subjects
- Double-Blind Method, Female, Humans, Immunization Schedule, Immunoglobulin A blood, Infant, Infant, Newborn, Male, New Zealand, Rotavirus Infections blood, Rotavirus Infections immunology, Rotavirus Infections virology, Vaccines, Attenuated, Antibodies, Viral blood, Rotavirus immunology, Rotavirus Infections prevention & control, Rotavirus Vaccines administration & dosage, Vaccination
- Abstract
Background: Despite the success of rotavirus vaccines, suboptimal vaccine efficacy in regions with a high burden of disease continues to present a challenge to worldwide implementation. A birth dose strategy with a vaccine developed from an asymptomatic neonatal rotavirus strain has the potential to address this challenge and provide protection from severe rotavirus disease from birth., Methods: This phase 2a randomised, double-blind, three-arm, placebo-controlled safety and immunogenicity trial was undertaken at a single centre in New Zealand between Jan 13, 2012, and April 17, 2014. Healthy, full-term (≥36 weeks gestation) babies, who weighed at least 2500 g, and were 0-5 days old at the time of randomisation were randomly assigned (1:1:1; computer-generated; telephone central allocation) according to a concealed block randomisation schedule to oral RV3-BB vaccine with the first dose given at 0-5 days after birth (neonatal schedule), to vaccine with the first dose given at about 8 weeks after birth (infant schedule), or to placebo. The primary endpoint was cumulative vaccine take (serum immune response or stool shedding of vaccine virus after any dose) after three doses. The immunogenicity analysis included all randomised participants with available outcome data. This trial is registered with the Australian New Zealand Clinical Trials Registry, ACTRN12611001212943., Findings: 95 eligible participants were randomised, of whom 89 were included in the primary analysis. A cumulative vaccine take was detected in 27 (90%) of 30 participants in the neonatal schedule group after three doses of RV3-BB vaccine compared with four (13%) of 32 participants in the placebo group (difference in proportions 0·78, 95% CI 0·55-0·88; p<0·0001). 25 (93%) of 27 participants in the infant schedule group had a cumulative vaccine take after three doses compared with eight (25%) of 32 participants in the placebo group (difference in proportions 0·68, 0·44-0·81; p<0·0001). A serum IgA response was detected in 19 (63%) of 30 participants and 20 (74%) of 27 participants, and stool shedding of RV3-BB was detected in 21 (70%) of 30 participants and 21 (78%) of 27 participants in the neonatal and infant schedule groups, respectively. The frequency of solicited and unsolicited adverse events was similar across the treatment groups. RV3-BB vaccine was not associated with an increased frequency of fever or gastrointestinal symptoms compared with placebo., Interpretation: RV3-BB vaccine was immunogenic and well tolerated when given as a three-dose neonatal or infant schedule. A birth dose strategy of RV3-BB vaccine has the potential to improve the effectiveness and implementation of rotavirus vaccines., Funding: Australian National Health and Medical Research Council, the New Zealand Health Research Council, and the Murdoch Childrens Research Institute., (Copyright © 2015 Elsevier Ltd. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
131. Ground-state phase structure of the spin-1/2 anisotropic planar pyrochlore.
- Author
-
Li PH and Bishop RF
- Abstract
We study the zero-temperature ground-state (GS) properties of the spin-1/2 anisotropic planar pyrochlore, using the coupled cluster method (CCM) implemented to high orders of approximation. The system comprises a J 1-J 2 model on the checkerboard lattice, with isotropic Heisenberg interactions of strength J 1 between all nearest-neighbour pairs of spins on the square lattice, and of strength J 2 between half of the next-nearest-neighbour pairs (in the checkerboard pattern). We calculate results for the GS energy and average local GS on-site magnetization, using various antiferromagnetic classical ground states as CCM model states. We also give results for the susceptibility of one of these states against the formation of crossed-dimer valence-bond crystalline (CDVBC) ordering. The complete GS phase diagram is presented for arbitrary values of the frustration parameter k≡J2/J1, and when each of the exchange couplings can take either sign.
- Published
- 2015
- Full Text
- View/download PDF
132. Australian Rotavirus Surveillance Program annual report, 2012.
- Author
-
Kirkwood CD, Roczo-Farkas S, Bishop RF, and Barnes GL
- Subjects
- 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, Population Surveillance, Rotavirus classification, Rotavirus genetics, Rotavirus Infections epidemiology, Rotavirus Infections virology
- 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., (copyright@health.gov.au)
- Published
- 2014
133. Valence-bond crystalline order in the s = 1/2 J1-J2 model on the honeycomb lattice.
- Author
-
Bishop RF, Li PH, and Campbell CE
- Abstract
Using the coupled cluster method we study the phase diagram of the spin-1/2 Heisenberg antiferromagnet on a honeycomb lattice with nearest-neighbour exchange coupling J1 > 0 and frustrating next-nearest-neighbour coupling J2 ≡ xJ1 > 0. In the range 0 < x < 1 we find four phases exhibiting respectively Néel, 6-spin plaquette, staggered dimer and Néel-II orderings, with quantum critical points at xc1 ≈ 0.207(3), xc2 ≈ 0.385(10) and xc3 ≈ 0.65(5). The transitions at xc1 and xc3 appear to be continuous (and hence deconfined) ones, while that at xc2 appears to be a direct first-order one.
- Published
- 2013
- Full Text
- View/download PDF
134. Bacteriophages in gut samples from pediatric Crohn's disease patients: metagenomic analysis using 454 pyrosequencing.
- Author
-
Wagner J, Maksimovic J, Farries G, Sim WH, Bishop RF, Cameron DJ, Catto-Smith AG, and Kirkwood CD
- Subjects
- Case-Control Studies, Child, Crohn Disease genetics, DNA, Viral genetics, Female, Humans, Male, Polymerase Chain Reaction, Sequence Analysis, DNA, Bacteriophages physiology, Colon virology, Crohn Disease virology, Gastrointestinal Tract virology, Ileum virology, Metagenomics
- Abstract
Background: The role of bacteriophage in Crohn's disease (CD) is unknown. This study investigated the abundance of phages in ileal and colonic samples from pediatric CD patients and controls., Methods: Ileal and colonic biopsies from 6 CD patients, gut wash samples from 3 CD patients, and ileal biopsies from 6 noninflammatory bowel disease patients (controls) were analyzed for the presence of bacteriophage using 454 high-throughput pyrosequencing. A sequence-independent single-primer amplification method was used to amplify viral sequences., Results: A total of 186,143 high quality reads were obtained from the 4 sample populations. Contigs and sequence clusters (generated from unassembled singletons) were aligned with sequences from the National Center for Biotechnology Information viral reference database and analyzed by MEGAN. The largest number of viral hits was obtained from the CD gut wash samples (n = 691), followed by CD ileal samples (n = 52), control ileum samples (n = 20), and CD colonic samples (n = 1). The most abundant virus sequences identified belonged to the Caudovirales phage., Conclusions: Our study characterized a diverse phage community in the gut of CD patients. In this study, we have identified differences in phage composition between CD patients and control individuals. The large abundance of phages in CD ileum tissue and CD gut wash sample suggests a role of phage in CD development. The role of phage dysbiosis in CD is currently unknown but opens up a new area of research.
- Published
- 2013
- Full Text
- View/download PDF
135. Phase I trial of RV3-BB rotavirus vaccine: a human neonatal rotavirus vaccine.
- Author
-
Danchin M, Kirkwood CD, Lee KJ, Bishop RF, Watts E, Justice FA, Clifford V, Cowley D, Buttery JP, and Bines JE
- Subjects
- Administration, Oral, Adult, Antibodies, Anti-Idiotypic blood, Antibodies, Anti-Idiotypic immunology, Antibodies, Neutralizing blood, Antibodies, Neutralizing immunology, Antibodies, Viral blood, Antibodies, Viral immunology, Child, Cohort Studies, Double-Blind Method, Feces virology, Female, Genotype, Humans, Immunoglobulin A blood, Infant, Male, Rotavirus physiology, Rotavirus Infections immunology, Rotavirus Infections virology, Rotavirus Vaccines administration & dosage, Rotavirus Vaccines immunology, Vaccines, Attenuated administration & dosage, Vaccines, Attenuated adverse effects, Vaccines, Attenuated immunology, Virus Replication drug effects, Virus Replication immunology, Young Adult, Rotavirus immunology, Rotavirus Infections prevention & control, Rotavirus Vaccines adverse effects
- Abstract
Introduction: RV3 is a human neonatal rotavirus strain (G3P[6]) that has been associated with asymptomatic neonatal infection and replicates well in the infant gut. RV3-BB rotavirus vaccine has been developed as a rotavirus vaccine candidate for administration at birth., Methods: A single-centre, double-blind, randomised placebo-controlled Phase I study evaluated the safety and tolerability of a single oral dose of the second generation RV3-BB rotavirus vaccine (8.3×10(6)FFU/mL) in 20 adults, 20 children and 20 infants (10 vaccine and 10 placebo per age cohort). Vaccine take was defined as seroconversion (a 3-fold increase in serum anti-rotavirus IgA or serum neutralising antibody (SNA) from baseline at day 28 post-dose) or evidence of RV3-BB viral replication in the faeces by RT-PCR analysis 3-6 days post-vaccination. RV3-BB presence was confirmed by sequence analysis., Results: The RV3-BB vaccine was well tolerated in all participants, with no pattern of adverse events shown to be associated with the study vaccine. In the infant cohort, vaccine take was demonstrated in 8/9 infants following a single dose of vaccine compared with 2/7 placebo recipients. In the infant vaccine group, 5/9 infants exhibited either IgA or SNA seroconversion and 7/9 infants had evidence of RV3-BB replication on days 3-6, compared with 2/7 infants who seroconverted and 0/10 infants with evidence of replication in the placebo group. Two infants in the placebo group had serological evidence of a rotavirus infection within the 28-day study period: one demonstrated an IgA and the other an SNA response, with wild-type virus replication detected in another infant., Conclusion: A single dose of RV3-BB rotavirus vaccine was well tolerated in adults, children and infants. Most infants (8/9) who received RV3-BB demonstrated vaccine take following a single dose. These data support progression of RV3-BB to Phase II immunogenicity and efficacy trials., (Copyright © 2013 Elsevier Ltd. All rights reserved.)
- Published
- 2013
- Full Text
- View/download PDF
136. The frustrated Heisenberg antiferromagnet on the honeycomb lattice: J1-J2 model.
- Author
-
Bishop RF, Li PH, Farnell DJ, and Campbell CE
- Abstract
We study the ground-state phase diagram of the frustrated spin-[Formula: see text] antiferromagnet with J(2) = xJ(1) > 0 (J(1) > 0) on the honeycomb lattice, using the coupled-cluster method. We present results for the ground-state energy, magnetic order parameter and plaquette valence-bond crystal (PVBC) susceptibility. We find a paramagnetic PVBC phase for x(c(1)) < x < x(c(2)), where x(c(1)) ≈ 0.207 ± 0.003 and x(c(2)) ≈ 0.385 ± 0.010. The transition at x(c(1)) to the Néel phase seems to be a continuous deconfined transition (although we cannot exclude a very narrow intermediate phase in the range 0.21 ≲ x ≲ 0.24), while that at x(c(2)) is of first-order type to another quasiclassical antiferromagnetic phase that occurs in the classical version of the model only at the isolated and highly degenerate critical point [Formula: see text]. The spiral phases that are present classically for all values x > 1/6 are absent for all x ≲ 1.
- Published
- 2012
- Full Text
- View/download PDF
137. Expression profile of genes involved in pathogenesis of pediatric Crohn's disease.
- Author
-
Sim WH, Wagner J, Cameron DJ, Catto-Smith AG, Bishop RF, and Kirkwood CD
- Subjects
- Adolescent, Biopsy, Case-Control Studies, Child, Child, Preschool, Crohn Disease metabolism, Crohn Disease microbiology, Crohn Disease pathology, Female, Gene Expression, Gene Expression Profiling methods, Gene Regulatory Networks, Genetic Predisposition to Disease, Humans, Ileum metabolism, Ileum pathology, Lithostathine biosynthesis, Lithostathine genetics, Male, Matrix Metalloproteinase 2 biosynthesis, Matrix Metalloproteinase 2 genetics, Nucleic Acid Hybridization methods, Real-Time Polymerase Chain Reaction methods, Up-Regulation, Crohn Disease genetics
- Abstract
Background and Aim: Expression profiling of genes specific to pediatric Crohn's Disease (CD) patients was performed to elucidate the molecular mechanisms underlying disease cause and pathogenesis at disease onset., Methods: We used suppressive subtractive hybridization (SSH) and differential screening analysis to profile the mRNA expression patterns of children with CD and age- and sex-matched controls without inflammatory bowel disease (IBD)., Results: Sequence analysis of 1000 clones enriched by SSH identified 75 functionally annotated human genes, represented by 430 clones. The 75 genes have potential involvement in gene networks, such as antigen presentation, inflammation, infection mechanism, connective tissue development, cell cycle and cancer. Twenty-eight genes were previously described in association with CD, while 47 were new genes not previously reported in the context of IBD. Additionally, 29 of the 75 genes have been previously implicated in bacterial and viral infections. Quantitative real-time reverse transcription polymerase chain reaction performed on ileal-derived RNA from 13 CD and nine non-IBD patients confirmed the upregulation of extracellular matrix gene MMP2 (P = 0.001), and cell proliferation gene REG1A (P = 0.063) in our pediatric CD cohort., Conclusion: The retrieval of 28 genes previously reported in association with adult CD emphasizes the importance of these genes in the pediatric setting. The observed upregulation of REG1A and MMP2, and their known impact on cell proliferation and extracellular matrix remodeling, agrees with the clinical behavior of the disease. Moreover, the expressions of bacterial- and virus-related genes in our CD-patient tissues support the concept that microbial agents are important in the etiopathogenesis of CD., (© 2011 Journal of Gastroenterology and Hepatology Foundation and Blackwell Publishing Asia Pty Ltd.)
- Published
- 2012
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138. Australian Rotavirus Surveillance Program annual report, 2010/11.
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Kirkwood CD, Roczo S, Boniface K, Bishop RF, and Barnes GL
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Australia epidemiology, Child, Child, Preschool, Genotype, Humans, Infant, Infant, Newborn, Middle Aged, Rotavirus classification, Rotavirus Infections prevention & control, Rotavirus Infections virology, Rotavirus Vaccines administration & dosage, Vaccines, Attenuated administration & dosage, Young Adult, Gastroenteritis epidemiology, Gastroenteritis virology, Rotavirus genetics, Rotavirus Infections epidemiology
- Abstract
The Australian Rotavirus Surveillance Program together with collaborating laboratories Australia-wide conducts a laboratory based rotavirus surveillance program. This report describes the genotypes of rotavirus strains responsible for the hospitalisation of children with acute gastroenteritis during 1 July 2010 to 30 June 2011. This report represents the fourth year of surveillance following introduction of rotavirus vaccines into the National Immunisation Program. One thousand one hundred and twenty-seven faecal samples were referred to the centre for G and P genotype analysis using hemi-nested multiplex reverse transcription-polymerase chain reaction. Eight hundred and sixteen samples were confirmed as rotavirus positive. Of these, 551 were collected from children under 5 years of age, while 265 were from older children and adults. Genotype analysis revealed that a change in the dominant type occurred in this reporting period, such that genotype G2P[4] was the dominant type nationally, representing 51% of samples, followed by genotype G1P[8] (26.1%). Genotypes G3P[8] represented 11% of samples while G4P[8] re-emerged as an important genotype, and was identified in 6% of samples. Uncommon rotavirus G and P combinations continue to be identified, with G2P[8] and G9P[4] identified during this survey. Differences in genotype distribution based on vaccine usage continue to be evident in Australian states. This survey continues to highlight the fluctuations in rotavirus genotypes, with an annual change in dominant genotypes suggesting a more dynamic wild-type population.
- Published
- 2011
139. Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn's disease: a longitudinal follow-up study.
- Author
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Wagner J, Sim W, Bishop RF, Catto-Smith AG, Cameron DJ, and Kirkwood CD
- Subjects
- Adolescent, Biopsy, Child, Crohn Disease microbiology, Endoscopy, Gastrointestinal, Female, Follow-Up Studies, Humans, Male, Paratuberculosis microbiology, Crohn Disease complications, Crohn Disease pathology, Mycobacterium avium subsp. paratuberculosis isolation & purification, Paratuberculosis complications
- Published
- 2011
- Full Text
- View/download PDF
140. Maternal antibodies to rotavirus: could they interfere with live rotavirus vaccines in developing countries?
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Chan J, Nirwati H, Triasih R, Bogdanovic-Sakran N, Soenarto Y, Hakimi M, Duke T, Buttery JP, Bines JE, Bishop RF, Kirkwood CD, and Danchin MD
- Subjects
- Adolescent, Adult, Developing Countries, Female, Humans, Immunoglobulin A analysis, Immunoglobulin A blood, Immunoglobulin G analysis, Immunoglobulin G blood, Indonesia, Pregnancy, Prospective Studies, Young Adult, Antibodies, Viral analysis, Antibodies, Viral blood, Colostrum immunology, Immunity, Maternally-Acquired, Milk, Human immunology, Rotavirus Infections immunology, Rotavirus Vaccines immunology
- Abstract
Introduction: Past experience with live oral vaccines including licensed rotavirus vaccines demonstrates a trend towards reduced vaccine efficacy in developing countries compared with developed countries. The reasons behind this disparity are not well understood. Transplacental transfer of maternal antibodies and breast milk ingestion may attenuate vaccine responses in infants in developing countries where rotavirus infections are endemic, and maternal antibody levels are high. We examined the prevalence and level of rotavirus antibody in maternal and cord serum, colostrum and breast milk in a developing country setting., Methods: 100 mother-infant pairs were prospectively recruited from December 2008 to February 2009 at Dr. Sardjito Hospital, Yogyakarta, Indonesia. Maternal and cord sera were collected during delivery. Colostrum and transitional breast milk were collected between day 0-3 and day 7-10 postpartum respectively. Rotavirus-specific IgA and IgG were estimated for all specimens and virus neutralization assays were conducted on a subset of milk specimens., Results: All maternal and cord serum samples were positive for rotavirus-specific IgG antibodies with a strong correlation between levels of rotavirus-specific IgG in mothers and levels transferred to infants in cord blood (r=0.86; p=0.001). 78% of colostrum and 67% of transitional breast milk specimens were positive for rotavirus-specific IgA. There was a median 4-fold decrease in rotavirus-specific IgA from colostrum to transitional breast milk. Neutralizing antibodies were present in 56% of colostrum specimens assayed (19/34) and in 41% of transitional milk specimens assayed (14/34)., Conclusions: Maternal serum and breast milk antibodies to rotavirus are highly prevalent in a developing country setting. Evaluation of the impact of maternal anti-rotavirus serum and breast milk antibody upon vaccine immunogenicity would help to inform rotavirus vaccination strategies, especially in developing settings., (Copyright © 2010 Elsevier Ltd. All rights reserved.)
- Published
- 2011
- Full Text
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141. Distribution of rotavirus genotypes after introduction of rotavirus vaccines, Rotarix® and RotaTeq®, into the National Immunization Program of Australia.
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Kirkwood CD, Boniface K, Barnes GL, and Bishop RF
- Subjects
- Australia epidemiology, Child, Child, Preschool, Diarrhea virology, Feces virology, Genotype, Hospitalization, Humans, Immunization Programs, Molecular Epidemiology, Prevalence, Rotavirus genetics, Rotavirus isolation & purification, Rotavirus Vaccines immunology, Vaccines, Attenuated administration & dosage, Vaccines, Attenuated immunology, Rotavirus classification, Rotavirus Infections epidemiology, Rotavirus Infections virology, Rotavirus Vaccines administration & dosage
- Abstract
Background: Rotavirus vaccines, RotaTeq and Rotarix, were introduced into the Australian National Immunization Program on July 1, 2007. The simultaneous introduction in different Australian states and territories provides a unique opportunity to compare the affect of each vaccine on the types of circulating rotavirus strains. This report describes the rotavirus genotypes responsible for the hospitalization of children during the first 2-year period after vaccine introduction., Methods: A total of 764 rotavirus-associated diarrheal cases were collected from children presenting to hospital in 10 Australian centers. Rotavirus genotype was determined using reverse transcription polymerase chain reaction assays., Results: G1P[8] was the dominant genotype nationally (52%), followed by G2P[4] (19.8%), G9P[8] (12.2%), and G3P[8] (11%). Differences in the prevalence rates of G2P[4] and G3P[8] were seen in the various states. G2P[4] strains were more prevalent in states using Rotarix, whereas G3P[8] strains were more prevalent in states using RotaTeq., Conclusions: Differences in rotavirus genotypes were observed across Australia, which suggest that different immune pressures are exerted by the different vaccines, but do not necessarily imply lack of protection by either vaccine. These differences may simply be related to the variation that can occur because of natural annual fluctuation in rotavirus strain prevalence.
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- 2011
- Full Text
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142. Australian Rotavirus Surveillance Program: annual report, 2009/2010.
- Author
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Kirkwood CD, Boniface K, Bishop RF, and Barnes GL
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Australia epidemiology, Child, Child, Preschool, Female, Humans, Infant, Infant, Newborn, Male, Middle Aged, Reverse Transcriptase Polymerase Chain Reaction, Rotavirus Infections prevention & control, Rotavirus Vaccines therapeutic use, Sentinel Surveillance, Young Adult, Gastroenteritis epidemiology, Gastroenteritis virology, Rotavirus genetics, Rotavirus Infections epidemiology
- Abstract
The Australian Rotavirus Surveillance Program together with 15 collaborating laboratories Australia-wide conducts a laboratory based rotavirus surveillance program. This report describes the genotypes of rotavirus strains responsible for the hospitalisation of children with acute gastroenteritis during the period 1 July 2009 to 30 June 2010, the 3rd year of surveillance following introduction of rotavirus vaccines into the National Immunisation Program. Seven hundred and seventy-eight faecal samples were referred to the centre for G and P genotype analysis using hemi-nested multiplex reverse transcription-polymerase chain reaction. Of the 422 confirmed as rotavirus positive, genotype G1P[8] was the dominant type nationally, representing 49.3%, followed by genotype G2P[4] (21.1%). Genotypes G3P[8], G4P[8] and G9P[8] each represented less than 3% of circulating strains nationally. The dominance of G1P[8] was in part associated with a large outbreak of severe gastroenteritis in the Northern Territory in 2010. The identification of uncommon rotavirus genotype combinations has increased since vaccine introduction, with G1P[4], G2P[8] and G9P[4] identified during this survey. Single strains of G1P[6] and G4P[6] were identified during this study period. This survey continues to highlight the fluctuations in rotavirus genotypes, and results from this survey suggest there is limited genotype selection based on vaccine usage. However, the large G1P[8] outbreak of gastroenteritis in the Northern Territory may have resulted from vaccine pressure on wild-type strains.
- Published
- 2010
143. Interaction of Crohn's disease susceptibility genes in an Australian paediatric cohort.
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Wagner J, Sim WH, Ellis JA, Ong EK, Catto-Smith AG, Cameron DJ, Bishop RF, and Kirkwood CD
- Subjects
- Australia, Chi-Square Distribution, Child, Cohort Studies, Crohn Disease pathology, GTP-Binding Proteins genetics, Gene Frequency, Genetic Association Studies, Genotype, Humans, Logistic Models, Membrane Proteins genetics, Molecular Chaperones, Muscle Proteins genetics, Nod2 Signaling Adaptor Protein genetics, Organic Cation Transport Proteins genetics, Phenotype, Receptors, Interleukin genetics, Receptors, Tumor Necrosis Factor, Member 6b genetics, Solute Carrier Family 22 Member 5, Symporters, Toll-Like Receptor 4 genetics, Crohn Disease genetics, Epistasis, Genetic, Genetic Predisposition to Disease genetics, Polymorphism, Single Nucleotide
- Abstract
Genetic susceptibility is an important contributor to the pathogenesis of Crohn's disease (CD). We investigated multiple CD susceptibility genes in an Australian paediatric onset CD cohort. Newly diagnosed paediatric onset CD patients (n = 72) and controls (n = 98) were genotyped for 34 single nucleotide polymorphisms (SNPs) in 18 genetic loci. Gene-gene interaction analysis, gene-disease phenotype analysis and genetic risk profiling were performed for all SNPs and all genes. Of the 34 SNPs analysed, four polymorphisms on three genes (NOD2, IL23R, and region 3p21) were significantly associated with CD status (p<0.05). All three CD specific paediatric polymorphisms on PSMG1 and TNFRSF6B showed a trend of association with p<0.1. An additive gene-gene interaction involving TLR4, PSMG1, TNFRSF6B and IRGM was identified with CD. Genes involved in microbial processing (TLR4, PSMG1, NOD2) were significantly associated either at the individual level or in gene-gene interactive roles. Colonic disease was significantly associated with disease SNP rs7517847 (IL23R) (p<0.05) and colonic and ileal/colonic disease was significantly associated with disease SNP rs125221868 (IBD5) and SLC22A4 & SLC22A4/5 variants (p<0.05). We were able to demonstrate genetic association of several genes to CD in a paediatric onset cohort. Several of the observed associations have not been reported previously in association with paediatric CD patients. Our findings demonstrate that CD genetic susceptibility in paediatric patients presents as a complex interaction between numerous genes.
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- 2010
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144. Novel Burkholderiales 23S rRNA genes identified in ileal biopsy samples from children: preliminary evidence that a subtype is associated with perianal Crohn's disease.
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Sim WH, Wagner J, Cameron DJ, Catto-Smith AG, Bishop RF, and Kirkwood CD
- Subjects
- Adolescent, Biopsy, Burkholderia isolation & purification, Child, Child, Preschool, Cluster Analysis, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 23S genetics, Sequence Analysis, DNA, Burkholderia classification, Burkholderia genetics, Crohn Disease microbiology, Ileum microbiology
- Abstract
A novel family of Burkholderiales bacteria was identified in ileal biopsy specimens from children presenting with symptoms of inflammatory bowel disease. A molecular subtyping approach based on sequencing of a variable region of the bacteria's 23S rRNA genes identified three variants. Pilot analysis identified one variant to be significantly associated with perianal Crohn's disease.
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- 2010
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145. Circulating human group A rotavirus genotypes in Malaysia.
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Zuridah H, Kirkwood CD, Bogdanovic-Sakran N, Bishop RF, and Yap KL
- Subjects
- Child, Preschool, Diarrhea epidemiology, Genotype, Hospitalization, Humans, Infant, Malaysia epidemiology, Molecular Epidemiology, Prevalence, Rotavirus isolation & purification, Rotavirus classification, Rotavirus genetics, Rotavirus Infections epidemiology, Rotavirus Infections virology
- Abstract
This study examined the temporal distribution of rotavirus genotypes in Malaysia. Rotaviruses from children with diarrhea admitted to hospitals in 1996 (n = 93) and 2007 (n = 12) in two different regions of Peninsular (West) Malaysia were analyzed for their G and P genotypes using a hemi-nested RT-PCR assay. In the 2007 samples, the dominant strain was G9P[8]. It was identified in 42% of the samples. Different strains all possessing the G1 genotype were identified in the rest of the samples. In contrast, 81% of the samples collected in 1996 were the G1P[8] strain. No strains with G9 genotype were detected in samples collected in 1996., (2010 Wiley-Liss, Inc.)
- Published
- 2010
- Full Text
- View/download PDF
146. Australian Rotavirus Surveillance Program annual report, 2008/2009.
- Author
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Kirkwood CD, Boniface K, Bishop RF, and Barnes GL
- Subjects
- Australia epidemiology, Child, Preschool, Genotype, Humans, Incidence, Infant, Infant, Newborn, Rotavirus Infections etiology, Rotavirus Infections genetics, Rotavirus Vaccines adverse effects, Population Surveillance, Rotavirus Infections epidemiology
- Abstract
The Australian Rotavirus Surveillance Program together with collaborating laboratories Australia-wide, conducts a laboratory based rotavirus surveillance program. This report describes the genotypes of rotavirus strains responsible for the hospitalisation of children with acute gastroenteritis during the period 1 July 2008 to 30 June 2009, the second year of surveillance following introduction of rotavirus vaccine into the National Immunisation Program. Five hundred and ninety-two faecal samples from across Australia were examined for G and P genotype using hemi-nested multiplex reverse transcription-polymerase chain reaction assays. Of the 445 confirmed as rotavirus positive, genotype G2P[4] was the dominant type nationally, representing 50.3%, followed by genotype G1P[8] (22.5%). Genotypes G3P[8], G4P[8] and G9P[8] each represented less than 5% of circulating strains nationally. Uncommon rotavirus genotype combinations, including G1P[4] (n = 6), G4P[4] (n = 2) and single strains of G1P[6] and G3P[6] were identified during this study period. The national dominance of G2P[4] was associated with a large outbreak of severe gastroenteritis in Alice Springs in early 2009. This is the first report to describe G2P[4] as the dominant genotype nationally. Whether vaccine pressure has resulted in emergence of this genotype is not yet known.
- Published
- 2009
147. Rotavirus strain surveillance--an Australian perspective of strains causing disease in hospitalised children from 1997 to 2007.
- Author
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Kirkwood CD, Boniface K, Bogdanovic-Sakran N, Masendycz P, Barnes GL, and Bishop RF
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- Age Distribution, Australia epidemiology, Child, Hospitalized statistics & numerical data, Child, Preschool, Diarrhea virology, Genotype, Humans, Infant, Molecular Epidemiology, Diarrhea epidemiology, Population Surveillance, Rotavirus genetics, Rotavirus Infections epidemiology
- Abstract
This study documents rotavirus strains causing severe disease in Australian children during the pre-vaccine era. During the period 1997-2007, rotavirus strains from national multi-centre hospital-based surveillance in Australia were analysed for G and P types. G1P[8] was the dominant genotype identified during the 11-year study, with intermittent peaks associated with genotypes G2P[4], G3P[8] and G9P[8]. The results provide baseline information of the G and P genotypes causing disease in Australian children, and highlight the unpredictable changes in genotype incidence that can occur on both a local and national level. To be optimally effective, rotavirus vaccines must prevent disease caused by all common rotavirus genotypes.
- Published
- 2009
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148. Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn's disease.
- Author
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Kirkwood CD, Wagner J, Boniface K, Vaughan J, Michalski WP, Catto-Smith AG, Cameron DJ, and Bishop RF
- Subjects
- Adolescent, Age of Onset, Base Sequence, Biopsy, Child, Child, Preschool, DNA, Bacterial genetics, DNA, Bacterial metabolism, Female, Humans, Leukocytes, Mononuclear microbiology, Male, Microbiological Techniques, Molecular Sequence Data, Mycobacterium avium subsp. paratuberculosis genetics, Paratuberculosis blood, Paratuberculosis pathology, Polymerase Chain Reaction, Crohn Disease complications, Crohn Disease microbiology, Intestinal Mucosa microbiology, Intestinal Mucosa pathology, Mycobacterium avium subsp. paratuberculosis isolation & purification, Paratuberculosis complications
- Abstract
Background: Mycobacterium avium subspecies paratuberculosis (MAP) is the most enduring infectious candidate that may be associated with inflammatory bowel disease (IBD). It is possible that the inconsistencies in the prevalence studies of MAP in adults reflect clinical differences in adult patients studied, including duration of disease and treatment regimens, and also in lack of specificity of some of the assays used. The aim was to determine the presence of MAP in children with symptoms of Crohn's disease (CD) and ulcerative colitis (UC), using gut biopsy tissue and peripheral blood mononuclear cells (PBMC) collected at initial endoscopic examination prior to clinical treatment., Methods: Mucosal biopsies and/or PBMC specimens were collected from a total of 142 children, comprising 62 with CD, 26 with UC, and 54 with non-IBD. MAP-specific IS900 polymerase chain reaction (PCR) analysis was performed on all biopsies and PBMC specimens. Conventional MAP culture technique was performed on a subset of 10 CD, 2 UC, and 4 non-IBD patients to isolate MAP., Results: MAP was identified by IS900 PCR significantly more often in mucosal biopsies from CD 39% (22/56) than from non-IBD 15% (6/39) patients (P < 0.05), and in PBMC from CD 16% (8/50) than from non-IBD 0% (0/31) patients (P < 0.05). Viable MAP were cultured from mucosal biopsies from 4/10 CD, 0/2 UC, and 0/4 non-IBD patients, but were not cultured from PBMC specimens., Conclusions: This unique study on the occurrence of MAP in gut tissue and blood from pediatric IBD patients suggests the possible involvement of MAP in the early stages of development of CD in children.
- Published
- 2009
- Full Text
- View/download PDF
149. Molecular characterization and epidemiology of rotavirus isolates obtained from children with diarrhoea in Malaysia.
- Author
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Zuridah H, Kirkwood CD, Bishop RF, Bogdanovic-Sakran N, and Yap KL
- Subjects
- Child, Female, Genotype, Humans, Malaysia epidemiology, Male, Molecular Epidemiology, Phylogeny, Polymerase Chain Reaction, Prevalence, RNA, Viral analysis, Retrospective Studies, Time Factors, Diarrhea epidemiology, Diarrhea genetics, Diarrhea virology, Rotavirus genetics, Rotavirus isolation & purification, Rotavirus Infections epidemiology, Rotavirus Infections genetics, Rotavirus Infections virology
- Abstract
This retrospective study examined the G/P type of rotavirus in RNA samples that have previously been e-typed by RNA-PAGE in 1996. The results were then compared to 2007 samples to ascertain the extent of changes that may have occurred in this 11-years time interval. The G and P genotypes were determined by hemi-nested PCR and further analysed by phylogenetic study. In 1996, the G/P combination G1P[8], G(UT)P[8] and G1P(UT) prevalence rate were 81%, 9% and 7%, respectively. As expected, the G9 genotype which has already emerged worldwide was identified in 42% of the 2007 samples with the remaining 33% G1P[8] and 25% G1P(UT) Analysis of the RNA pattern showed that majority of the isolates were long e-type in both series, nevertheless minor differences within electropherotypes were observed. Genetic diversity in some strains of the human group A rotaviruses was analysed by phylogenetic methods. These findings will help in the decision to introduce rotavirus vaccines within the next decade.
- Published
- 2009
150. Australian Rotavirus Surveillance Program annual report, 2007/08.
- Author
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Kirkwood CD, Cannan D, Boniface K, Bishop RF, and Barnes GL
- Subjects
- Age Distribution, Annual Reports as Topic, Australia epidemiology, Child, Preschool, Communicable Disease Control, Diarrhea, Infantile virology, Disease Notification, Female, Humans, Infant, Infant, Newborn, Male, National Health Programs, Population Surveillance, Prevalence, Rotavirus classification, Rotavirus Infections virology, Serotyping, Diarrhea, Infantile epidemiology, Rotavirus isolation & purification, Rotavirus Infections epidemiology
- Abstract
The National Rotavirus Reference Centre together with collaborating laboratories Australia-wide conducts a laboratory based rotavirus surveillance program. This report describes the types of rotavirus strains responsible for the hospitalisation of children with acute gastroenteritis during the period 1 July 2007 to 30 June 2008, the first complete year of surveillance following introduction of rotavirus into the National Immunisation Program. Six hundred faecal samples from across Australia were examined using a combined approach of monoclonal antibody immunoassays and reverse transcription-polymerase chain reaction. Of the 419 confirmed as rotavirus positive, serotype G1 was the dominant serotype nationally, representing 52% of specimens, followed by serotype G2 (19.8%), serotype G9 (12.2%), and serotype G3 (11%). No serotype G4 strains were identified. All G1, G3 and G9 strains assayed for P genotype contained the P[8] genotype, while all G2 strains contained the P[4] genotype, except one G2 strain which possessed a P[8]. Uncommon rotavirus genotypes, G8 (n = 2) and P[9] (n = 2) were identified during this study period. There was no evidence of unexpected changes in serotype distribution during the first 12 months of rotavirus vaccine use in the National Immunisation Program.
- Published
- 2008
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