The efficacy and safety of rotavirus vaccines in countries in Africa and Asia with high child mortality.

Rotavirus remains a leading cause of diarrhoeal morbidity and mortality in young children and rotavirus vaccines are critical for reducing global disease burden. This report addresses the performance of rotavirus vaccines in countries with high child mortality. We performed a sensitivity analysis as part of a systematic review on rotavirus vaccines to inform development of World Health Organization vaccine recommendations. The efficacy of four prequalified vaccines against severe rotavirus gastroenteritis was similar across high mortality settings in Asia and Africa. Within the first year following vaccination, vaccine efficacy for the four vaccines ranged from 48% to 57% while in the second year, efficacy ranged from 29% to 54%. The four vaccines showed no increase in intussusception risk in these settings. All four vaccines appear to prevent significant numbers of severe rotavirus gastroenteritis episodes with no measurable increase in intussusception risk in high mortality settings in Africa and Asia.

Understanding norovirus reporting patterns in England: a mixed model approach.

BACKGROUND: Norovirus has a higher level of under-reporting in England compared to other intestinal infectious agents such as Campylobacter or Salmonella, despite being recognised as the most common cause of gastroenteritis globally. In England, this under-reporting is a consequence of the frequently mild/self-limiting nature of the disease, combined with the passive surveillance system for infectious diseases reporting. We investigated heterogeneity in passive surveillance system in order to improve understanding of differences in reporting and laboratory testing practices of norovirus in England. METHODS: The reporting patterns of norovirus relating to age and geographical region of England were investigated using a multivariate negative binomial model. Multiple model formulations were compared, and the best performing model was determined by proper scoring rules based on one-week-ahead predictions. The reporting patterns are represented by epidemic and endemic random intercepts; values close to one and less than one imply a lower number of reports than expected in the given region and age-group. RESULTS: The best performing model highlighted atypically large and small amounts of reporting by comparison with the average in England. Endemic random intercept varied from the lowest in East Midlands in those in the under 5 year age-group (0.36, CI 0.18-0.72) to the highest in the same age group in South West (3.00, CI 1.68-5.35) and Yorkshire & the Humber (2.93, CI 1.74-4.94). Reporting by age groups showed the highest variability in young children. CONCLUSION: We identified substantial variability in reporting patterns of norovirus by age and by region of England. Our findings highlight the importance of considering uncertainty in the design of forecasting tools for norovirus, and to inform the development of more targeted risk management approaches for norovirus disease.

Direct and possible indirect effects of vaccination on rotavirus hospitalisations among children in Malawi four years after programmatic introduction.

INTRODUCTION: Despite increased use of vaccine in routine immunisation, rotavirus remains a major cause of acute gastroenteritis (AGE) in low-income countries. We describe rotavirus prevalence and hospitalisation in Malawi pre and four years post vaccine introduction; provide updated vaccine effectiveness (VE) estimates; and assess rotavirus vaccine indirect effects. METHODS: Children under five years of age presenting to a referral hospital in Blantyre with AGE were recruited. Stool samples were tested for rotavirus using Enzyme Immunoassay. The change in rotavirus prevalence was evaluated using Poisson regression. Time series analysis was used to further investigate trends in prevalence over time. VE against rotavirus diarrhoea of any severity was estimated using logistic regression. Indirect effects were estimated by evaluating rotavirus prevalence in unvaccinated children over time, and by comparing observed reductions in incidence of rotavirus hospitalisation to those expected based on vaccine coverage and trial efficacy estimates. RESULTS: 2320 children were included. Prevalence of rotavirus in hospitalised infants (<12 months) with AGE decreased from 69/139(49.64%) prior to vaccine introduction to 197/607(32.45%) post-vaccine introduction (adjusted RR 0.67[95% CI 0.55, 0.82]). Prevalence in children aged 12-23 months demonstrated a less substantial decline: 15/37(40.54%) pre- and 122/352(34.66%) post-vaccine introduction (adjusted RR 0.85, 95% CI 0.57, 1.28). Adjusted VE was 61.89%(95% CI 28.04-79.82), but lower in children aged 12-23 months (31.69% [95% CI -139.03 to 80.48]). In hospitalised infants with rotavirus disease, the observed overall effect of the vaccine was 9% greater than expected according to vaccine coverage and efficacy estimates. Rotavirus prevalence among unvaccinated infants declined post-vaccine introduction (RR 0.70[95% CI 0.55-0.80]). CONCLUSIONS: Following rotavirus vaccine introduction in Malawi, prevalence of rotavirus in hospitalised children with AGE has declined significantly, with some evidence of an indirect effect in infants. Despite this, rotavirus remains an important cause of severe diarrhoea in Malawian children, particularly in the second year of life.

Detection of rotavirus in paediatric oncology patients with diarrhoea: the impact of rotavirus vaccine.

Seven years' data were reviewed to examine stool-testing for rotavirus in patents treated in a regional paediatric oncology unit before and after the introduction of UK-wide rotavirus immunization in July 2013. The prevalence of rotavirus positivity has diminished since the introduction of rotavirus immunization, with 21 of 416 positive samples between 2010 and 2012, but only one positive test out of 122 samples in 2015 and 2016. Based on these results, there seems to be little use for routine rotavirus-testing in children and young people with cancer presenting with diarrhoea.

Clinical value of stool culture in paediatric oncology patients: hospital evaluation and UK survey of practice.

Diarrhoea is a frequently occurring symptom in paediatric oncology patients. The role of routine testing for enteric bacteria in hospitalized patients with diarrhoea is considered limited, but the diagnostic value of testing in children with oncological conditions has not been reported. Therefore, we conducted a five-year retrospective service evaluation in our tertiary paediatric oncology unit together with a national survey of 21 centres to estimate the utility of stool cultures in oncology patients with diarrhoea and the national approach to testing. Our local survey demonstrated very low diagnostic yield using routine enteric stool cultures with only one sample out of 842 (0.1%) testing positive. The national survey demonstrated considerable variation in practice. There is little evidence to support the use of conventional stool culture for enteric bacteria in children with cancer in our centre. These findings should inform national testing policies.

Whole-genome characterisation of G12P[6] rotavirus strains possessing two distinct genotype constellations co-circulating in Blantyre, Malawi, 2008.

Rotavirus A strains detected in diarrhoeal children commonly possess any one of the genotypes G1, G2, G3, G4, and G9, with a recent increase in G12 detection globally. G12P[6] strains possessing short RNA (DS-1-like) and long RNA (Wa-like) migration patterns accounted for 27 % of the strains circulating in Blantyre, Malawi, between 2007 and 2008. To understand how the G12P[6] strains with two distinct genetic backgrounds emerged in Malawi, we conducted whole-genome analysis of two long-RNA and two short-RNA strains. While the former had a typical Wa-like genotype constellation of G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, the latter was found to have G12-P[6]-I2-R2-C2-M1-A2-N2-T2-E2-H2: a VP3 gene mono-reassortant on the DS-1-like backbone. Phylogenetic and Bayesian Markov chain Monte Carlo analyses showed that the short-RNA G12P[6] strains were generated around 2006 by reassortment between an African Wa-like G12P[6] strain donating three genes (the VP7, VP4, and VP3 genes) and a G2P[4] strain similar to the one circulating in Thailand or the United States of America that donated the remaining eight genes. On the other hand, the long-RNA strains were generated as a result of reassortment events within Wa-like G12 and non-G12 strains commonly circulating in Africa; only the VP4 gene was from a Malawian G8P[6] strain. In conclusion, this study uncovered the evolutionary pathways through which two distinct G12P[6] strains emerged in Malawi.

A dynamic relationship between mucosal T helper type 17 and regulatory T-cell populations in nasopharynx evolves with age and associates with the clearance of pneumococcal carriage in humans.

Pneumococcal carriage is common in young children, which may account for the high incidence of disease in this age group. Host factors determining the clearance of carriage in humans remain unclear. We aimed to study the relationships between T helper type 17 (Th17) and Foxp3(+) regulatory T (Treg) cells in nasopharynx-associated lymphoid tissue (NALT) and carriage in children and adults. Frequencies of Th17 and Treg cells in NALT were analysed by flow cytometry in association with age and pneumococcal carriage status. Cytokine responses following pneumococcal stimulation were analysed by cytometric beads array. The frequencies of Th17 and Treg cells in NALT were inversely correlated (R -0.60). Whereas Treg cell frequency decreased with age (R -0.63), both Th17 and the Th17: Treg ratio increased with age (R 0.62 and R 0.64, respectively). Also, the Th17: Treg ratio was higher in carriage-negative than in carriage-positive children (p <0.01). Pneumococcal stimulation of tonsillar cells increased both Th17 and Treg cell numbers, but the Th17: Treg ratio and pattern of cytokine responses differed between carriage-negative and carriage-positive children. The former showed markedly higher Th17: Treg and interleukin-17A: interleukin-10 ratios than in the latter (p <0.01). Pneumococcal stimulation also induces Th17, although the capacity of this Th17 differentiation from naive T cells of young children was low, but increased with age. We demonstrated a dynamic relationship between Th17 and Treg cells in human nasopharynx that evolves with age. The balance between Th17 and Treg cells in NALT appears to be a major host factor closely associated with the clearance of Streptococcus pneumoniae from the nasopharynx.

Early impact of rotavirus vaccination in a large paediatric hospital in the UK.

The impact of routine rotavirus vaccination on community-acquired (CA) and healthcare-associated (HA) rotavirus gastroenteritis (RVGE) at a large paediatric hospital, UK, was investigated over a 13-year period. A total of 1644 hospitalized children aged 0-15 years tested positive for rotavirus between July 2002 and June 2015. Interrupted time-series analysis demonstrated that, post vaccine introduction (July 2013 to June 2015), CA- and HA-RVGE hospitalizations were 83% [95% confidence interval (CI): 72-90%) and 83% (95% CI: 66-92%] lower than expected, respectively. Rotavirus vaccination has rapidly reduced the hospital rotavirus disease burden among both CA- and HA-RVGE cases.

Methodological challenges in measuring vaccine effectiveness using population cohorts in low resource settings.

Post-licensure real world evaluation of vaccine implementation is important for establishing evidence of vaccine effectiveness (VE) and programme impact, including indirect effects. Large cohort studies offer an important epidemiological approach for evaluating VE, but have inherent methodological challenges. Since March 2012, we have conducted an open prospective cohort study in two sites in rural Malawi to evaluate the post-introduction effectiveness of 13-valent pneumococcal conjugate vaccine (PCV13) against all-cause post-neonatal infant mortality and monovalent rotavirus vaccine (RV1) against diarrhoea-related post-neonatal infant mortality. Our study sites cover a population of 500,000, with a baseline post-neonatal infant mortality of 25 per 1000 live births. We conducted a methodological review of cohort studies for vaccine effectiveness in a developing country setting, applied to our study context. Based on published literature, we outline key considerations when defining the denominator (study population), exposure (vaccination status) and outcome ascertainment (mortality and cause of death) of such studies. We assess various definitions in these three domains, in terms of their impact on power, effect size and potential biases and their direction, using our cohort study for illustration. Based on this iterative process, we discuss the pros and cons of our final per-protocol analysis plan. Since no single set of definitions or analytical approach accounts for all possible biases, we propose sensitivity analyses to interrogate our assumptions and methodological decisions. In the poorest regions of the world where routine vital birth and death surveillance are frequently unavailable and the burden of disease and death is greatest We conclude that provided the balance between definitions and their overall assumed impact on estimated VE are acknowledged, such large scale real-world cohort studies can provide crucial information to policymakers by providing robust and compelling evidence of total benefits of newly introduced vaccines on reducing child mortality.

Determination of a Viral Load Threshold To Distinguish Symptomatic versus Asymptomatic Rotavirus Infection in a High-Disease-Burden African Population.

We evaluated quantitative real-time PCR to establish the diagnosis of rotavirus gastroenteritis in a high-disease-burden population in Malawi using enzyme immunoassay as the gold standard diagnostic test. In 146 children with acute gastroenteritis and 65 asymptomatic children, we defined a cutoff point in the threshold cycle value (26.7) that predicts rotavirus-attributable gastroenteritis in this population. These data will inform the evaluation of direct and indirect rotavirus vaccine effects in Africa.

Molecular epidemiology of rotavirus in cats in the United Kingdom.

Rotaviruses are leading causes of gastroenteritis in the young of many species. Molecular epidemiological studies in children suggest that interspecies transmission contributes to rotavirus strain diversity in people. However, population-based studies of rotaviruses in animals are few. We investigated the prevalence, risk factors for infection, and genetic diversity of rotavirus A in a cross-sectional survey of cats housed within 25 rescue catteries across the United Kingdom. Morning litter tray fecal samples were collected during the winter and summer in 2012 from all pens containing kittens and a random sample of those housing adult cats. Group A rotavirus RNA was detected by real-time reverse transcription-PCR, and positive samples were G and P genotyped using nested VP4 and VP7 PCR assays. A total of 1,727 fecal samples were collected from 1,105 pens. Overall, the prevalence of rotavirus was 3.0% (95% confidence interval [CI], 1.2 to 4.9%). Thirteen out of 25 (52%; 95% CI, 31.3 to 72.2%) centers housed at least one rotavirus-positive cat. The prevalence of rotavirus was associated with season (odds ratio, 14.8 [95% CI, 1.1 to 200.4]; P = 0.04) but not age or diarrhea. It was higher during the summer (4.7%; 95% CI, 1.2 to 8.3%) than in winter (0.8%; 95% CI, 0.2 to 1.5%). Asymptomatic epidemics of infection were detected in two centers. G genotypes were characterized for 19 (33.3%) of the 57 rotavirus-positive samples and P genotypes for 36 (59.7%). Two rotavirus genotypes were identified, G3P[9] and G6P[9]. This is the first population-based study of rotavirus in cats and the first report of feline G6P[9], which questions the previous belief that G6P[9] in people is of bovine origin.

Emergence of carbapenem-resistant Enterobacteriaceae in a UK paediatric hospital.

BACKGROUND: Carbapenem-resistant Enterobacteriaceae are an emerging global infection threat. However, there are few data describing their clinical importance in children. AIM: This retrospective study reviewed the prevalence and resistance mechanisms of carbapenem-resistant Enterobacteriaceae grown from clinical and surveillance samples in a large tertiary referral children's hospital in the UK. METHODS: Carbapenem-resistant Enterobacteriaceae were sought in specimens submitted for diagnostic and surveillance purposes at Alder Hey Children's NHS Foundation Trust, Liverpool, between September 2011 and August 2012. Mechanisms of resistance were identified using phenotypic and/or molecular methods. Variable number tandem repeat profiling was used to type carbapenemase-producing strains. FINDINGS: During the 12-month study period, carbapenem-resistant Enterobacteriaceae were recovered from 24 patients. Five isolates were from clinical diagnostic specimens whereas 19 of 421 patients had positive rectal surveillance swabs (4.5%). Of the 24 isolates, seven (all Klebsiella spp.) harboured carbapenemases: three had blaKPC and four blaNDM, whereas 17 had resistance due to combinations of AmpC or extended-spectrum ß-lactamase activity plus impermeability. CONCLUSION: Carbapenem-resistant Enterobacteriaceae and, in particular, those with carbapenemases, are an emerging infection problem in a major paediatric hospital in the UK. Active surveillance is required to monitor and control their spread.

The occurrence of amino acid substitutions D96N and S242N in VP7 of emergent G2P[4] rotaviruses in Nepal in 2004-2005: a global and evolutionary perspective.

Rotavirus is the leading cause of severe diarrhea among children worldwide. Strains with G2P[4] have captured recent attention because of its abrupt increase or re-emergence in many locations in the world. In Nepal, G2P[4] strains were detected at a rate of 1% in 2003-2004, but increased to 33% in 2004-2005. Thus, the VP7 genes of 45 emergent G2 strains from Nepal were sequenced and analyzed together with a total of 339 G2VP7 sequences detected over the last 34 years that were compiled from the DNA database. We found that all Nepalese VP7 sequences had a substitution from aspartic acid to asparagine at residue 96 (D96N) that was the hallmark of the lineage termed sublineage IVa, which replaced virtually all globally circulating G2 strains during the last decade. Within sublineage IVa, further sublineages emerged, of which a sublineage termed IVa-3 was identified to have another amino acid substitution from serine to asparagine at 242 (S242N). This sublineage, to which all Nepalese sequences belonged, now became the most frequent G2 sequence globally. In conclusion, the G2VP7 gene evolved in a dynamic fashion such that new lineages emerged within the previously dominant lineage, one of which became subsequently dominant.

Molecular characterization of rotavirus strains circulating among children with acute gastroenteritis in Madagascar during 2004-2005.

A survey was undertaken of the etiology of acute gastroenteritis in children <16 years of age in Antananarivo, Madagascar, from May 2004 through May 2005. With use of electron microscopy of fecal specimens, 104 (36%) of 285 children were found to be infected with rotavirus. Rotavirus strain characterization was undertaken using enzyme-linked immunosorbent assay, electropherotyping, reverse-transcription polymerase chain reaction genotyping, and nucleotide sequencing. The predominant group A rotavirus strain types identified were P[4]G2 (62%) and P[8]G9 (23%). Nucleotide sequence analysis of the VP7 genes of selected Malagasy G2 and G9 strains demonstrated similarity with those of other recently identified African rotavirus strains belonging to the same genotype.

Detection of coronaviruses in children with acute gastroenteritis in Maddina, Saudi Arabia.

BACKGROUND: The role of coronaviruses in paediatric gastro-enteritis is not well defined. We investigated the detection rate and epidemiological features of infection with coronavirus in children receiving hospital care for acute gastro-enteritis in Maddina, Saudi Arabia. METHODS: Stool specimens were collected from children less than 5 years of age who were either hospitalised in Maddina or given oral rehydration therapy as outpatients between April 2004 and April 2005. Coronaviruses were detected by electron microscopy. RESULTS: Coronaviruses were detected in 63 (6%) of 984 children with acute gastro-enteritis and were more commonly detected in outpatients (47/423, 11%) than in inpatients (16/561, 3%). The median age (range) of children with coronavirus infection was 42 months (10-60). Coronaviruses were detected throughout the year with the highest detection rate at the end of the winter season. CONCLUSIONS: Coronaviruses were commonly identified in children with diarrhoea in Saudi Arabia. Their role in paediatric gastro-enteritis warrants further evaluation.

Norovirus infection among children with acute gastroenteritis in Recife, Brazil: disease severity is comparable to rotavirus gastroenteritis.

Norovirus has captured increasing attention as an agent of childhood diarrhoea. However, it is not known whether norovirus causes as severe diarrhoea as rotavirus, particularly among children in developing countries. In a 1-year study conducted between May 2004 and April 2005 in Recife, Brazil, norovirus was detected by ELISA in 34/233 (15%) diarrhoeal children less than 5 years of age. The severity of clinical illness, as indicated by the presence of dehydration, the requirement for hospitalization, and the duration of hospital stay, was similar between children with norovirus and rotavirus infection. These data underscore the importance of norovirus as a cause of severe diarrhoea in children.

Apparent extinction of non-G2 rotavirus strains from circulation in Recife, Brazil, after the introduction of rotavirus vaccine.

The introduction of a G1P[8] rotavirus vaccine in Recife, Brazil, caused a decrease in rotavirus detection from 27% (March-May, 2006) to 5.0% (March-May, 2007), with all strains becoming G2, against which less protection had been predicted.

Healthcare-associated rotavirus gastroenteritis in a large paediatric hospital in the UK.

Rotavirus is a major cause of acute, community-acquired gastroenteritis in infants and young children but its importance in healthcare-associated paediatric gastroenteritis is much less well understood. A prospective study was undertaken at the Royal Liverpool Children's NHS Trust, Liverpool, UK. We enrolled 243 children with acute gastroenteritis (AGE) who were hospitalised between January and May 2006. Rotavirus was detected in faecal specimens by enzyme immunoassay. This virus was responsible for 17/91 cases (19%) of healthcare-associated AGE and 54/152 cases (36%) of community-acquired AGE. Sixteen children with healthcare-associated acute rotavirus gastroenteritis required source isolation and eight received intravenous rehydration. We conclude that rotavirus is an important cause of healthcare-associated AGE in a large paediatric hospital. Rotavirus vaccines represent a public health tool that could prevent the majority of symptomatic rotavirus infections within this healthcare setting.

Epidemiology of rotavirus diarrhoea in Iranian children.

Human rotavirus is the most important cause of severe diarrhoea in infants and young children worldwide. We describe the aetiology of viral diarrhoea and the characteristics of rotavirus infection in Shahrekord, Iran. Two hundred and fifty nine children <5 years old admitted to Hajar Hospital, 245 children with acute diarrhoea attending primary health centres in Shahrekord, and 114 children hospitalised for elective surgery were selected from October 2001 to August 2002. Stool samples were screened for enteric viruses using EM. Rotaviruses were characterised using ELISA, reverse transcription-polymerase chain reaction (RT-PCR), and electropherotyping. One hundred and eighty six viruses were identified, of which 146 (78%) were rotavirus. The second most frequent virus was coronavirus, followed by calicivirus. Rotaviruses exhibited a marked seasonal variation, being most frequently isolated from November to February (50% of rotavirus recovered) and affected mostly children <2 years old. The RT-PCR successfully typed 139 of the 146 (95%) rotavirus G types and 124 (85%) P types. The most frequent P type was, P[8] in 108 (74%), P[4] in 16 (11%), and was P non-typeable in 22 (15%). Among the G types, G1 was identified in 120 (82%), G2 in 19 (13%), and was G-non-typeable in 7 (5%). Our results are the first report of rotavirus genotypes affecting Iranian children. The most frequent G and P types (G1, G2, P[8], and P[4]) are similar to those reported from around the world and will be covered by existing rotavirus vaccines targeting G types G1-G4.

Characterization of rotaviruses causing diarrhoea in Vietnamese children.

Faecal samples from 123 children admitted to the Centre for Tropical Diseases in Ho Chi Minh city, Vietnam, with acute watery diarrhoea were screened by negative-stain electron microscopy for viral enteropathogens. In addition to the 48 children who were found to be infected with rotavirus only, one had both rotavirus and astrovirus, two had adenovirus 40/41, and one had astrovirus only. The rotaviruses were subjected to molecular analysis by electropherotyping, G- and P-genotyping (by reverse-transcriptase PCR), and amplicon sequencing. By use of newly designed PCR primers, all 49 isolates could be G-genotyped and all but one P-genotyped. Novel variants of G1-G1*--were the most commonly detected G-genotype and such variants of P[8]-P[8*]--were the second commonest P-genotype. The P[8*] and G1* amplicons were, respectively, only 92%-93.4% and 88.1%-89% similar to the corresponding sequences from the prototype P[8] G1 rotavirus, Wa. Several unusual P- and G-genotype combinations were detected. Four (8%) of the children investigated were each found to be co-infected with two different rotaviruses. These data add to our knowledge of the continuing evolution and diversity of human rotaviruses, and should help in the rational design of vaccines.