Water-Based Epidemiological Investigation of Hepatitis E Virus in South Africa

Hepatitis E virus (HEV) is an emerging zoonotic pathogen that exhibits great host diversity. The primary means of transmission of the virus in low- and middle-income countries is contaminated water, often due to a lack of access to proper sanitation, which leads to faecal contamination of water sources. Environmental surveillance is an important tool that can be used to monitor virus circulation and as an early warning system for outbreaks. This study was conducted to determine the prevalence and genetic diversity of HEV in wastewater, surface water (rivers and standpipe/ablution water), and effluent from a piggery in South Africa. A total of 536 water samples were screened for HEV using real-time reverse transcription-polymerase chain reaction. Overall, 21.8% (117/536) of the wastewater, river, and ablution water samples tested positive for HEV, whereas 74.4% (29/39) of the samples from the piggery tested positive. Genotyping revealed sequences belonging to HEV genotypes 3 (98%, 53/54) and 4 (2%, 1/54), with subtypes 3c, 3f, and 4b being identified.

Quantification and Potential Viability of Human Noroviruses in Final Effluent from Wastewater Treatment Works in Pretoria, South Africa

Growing global concerns over water scarcity, worsened by climate change, drive wastewater reclamation efforts. Inadequately treated wastewater presents significant public health risks. Previous studies in South Africa (SA) have reported high norovirus levels in final effluent and sewage-polluted surface water, indicating pathogen removal inefficiency. However, the viability of these virions was not explored. This study assessed human norovirus viability in final effluent from wastewater treatment works (WWTWs) in Pretoria, SA. Between June 2018 and August 2020, 200 samples were collected from two WWTWs, including raw sewage and final effluent. Norovirus concentrations were determined using in-house RNA standards. Viability of noroviruses in final effluent was assessed using viability RT-qPCR (vPCR) with PMAxx™-Triton X-100. There was no significant difference in GI concentrations between raw sewage (p = 0.5663) and final effluent (p = 0.4035) samples at WWTW1 and WWTW2. WWTW1 had significantly higher GII concentrations in raw sewage (p < 0.001) compared to WWTW2. No clear seasonal pattern was observed in norovirus concentrations. At WWTW1, 50% (7/14) of GI- and 64.9% (24/37) of GII-positive final effluent samples had no quantifiable RNA after vPCR. At WWTW2, the majority (92.6%, 25/27) of GII-positive final effluent samples showed a 100% RNA reduction post vPCR. PMAxx™-Triton X-100 vPCR provides a more accurate reflection of discharge of potentially viable noroviruses in the environment than standard RT-qPCR. Despite significant reductions in potentially viable noroviruses after wastewater treatment, the levels of potentially viable viruses in final effluent are still of concern due to the high initial load and low infectious dose of noroviruses.

Norovirus Genetic Diversity in Children under Five Years Old with Acute Diarrhea in Mozambique (2014-2015)

Norovirus (NoV) is the second most important cause of viral diarrheal disease in children worldwide after rotavirus and is estimated to be responsible for 17% of acute diarrhea in low-income countries. This study aimed to identify and report NoV genotypes in Mozambican children under the age of five years with acute diarrhea. Between May 2014 and December 2015, stool specimens were collected within the Mozambique Diarrhea National Surveillance (ViNaDia) and tested for NoV genogroups I (GI) and II (GII) using conventional reverse transcriptase-polymerase chain reaction (RT-PCR). Partial capsid and RNA-dependent RNA polymerase (RdRp) nucleotide sequences were aligned using the Muscle tool, and phylogenetic analyses were performed using MEGA X. A total of 204 stool specimens were tested for NoV. The detection rate of NoV was 14.2% (29/204). The presence of NoV was confirmed, by real-time RT-PCR (RT-qPCR), in 24/29 (82.8%) specimens, and NoV GII predominated (70.8%; 17/24). NoV GII.4 Sydney 2012[P31] was the predominant genotype/P-type combination detected (30.4%; 7/23). This is the first study which highlights the high genetic diversity of NoV in Mozambican children and the need to establish a continuous NoV surveillance system.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Investigation of two suspected diarrhoeal-illness outbreaks in Northern Cape and KwaZulu-Natal provinces, South Africa, April-July 2013: The role of rotavirus

BACKGROUND

Suspected diarrhoeal-illness outbreaks affecting mostly children < 5 years were investigated between May and July 2013 in Northern Cape province (NCP) and KwaZulu-Natal (KZN) province. This study describes the epidemiological, environmental and clinical characteristics and diarrhoeal-illnesses causative agent(s).

METHODS

A descriptive cross-sectional study was conducted. Cases were patients presenting at healthcare facilities with diarrhoeal-illness between 09 April and 09 July 2013 in NCP and 01 May and 31 July 2013 in KZN. Laboratory investigations were performed on stools and water samples using microscopy, culture and sensitivity screening and molecular assays.

RESULTS

A total of 953 cases including six deaths (case fatality rate [CFR]: 0.6%) were recorded in the Northern Cape province outbreak. Children < 5 years accounted for 58% of cases. Enteric viruses were detected in 51% of stools, with rotavirus detected in 43%. The predominant rotavirus strains were G3P[8] (45%) and G9P[8] (42%). Other enteric viruses were detected, with rotavirus co-infections (63%). No enteric pathogens detected in water specimens. KwaZulu-Natal outbreak: A total of 1749 cases including 26 deaths (CFR: 1.5%) were recorded. Children < 5 years accounted for 95% of cases. Rotavirus was detected in 55% of stools; other enteric viruses were detected, mostly as rotavirus co-infections. The predominant rotavirus strains were G2P[4] (54%) and G9P[8] (38%).

CONCLUSION

Although source(s) of the outbreaks were not identified, the diarrhoeal-illnesses were community-acquired. It is difficult to attribute the outbreaks to one causative agent(s) because of rotavirus co-infections with other enteric pathogens. While rotavirus was predominant, the outbreaks coincided with the annual rotavirus season.

Feasibility of the Bag-Mediated Filtration System for Environmental Surveillance of Poliovirus in Kenya

The bag-mediated filtration system (BMFS) was developed to facilitate poliovirus (PV) environmental surveillance, a supplement to acute flaccid paralysis surveillance in PV eradication efforts. From April to September 2015, environmental samples were collected from four sites in Nairobi, Kenya, and processed using two collection/concentration methodologies: BMFS (> 3 L filtered) and grab sample (1 L collected; 0.5 L concentrated) with two-phase separation. BMFS and two-phase samples were analyzed for PV by the standard World Health Organization poliovirus isolation algorithm followed by intratypic differentiation. BMFS samples were also analyzed by a cell culture independent real-time reverse transcription polymerase chain reaction (rRT-PCR) and an alternative cell culture method (integrated cell culture-rRT-PCR with PLC/PRF/5, L20B, and BGM cell lines). Sabin polioviruses were detected in a majority of samples using BMFS (37/42) and two-phase separation (32/42). There was statistically more frequent detection of Sabin-like PV type 3 in samples concentrated with BMFS (22/42) than by two-phase separation (14/42, p = 0.035), possibly due to greater effective volume assayed (870 mL vs. 150 mL). Despite this effective volume assayed, there was no statistical difference in Sabin-like PV type 1 and Sabin-like PV type 2 detection between these methods (9/42 vs. 8/42, p = 0.80 and 27/42 vs. 32/42, p = 0.18, respectively). This study demonstrated that BMFS can be used for PV environmental surveillance and established a feasible study design for future research.

Molecular epidemiology of human bocavirus infection in hospitalized children with acute gastroenteritis in South Africa, 2009-2015

Human bocavirus (HBoV) is known to be associated with a variety of clinical manifestation including acute gastroenteritis (AGE). Despite their global prevalence, no data is available on the epidemiology of HBoV associated with AGE in South Africa (SA). Between April 2009 and April 2015, 3765 stool specimens were collected from children less than 5 years of age hospitalized with diarrhea. Specimens were screened for selected enteric viruses by enzyme immunoassay and quantitative polymerase chain reaction, bacteria by culture and parasites by staining and microscopy. HBoV was detected in 5.63% (212 of 3765) of cases, the majority of which were children ≤2 years (92%, 195 of 212), and were common in the summer and autumn months (60%; 128 of 212). Further investigations of coinfections showed that bacteria (adjusted odds ratio [aOR] = 2.20; 95% confidence interval [CI], 1.41-3.45; P = .001) and sapovirus (aOR = 2.05; 95% CI, 1.08-3.86; P = .027) were significantly associated with HBoV in multivariate analysis. HBoV genotyping was successful in 191 of the 212 samples with HBoV-1 being the most prevalent genotype observed (79.6%; 152 of 191) followed by HBoV-3 (13.6%; 26 of 191), HBoV-2 (5.2%; 10 of 191), and HBoV-4 (1.6%; 3 of 191). The high prevalence of HBoV-1, a virus known to be associated with respiratory infections, and the association between HBoV-positive specimens and already established AGE agents, suggests that HBoV may play a limited role in the observed AGE cases in SA.

Detection of potentially pathogenic enteric viruses in environmental samples from Kenya using the bag-mediated filtration system

Enteric virus environmental surveillance via a highly sensitive method is critical, as many enteric viruses have low infectious doses and can persist in the environment for extended periods. This study determined the potential of the novel bag-mediated filtration system (BMFS) to recover human enteric viruses and pepper mild mottle virus (PMMoV) from wastewater and wastewater-impacted surface waters, examined PMMoV use as a fecal contamination indicator in Kenya, and identified potential BMFS process controls. From April 2015 to April 2016, BMFS samples were collected from seven sites in Kenya (n = 59). Enteroviruses and PMMoV were detected in 100% of samples, and human adenovirus, human astrovirus, hepatitis A virus, norovirus GI, norovirus GII, sapovirus, and human rotavirus were detected in the majority of samples. The consistent detection of enteroviruses and PMMoV suggests that these viruses could be used as indicators in similarly fecally contaminated sites and BMFS process controls. As contamination of surface water sources remains a global issue, enteric virus environmental surveillance is necessary. This study demonstrates an effective way to sample large volumes of wastewater and wastewater-impacted surface waters for the detection of multiple enteric viruses simultaneously.

Epidemiology of human astroviruses among children younger than 5 years: Prospective hospital-based sentinel surveillance in South Africa, 2009-2014

BACKGROUND

The epidemiology of human astroviruses (HAstVs) in hospitalised patients less than 5 years of age from selected sites in South Africa was investigated. Diarrheagenic stool specimens collected from April 2009 to May 2014 were screened retrospectively for selected viruses, bacteria and parasites.

METHOD

Patient data were analysed to identify epidemiologic factors most frequently detected with HAstV infections. The following case-comparisons were investigated; HAstV-positive and HAstV-negative children, human immunodeficiency virus (HIV)-infected and HIV-uninfected (HAstV-positive) children and HIV-exposed and unexposed (HAstV-positive HIV-uninfected) children.

RESULTS

Astrovirus was identified in 7.0% (234/3340) of cases and most frequently in ages 7 to 12 months (9.2%; 90/975) compared with 5.8% to 6.6% in other 6-month age groups. No seasonal trends were observed. More HAstVs were detected in children from homes that used outdoor water sources (7.6%) compared to indoor sources [5.7%; adjusted odds ratio (aOR), 1.5; 95% CI, 1.1-2.1; P = 0.009]. Astroviruses were detected in 8.4% (67/799) of HIV-uninfected patients that were exposed to HIV compared with 5.9% (74/1257) of HIV-unexposed patients ( P = 0.032).

CONCLUSION

Astroviruses were most prevalent in children aged 7 to 12 months and were detected throughout the study period. The study was limited as only hospitalised patients were investigated and no comparisons were made to diarrhoea-free control groups. Future HAstV surveillance should include community-based studies and children presenting at outpatient facilities.

Composition of gut microbiota and its influence on the immunogenicity of oral rotavirus vaccines

The introduction of oral rotavirus vaccines (ORVVs) has led to a reduction in number of hospitalisations and deaths due to rotavirus (RV) infection. However, the efficacy of the vaccines has been varied with low-income countries showing significantly lower efficacy as compared to high-income countries. The reasons for the disparity are not fully understood but are thought to be multi-factorial. In this review article, we discuss the concept that the disparity in the efficacy of oral rotavirus vaccines between the higher and lower socio-economical countries could be due the nature of the bacteria that colonises and establishes in the gut early in life. We further discuss recent studies that has demonstrated significant correlations between the composition of the gut bacteria and the immunogenicity of oral vaccines, and their implications in the development of novel oral RV vaccines or redesigning the current ones for maximum impact.

Environmental Surveillance for Noroviruses in Selected South African Wastewaters 2015-2016: Emergence of the Novel GII.17

Norovirus (NoV) GII.4 is the predominant genotype associated with gastroenteritis pandemics and new strains emerge every 2-3 years. Between 2008 and 2011, environmental studies in South Africa (SA) reported NoVs in 63% of the sewage-polluted river water samples. The aim of this study was to assess whether wastewater samples could be used for routine surveillance of NoVs, including GII.4 variants. From April 2015 to March 2016, raw sewage and effluent water samples were collected monthly from five wastewater treatment plants in SA. A total of 108 samples were screened for NoV GI and GII using real-time RT-qPCR. Overall 72.2% (78/108) of samples tested positive for NoVs with 4.6% (5/108) GI, 31.5% (34/108) GII and 36.1% (39/108) GI + GII strains being detected. Norovirus concentrations ranged from 1.02 × 10² to 3.41 × 10⁶ genome copies/litre for GI and 5.00 × 10³ to 1.31 × 10⁶ genome copies/litre for GII. Sixteen NoV genotypes (GI.2, GI.3, GI.4, GI.5, GI.6, GII.2, GII.3, GII.4, GII.7, GII.9, GII.10, GII.14, GII.16, GII.17, GII.20, and GII.21) were identified. Norovirus GII.2 and GII.17 co-dominated and the majority of GII.17 strains clustered with the novel Kawasaki 2014 variant. Sewage surveillance facilitated detection of Kawasaki 2014 in SA, which to date has not been detected with surveillance in children with gastroenteritis <5 years of age. Combined surveillance in the clinical setting and environment appears to be a valuable strategy to monitor emergence of NoV strains in countries that lack NoV outbreak surveillance.

Quantitative microbial risk assessment to estimate the health risk from exposure to noroviruses in polluted surface water in South Africa

This study assessed the risks posed by noroviruses (NoVs) in surface water used for drinking, domestic, and recreational purposes in South Africa (SA), using a quantitative microbial risk assessment (QMRA) methodology that took a probabilistic approach coupling an exposure assessment with four dose-response models to account for uncertainty. Water samples from three rivers were found to be contaminated with NoV GI (80-1,900 gc/L) and GII (420-9,760 gc/L) leading to risk estimates that were lower for GI than GII. The volume of water consumed and the probabilities of infection were lower for domestic (2.91 × 10^-8 to 5.19 × 10^-1) than drinking water exposures (1.04 × 10^-5 to 7.24 × 10^-1). The annual probabilities of illness varied depending on the type of recreational water exposure with boating (3.91 × 10^-6 to 5.43 × 10^-1) and swimming (6.20 × 10^-6 to 6.42 × 10^-1) being slightly greater than playing next to/in the river (5.30 × 10^-7 to 5.48 × 10^-1). The QMRA was sensitive to the choice of dose-response model. The risk of NoV infection or illness from contaminated surface water is extremely high in SA, especially for lower socioeconomic individuals, but is similar to reported risks from limited international studies.

Norovirus Epidemiology in Africa: A Review

Norovirus (NoV) is recognised as a leading cause of gastroenteritis worldwide across all age groups. The prevalence and diversity of NoVs in many African countries is still unknown, although early sero-prevalence studies indicated widespread early infection. Reports on NoVs in Africa vary widely in terms of study duration, population groups and size, inclusion of asymptomatic controls, as well as genotyping information. This review provides an estimate of NoV prevalence and distribution of genotypes of NoVs in Africa. Inclusion criteria for the review were study duration of at least 6 months, population size of >50 and diagnosis by RT-PCR. As regions used for genotyping varied, or genotyping was not always performed, this was not considered as an inclusion criteria. A literature search containing the terms norovirus+Africa yielded 74 publications. Of these 19 studies from 14 out of the 54 countries in Africa met the inclusion criteria. Data from studies not meeting the inclusion criteria, based on sample size or short duration, were included as discussion points. The majority of studies published focused on children, under five years of age, hospitalised with acute gastroenteritis. The mean overall prevalence was 13.5% (range 0.8–25.5%) in children with gastroenteritis and 9.7% (range 7–31%) in asymptomatic controls, where tested. NoV GII.4 was the predominant genotype identified in most of the studies that presented genotyping data. Other prevalent genotypes detected included GII.3 and GII.6. In conclusion, NoV is a common pathogen in children with diarrhoea in Africa, with considerable carriage in asymptomatic children. There is however, a paucity of data on NoV infection in adults.

Molecular detection and characterisation of mumps virus in cerebrospinal fluid in a Gauteng laboratory

The study aimed to determine the presence of mumps virus (MuV) in cerebrospinal fluid (CSF) specimens and to genetically characterise detected MuV strains. A real-time reverse transcription-polymerase chain reaction (RT-PCR) was used to detect the MuV F gene, and characterisation was performed by sequencing of the SH gene. Mumps virus was detected in 1.2% (3/260) of specimens. Phylogenetic analysis of one MuV strain revealed that it clustered with the Jeryl-Lynn and RIT4385 vaccine strains. As far as the authors could ascertain this is the first study to provide viral proof that these vaccine-like strains may be associated with aseptic meningitis.

Sapovirus prevalence in children less than five years of age hospitalised for diarrhoeal disease in South Africa, 2009-2013

BACKGROUND

Although sapovirus (SaV) has been detected in 2.2-12.7% of gastroenteritis cases globally, there are limited data on SaV epidemiology.

OBJECTIVES

Describe the epidemiology, clinical characteristics and factors associated with SaV gastroenteritis in hospitalised children <5 years of age in South Africa.

STUDY DESIGN

Between 2009 and 2013 during prospective diarrhoeal surveillance, stool specimens were collected from four sites and screened for SaVs and associated enteric pathogens using ELISA, microscopy, conventional and real-time PCR. Epidemiological and clinical data were compared in patients with or without SaV. Odds ratios were assessed by bivariate and stepwise multivariable logistic regression analysis.

RESULTS

Sapoviruses were detected in 7.7% (238/3103) of children admitted to hospital and 11.4% (9/79) of deaths. Sapovirus was detected more commonly in children 19-24 months compared to<6months (aOR=2.3; p=0.018) and in males (aOR=2.0; p=0.001). Additional factors associated with SaV detection included residing with≥7 inhabitants compared to ≤3 (aOR=2.2; p=0.011) and concomitant norovirus infections (aOR=3.0; p=0.003). HIV-infected children with SaV were more likely to have bloody stools (aOR=16.8; p<0.001), low birth weight (<2.5kg; aOR=5.8; p=0.007) and live in environments without flush toilets (aOR=8.1; p=0.003) compared to HIV-uninfected children.

CONCLUSIONS

Sapoviruses, which are perceived to cause mild diarrhoea, were detected in hospitalised children and diarrhoeal deaths in South Africa. Determinants increasing the odds of SaV included overcrowding and concomitant infections while HIV-infected children with SaV displayed bloody stools, low birth weight and reduced access to proper sanitation. Mitigation strategies against SaV infections include improved sanitation.

Diverse sapovirus genotypes identified in children hospitalised with gastroenteritis in selected regions of South Africa

BACKGROUND

Sapoviruses (SaVs) are recognised as causative agents of gastroenteritis worldwide. However, data on the genetic diversity of this virus in Africa are lacking, particularly in the form of current long-term studies.

OBJECTIVE

To determine the genetic diversity of SaVs in children hospitalised with gastroenteritis in South Africa (SA).

STUDY DESIGN

From April 2009 to December 2013, SaVs were characterised from stool specimens from children hospitalised with gastroenteritis in four provinces of SA.

RESULTS

Fourteen different SaV genotypes were identified from the 221 strains that were characterised. Genogroup (G) IV predominated overall and was detected in 24% (53/221) of specimens. The other identified genotypes included six belonging to GI (GI.1-GI.3, GI.5, GI.6, and GI.7) and seven belonging to GII (GII.1-GII.7).

CONCLUSION

This study has provided the first comprehensive data on the genetic diversity of SaVs in a clinical setting in SA, contributing to the global knowledge of this virus.

Quantification and molecular characterisation of human sapoviruses in water sources impacted by highly polluted discharged wastewater in South Africa

Sapoviruses (SaVs) were detected and quantified in 8/10 water samples collected from wastewater treatment works (WWTWs) and water sources impacted by these WWTWs in Limpopo Province, South Africa. The median SaV concentration was 2.45 × 10⁶ copies/L and SaV genotypes I.2 and IV were characterised. This study provides new data on the high concentrations of clinically relevant SaVs in rivers and dams impacted by poor-performing WWTWs.

Genetic characterization of a novel hepatitis a virus strain in irrigation water in South Africa

Hepatitis A virus (HAV) was detected, by real-time reverse transcription-polymerase chain reaction, in irrigation water from a dam on a commercial fresh produce farm in South Africa (SA). The virus was characterized by nucleotide sequence and phylogenetic analysis of a consensus sequence spanning the VP1 and VP1/P2B genomic regions. Amino acid sequence and phylogenetic analysis indicated that the HAV strain was closely related to HAV genotype V and possibly of simian origin. This suggests that a novel HAV may be circulating in SA and its presence in irrigation water highlights the potential for zoonotic or anthroponotic cross-species transmission via environmental food and water sources.

Norovirus GII.17 Predominates in Selected Surface Water Sources in Kenya

In this study, the prevalence and genotypes of noroviruses (NoVs) in selected water sources from rural, urban and refugee settings in Kenya were investigated. Ten litres each of river, household and borehole water was collected in rural (Mboone River), urban (Nairobi and Mutoine River) and refugee (Dadaab refugee camp) settings. NoVs were recovered from the water samples by a glass wool adsorption-elution technique and/or PEG/NaCl precipitation. Nucleic acid was extracted using the automated MagNA Pure platform. NoVs were detected with singleplex real-time reverse transcription-polymerase chain reaction assays and characterised by nucleotide sequence analysis. NoVs were detected in 63% (25/40) of the selected water samples comprising GII (42.5%), GI (2.5%) and mixed GI/GII (17.5%) positive samples. The prevalence of NoVs in the Mutoine River (urban area) was higher than in the Mboone River (rural area) (P = 0.0013). Noroviruses GI.1, GI.3, GI.9, GII.4, GII.6, GII.12, GII.16 and GII.17 were identified, with GII.17 accounting for 76% (16/21) of the typed strains. The NoV GII.17 predominance differs to other studies in Africa and further surveillance of NoVs in clinical and environmental settings is required to clarify/elucidate this observation. As information regarding NoVs in Kenyan water sources is limited this report provides valuable new data on NoV genotypes circulating in environmental water sources and the surrounding communities in Kenya.

Novel norovirus recombinants detected in South Africa

Background

Noroviruses (NoV) are the leading cause of viral gastroenteritis worldwide. Recombination frequently occurs within and between NoV genotypes and recombinants have been implicated in sporadic cases, outbreaks and pandemics of NoV. There is a lack of data on NoV recombinants in Africa and therefore their presence and diversity was investigated in South Africa (SA).

Results

Between 2010 and 2013, eleven types of NoV recombinants were identified in SA. Amplification of the polymerase/capsid region spanning the ORF1/2 junction and phylogenetic analysis confirmed each of the recombinant types. SimPlot and maximum x² analysis indicated that all recombinants had a breakpoint in the region of the ORF1/2 junction (P < 0.05). The majority (9/11) were intergenotype recombinants, but two intragenotype GII.4 recombinants were characterised. Three combinations represent novel recombinants namely GII.P not assigned (NA)/GII.3, GII.P4 New Orleans 2009/GII.4 NA and GII.P16/GII.17. Several widely reported recombinants were identified and included GII.P21/GII.2, GII.P21/GII.3, GII.Pe/GII.4 Sydney 2012, and GII.Pg/GII.12. Other recombinants that were identified were GII.Pg/GII.1, GII.Pe/GII.4 Osaka 2007, GII.P4 New Orleans 2009/GII.4 Sydney 2012, GII.P7/GII.6. To date these recombinant types all have a reportedly restricted geographic distribution. This is the first report of the GII.P4 New Orleans 2009/GII.4 Sydney 2012 recombinant in Africa.

Conclusions

Over the past four years, remarkably diverse NoV recombinants have been circulating in SA. Pandemic strains such as the GII.Pe/GII.4 Sydney 2012 recombinant co-circulated with novel and emerging recombinant strains. Combined polymerase- and capsid-based NoV genotyping is essential to determine the true diversity and global prevalence of these viruses.

Molecular characterisation of hepatitis A virus strains from water sources in South Africa

Hepatitis A virus (HAV) strains found in selected South African (SA) surface waters were characterised to establish what HAV types are circulating in the environment, thus reflecting circulation in the surrounding communities. Surface water samples used for irrigation or domestic purposes, and water samples from the outflow of wastewater plants were collected from six provinces. Viruses were recovered from the samples using a glass wool adsorption-elution method and then further concentrated using polyethylene glycol/sodium chloride precipitation. After automated nucleic acid extraction, samples were analysed for HAV by real-time reverse-transcriptase polymerase chain reaction. HAV strains were genotyped by nucleotide sequence analysis of the capsid gene VP1 and the VP1/P2B junction. HAVs were detected in 76% (16/21) of the surface water samples and in 37% (19/51) of the samples from the wastewater plants. Strains were characterised from 32 of the 35 samples and classified within genotype IB. The presence of genotype IB in the water sources confirms human faecal contamination. Hence, these faecally-contaminated water sources may be a potential transmission route of HAV infection and a potential source of contamination of irrigated fresh produce in SA.

Human caliciviruses detected in HIV-seropositive children in Kenya

The human caliciviruses (HuCVs) are important causes of gastroenteritis worldwide. Norovirus (NoV) and sapovirus (SaV) have been detected in HIV-seropositive children but the genetic diversity of HuCVs circulating in these individuals is largely unknown. In this study the prevalence and genotype diversity of HuCVs circulating in Kenyan HIV-positive children, with or without diarrhea, from the year 1999 to 2000 was investigated. The overall prevalence of HuCVs was 19% with NoV predominating at 17% (18/105) and SaV present in 5.7% (6/105) of specimens. Human CVs were detected in both symptomatic (24%) and asymptomatic (16%) children. Co-infections with other enteric viruses were detected in 21.6% of children with diarrhea but only in 4.4% of children without diarrhea. Remarkable genetic diversity was observed with 12 genotypes (7 NoV, 5 SaV) being identified in 20 HuCV-infected children. NoV genogroup II (GII) strains predominated with GII.2 and GII.4 each representing 27% of the NoV-positive strains. The GII.4 strain was most closely related to the nonepidemic GII.4 Kaiso 2003 variant. Other NoV genotypes detected were GI.3, GII.6, GII.12, GII.14, and GII.17. Five different SaV genotypes (GI.2, GI.6, GII.1, GII.2, and GII.4) were characterized from six specimens. Diarrheal symptoms were not associated with any specific HuCV genotype. Overall the HuCV genotype distribution detected in this study reflects those in other studies worldwide. The strains detected are closely related to genotypes that have circulated on several continents since the year 2000.

Commissioning dose computation models for spot scanning proton beams in water for a commercially available treatment planning system

PURPOSE

To present our method and experience in commissioning dose models in water for spot scanning proton therapy in a commercial treatment planning system (TPS).

METHODS

The input data required by the TPS included in-air transverse profiles and integral depth doses (IDDs). All input data were obtained from Monte Carlo (MC) simulations that had been validated by measurements. MC-generated IDDs were converted to units of Gy mm(2)/MU using the measured IDDs at a depth of 2 cm employing the largest commercially available parallel-plate ionization chamber. The sensitive area of the chamber was insufficient to fully encompass the entire lateral dose deposited at depth by a pencil beam (spot). To correct for the detector size, correction factors as a function of proton energy were defined and determined using MC. The fluence of individual spots was initially modeled as a single Gaussian (SG) function and later as a double Gaussian (DG) function. The DG fluence model was introduced to account for the spot fluence due to contributions of large angle scattering from the devices within the scanning nozzle, especially from the spot profile monitor. To validate the DG fluence model, we compared calculations and measurements, including doses at the center of spread out Bragg peaks (SOBPs) as a function of nominal field size, range, and SOBP width, lateral dose profiles, and depth doses for different widths of SOBP. Dose models were validated extensively with patient treatment field-specific measurements.

RESULTS

We demonstrated that the DG fluence model is necessary for predicting the field size dependence of dose distributions. With this model, the calculated doses at the center of SOBPs as a function of nominal field size, range, and SOBP width, lateral dose profiles and depth doses for rectangular target volumes agreed well with respective measured values. With the DG fluence model for our scanning proton beam line, we successfully treated more than 500 patients from March 2010 through June 2012 with acceptable agreement between TPS calculated and measured dose distributions. However, the current dose model still has limitations in predicting field size dependence of doses at some intermediate depths of proton beams with high energies.

CONCLUSIONS

We have commissioned a DG fluence model for clinical use. It is demonstrated that the DG fluence model is significantly more accurate than the SG fluence model. However, some deficiencies in modeling the low-dose envelope in the current dose algorithm still exist. Further improvements to the current dose algorithm are needed. The method presented here should be useful for commissioning pencil beam dose algorithms in new versions of TPS in the future.

Patterns of recurrence of gastrointestinal stromal tumour (GIST) following complete resection: implications for follow-up

AIM

To determine the frequency, time course and sites of recurrence following surgical resection of gastrointestinal stromal tumours (GIST) and to evaluate the performance of a risk-based surveillance protocol in detection of recurrence.

METHODS

Eighty-one patients on surveillance following complete resection of GIST were included. Patients were stratified into risk groups according to accepted histopathological criteria. Computed tomography (CT) examinations were retrospectively reviewed to determine rates, sites and imaging characteristics of recurrence and to assess compliance with the local follow-up protocol.

RESULTS

The median time of follow-up was 41 months. Nineteen patients suffered recurrence, all of whom were in the high-risk group. Fifty-eight percent of relapses occurred within 1 year and 84% within 3 years. Even within the high-risk group, patients with relapse had significantly larger (mean 15 versus 10.4 cm, p < 0.05) and more mitotically active primary tumours (mean 33.7 versus 5.6 mitoses per 50 high-power fields; p < 0.05) than those with no relapse. Relapse was to the liver in 12 cases (63%) and to the omentum and mesentery in nine cases (47%), and was asymptomatic in three-quarters of patients.

CONCLUSIONS

The high incidence of GIST recurrence in the high-risk group in the first 3 years after surgery supports the use of intensive imaging surveillance in this period. Relapse is often asymptomatic and commonly occurs to the liver, omentum and mesentery. Stratification by tumour factors may enable improved tailoring of surveillance protocols within the high-risk group in the future.

Human calicivirus diversity in wastewater in South Africa

AIM

To investigate the diversity of human caliciviruses (HuCVs) in wastewater from small- to medium-sized communities in five provinces of South Africa (SA).

METHODS AND RESULTS

Wastewater samples (51) were screened for norovirus (NoV) GI, GII, GIV and sapovirus (SaV) using real-time reverse transcription (RT)-PCR. Partial capsid nucleotide sequences were analysed for genotyping. At least one HuCV was detected in 42 samples (82%) with NoV GI being detected in 15 (29%), NoV GII in 32 (63%) and SaV in 37 (73%) samples. NoV GIV was not detected. Five NoV GI genotypes (GI.1, GI.3, GI.4, GI.8 and GI.unassigned), eight NoV GII genotypes (GII.2, GII.3, GII.4, GII.6, GII.7, GII.12, GII.13 and GII.17) and six SaV genotypes (GI.2, GI.3, GI.6, GI.7, GII.1 and GII.2) were characterized.

CONCLUSIONS

Many NoV and SaV genotypes were detected in wastewater, demonstrating a high genetic diversity of HuCVs in the surrounding communities. Caliciviruses were characterized from several provinces in SA, indicating widespread occurrence in the country.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides valuable new data on CVs circulating in SA, including the first data on SaV strains from wastewater in Africa. Environmental surveillance is especially important in countries like SA where outbreak reporting systems or routine HuCV surveillance is lacking.

Application of a competitive internal amplification control for the detection of sapoviruses in wastewater

In this study, a competitive internal amplification control (IAC) was constructed for application in the real-time reverse transcription-polymerase chain reaction detection of sapoviruses (SaVs). A SaV RNA standard was also created for quantification of the virus. The IAC was included in the screening of environmental samples for SaVs. From August 2010 to December 2011, 51 wastewater samples were collected from five provinces in South Africa. SaVs were found in 72.5 % (37/51) of samples, including four samples where detection was initially inhibited. SaV concentrations ranged from 4.24 × 10(3) to 1.31 × 10(6) copies/ml. The IAC successfully identified samples which contained inhibitors and inclusion of an IAC is necessary to ensure the prevalence of SaVs is accurately determined. SaVs are present at high concentrations in wastewater in several provinces of South Africa. This widespread occurrence indicates that SaV circulation in the South African population may be underestimated.

First detection of human sapoviruses in river water in South Africa

Over a 2-year period, from January 2009 to December 2010, water samples were collected from three rivers (Klip, Rietspruit and Suikerbosrand) in the Vaal River System, South Africa. Enteric viruses were recovered by a glass wool adsorption-elution method and concentrated using polyethylene glycol/sodium chloride precipitation. Sapoviruses (SaVs) were detected using published sapovirus (SaV)-specific primers and Taqman probes in a two-step real-time reverse transcription-polymerase chain reaction assay. Based on sequence analysis of the 5'-end of the capsid gene, SaVs were genotyped. In 2009, SaVs were detected in 39% (15/38) of samples from the Klip river, 83% (5/6) from the Rietspruit and 14% (1/7) of samples from the Suikerbosrand river. In 2010, SaVs were detected in 54% (14/26) of Klip river samples, 92% (11/12) from the Rietspruit and 20% (2/10) of samples from the Suikerbosrand river. SaV strains identified in the water samples were characterised into several GI and GII genotypes. The presence of SaVs in these rivers indicates human faecal contamination which may pose a potential health risk to persons exposed to these water sources during domestic or recreational activities.

A prospective study of bacterial flora in nasal cavity of patients with persistent allergic rhinitis

It remains unanswered whether persistent allergic inflammation in nasal mucosa alters bacterial colonization and infection. The aim of this study was to investigate the bacterial flora in the nasal cavity of patients with persistent allergic rhinitis (PAR) and to correlate the bacteriological findings with presence of nasal symptoms, nasal eosinophil and neutrophil counts. A total of 255 subjects, aged between 6 - 74 years (mean 33.9 years) was randomly selected from a population-based rhinitis survey study in Singapore. All subjects went through a thorough medical history and nasal examinations. Serum specific IgE to a panel of common house dust mites, nasal cytological and microbiological examinations were performed. PAR was diagnosed in 107 patients and none of them had received previous regular therapy. There is a significant relationship between PAR and eosinophil grades, but not with neutrophil count. No statistically significant difference was found in quantitative and qualitative bacterial flora in nasal cavity between PAR patients and subjects with non-rhinitis or with non-allergic rhinitis. There is a significant inverse correlation between ongoing rhinorrhoea and quantitative bacterial load, and between signs of nasal mucosa (pale and edema) and the presence and type of bacterial pathogens. In conclusion, our study demonstrates that patients with untreated (or using PRN medicine) PAR do not result in a significant change in bacterial flora in their nasal cavity.

Carcinoma of unknown primary: key radiological issues from the recent National Institute for Health and Clinical Excellence guidelines

Carcinoma of unknown primary origin (CUP) accounts for 3-5% of cancer cases and is the fourth most common cause of cancer death in the UK. CUP management is challenging, partly owing to the heterogeneity of the condition and its presentation, but also owing to the lack of dedicated clinical services for these patients. The recent National Institute for Health and Clinical Excellence (NICE) guidelines on metastatic malignancy of unknown primary origin were developed to improve the co-ordination of diagnostic and clinical services at hospitals treating cancer patients in England and Wales, in particular by the setting up of CUP teams to manage these patients. Radiologists have a vital role in the diagnosis of these patients and should work closely with the CUP team to streamline the diagnostic pathway. This article summarises areas of the NICE guidelines relevant to radiology and discusses the radiological management of patients with CUP, including initial investigation, the importance of biopsy, the management of specific presentations, special investigations and organisational issues.

Is dual-phase abdominal CT necessary for the optimal detection of metastases from renal cell carcinoma?

AIM

To determine whether dual-phase abdominal computed tomography (CT) detected more metastases than portal-phase CT alone in patients with renal cell carcinoma (RCC).

MATERIALS AND METHODS

Audit committee approval was obtained. A retrospective audit was undertaken in 100 patients who underwent both arterial and portal phase CT. The CT images were independently reviewed by two consultant radiologists. The presence of metastases in the liver, pancreas, and contralateral kidney were recorded for each phase of contrast enhancement.

RESULTS

Metastases were identified in the liver in 27 patients, pancreas in 12, and contralateral kidney in 23 patients. Nine of the 27 (33%) liver metastases, three of the 12 (25%) pancreatic metastases, and two of the 23 (9%) renal metastases were only detected in the arterial phase, whilst four of the 27 (15%) liver metastases, three of the 12 (25%) pancreatic metastases, and two of the 23 (9%) renal metastases were only detected in the portal phase. Nine patients (9%) had metastases only visualized in the arterial phase, and six (6%) only in the portal phase. Detection of metastases only visible in the arterial phase led to a change of management in two patients (2%).

CONCLUSION

The audit results support our current standard of dual-phase abdominal CT for optimal detection of RCC metastases.

The detection of enteric viruses in selected urban and rural river water and sewage in Kenya, with special reference to rotaviruses

AIM

To determine the occurrence of eight human enteric viruses in surface water and sewage samples from different geographical areas in Kenya.

METHODS AND RESULTS

Enteric viruses were recovered from the water and sewage sources by glass-wool adsorption elution and/or polyethylene glycol/NaCl precipitation and detected by singleplex real-time and conventional PCR and reverse transcriptase-PCR assays. One or more enteric viruses were detected in nearly all sewage and river water samples except the urban Mbagathi River. The VP7 (G types) and the VP4 (P types) of the rotaviruses (RV) were characterized by multiplex nested PCR methods. The G and P types could be determined in 95·5% of the RV strains, respectively. Mixed G types were detected with G12 and G1 predominating, and unusual G types, G5 and G10, were present. P[4] predominated in the urban Karen sewage samples, while P[8] predominated in the urban and rural streams.

CONCLUSIONS

The high prevalence of RVs in surface water highlights the importance of assessing the water sources used for domestic purposes for viral contamination.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates the benefit of environmental surveillance as an additional tool to determine the epidemiology of RVs and other enteric viruses circulating in a given community.

Comparison of dynamic contrast-enhanced MRI and dynamic contrast-enhanced CT biomarkers in bladder cancer

Dynamic contrast-enhanced MRI (DCE-MRI) is frequently used to provide response biomarkers in clinical trials of novel cancer therapeutics but assessment of their physiological accuracy is difficult. DCE-CT provides an independent probe of similar pharmacokinetic processes and may be modeled in the same way as DCE-MRI to provide purportedly equivalent physiological parameters. In this study, DCE-MRI and DCE-CT were directly compared in subjects with primary bladder cancer to assess the degree to which the model parameters report modeled physiology rather than artefacts of the measurement technique and to determine the interchangeability of the techniques in a clinical trial setting. The biomarker K(trans) obtained by fitting an extended version of the Kety model voxelwise to both DCE-MRI and DCE-CT data was in excellent agreement (mean across subjects was 0.085 ± 0.030 min(-1) for DCE-MRI and 0.087 ± 0.033 min(-1) for DCE-CT, intermodality coefficient of variation 9%). The parameter v(p) derived from DCE-CT was significantly greater than that derived from DCE-MRI (0.018 ± 0.006 compared to 0.009 ± 0.008, P = 0.0007) and v(e) was in reasonable agreement only for low values. The study provides evidence that the biomarker K(trans) is a robust parameter indicative of the underlying physiology and relatively independent of the method of measurement.

Prevalence and diversity of rotavirus strains in children with acute diarrhea from rural communities in the Limpopo Province, South Africa, from 1998 to 2000

BACKGROUND

Data regarding the prevalence and molecular epidemiology of rotavirus infection in rural areas of Africa are limited. In this study the prevalence and genetic diversity of rotaviruses in a rural South African setting were investigated.

METHODS

During June 1998 to June 2000, 420 stool specimens were collected from children with acute diarrhea who visited primary health care clinics in the rural Vhembe region, Limpopo Province, South Africa. Group A rotaviruses were detected by enzyme-linked immunosorbent assay, and the G and P types were determined by reverse-transcription polymerase chain reaction.

RESULTS

Of the 420 specimens, 111 (26.4%) were positive for group A rotavirus; P[6]G1 strains predominated (32.4%), followed by P[8]G1 (13.5%), P[6]G9 (4.5%), P[4]G8 (3.6%), P[4]G1 (3.6%), P[6]G8 (3.6%), and P[6]G2 (2.7%). Dual infections, with >1 P type, were seen in 33 (37.1%) of the positive specimens.

CONCLUSION

The unusual serotype and genotype combinations of rotavirus circulating in the rural communities of the Limpopo Province highlight the need for more studies to monitor the geographic distribution of rotavirus strains in rural African settings.

Efficacy and tolerability of limited field radiotherapy with concurrent capecitabine in locally advanced pancreatic cancer

AIMS

Patients with locally advanced pancreatic cancer (LAPC) are most commonly managed with chemotherapy or concurrent chemoradiotherapy (CRT), which may or may not include non-involved regional lymph nodes in the clinical target volume. We present our results of CRT for LAPC using capecitabine and delivering radiotherapy to a limited radiation field that excluded non-involved regional lymph nodes from the clinical target volume.

MATERIALS AND METHODS

Thirty patients were studied. Patients received 50.4 Gy external beam radiotherapy in 28 fractions, delivered to a planning target volume expanded from the primary tumour and involved nodes only. Capecitabine (500-600 mg/m2) was given twice daily continuously during radiotherapy. Toxicity and efficacy data were prospectively collected.

RESULTS

Nausea, vomiting and tumour pain were the most common grade 2 toxicities. One patient developed grade 3 nausea. The median time to progression was 8.8 months, with 20% remaining progression free at 1 year. The median overall survival was 9.7 months with a 1 year survival of 30%. Of 21 patients with imaged progression, 13 (62%) progressed systemically, three (14%) had local progression, two (10%) had locoregional progression and three (14%) progressed with both local/locoregional and systemic disease.

CONCLUSION

CRT using capecitabine and limited field radiotherapy is a well-tolerated, relatively efficacious treatment for LAPC. The low toxicity and low regional progression rates support the use of limited field radiotherapy, allowing evaluation of this regimen with other anti-cancer agents.

High prevalence of species D human adenoviruses in fecal specimens from Urban Kenyan children with diarrhea

Human adenoviruses (HAdVs) cause a wide range of clinical syndromes and are classified in seven species, A-G, comprising 52 serotypes. HAdV-A31, -F40, and -F41 have been associated with diarrhea in infants and young children. In developing countries gastroenteritis is a major cause of morbidity and mortality in children and, in comparison to rotaviruses, there are no data on the HAdVs associated with diarrhea in pediatric patients in Kenya. This study investigates the prevalence and genotypes of HAdVs in 278 stool specimens (211 diarrheal; 67 non-diarrheal) from children < or =14 years of age in urban and rural areas in Kenya. Stool specimens were screened for HAdVs using a nested polymerase chain reaction and the HAdVs genotyped by sequence analysis of a conserved hexon gene fragment. HAdVs were detected in 104/278 (37.4%) of the stool specimens: 35/43 (81.4%) of diarrheal and 10/61 (16.4%) of non-diarrheal stool specimens from children in an urban hospice; 25/94 (26.6%) of diarrheal specimens from urban children and 34/80 (42.5%) of diarrheal specimens from children in a rural area. Species D HAdVs were identified as the most prevalent HAdV species in diarrheal stool specimens from urban children comprising 18/37 (48.6%) of the strains identified. In contrast HAdV species F predominated in pediatric diarrheal specimens from the rural area, being identified in 7/16 (43.8%) of the characterized strains. This study provides valuable new data on the prevalence and distribution of HAdV genotypes in diarrheal stool specimens in Kenya and Africa, and highlights the necessity for further investigations.

The origin of preferred orientation during carbon film growth

Carbon films were prepared using a filtered cathodic vacuum arc deposition system operated with a substrate bias varying linearly with time during growth. Ion energies were in the range between 95 and 620 eV. Alternating dark, high density (sp(3) rich) bands and light, low density (sp(2) rich) bands were observed using cross-sectional transmission electron microscopy, corresponding to abrupt transitions between materials with densities of approximately 3.1 and 2.6 g cm(-3). No intermediate densities were observed in the samples. The low density bands show strong preferred orientation with graphitic sheets aligned normal to the film. After annealing, the low density bands became more oriented and the thinner high density layers were converted to low density material. In molecular dynamics modelling of film growth, temperature activated structural rearrangements occurring over long timescales ([Formula: see text] ps) caused the transition from sp(3) rich to oriented sp(2) rich structure. Once this oriented growth was initiated, the sputtering yield decreased and channelling was observed. However, we conclude that sputtering and channelling events, while they occur, are not the cause of the transition to the oriented structure.

Role of astrovirus in intussusception in Nigerian infants

Intussusception (IS) is a form of intestinal obstruction in which a segment of the bowel prolapses into a more distal segment. Viral infections, mostly adenovirus, enteroviruses, human herpesvirus and Epstein-Barr virus are reported in 20-50% of childhood cases of IS. Between January and July 2004, six stool specimens collected from infants 0- to 8-months old diagnosed and admitted for IS were investigated for the presence of rotavirus, astrovirus and adenovirus antigens. Astrovirus antigen was detected in three of the six stool specimens by enzyme immune assay (EIA) and confirmed in two specimens by reverse transcription-polymerase chain reaction (RT-PCR). Rotavirus, non-enteric adenovirus and astrovirus were detected by EIA, as mixed infections in a single specimen. The rotavirus strain revealed a SGI+II, mixed G1G2G8P[6] genotype and had no visible electrophoretic profile. A larger study is needed to determine the extent of involvement of astroviruses in IS in infants and the virus should be included in studies investigating the aetiology of IS.

A phase II study evaluating the use of concurrent mitomycin C and capecitabine in patients with advanced unresectable pseudomyxoma peritonei

Pseudomyxoma peritonei (PMP) is a rare neoplastic process characterised by progressive intra-abdominal dissemination of mucinous tumour, and generally considered resistant to systemic chemotherapy. A phase II study in patients with advanced unresectable PMP was undertaken to evaluate the combination of systemic concurrent mitomycin C (7 mg m(-2) i.v. on day 1) and capecitabine (1250 mg m(-2) b.d. on days 1-14) in a 3-weekly cycle (MCap). Response was determined by semiquantitative assessment of disease volume on serial computed tomographic (CT) scans and serum tumour marker (CEA, CA125, CA19-9) changes at 12 weeks. Between 2003 and 2006, 40 patients were recruited through a national centre for the treatment of peritoneal surface tumours. At baseline, 23 patients had progressive disease and 17 had stable disease. Of 39 assessable patients, 15 (38%, 95% confidence intervals (CIs): 25, 54%) benefited from chemotherapy in the form of either reductions in mucinous deposition or stabilisation of progressive pretreatment disease determined on CT scan. Notably, two patients, originally considered unresectable, following MCap and re-staging underwent potentially curative cytoreductive surgery. Grade 3/4 toxicity rates were low (6%, 95% CIs: 4, 9%). Twenty out of 29 assessed patients (69%, 95% CIs: 51, 83%) felt that their Global Health Status improved during chemotherapy. This is the first trial to demonstrate an apparent benefit of systemic chemotherapy in patients with advanced unresectable PMP.

Abrupt stress induced transformation in amorphous carbon films with a highly conductive transition phase

We demonstrate that when, and only when, the biaxial stress is increased above a critical value of 6+/-1 GPa during the growth of a carbon film at room temperature, tetrahedral amorphous carbon is formed. This confirms that the stress present during the formation of an amorphous carbon film determines its sp;{3} bonding fraction. In the vicinity of the critical stress, a highly oriented graphitelike material is formed which exhibits low electrical resistance and provides Ohmic contacts to silicon. Atomistic simulations reveal that the structural transitions are thermodynamically driven and not the result of dynamical effects.

Magnetic resonance imaging of primary vaginal carcinoma

AIMS

To describe the magnetic resonance imaging (MRI) features of vaginal carcinoma and to suggest a role for MRI in its management.

MATERIALS AND METHODS

Twenty-five patients with primary vaginal carcinoma treated at our institution between 1996 and 2005 were included in the study. The MRI examinations were reviewed and tumour dimensions, signal characteristics and involvement of pelvic structures were documented, as were sites of enlarged lymph nodes and metastases. Details of patient treatment and outcome were obtained from the clinical notes.

RESULTS

The median patient age was 54 years (range 31-86 years). Tumour maximum diameter ranged from 1.6-11.3 cm (mean 3.7 cm). Most tumours were of iso-intense signal to muscle on T1-weighted images and hyper-intense to muscle on T2-weighted images. Eighty-eight percent of patients had tumour extending beyond the vagina and 56% of patients had Figo stage III or above tumours. Sixteen patients were treated with radiotherapy (two with chemoradiotherapy), five with surgery and four with supportive care. Ten patients (40%) died of their disease during the study period. The MRI stage of the tumour correlated with survival.

CONCLUSION

MRI identified over 95% of primary vaginal tumours in the present study, enabled radiological staging, which correlated with outcome, and provided information of use in treatment planning.

Astrovirus infection in young Kenyan children with diarrhoea

Human astroviruses (HAstV) have been commonly identified worldwide as important aetiological agents of acute gastroenteritis in all age groups including the young, elderly and immunocompromised. However, limited data exist on the prevalence of this important pathogen in Kenya. The aim of this study was therefore to determine the prevalence of astrovirus (AstV) infection in Kenyan children younger than 10 years of age with diarrhoea. During the period February 1999 to September 2005, stool samples were collected from 476 children attending clinics in Nairobi (and its environs) and the Maua Methodist Hospital, Meru North, Kenya. The faecal specimens were tested by a commercial enzyme immunoassay kit for HAstV. AstV prevalence rates were found to be 6.3%. There was significantly high prevalence of AstV infection in children <or=5 years [5.3% (25/476)] than those >5 years [0.2% (1/476)] ( p < 0.01). Also, we showed a significantly high prevalence of AstV infection in children of <or=5 years [5.8% (20/341)] in Nairobi (urban setting) as compared with those of similar age in Maua (a rural setting) [3.7% (5/135)] ( p < 0.01). This study indicates that HAstV is an important pathogen associated with diarrhoea in young Kenyan children.

Hepatitis A virus in surface water in South Africa: what are the risks?

The aim of this study was to assess the potential risk of infection constituted by HAV to persons using surface dam and river water for domestic and recreational purposes. It estimates the potential risk using a deterministic exponential risk assessment model with mean values and conservative assumptions. Hepatitis A virus was detected in 17.5% of river and 14.9% of dam water samples tested. The number of indicator organisms in these sources exceeded drinking and recreational water quality guidelines set by the United States Environmental Protection Agency (US EPA), indicating possible health risks to recreational water users. Based on the available data and taking all the assumptions into consideration, the probability of infection (Pinf) to the higher socio-economic population using the river water for recreational purposes was 1.1 x 10(-3) per day and 3.3 x 10(-1) per annum if 100 ml was ingested per day. For recreation in the dam water the Pinf value was 1.2 x 10(-4) per day and 4.2 x 10(-2) per annum. For the lower socio-economic population, risk values for drinking purposes (2 L day(-1)) were ten-fold greater. These surface waters therefore did not conform to the US EPA guidelines of 1 infection per 10,000 consumers per year for drinking water or eight gastrointestinal illnesses per 1,000 bathers per day in environmental waters used for recreational purposes. This is the first risk assessment study addressing the risk of infection by HAV in surface water to different socio-economic populations in South Africa.

Molecular epidemiology of group A rotaviruses in water sources and selected raw vegetables in southern Africa

Group A rotaviruses (RVs) are the most important cause of acute viral gastroenteritis in infants and young children. In this study raw and treated drinking water supplies at plants in two geographic areas, as well as selected irrigation water and corresponding raw vegetables in three regions of southern Africa, were screened for the presence of RVs using molecular techniques. Group A RVs were detected in 11.8% of partially treated and 1.7% of finally treated drinking water samples and in 14% of irrigation water samples and 1.7% of corresponding raw vegetable samples. Type-specific reverse transcriptase-PCR and sequence analysis revealed the presence of multiple types (G1, G2, G8, and G9) in irrigation water and single types (G1 or G3) in raw and treated drinking water. Group A RVs detected in all samples consisted of mixed P types (P[4], P[6], P[8], and P[9]), with P[6] predominating. The detection of types G8, G9, and P[6] reflects the emergence of these types in clinical infections. The similarity of environmental types to those in patients with clinical RV infections confirms the value of wastewater screening as a tool for assessing RVs circulating in communities, with the benefit of detecting types that cause both clinical and subclinical infections. The results provide new information on RV types in water and related environments and identify the potential risk of waterborne transmission. In addition, the presence of RVs in drinking water underlines shortcomings in quality specifications. These data provide valuable information regarding the prevalence of RVs in environmental sources, with important implications for vaccine development.

Response evaluation in gastrointestinal stromal tumours treated with imatinib: misdiagnosis of disease progression on CT due to cystic change in liver metastases

Imatinib is a highly effective treatment for patients with metastatic gastrointestinal stromal tumours (GIST). In most instances, response to imatinib treatment is assessed with CT. We present two cases where CT demonstrated the appearance of new low density liver lesions after 8-12 weeks of imatinib treatment. While this finding is consistent with progressive disease due to new lesions appearing at a previously uninvolved site, we hypothesise that the appearance of new liver lesions is in fact due to cystic change within previously occult, solid metastases. These untreated solid metastases were not visible on conventional portal phase CT due to their small size and vascular nature. Our hypothesis is supported by the observation that extrahepatic sites of disease had reduced in size over the same period of imatinib treatment and by the subsequent disease outcomes of these two cases. One patient, who continued imatinib because of significant symptomatic improvement despite the CT findings, remained stable on the same dose of imatinib for 18 months. The other patient, whose disease progressed when imatinib was withdrawn, had a dramatic response to treatment when imatinib was restarted at the same dose 2 years later. It is important that radiologists and oncologists who are involved in the management of GIST recognize that the appearance of new, low-density liver lesions on CT may represent a response to treatment. This finding must be correlated with symptomatic response and with tumour sites outside the liver before erroneously withdrawing effective imatinib treatment.

The evolution of teaching and learning medical microbiology and infectious diseases at NUS

Infectious diseases were rife during the early years of the Singapore Medical College, which was established in 1905. The current Department of Microbiology in the National University of Singapore (NUS) has its historical roots in the Departments of Bacteriology and Parasitology, which were established in 1925 and 1950 respectively. With the achievements since its inception, and with its present research focus on Infectious Diseases, Immunology, Applied and Environmental Microbiology, it is poised to face the microbiological challenges of the 21st century. Over the decades, the structure of the medical microbiology course in NUS has modernised, culminating in the current emphasis on its practical utility in clinical practice. Coordinated by the Department of Microbiology, the Microbiology and Infectious Diseases module and the Immunology module both adopt integrated multidisciplinary approaches that aim to introduce students to the language and fundamental concepts in microbiology, infectious diseases and immunology.

Comparison of caudal steroid epidural with targeted steroid placement during spinal endoscopy for chronic sciatica: a prospective, randomized, double-blind trial

BACKGROUND

Chronic sciatica can be managed by caudal steroid epidural or by targeted steroid placement during spinal endoscopy. Spinal endoscopy is a new unproven procedure. We aimed to compare the two pain management techniques and to investigate whether the site of steroid placement within the epidural space was significant.

METHODS

We randomized 60 patients with a 6-18 months history of sciatica to either targeted epidural local anaesthetic and steroid placement with a spinal endoscope or caudal epidural local anaesthetic and steroid treatment. Pre-treatment and 6-week, 3-month, and 6-month SF-MPQ and HAD scores were recorded.

RESULTS

No significant differences were found between the groups for any of the measures at any time. However, there were significant differences within both groups compared with pre-treatment values. For the caudal group, significant improvements were found for descriptive pain at 6 months (P=0.031), VAS at 6 weeks (P=0.036), 3 months (P=0.026), and 6 months (P=0.003), present pain intensity (PPI) at 3 months (P=0.013) and 6 months (P=0.01); anxiety at 6 weeks (P=0.008), 3 months (P=0.004), and 6 months (P=0.001) and depression at 6 months only (P=0.037). For the epiduroscopy group there were fewer significant changes. PPI was significantly reduced at 6 weeks (P=0.004) and at 6 months (P=0.02). Anxiety was reduced at 6 months only (P=0.03).

CONCLUSION

The targeted placement of epidural steroid onto the affected nerve root causing sciatica does not significantly reduce pain intensity and anxiety and depression compared with untargeted caudal epidural steroid injection. When analysed individually, both techniques benefited patients.