Enteric virus infections and diarrhea in healthy and human immunodeficiency virus-infected children

Evaluation of the detection of diarrhoea-associated RNA viruses in immunocompromised children in Iran

Background

Gastroenteritis accounts for about 10% of the deaths among children, especially in immunocompromised children. Few studies on the prevalence of gastrointestinal infections caused by RNA viruses have been done in Iran. The aim of the study was to evaluate the detection of RNA viruses causing diarrhoea using a multiplex PCR.

Methods

Stool samples were collected from 130 paediatric patients with diarrhoea who had acute lymphocytic leukaemia, non-Hodgkin lymphoma, and retinoblastoma. After RNA extraction and synthesis of cDNA, multiplex PCR was done to evaluate the presence of rotavirus, norovirus, astrovirus, and enterovirus.

Results

There were 9 (6.9%), 7 (5.4%), 3 (2.3%), and 6 (4.6%) cases of rotavirus, norovirus, astrovirus, and enterovirus detected, respectively. One case of co-infection with astrovirus and norovirus was observed.

Conclusions

This is the first report from Iran which identified the presence of common RNA viruses causing diarrhoea in immunocompromised children. Increased awareness of these viruses will enable healthcare professionals to improve strategies and policies to control spread and infection caused by these viruses.

Leveraging machine learning for taxonomic classification of emerging astroviruses

Astroviruses are a family of genetically diverse viruses associated with disease in humans and birds with significant health effects and economic burdens. Astrovirus taxonomic classification includes two genera, Avastrovirus and Mamastrovirus. However, with next-generation sequencing, broader interspecies transmission has been observed necessitating a reexamination of the current host-based taxonomic classification approach. In this study, a novel taxonomic classification method is presented for emergent and as yet unclassified astroviruses, based on whole genome sequence k-mer composition in addition to host information. An optional component responsible for identifying recombinant sequences was added to the method's pipeline, to counteract the impact of genetic recombination on viral classification. The proposed three-pronged classification method consists of a supervised machine learning method, an unsupervised machine learning method, and the consideration of host species. Using this three-pronged approach, we propose genus labels for 191 as yet unclassified astrovirus genomes. Genus labels are also suggested for an additional eight as yet unclassified astrovirus genomes for which incompatibility was observed with the host species, suggesting cross-species infection. Lastly, our machine learning-based approach augmented by a principal component analysis (PCA) analysis provides evidence supporting the hypothesis of the existence of human astrovirus (HAstV) subgenus of the genus Mamastrovirus, and a goose astrovirus (GoAstV) subgenus of the genus Avastrovirus. Overall, this multipronged machine learning approach provides a fast, reliable, and scalable prediction method of taxonomic labels, able to keep pace with emerging viruses and the exponential increase in the output of modern genome sequencing technologies.

Screening for viral pathogens in the gastrointestinal tract from cases of sudden unexpected death in infancy at the Tygerberg Medico-legal Mortuary

Sudden and unexpected death in infancy (SUDI) may be triggered by an external risk or exposure. Intestinal infections with enteric viruses may disrupt the gut and enhance bacterial toxins present in SUDI cases. While diarrhoeal disease deaths have decreased worldwide, approximately half a million deaths still occur in children in Sub- Saharan Africa and South Asia. Furthermore, the role of viral enteropathogens in SUDI cases have not been investigated. The aim of this study was to describe specific viral pathogens in stool samples collected from SUDI cases and age-matched, apparently healthy infants in Cape Town, South Africa. Stool samples were collected from 176 SUDI cases between June 2017 and May 2018. In addition, stool samples were collected from the nappies of 30 age-matched, apparently healthy infants as a control group. Real-time polymerase chain reaction was performed on the stool samples for viral detection. A total of 111 SUDI cases were positive for viruses, with rotavirus (38.6%; 68/176) and norovirus GI and GII (30.0%; 53/176) were prevalent in SUDI cases. Adenovirus Type F was present in only 15.9% (28/176), astrovirus in 9.7% (17/176), and sapovirus in 0.6% (1/176) of cases. In the control samples, norovirus GII was detected most frequently (36.7%; 11/30), followed by rotavirus (33.3%; 10/30), and sapovirus in 6.7% (2/30). While there was no significant association between SUDI cases and enteric viruses, the majority of viruses were significantly associated with the seasons. The study confirms the importance of rotavirus vaccination and describes the significance of norovirus infection in children, post rotavirus vaccine introduction.

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

AIM

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

METHODS

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

RESULTS

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

CONCLUSION

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

HUMAN COSAVIRUS INFECTION IN HIV SUBJECTS WITH DIARRHOEA: PERSISTENT DETECTION ASSOCIATED WITH FATAL OUTCOME

BACKGROUND

Human cosavirus (HCoSV) is a new member of the Picornaviridae family, geographically widespread among humans. It has been suggested as a causative agent of acute gastroenteritis, but its pathogenicity is not currently certain. In HIV-infected subjects, diarrhoea is one of the most frequent gastrointestinal manifestations, whose aetiology remains often unexplained.

OBJECTIVES

To identify the cause of viral diarrhoea among HIV infected patients by molecular assays.

STUDY DESIGN

A total of 143 stool samples from HIV subjects with and without diarrhoea, were screened for conventional enteric viruses (rotavirus, adenovirus, norovirus and astrovirus) by molecular assays. The presence of HCoSV genome was investigated by nested RT-PCR for the 5'UTR region. Positive samples were further characterized by sequencing and phylogenetic analysis.

RESULTS

Enteric viruses were more frequently found in diarrhoea cases (9/82) than controls (0/61) (p=0.007). HCoSV was detected in five (3.5%) of the subjects affected by diarrhoea. Phylogenetic analysis revealed the predominance of the HCoSV species D. One patient suffered a persistent cosavirus infection with a same strain and after eight months he had a fatal outcome. No other pathogens could be detected.

CONCLUSIONS

The results suggest a role of non-conventional enteric viruses, as HCoSV, as a potential opportunistic agent causing persistent infection and deterioration of the clinical conditions in HIV-infected patients. Screening procedures and monitoring including such viruses would be helpful in the clinical management of such patients.

Enteric Viral Co-Infections: Pathogenesis and Perspective

Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of all ages globally. Despite virus–virus co-infection events in the intestine being increasingly detected, little is known about their impact on disease outcomes or human health. Here, we review what is currently known about the clinical prevalence of virus–virus co-infections and how co-infections may influence vaccine responses. While experimental investigations into enteric virus co-infections have been limited, we highlight in vivo and in vitro models with exciting potential to investigate viral co-infections. Many features of virus–virus co-infection mechanisms in the intestine remain unclear, and further research will be critical.

Occurrence of human astrovirus associated with gastroenteritis among Congolese children in Brazzaville, Republic of Congo

INTRODUCTION

Acute viral gastroenteritis is a major public health concern, especially among children younger than 5 years of age. The aim of this study was to determine the occurrence of human astrovirus infection in children with acute gastroenteritis.

METHODS

Stool specimens were collected from 506 children under 5 years of age hospitalized with acute diarrhoea (289 male and 208 female), and human astrovirus was investigated by RT-PCR. Associations of socio-demographic, clinical, and behavioural conditions with infection were analysed.

RESULTS

The overall prevalence of human astrovirus was found to be 10.3%. The mean age of positive cases was 12.41 ± 6.21 months and this was associated with infection (p = 0.013). Children >18 months of age were at three times the risk of infection when compared to those aged 0-6 months (odds ratio (OR) 3.19, 95% confidence interval (CI) 1.15-8.88; p = 0.026). Children living in houses with more than one room (OR 0.60, 95% CI 0.28-0.96; p = 0.036) and mothers using treated water (OR 0.47, 95% CI 0.25-0.86; p = 0.015) were associated with reduced infection.

CONCLUSIONS

In this study, infection with astrovirus was common in acute gastroenteritis cases among children younger than 5 years of age. Drinking treated water and living in non-crowded environments protected the children from infection.

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.

Healthcare utilization for common infectious disease syndromes in Soweto and Klerksdorp, South Africa

Introduction

Understanding healthcare utilization helps characterize access to healthcare, identify barriers and improve surveillance data interpretation. We describe healthcare-seeking behaviors for common infectious syndromes and identify reasons for seeking care.

Methods

We conducted a cross-sectional survey among residents in Soweto and Klerksdorp, South Africa. Households were interviewed about demographic characteristics; recent self-reported episodes of pneumonia, influenza-like illness (ILI), chronic febrile respiratory illness and meningitis in individuals of all ages; recent diarrhea in children aged < 5 years; and consultation with healthcare facilities and providers.

Results

From July-October 2012, we interviewed 1,442 households in Klerksdorp and 973 households in Soweto. Public clinics were consulted most frequently for pneumonia, ILI and diarrhea in a child <5 years old at both sites; public hospitals were most frequently consulted for chronic respiratory and meningitis syndromes. Of all illness episodes reported, there were 110 (35%) in Klerksdorp and 127 (32%) in Soweto for which the person did not seek care with a licensed medical provider. Pharmacies were often consulted by individuals with pneumonia (Klerksdorp: 17, 16%; Soweto: 38, 22%) or ILI (Klerksdorp: 35, 24%; 44, 28%). Patients who did not seek care with a licensed provider reported insufficient time (Klerksdorp: 7%; Soweto, 20%) and lack of medications at the facility (Klerksdorp: 4%; Soweto: 8%) as barriers.

Conclusion

Public government healthcare facilities are commonly consulted for infectious syndromes and pharmacies are frequently consulted particularly for respiratory diseases. Improving medication availability at healthcare facilities and streamlining healthcare delivery may improve access of licensed providers for serious illnesses.

Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees?

Enteroviruses are among the best studied small non-enveloped enteric RNA viruses. Most enteroviruses are easy to isolate in cell culture, and many non-polio enterovirus strains were archived worldwide as a byproduct of the WHO poliovirus surveillance system. Common outbreaks and epidemics, most prominently the epidemic of hand-foot-and-mouth disease with severe neurological complications in East and South-East Asia, justify practical interest of non-polio enteroviruses. As a result, there are over 50 000 enterovirus nucleotide sequences available in GenBank. Technical possibilities have been also improving, as Bayesian phylogenetic methods with an integrated molecular clock were introduced a decade ago and provided unprecedented opportunities for phylogenetic analysis. As a result, hundreds of papers were published on the molecular epidemiology of enteroviruses. This review covers the modern methodology, structure, and biases of the sequence dataset available in GenBank. The relevance of the subtype classification, findings of co-circulation of multiple genetic variants, previously unappreciated complexity of viral populations, and global evolutionary patterns are addressed. The most relevant conclusions and prospects for further studies on outbreak emergence mechanisms are discussed.

Persistent Infections with Diverse Co-Circulating Astroviruses in Pediatric Oncology Patients, Memphis, Tennessee, USA

Human astroviruses are a major cause of pediatric gastroenteritis, especially in immunocompromised children. We conducted a retrospective study to demonstrate that diverse astrovirus genotypes can co-circulate in pediatric oncology patients. A subset of cases is associated with long-term virus shedding (range 17–183 days).

Vaccine-related poliovirus shedding in trivalent polio vaccine and human immunodeficiency virus status: analysis from under five children

Background

Poliomyelitis is an acute viral infection caused by poliovirus and transmitted via the fecal–oral route. The causative agent is one of the three serotypes of poliovirus (serotypes 1, 2, 3) that differ slightly in capsid protein. Prolonged vaccine-related poliovirus shedding in human immunodeficiency virus (HIV) positive individuals has been linked to possible reservoir for reintroduction of polioviruses after eradication. The study therefore aimed at estimating the duration for vaccine-related poliovirus shedding among potentially and HIV-infected persons.

Methods

Poliovirus excretion was studied following vaccination of children aged ≤ 59 month per human immunodeficiency virus status after national immunization days. Their medical records were reviewed to identify the child’s HIV status, demographic and immunization data. Sequential stool samples were collected at site 2nd, 4th and 8th week after trivalent oral poliovirus vaccine (tOPV) was administered. To isolate suspected polioviruses and non-polio enteroviruses, characterize poliovirus subtypes by intratypic differentiation and Sabin vaccine derived poliovirus, real time polymerase chain reaction was applied. Shedding for ≥ 24 weeks was defined as long-term persistence.

Results

The mean age of the study population was 28.6 months, while the median age was 24 months. Of the children recruited, majority were in the 25–48 months (n = 12; 46.2%) age category. All the HIV-positive children (n = 10) had mild symptomatic HIV status and did shed vaccine-related polioviruses between weeks 2 and 4 respectively. No participant shed polioviruses for ≥ 6 weeks.

Conclusions

It was evident mildly symptomatic HIV+ children sustain the capacity to clear vaccine-related poliovirus. The oral poliovirus vaccine-2 (Sabin like) that was detected in one HIV-infected child’s stool 6 weeks after the national immunization days was predominantly non revertant. There was no evident prolonged poliovirus shedding among the participants enlisted in the present study. High powered studies are desired to further corroborate these findings.

Enteric viruses in HIV-1 seropositive and HIV-1 seronegative children with diarrheal diseases in Brazil

Diarrheal diseases (DD) have distinct etiological profiles in immune-deficient and immune-competent patients. This study compares detection rates, genotype distribution and viral loads of different enteric viral agents in HIV-1 seropositive (n = 200) and HIV-1 seronegative (n = 125) children hospitalized with DD in Rio de Janeiro, Brazil. Except for group A rotavirus (RVA), which were detected through enzyme immunoassay, the other enteric viruses (norovirus [NoV], astrovirus [HAstV], adenovirus [HAdV] and bocavirus [HBoV]) were detected through PCR or RT-PCR. A quantitative PCR was performed for RVA, NoV, HAstV, HAdV and HBoV. Infections with NoV (19% vs. 9.6%; p<0.001), HBoV (14% vs. 7.2%; p = 0.042) and HAdV (30.5% vs. 14.4%; p<0.001) were significantly more frequent among HIV-1 seropositive children. RVA was significantly less frequent among HIV-1 seropositive patients (6.5% vs. 20%; p<0.001). Similarly, frequency of infection with HAstV was lower among HIV-1 seropositive children (5.5% vs. 12.8%; p = 0.018). Among HIV-1 seropositive children 33 (16.5%) had co-infections, including three enteric viruses, such as NoV, HBoV and HAdV (n = 2) and NoV, HAstV and HAdV (n = 2). The frequency of infection with more than one virus was 17 (13.6%) in the HIV-1 negative group, triple infection (NoV + HAstV + HBoV) being observed in only one patient. The median viral load of HAstV in feces was significantly higher among HIV-1 positive children compared to HIV-1 negative children. Concerning children infected with RVA, NoV, HBoV and HAdV, no statistically significant differences were observed in the medians of viral loads in feces, comparing HIV-1 seropositive and HIV-1 seronegative children. Similar detection rates were observed for RVA, HAstV and HAdV, whilst NoV and HBoV were significantly more prevalent among children with CD4⁺ T lymphocyte count below 200 cells/mm³. Enteric viruses should be considered an important cause of DD in HIV-1 seropositive children, along with pathogens more classically associated with intestinal infections in immunocompromised hosts.

Enteroviruses and Parechoviruses

Infections with enteroviruses and human parechoviruses are highly prevalent, particularly in neonates, where they may cause substantial morbidity and mortality. Individuals with B-cell-related immunodeficiencies are at risk for severe enteroviral infections, usually a chronic and fatal meningoencephalitis. In transplant recipients and patients with malignancy, enterovirus infections typically involve the respiratory tract, but cases of severe, disseminated infection have been described. The mainstay of diagnosis for enterovirus and human parechovirus infections involves the use of molecular diagnostic techniques. However, routine nucleic acid-detection methods for enteroviruses will not detect human parechoviruses. Laboratory diagnosis of these viral infections is important in determining a patient's prognosis and guiding clinical management.

Seroprevalence of antibodies to astrovirus in chickens in Grenada, West Indies

Aim:

Chicken astroviruses (CAstV) are known to cause mild gastroenteritis, growth depression, and even mortality in poultry, especially in chickens, turkeys, and ducks. To the best our knowledge, there is no published information on CAstV in Grenada. This study was conducted to determine the prevalence of astrovirus in chickens in Grenada.

Materials and Methods:

Blood samples from 366 indigenous chickens and 92 commercial chicken layers were collected from all parishes of the island and tested for antibodies against CAstV using commercial enzyme-linked immunosorbent assay.

Results:

The seroprevalence of antibodies against astrovirus was 57.6% (95%, Confidence interval [CI]: 47.4-67.2) in commercial layers and 61.5% (95%, CI: 56.4-66.3) in indigenous chickens. The results show the presence of infection throughout the island.

Conclusion:

The results show the infection with CAstV in approximately half of the chicken population in Grenada. This is the first report on the prevalence of CAstV in chickens in Grenada and the Caribbean region.

Epidemiology of Classic and Novel Human Astrovirus: Gastroenteritis and Beyond

Since they were identified in 1975, human astroviruses have been considered one of the most important agents of viral acute gastroenteritis in children. However, highly divergent astroviruses infecting humans have been recently discovered and associated with extra-intestinal infections. The report of cases of fatal meningitis and encephalitis, especially in immunocompromised individuals, has broadened their disease spectrum. Although zoonotic transmission among animal and human astroviruses has not been clearly recognized, the genetic similarity between some human and animal viruses makes it likely to occur. This review provides an update on the epidemiology of both classic and novel human astroviruses, and a comprehensive view on confirmed or potential association between astrovirus and human disease.

Implementation and Operational Research: Risk Factors of Loss to Follow-up Among HIV-Positive Pediatric Patients in Dar es Salaam, Tanzania

OBJECTIVE

To identify risk factors for loss to follow-up (LTFU) in an HIV-infected pediatric population in Dar es Salaam, Tanzania, between 2004 and 2011.

DESIGN

Longitudinal analysis of 6236 HIV-infected children.

METHODS

We conducted a prospective cohort study of 6236 pediatric patients enrolled in care and treatment in Dar es Salaam from October 2004 to September 2011. LTFU was defined as missing a clinic visit for >90 days for patients on ART and for >180 days for patients in care and monitoring. The relationship of baseline and time-varying characteristics to the risk of LTFU was examined using a Cox proportional hazards model.

RESULTS

A total of 2130 children (34%) were LTFU over a median follow-up of 16.7 months (interquartile range, 3.4-36.9). Factors independently associated with a higher risk of LTFU were age ≤2 years (relative risk [RR] = 1.59, 95% CI: 1.40 to 1.80), diarrhea at enrollment (RR = 1.20, 95% CI: 1.03 to 1.41), a low mid-upper arm circumference for age (RR = 1.20, CI: 1.05 to 1.37), eating protein-rich foods ≤3 times a week (RR = 1.39, 95% CI: 1.05 to 1.90), taking cotrimoxazole (RR = 1.39, 95% CI: 1.06 to 1.81), initiating onto antiretrovirals (RR = 1.37, 95% CI: 1.17 to 1.61), receiving treatment at a hospital instead of a local facility (RR = 1.39, 95% CI: 1.06 to 1.41), and starting treatment in 2006 or later (RR = 1.10, 95% CI: 1.04 to 1.16).

CONCLUSIONS

Health workers should be aware of pediatric patients who are at a greatest risk of LTFU, such as younger and undernourished patients, so that they can proactively counsel families about the importance of visit adherence. Findings support decentralization of HIV care to local facilities as opposed to hospitals.

Prevalence and molecular characterisation of human adenovirus in diarrhoeic children in Tanzania; a case control study

BACKGROUND

Human adenovirus (HAdV) causes acute diarrhoea sporadically, as well as in outbreaks. Understanding the prevalence and types of HAdV in diarrhoea is important for control and preventive measures, especially in the African region where there is a high burden of diarrhoeal disease. The present study assessed the prevalence, molecular characteristics, seasonality and associated clinical features of HAdV infection Tanzanian children below two years of age with and without diarrhoea between 2010-2011.

METHODS

Stool specimens, demographic and clinical information were collected in 690 cases and 545 controls. All stool samples were screened for HAdV-antigen using ELISA. Positive samples subsequently underwent real-time PCR and sequencing for molecular typing.

RESULTS

HAdV was detected in 37 children, corresponding to a prevalence of 3.5% (24/690) in diarrhoeic and 2.4% (13/545) in non-diarrhoeic children (P > 0.05). Among HAdV-infected children, the median age was significantly lower in diarrhoeic than in non-diarrhoeic children (10 vs. 14 months, P˂0.001). More than half of HAdV infected (54.2%) were dehydrated as compared to diarrhoeic children without HAdV (45.8%, P = 0.01). The proportion of the enteric HAdV type 40/41 in diarrhoeic and non-diarrhoeic children was (50.0%, 12/24) and (46.2%, 6/13) respectively. Other HAdV types detected were; 1, 2, 7, 18, 19 and 31. The prevalence of adenovirus was not significantly different between rainy and dry seasons. HAdV was not detected in the 33 known HIV positive children. There was no significant association between HAdV infection and gender, nutritional status of the child and parent educational level.

CONCLUSION

The present study provides further evidence of the contribution of adenovirus in causing gastroenteritis in young children, with symptomatic infection being significantly more prevalent in children below one year. We found similar prevalence of adenovirus in non-diarrhoeic children and in diarrhoeic children. This first report on molecular epidemiology of human adenovirus in Tanzania observed diversity of HAdV types that circulate the study setting. The study findings suggest that HAdV is not an important cause of diarrhoea in young HIV-positive children.

Genetic diversity of circulating rotavirus strains in Tanzania prior to the introduction of vaccination

Background

Tanzania currently rolls out vaccination against rotavirus-diarrhea, a major cause of child illness and death. As the vaccine covers a limited number of rotavirus variants, this study describes the molecular epidemiology of rotavirus among children under two years in Dar es Salaam, Tanzania, prior to implementation of vaccination.

Methods

Stool specimens, demographic and clinical information, were collected from 690 children admitted to hospital due to diarrhea (cases) and 545 children without diarrhea (controls) during one year. Controls were inpatient or children attending child health clinics. Rotavirus antigen was detected using ELISA and positive samples were typed by multiplex semi-nested PCR and sequencing.

Results

The prevalence of rotavirus was higher in cases (32.5%) than in controls (7.7%, P<0.001). The most common G genotypes were G1 followed by G8, G12, and G4 in cases and G1, G12 and G8 in controls. The Tanzanian G1 variants displayed 94% similarity with the Rotarix vaccine G1 variant. The commonest P genotypes were P[8], P[4] and P[6], and the commonest G/P combination G1 P[8] (n = 123), G8 P[4] and G12 P[6]. Overall, rotavirus prevalence was higher in cool (23.9%) than hot months (17.1%) of the year (P = 0.012). We also observed significant seasonal variation of G genotypes. Rotavirus was most frequently found in the age group of four to six months. The prevalence of rotavirus in cases was lower in stunted children (28.9%) than in non-stunted children (40.1%, P = 0.003) and lower in HIV-infected (15.4%, 4/26) than in HIV-uninfected children (55.3%, 42/76, P<0.001).

Conclusion

This pre-vaccination study shows predominance of genotype G1 in Tanzania, which is phylogenetically distantly related to the vaccine strains. We confirm the emergence of genotype G8 and G12. Rotavirus infection and circulating genotypes showed seasonal variation. This study also suggests that rotavirus may not be an opportunistic pathogen in children infected with HIV.

Norovirus infection in pediatric hematopoietic stem cell transplantation recipients: incidence, risk factors, and outcome

Norovirus infections are increasingly being recognized as important causes of diarrhea in hematopoietic stem cell transplantation (HSCT) recipients. This retrospective study aimed to evaluate the cumulative incidence, risk factors, and outcomes of norovirus infection in pediatric HSCT recipients. Among 55 patients age <21 years who underwent first HSCT between July 2007 and June 2011, 49 patients developed diarrhea and had stool tested for norovirus. Eight of these patients were found to be infected with norovirus. All were sporadic cases and manifested with nausea, vomiting, and diarrhea. The median age of these patients was 5.2 years (range, 0.5-18.5 years). Six were males. Seven patients underwent unrelated donor HSCT, and 1 patient underwent autologous cord blood HSCT. Two patients had norovirus infection before HSCT that persisted after transplantation. In the remaining 6 patients, norovirus developed at a median of 36.5 days posttransplantation (range, 5-517 days). The cumulative incidence of norovirus infection was 12.9% at 2 years posttransplantation. Risk factors for norovirus infection included the use of peripheral blood or cord blood as the stem cell source (P = .043) and administration of fludarabine (P = .002) and alemtuzumab (P = .011). The median time to viral clearance was 145 days (range, 13-263 days). Four-year survival was similar in norovirus-infected patients and noninfected patients (56.3% versus 58.3%).

The role of prolonged viral gastrointestinal infections in the development of immunodeficiency-related enteropathy

Patients with primary immunodeficiencies are prone to develop enteropathy of unknown pathogenesis. We hypothesize that ineffective clearance of gastrointestinal pathogens, particularly viruses, in combination with defective immune regulation may cause inflammatory enteropathy in certain immunodeficient hosts. We reviewed publications related to prolonged enteric viral infection, immunodeficiency, and the subsequent development of inflammatory enteropathy. Prolonged infection with especially enteroviral infections was reported more often in immunocompromised hosts than in healthy individuals. Protracted enteric viral shedding was not always associated with the presence or duration of gastrointestinal symptoms. The development of immunodeficiency-associated enteropathy after prolonged viral infections was described in sporadic cases. Clinical consequences of viral gut infections in immunocompromised hosts comprise isolation issues and supportive care. Prospective studies in cohorts of immunodeficient patients are required to study the impact of prolonged enteric viral replication with respect to the pathogenesis of non-infectious enteropathy.

Picobirnavirus infections: viral persistence and zoonotic potential

Picobirnaviruses (PBVs) are small, non-enveloped, bisegmented double-stranded RNA genomic viruses of vertebrate hosts. Since their discovery in the late 1980s in clinical specimens from outbreaks of acute gastroenteritis in children, significant efforts have been made to investigate the role of PBV in diarrheic diseases. PBV has been detected in sporadic episodes of diarrhea as sole pathogen or coinfection as well as in outbreaks of acute gastroenteritis and in immunocompromised patients with diarrhea. However, PBV is frequently detected in non-diarrheic healthy hosts, and prolonged shedding has been observed in some individuals. Of interest, similar patterns of PBV infection have also been observed in pigs and other animal hosts. The increasing amount of PBV sequence data gathered from molecular epidemiological studies has evidenced a great sequence diversity of PBVs in various hosts and environmental samples. Importantly, evidence has been found for genetic relatedness between human and animal PBV strains, suggesting extant crossing points in the ecology and evolution of heterologous PBV strains. At present, no cell culture and animal model exists for PBVs. Well-structured epidemiological studies are still the only alternative to demonstrate the potential etiological role of PBVs in acute gastroenteritis or other diseases. This review aims to analyze the public health aspects of PBV infection, especially its possible association with zoonosis.

Serological studies confirm the novel astrovirus HMOAstV-C as a highly prevalent human infectious agent

Molecular identification of a microbe is the first step in determining its prevalence of infection and pathogenic potential. Detection of specific adaptive immune responses can provide insights into whether a microbe is a human infectious agent and its epidemiology. Here we characterized human anti-IgG antibody responses by luciferase immunoprecipitation systems (LIPS) against two protein fragments derived from the capsid protein of the novel HMOAstV-C astrovirus. While antibodies to the N-terminal fragment were not informative, the C-terminal capsid fragment of HMOAstV-C showed a high frequency of immunoreactivity with serum from healthy blood donors. In contrast, a similar C-terminal capsid fragment from the related HMOAstV-A astrovirus failed to show immunoreactivity. Detailed analysis of adult serum from the United Sates using a standardized threshold demonstrated HMOAstV-C seropositivity in approximately 65% of the samples. Evaluation of serum samples from different pediatric age groups revealed that the prevalence of antibodies in 6-12 month, 1-2 year, 2-5 year and 5-10 year olds was 20%, 23%, 32% and 36%, respectively, indicating rising seroprevalence with age. Additionally, 50% (11/22) of the 0-6 month old children showed anti-HMOAstV-C antibody responses, likely reflecting maternal antibodies. Together these results document human humoral responses to HMOAstV-C and validate LIPS as a facile and effective approach for identifying humoral responses to novel infectious agents.

Chronic norovirus infection in pediatric hematopoietic stem cell transplant recipients: a cause of prolonged intestinal failure requiring intensive nutritional support

Norovirus infection is a major cause of nonbacterial gastroenteritis. In immunocompetent individuals the illness caused by norovirus is mostly self limiting. Excretion of norovirus has been reported to be prolonged in the immunocompromised including adult HSCT recipients. We report a case series of 13 children who received HSCT and required prolonged parenteral and enteral nutrition due to severe gut dysfunction accompanying protracted norovirus excretion that was monitored by RT-PCR. The median duration of viral excretion was 150 days (range 60-380) and the eventual clearance of norovirus from feces was closely associated with donor T cell recovery in the peripheral blood. There was no disease manifestation beyond the gut but the severity and length of norovirus associated illness suggests that HSCT should be delayed where possible in patients excreting the virus prior to conditioning therapy.

Rediscovery and genomic characterization of bovine astroviruses

The genus Mamastrovirus belongs to the family Astroviridae and consists of at least six members infecting different mammalian hosts, including humans, cattle and pigs. In recent years, novel astroviruses have been identified in other mammalian species like roe deer, bats and sea lions. While the bovine astrovirus was one of the earliest astroviruses to have been studied, no further research has been performed recently and its genome sequence remains uncharacterized. In this report, we describe the detection and genomic characterization of astroviruses in bovine faecal specimens obtained in Hong Kong. Five of 209 specimens were found to be positive for astrovirus by RT-PCR. Two of the positive specimens were found to contain sequences from two different astrovirus strains. Complete genome sequences of approximately 6.3 kb in length were obtained for four strains, which showed similar organization of the genome compared to other astroviruses. Phylogenetic analysis confirmed their identities as members of the genus Mamastrovirus, and showed them to be most closely related to the Capreolus capreolus astrovirus. Based on the pairwise genetic distances among their full-length ORF2 sequences, these bovine astroviruses may be assigned into at least three different genotype species. Sequence analysis revealed evidence of potential recombination in ORF2. In summary, we report the first genome sequences of bovine astroviruses and clearly establish the species status of the virus. Additionally, our study is among the first to report co-infection by different astrovirus genotypes in the same host, which is an essential step for recombination to occur.

The picobirnavirus: an integrated view on its biology, epidemiology and pathogenic potential

Picobirnaviruses (PBV) are a group of small, nonenveloped viruses with bi-segmented dsRNA genomes. The large genomic segment encodes for the capsid protein while the small segment encodes for the RNA-dependent RNA polymerase. PBV are widely distributed and have been detected in the feces of a large variety of vertebrate species, including farm and captive animals and also in humans. Their etiological role as a cause of diarrhea remains elusive. Still, compelling evidence indicates that PBV may be opportunistic pathogens associated with diarrhea in immunocompromised individuals. The partial molecular characterization of human and animal strains revealed that PBVs are highly variable, and at least two distinct genogroups have been recognized. In addition, the possibility of interspecies transmission has been suggested. This article examines the molecular epidemiology and the biology of PBV and highlights the major challenges in the field.

Water quality issues and infant diarrhoea in a South American province

In the province of Salta, in the Northwest region of Argentina, almost two-thirds of the population live in absolute poverty, and diseases associated with poverty are rampant. Almost 12% of the total population of the province are children below 5 years of age; almost half of these infants are living in situations where the basic necessities are not available. Primitive sanitary conditions, including widespread contamination of available water supplies with pathogens, contribute to a major public health problem. Infant mortality was 17% higher for Salta than for Argentina as a whole in 2001. A major cause of death for these children is infectious disease, especially respiratory and intestinal diseases. In Salta, more than half of the total population of infants is affected by diarrhoea annually. The infectious pathogens are diverse: bacteria (predominantly in spring and summer), viruses (especially in the winter) and parasites (endemic in some situations). This paper evaluates current methods used to test for the presence of pathogens in drinking water; discusses why these methods are less than adequate; documents an episode of contamination in a local water supply source; and suggests appropriate methods that can be used to better address this major public health issue effectively.

Rotavirus infections among HIV-infected children in Nairobi, Kenya

Human rotaviruses have emerged as a leading cause of acute diarrhea in children <5 years of age worldwide. Although there are previous reports relating to various aspects of rotaviruses, there is limited data on the involvement of rotavirus infection in HIV-infected children. We therefore evaluated the importance of rotavirus infections in HIV-related diarrhea in Kenyan children. Fecal samples were collected from a total of 207 children during the period February 1999 to June 2000 and screened for HRV antigen by enzyme-linked immunosorbent assay (ELISA). Positive samples were analyzed by VP6 subgroup specificity assay, by polyacrylamide gel electrophoresis (PAGE) and reverse transcriptase/polymerase chain reaction (RT-PCR). Fourteen percent (29/207) of the samples were positive. HIV-seropositive children with diarrhea were more likely than their counterparts without diarrhea to have rotaviruses [23.3% (10/43) versus 2.9% (2/70); p = 0.0001]. Rotavirus strain G3P[6] was predominant. These results indicate that rotavirus is an important viral etiological agent causing diarrhea in HIV-seropositive children.

Limited duration of vaccine poliovirus and other enterovirus excretion among human immunodeficiency virus infected children in Kenya

Background

Immunodeficient persons with persistent vaccine-related poliovirus infection may serve as a potential reservoir for reintroduction of polioviruses after wild poliovirus eradication, posing a risk of their further circulation in inadequately immunized populations.

Methods

To estimate the potential for vaccine-related poliovirus persistence among HIV-infected persons, we studied poliovirus excretion following vaccination among children at an orphanage in Kenya. For 12 months after national immunization days, we collected serial stool specimens from orphanage residents aged <5 years at enrollment and recorded their HIV status and demographic, clinical, immunological, and immunization data. To detect and characterize isolated polioviruses and non-polio enteroviruses (NPEV), we used viral culture, typing and intratypic differentiation of isolates by PCR, ELISA, and nucleic acid sequencing. Long-term persistence was defined as shedding for ≥ 6 months.

Results

Twenty-four children (15 HIV-infected, 9 HIV-uninfected) were enrolled, and 255 specimens (170 from HIV-infected, 85 from HIV-uninfected) were collected. All HIV-infected children had mildly or moderately symptomatic HIV-disease and moderate-to-severe immunosuppression. Fifteen participants shed vaccine-related polioviruses, and 22 shed NPEV at some point during the study period. Of 46 poliovirus-positive specimens, 31 were from HIV-infected, and 15 from HIV-uninfected children. No participant shed polioviruses for ≥ 6 months. Genomic sequencing of poliovirus isolates did not reveal any genetic evidence of long-term shedding. There was no long-term shedding of NPEV.

Conclusion

The results indicate that mildly to moderately symptomatic HIV-infected children retain the ability to clear enteroviruses, including vaccine-related poliovirus. Larger studies are needed to confirm and generalize these findings.

Multiple novel astrovirus species in human stool

Diarrhoea remains a significant cause of morbidity and mortality in developing countries where numerous cases remain without identified aetiology. Astroviruses are a recently identified cause of animal gastroenteritis which currently includes two species suspected of causing human diarrhoea. Using pan-astrovirus RT-PCR, we analysed human stool samples from different continents for astrovirus-related RNA sequences. We identified variants of the two known human astrovirus species plus, based on genetic distance criteria, three novel astrovirus species all distantly related to mink and ovine astroviruses, which we provisionally named HMOAstV species A-C. The complete genome of species A displayed all the conserved characteristics of mammalian astroviruses. Each of the now three groups of astroviruses found in human stool (HAstV, AstV-MLB and HMOAstV) were more closely related to animal astroviruses than to each other, indicating that human astroviruses may periodically emerge from zoonotic transmissions. Based on the pathogenic impact of their closest phylogenetic relatives in animals, further investigations of the role of HMOAstV, so far detected in Nigeria, Nepal and Pakistan, in human gastroenteritis are warranted.

New real-time PCR detects prolonged norovirus excretion in highly immunosuppressed patients and children

Noroviruses (NoV) are a major cause of epidemic nonbacterial gastroenteritis and affect all age groups worldwide. Three of five NoV genogroups, namely, genogroup I (GI), GII, and GIV, are associated with human disease. Unfortunately, these genogroups demonstrate a high degree of sequence diversity, complicating the design of pan-NoV diagnostic PCR tests. To decrease the risk of false-negative test results, we have developed a new one-step real-time TaqMan reverse transcription-PCR protocol. This protocol detects all human NoV genogroups in one reaction with a sensitivity of 400 virus genome equivalents/reaction for both GI and GII. The use of in vitro-transcribed NoV RNA as an external standard allows (semi)quantification of viral loads in samples. In a retrospective analysis of 206 stool samples from 77 patient episodes, the duration of NoV excretion and the amount of virus excreted were determined. Twenty (26.0%) of these episodes lasted longer than 10 days. Univariate risk factor analysis revealed the patient status after organ transplantation (odds ratio [OR], 7.49 [95% confidence interval, 2.06 to 28.32]; P < 0.001), immunosuppression (OR, 9.19 [95% confidence interval, 2.50 to 35.39]; P < 0.001), and age of less than 10 years (OR, 4.58 [95% confidence interval, 1.36 to 15.77]; P = 0.004) as risk factors for a NoV excretion period of more than 10 days. These findings were confirmed by time-dependent Kaplan-Meier analyses, whereas multivariate Cox regression analyses identified immunosuppression as the sole risk factor. Surprisingly, in contrast to the excretion periods, the viral loads in stools did not increase in connection with age or immunosuppressive status. This fact may be one important piece in the pattern of high-level NoV transmissibility and may have an impact on the development of transmission prevention strategies.

Etiological agents of diarrhea in patients infected by the human immunodeficiency virus-1: a review

Despite the importance of understanding the epidemiology of agents responsible for infectious diarrhea in human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) population, the number of articles about this subject is relatively few. The current article summarizes published data on bacterial, fungal, viral and parasitic enteropathogens in the HIV/AIDS seropositive subjects in different countries, regions and localities. In general, there is a great difference in the frequencies of etiological agents due to factors which include immune status, geographical location, climate and socioeconomic conditions. It is important to stress that a great prevalence of infection by emergent agents has been reported in the more advanced stages of AIDS. Therefore, to establish specific treatment depends directly on knowledge of these agents and risk factors associated to their distribution. Moreover, the colonization by potential pathogenic agents verified in these individuals is high thus implicating that they act as carriers. Finally, public health measures of control and prevention must take into consideration the regional previously identified enteropathogens, especially in areas where HIV prevalence is high.

Gastrointestinal norovirus infection associated with exacerbation of inflammatory bowel disease

OBJECTIVE

In this study we aimed to determine, in pediatric patients, whether norovirus infection could be associated with exacerbations of inflammatory bowel disease (IBD) and ascertain whether the clinical expression of norovirus gastroenteritis was similar in patients with IBD compared with non-IBD controls.

MATERIALS AND METHODS

We performed a case-control retrospective chart review, over a 10-month interval, of patients with IBD with an exacerbation of their disease. The presence of norovirus in stool and/or rectal swab samples, as determined by an enzyme-linked immunoassay, was assessed. In addition, sex, age, type of IBD, presence or absence of diarrhea, hematochezia, and the need for hospitalization were determined. A similar number of control patients who did not have IBD were used as controls.

RESULTS

Nine patients with IBD (8 ulcerative colitis/1 Crohn disease) had exacerbations with diarrhea. Eight had norovirus antigen in at least 1 sample. All 9 patients with IBD presented with bloody diarrhea and 6 of the 8 norovirus-positive patients with IBD required hospitalization. All of the control patients experienced diarrhea; however, no hematochezia was noted and no hospitalization was required. Several patients with IBD and controls remained positive for norovirus months after the initial positive stool and/or rectal swab sample. The virus appeared to be more common during winter months.

CONCLUSIONS

We conclude that norovirus may be associated with exacerbations of IBD. When norovirus accompanies IBD it is more likely to be associated with hematochezia than when the infection occurs in the absence of IBD.

Prevalence of rotavirus, adenovirus and enteric parasites among pediatric patients attending Saint Camille Medical Centre in Ouagadougou

The present study carried out in the Saint Camille Medical Centre of Ouagadougou and related to the prevalence of Rotaviruses, Adenoviruses and enteric parasites infections among HIV-seropositive and HIV-seronegative children allowed to include 66 children aged from 2 to 60 months presenting acute diarrhea. The results revealed that 10.60% were infected by HIV. Stool samples analysis by direct microscopy and immunochromatographic tests (Rota-strip and Adeno-strip) showed 42.42% of global infections, among these, 18.18% parasitic infections and 24.24% viral infections, predominantly rotaviruses (22.73 and 1.52% for Rotaviruses and Adenoviruses, respectively). Among parasitic infections, Protozoan were most common than Helminthes (12.12% versus 6.06%). According to present results, Rotaviruses appeared as the major etiological agents in children aged from 2 to 11 months. However high rate of protozoan and helminthes was found in children aged from 12 to 60 months. Thus, virus, particularly Rotavirus must be painstaking as the principal etiologic agent of infant diarrhea in our country.

Detection of viral agents of gastroenteritis: Norovirus, Sapovirus and Astrovirus

Norovirus, Sapovirus and Astrovirus are causative agents of viral gastroenteritis affecting all age groups, but most frequently the young, the elderly and persons in semi-closed communities such as hospitals, nursing homes, military bases and cruise ships. The sensitive and rapid detection of causative agents of viral gastroenteritis is key to the effective implementation of infection control systems. Traditional detection methods such as electron microscopy and antigen detection assays lack sensitivity. The detection of gastrointestinal viruses by molecular methods has resulted in increased levels of detection, and enables the epidemiological investigation of viral strains. The significant diversity of gastrointestinal viruses, in particular Norovirus and Sapovirus, are compounded by increasing reports of virus recombination, and pose an ongoing challenge to the development of sensitive and specific molecular detection assays.

Picobirnavirus (PBV) natural hosts in captivity and virus excretion pattern in infected animals

A picobirnavirus (PBV) analysis was carried out by polyacrylamide gel electrophoresis of 513 stool samples obtained from 150 animal species collected from the Córdoba city zoo. The purpose of the present study was to determine susceptible species for PBV infection, the viral excretion pattern in infected animals, and the potential association with PBV diarrheic illness. Our findings suggest that PBVs are widespread in animals and could have a similar excretion behavior to that previously detected in infected humans. No disease association with PBV infection could be demonstrated. Thus, infected animals could be persistently infected asymptomatic carriers and could serve as reservoirs of infection.

Poliovirus excretion in Guatemalan adults and children with HIV infection and children with cancer

More than 20 patients with persistent poliovirus infections have been identified and reported to WHO. To date, almost all of these patients have had B-cell immune deficiency disorders. Since there are limited data on patients with HIV infection who have received oral poliovirus vaccine (OPV), we studied adults and children to determine if persons with acquired immunodeficiency due to HIV infection or cancer chemotherapy in a developing country setting had prolonged excretion of polioviruses. Stool samples from 94 HIV-infected children and 101 adults and 50 children surviving cancer in Guatemala City were cultured for polioviruses. No polioviruses were detected in any of the 195 persons with HIV infection or the 50 with cancer. The evidence from this and other studies indicates that the persistent poliovirus excretion in HIV-infected individuals is an unlikely event.

[Picobirnavirus]

Picobirnavirus is named after the small birnavirus which contains two double-stranded RNA segments as a genome. However, their properties are quite different to each other. Although the virus has been detected mainly from the stools of gastroenteritis patients and several mammals and birds, the pathogenicity of the virus has not been established. Characterizations of the virus are hampered due to the lack in the system for multiplication of the virus in cultured cells or experimental animals. Recently, complete nucleotide sequences of two RNA segments of a human picobirnavirus detected in Thailand were determined.

Use of a heminested reverse transcriptase PCR assay for detection of astrovirus in environmental swabs from an outbreak of gastroenteritis in a pediatric primary immunodeficiency unit

An outbreak of astrovirus gastroenteritis occurred in the Primary Immunodeficiency Unit at Newcastle General Hospital in March 2004. Environmental swabbing of the unit was undertaken after the outbreak, with multiple sites swabbed pre- and postcleaning. Astroviruses were detected in four environmental swabs and from two patient fecal samples using heminested reverse transcriptase PCR. An astrovirus genotype 3 strain was identified in both environmental swabs and fecal specimens and was the strain identified as being responsible for the outbreak. Environmental transmission of the virus was thought to have occurred by contamination of a syringe pump outside the laminar-flow curtain of a patient who was admitted with astrovirus gastroenteritis. This was subsequently transmitted to a cubicle next door and to a television/games console in a parents' room in the ward. Environmental monitoring of surfaces/equipment, using PCR assays for gastroenteric viruses in hospital situations where infection can give rise to serious clinical complications, may have a role in controlling and monitoring cleaning and the subsequent prevention of nosocomial transmission of gastroenteritis.

Complete nucleotide sequences of two RNA segments of human picobirnavirus

Picobirnaviruses are unclassified, non-enveloped, spherical, small viruses with a genome comprising two double-stranded RNA segments. Only incomplete sequence data on picobirnaviruses are available so far. By cloning involving single primer amplification, full-length cDNAs were prepared corresponding to RNA segments 1 and 2 of a picobirnavirus (strain Hy005102) isolated from a stool specimen from an infant with acute non-bacterial gastroenteritis in Thailand, and the complete nucleotide sequences were determined. RNA segments 1 and 2 are 2,525 and 1,745 base pairs in length, respectively. RNA segment 1 encodes two open reading frames (ORFs) of 224 and 552 amino acids, and RNA segment 2 codes for a single ORF of 534 amino acids. On comparison with a part of the nucleotide sequences of the RNA segment, 2 of the other published picobirnavirus strains, the Thai strain was found to be related most closely to one of the US strains.