A first report on the characterization of rotavirus strains in Sierra Leone

Genetic Profile of Rotavirus Type A in Children under 5 Years Old in Africa: A Systematic Review of Prevalence

Human type A rotavirus (RV-A) is world-recognized as the major pathogen causing viral gastroenteritis in children under 5 years of age. The literature indicates a substantial increase in the diversity of rotavirus strains across continents, especially in Africa, which can pose significant challenges including an increase of disease burden and a reduction of vaccines' effectiveness. However, few studies have mapped the variety of circulating virus strains in different regions, which may hamper decisions on epidemiological surveillance and preventive public health measures. Thus, our aim was to compile the most updated available evidence on the genetic profile of RV-A among children in Africa and determine the prevalence of different genotypes according to the geographical regions by means of a broad systematic review. Systematic searches were performed in PubMed, Scopus, Web of Science, and Scielo without language, time limits, or geographical restrictions within the African continent. We selected full-text peer-reviewed articles assessing the genetic profile (i.e., genotyping) of RV-A in children up to 5 years old in Africa. Overall, 682 records were retrieved, resulting in 75 studies included for evidence synthesis. These studies were published between 1999 and 2022, were conducted in 28 countries from the five African regions, and 48% of the studies were carried out for 24 months or more. Most studies (n = 55; 73.3%) evaluated RV-A cases before the introduction of the vaccines, while around 20% of studies (n = 13) presented data after the vaccine approval in each country. Only seven (9.3%) studies compared evidence from both periods (pre- and post-vaccine introduction). Genotyping methods to assess RV-A varied between RT-PCR, nested or multiplex RT-PCR, testing only the most common P and G-types. We observed G1 and P[8] to be the most prevalent strains in Africa, with values around 31% and 43%, respectively. Yet if all the genotypes with the following highest prevalence were added ((G1 + G2, G3, G9) and (P[8] + P[6], P[4])), these figures would represent 80% and 99% of the total prevalence. The combination G1P[8] was the most reported in the studies (around 22%). This review study demonstrated an increased strain diversity in the past two decades, which could represent a challenge to the efficacy of the current vaccine.

Prevalence and seasonal pattern of enteric viruses among hospitalized children with acute gastroenteritis in Samawah, Iraq

Almost all of the deaths happening under the age of 5 occur in the developed countries of Africa and Asia. This study included children admitted to the surgical care, aged 6 months to 5 years, who suffered from acute gastroenteritis and received treatment at Samawah, Iraq, from December 2018 to December 2019. Test results detected different types of rotaviruses, adenoviruses, astroviruses using ELISA. 56.6% of the infections were attributed to a viral pathogen. The main cause was attributed to rotavirus and adenovirus. The causative agents of diarrheal diseases in 28.1% of cases are rotaviruses, in 17.05% – adenoviruses, in 11.43% – astroviruses. Viral mono-infections are detected more often than mixed infections. Viral intestinal infections are characterized by seasonality and rise in the cold season, with a peak incidence of rotavirus infection in April, adenovirus infection in November, and astrovirus infection in December.

Epidemiology of Group A Rotavirus Diarrhea among Children Hospitalized for Acute Gastroenteritis in Ondo State, Nigeria

Globally, infective group A rotavirus (RVA) enteric infection in children culminates in acute diarrheal disease, severe dehydration, and mortality in children under the age of 5 years, particularly in sub-Saharan Africa. This research sought to determine the prevalence of RVA diarrhea among children aged below 5 years in Ondo state, as one of the necessary frameworks before instituting a vaccine campaign, and to expand knowledge on the epidemiology of RVA diarrhea in Nigeria.

In a cross-sectional descriptive study between October 2012 and September 2014, convenience sampling was adopted to obtain demographic information, clinical details, and stool samples from accented under five children who sought treatment for acute gastroenteritis at designated hospitals in Akure and Owo, Nigeria. A total of 390 stool samples were collected from children with acute diarrhea and tested for VP6 RVA antigen using enzyme immunoassay. Data generated were analyzed using descriptive statistics and chi-square at α 0.05.

From the 390 children hospitalized for diarrhea, 240 samples (240/390; 61.5%) were from males, while 150 samples (150/390; 38.5%) were from females, representing a male:female ratio of 1.6:1. RVAs were found in 24.2% (58/240) males and 28% (42/150) females, giving a male-female ratio of 1:1.2 and total prevalence of 25.6% (100/390). RVA infection was inversely proportional to the age as a rate of 11.8% was observed in children aged above 36 months and 31.8% (35/110) in children 7 to 12 months, while the highest rate (45.7%) was among children ≤ 6 months old. No significant difference was found (chi-square = 0.712) in the induction of diarrhea in children from Akure and Owo, neither was there any significant difference in the rates of infection between the boys and girls in Akure (chi-square = 0.576) nor in Owo (chi-square = 0.333). Seasonal association (chi-square = 5.802) in RVA infection was observed in the rainy season of year 2013/2014 period.

RVA diarrhea occurred year-round at a prevalence of 25.6%, predominantly in females. A seasonal fluctuation was observed in the rainy and dry seasons of the 2-year period. RVA diarrhea occurred predominantly in children aged below 18 months of age, and may thus help in determining the optimal period/schedule of any immunization program.

Global occurrence and emission of rotaviruses to surface waters

Group A rotaviruses (RV) are the major cause of acute gastroenteritis in infants and young children globally. Waterborne transmission of RV and the presence of RV in water sources are of major public health importance. In this paper, we present the Global Waterborne Pathogen model for RV (GloWPa-Rota model) to estimate the global distribution of RV emissions to surface water. To our knowledge, this is the first model to do so. We review the literature to estimate three RV specific variables for the model: incidence, excretion rate and removal during wastewater treatment. We estimate total global RV emissions to be 2 × 1018 viral particles/grid/year, of which 87% is produced by the urban population. Hotspot regions with high RV emissions are urban areas in densely populated parts of the world, such as Bangladesh and Nigeria, while low emissions are found in rural areas in North Russia and the Australian desert. Even for industrialized regions with high population density and without tertiary treatment, such as the UK, substantial emissions are estimated. Modeling exercises like the one presented in this paper provide unique opportunities to further study these emissions to surface water, their sources and scenarios for improved management.

Rotavirus surveillance in Kisangani, the Democratic Republic of the Congo, reveals a high number of unusual genotypes and gene segments of animal origin in non-vaccinated symptomatic children

Group A rotavirus (RVA) infections form a major public health problem, especially in low-income countries like the Democratic Republic of the Congo (COD). However, limited data on RVA diversity is available from sub-Saharan Africa in general and the COD in particular. Therefore, the first aim of this study was to determine the genetic diversity of 99 RVAs detected during 2007–2010 in Kisangani, COD. The predominant G-type was G1 (39%) and the most predominant P-type was P[6] (53%). A total of eight different G/P-combinations were found: G1P[8] (28%), G8P[6] (26%), G2P[4] (14%), G12P[6] (13%), G1P[6] (11%), G9P[8] (4%), G4P[6] (2%) and G8P[4] (1%). The second aim of this study was to gain insight into the diversity of P[6] RVA strains in the COD. Therefore, we selected five P[6] RVA strains in combination with the G1, G4, G8 (2x) or G12 genotype for complete genome analysis. Complete genome analysis showed that the genetic background of the G1P[6] and G12P[6] strains was entirely composed of genotype 1 (Wa-like), while the segments of the two G8P[6] strains were identified as genotype 2 (DS-1-like). Interestingly, all four strains possessed a NSP4 gene of animal origin. The analyzed G4P[6] RVA strain was found to possess the unusual G4-P[6]-I1-R1-C1-M1-A1-N1-T7-E1-H1 constellation. Although the majority of its genes (if not all), were presumably of porcine origin, this strain was able to cause gastro-enteritis in humans. The high prevalence of unusual RVA strains in the COD highlights the need for continued surveillance of RVA diversity in the COD. These results also underline the importance of complete genetic characterization of RVA strains and indicate that reassortments and interspecies transmission among human and animal RVAs strains occur regularly. Based on these data, RVA vaccines will be challenged with a wide variety of different RVA strain types in the COD.

Importance of viral pathogens in children with acute gastroenteritis in the south of Iran

BACKGROUND AND OBJECTIVES

Different types of viruses are the leading cause of acute diarrhea among infants and young children worldwide. Epidemiological surveillance of viral agents is critical for the develop.ment of effective preventive measures, including vaccines. This study aimed to determine the prevalence of the four major enteropathogenic viruses-rotavirus, norovirus, adenovirus and astrovirus-in children over 7 years of age.

DESIGN AND SETTING

A cross-sectional descriptive study conducted on stool specimens of children with acute gastroenteritis admitted to the Pediatrics Unit of 17 Shahrivar Hospital in Borazjan, Iran from October 2008 to September 2010.

PATIENTS AND METHODS

Acute gastroenteritis was defined as >=3 loose watery stools per 24 hours. A total of 375 stool samples were collected from hospitalized children aged < 7 years old with acute gastroenteritis. All samples were investigated by using enzyme-linked immunosorbent assay for the presence of viral antigens.

RESULTS

Rotavirus was detected in 91 (24.3%) of the patients whereas the prevalence of norovirus, adenovirus and astrovirus was 12.5%, 5.1% and 2.4%, respectively. On average, 75.9% of children with viral diarrhea were younger than 2 years old (P=.023). All the strains of viral gastroenteritis studied peaked in the autumn, except for adenovirus which peaked in spring (P=.015). The most common clinical symptoms included diarrhea (92.2%), vomiting (68.7%), abdominal cramp (60.8%) and moderate dehydration (57.2%).

CONCLUSION

Since nearly half of gastroenteritis cases (44.3%) were due to viral agents, testing for the viral antigens may guide the clinical approach to those patients with acute diarrhea particularly in the case of children less than 2 years old, and during cold seasons.

Rotavirus in diarrheal children in rural Burkina Faso: high prevalence of genotype G6P[6]

Group A rotavirus (RVA) is the most common cause of severe gastroenteritis in young children globally, and responsible for a significant number of deaths in African countries. While vaccines are available, trials have shown a lesser efficacy in Africa. One of the reasons could be the prevalence and/or emergence of unusual or novel RVA strains, as many strains detected in African countries remain uncharacterized. In this study, we characterized RVA positive specimens from two remote rural areas in Burkina Faso, West Africa. In total 56 RVA positive specimens were subgrouped by their VP6 gene, and G-and P typed by PCR and/or sequencing of the VP7 and VP4 genes, respectively. Notably, we found a high prevalence of the unusual G6P[6]SGI strains (23%). It was the second most common constellation after G9P[8]SGII (32%); and followed by G1P[8]SGII (20%) and G2P[4]SGI (9%). We also detected a G8P[6]SGI strain, for the first time in Burkina Faso. The intra-genetic diversity was high for the VP4 gene with two subclusters within the P[8] genotype and three subclusters within the P[6] genotype which were each associated with a specific G-type, thereby suggesting a genetic linkage. The G6P[6]SGI and other SGI RVA strains infected younger children as compared to SGII strains (p<0.05). To conclude, in this study we observed the emergence of unusual RVA strains and high genetic diversity of RVA in remote rural areas of Burkina Faso. The results highlight the complexity of RVA epidemiology which may have implication for the introduction of rotavirus vaccines currently being evaluated in many African countries.

Burden and typing of rotavirus group a in children with acute gastroenteritis in shiraz, southern iran

BACKGROUND

Human Rotavirus is a significant cause of severe gastroenteritis in infants and young children worldwide. In recent years, Rotavirus genotyping by RT-PCR has provided valuable information about the diversity of Rotaviruses circulating worldwide. The purpose of the present study is to monitor the prevalence of the different G types of Rotaviruses circulating in Shiraz, Southern Iran and detect any uncommon or novel types.

METHODS

During the period from December 2007 to November 2008, a total of 138 stool samples were collected from children less than 5 years old who were hospitalized for acute gastroenteritis. Rotavirus-associated diarrhea was investigated in fecal specimens with enzyme immunoassays (EIA). Rotavirus-positive specimens were typed by the Nested RT-PCR and by using different types of specific primers.

RESULTS

Out of the 138 collected samples, 34.78% (48 cases) tested positive for Rotavirus. The frequency of G1, G2 and G4 types was 6.25%, 2.08% and 27.08%, respectively. Mixed and non-typeable infections were detected in 33.34% and 31.25% of hospitalized children with acute diarrhea, respectively. This is the first time mixed Rotavirus infections with G1/G3 have been reported in Iran.

CONCLUSION

The high frequency of Rotavirus detection indicates the severity and the burden of Rotavirus disease may be able to reduce through the implementation of an effective vaccine and continual surveillance for the detection of Rotavirus genotypes circulating in other regions of Iran. Regarding to the noticeable frequency of non-typeable and mixed infections, it is suggested to use the other specific primers and further studies to detection of other novel and unusual types.

Whole-genome analysis reveals the complex evolutionary dynamics of Kenyan G2P[4] human rotavirus strains

Although G2P[4] rotaviruses are common causes of acute childhood diarrhoea in Africa, to date there are no reports on whole genomic analysis of African G2P[4] strains. In this study, the nearly complete genome sequences of two Kenyan G2P[4] strains, AK26 and D205, detected in 1982 and 1989, respectively, were analysed. Strain D205 exhibited a DS-1-like genotype constellation, whilst strain AK26 appeared to be an intergenogroup reassortant with a Wa-like NSP2 genotype on the DS-1-like genotype constellation. The VP2-4, VP6-7, NSP1, NSP3 and NSP5 genes of strain AK26 and the VP2, VP4, VP7 and NSP1–5 genes of strain D205 were closely related to those of the prototype or other human G2P[4] strains. In contrast, their remaining genes were distantly related, and, except for NSP2 of AK26, appeared to originate from or share a common origin with rotavirus genes of artiodactyl (ruminant and camelid) origin. These observations highlight the complex evolutionary dynamics of African G2P[4] rotaviruses.