Molecular characterization of rotavirus gastroenteritis strains, Iraqi Kurdistan

Molecular epidemiology, genetic diversity, and vaccine availability of viral acute gastroenteritis in the middle East and North Africa (MENA) region

Acute gastroenteritis is the cause of considerable mortality and morbidity worldwide, particularly among children under five years in underdeveloped countries. Most acute gastroenteritis (AGE) cases are attributed to viral etiologies, including rotavirus, norovirus, adenovirus, astrovirus, and sapovirus. This paper aimed to determine the prevalence rate of different viral etiologies of AGE in the Middle East and North Africa (MENA) region. Moreover, this paper explored rotavirus phylogenetic relatedness, compared VP7 and VP4 antigenic regions of rotavirus with vaccine strains, and explored the availability of vaccines in the MENA region. The literature search identified 160 studies from 18 countries from 1980 to 2019. The overall prevalence of rotavirus, norovirus, adenovirus, astrovirus, and sapovirus were 29.8 %, 13.9 %, 6.3 %, 3.5 %, and 3.2 % of tested samples, respectively. The most common rotavirus genotype combinations in the MENA region were G1P[8], G9P[9], and G2P[4], whereas GII.4 was the predominant norovirus genotype all of which were reported in almost all the studies with genotyping data. The comparison of VP7 and VP4 between circulating rotavirus in the MENA region and vaccine strains has revealed discrete divergent regions, including the neutralizing epitopes. Rotavirus vaccine was introduced to most of the countries of the MENA region; however, only a few studies have assessed the effectiveness of vaccine introduction. This paper provides a comprehensive update on the prevalence of the different viral agents of AGE in the MENA region.

Epidemiological, molecular, and clinical features of rotavirus infections among pediatrics in Qatar

Acute gastroenteritis (AGE) remains a major cause of diarrhea in developing and developed countries. Rotavirus (RV) is a leading cause of severe pediatric diarrhea worldwide. Here we report on the prevalence of circulating genotypes in association with demographics and clinical manifestations outcomes in Qatar. A total of 231 RV-positive fecal samples were collected from children suffering from AGE during 3 years study period between June 2016 and June 2019. The age of the subjects ranged between 2 months and 14 years (median of 16 months). The VP4 and VP7 were amplified and sequenced. Phylogenetic analyses were performed using MEGA7.0. Pearson's chi-squared test was used to determine significant differences for comparisons of general categorical variables. RV infections were most common in children between 1 and 3 years of age (49%), followed by those < 1 year and > 3 years of age (33% and 28%, respectively). RV infections were more frequent in males than females, with a ratio of 1.4:1. RV infections occurred throughout the year, with a noticeable increase in summer (42.8%) and a drop in winter (20.1%). RV genotypes G3P[8] (30.8%), G2P[8] (12.3%), G4P[8] (11.7%), and G1P[8] (10.4%) were the common genotypes during the study period. The G3P[8] strain detected in our study revealed similarities to the equine-like G3P[8] (10.3%; 24/231) (KT988229.1), Wa-like genomic constellation (9%; 21/231) (MF563894.1), and DS-1-like strains (6.4%; 15/231) (LC386081.1). Based on the Vesikari score system, severe clinical illness including diarrhea and vomiting (average frequency: 4 to 5 times/day) was recorded for G3P[8] group, followed by G9P[8], G4P[8], and G1P[8]. Higher incidence for G3P[8], G2P[8], G4P[8], and G1P[8] were reported in Qatari subjects compared to other nationalities. The multinational status of a small country explains the wide diversity of circulating RV genotypes in Qatar. The highest prevalence and severe illnesses were recorded to G3P[8], which is different from other surrounding countries/global levels.

Systematic review of the rotavirus infection burden in the WHO-EMRO region

Rotavirus gastroenteritis imposes a heavy burden on low- and middle-income countries. The World Health Organization defines the Eastern Mediterranean region (WHO-EMRO) as a diverse area in terms of socioeconomic status and health indicators. Rotavirus vaccination has been introduced, at least partially, in 19 out of the 22 EM countries; however, vaccine coverage remains low, and data on rotavirus disease burden is scarce.Available data on rotavirus prevalence, seasonality, vaccination status, and genotype evolution was systematically compiled following a literature review that identified 165 relevant WHO-EMRO epidemiology studies published between 1990 and 2017.Although the infectious agents responsible for acute gastroenteritis vary over time, rotavirus remained the leading cause of acute gastroenteritis in children, as seen in 76.3% of reviewed publications. Younger children (<2 years old) were at higher risk and thus increased vaccination coverage and surveillance systems are required to reduce the rotavirus gastroenteritis burden in WHO-EMRO countries.

Circulating rotavirus G and P strains post rotavirus vaccination in Eastern Mediterranean Region

OBJECTIVE

To detect changes in circulating strains of rotavirus in the Eastern Mediterranean Region post rotavirus immunization drive.

METHODS

We searched MEDLINE, PubMed, ScienceDirect, and the Cochrane Library and specific database website (Nutrition and Food Sciences) for relevant articles. Our search included websites of a number of relevant organizations in addition to gray literature search. Of the 2198 articles found, we included only 35 studies after excluding irrelevant, ineligible, duplicated, and very low-quality papers.

RESULTS

Thirty pre-vaccination studies reported frequent rotavirus strains among children below 5 years of age. G1P[8] has been identified as the most dominant type prior to vaccination in Eastern Mediterranean Region (EMR) countries. Five post-vaccination studies conducted in 3 countries (Saudi Arabia, Morocco, and Yemen) illustrated that G1P[8] is the most prevalent strain in Saudi Arabia, and the incidence of G2P[4] has increased from 21.6% to 33.3%. In Yemen, G1P[4] is the most prevalent strain (87.5%), followed by G9P[8] (57%) and G1P[8] (18.5%). Furthermore, in Yemen, G9P[8] were the most prevalent strains accounting to 57% and 14% in G9P[4], post vaccination. Finally, in Morocco, G1P[8] was not reported 3 years post vaccination; however, incidence of G9P[8] was reported at 67% and G2P[4] at 33%.

CONCLUSIONS

Rotavirus circulating strain prevalence in EMR countries has changed post vaccination, and G9P[8], G2P[4], and G9P[4] have become more dominant. Proportion of rotavirus strains in these countries after vaccination has significantly reduced. There is an increase in circulating strain G2P[4] in the post-vaccination period, which needs further monitoring.

Prevalence, risk factors and antimicrobial resistance of Salmonella diarrhoeal infection among children in Thi-Qar Governorate, Iraq

We conducted a hospital-based cross-sectional study among children aged <5 years in Thi-Qar Governorate, south-eastern Iraq, in order to examine the prevalence, risk factors and antimicrobial resistance associated with gastroenteritis caused by Salmonella infection. From 320 diarrhoea cases enrolled between March and August 2016, 33 (10·3%, 95% confidence interval (CI) 8·4-12·4) cases were stool culture-positive for non-typhoidal Salmonella enterica. The most commonly identified serovar was Typhimurium (54%). Multivariable logistic regression analysis indicated that the odds of Salmonella infection in children from households supplied by pipe water was 4·7 (95% CI 1·6-13·9) times higher compared with those supplied with reverse osmosis treated water. Similarly, children from households with domestic animals were found to have a higher odds (OR 10·5; 95% CI 3·8-28·4) of being Salmonella stool culture-positive. The likelihood of Salmonella infection was higher (OR 3·9; 95% CI 1·0-6·4) among children belonging to caregiver with primary vs. tertiary education levels. Lower odds (OR 0·4; 95% CI 0·1-0·9) of Salmonella infection were associated with children exclusively breast fed as compared with those exclusively bottle fed. Salmonella infection was three times lower (95% CI 0·1-0·7) in children belonging to caregiver who reported always washing hands after cleaning children following defecation, vs. those belonging to caregivers who did not wash hands. The antimicrobial resistance profile by disc diffusion revealed that non-susceptibility to tetracycline (78·8%), azithromycin (66·7%) and ciprofloxacin (57·6%) were the most commonly seen, and 84·9% of Salmonella isolates were classified as multi-drug resistant. This is the first study on prevalence and antimicrobial resistance of Salmonella infection among children in this setting. This work provides specific epidemiological data which are crucial to understand and combat paediatric diarrhoea in Iraq.

Update on the epidemiology of rotavirus in the Middle East and North Africa

Rotavirus (RV) is the leading cause of severe acute gastroenteritis (AGE) worldwide. Consequently, we conducted a systematic literature review on articles studying RV in the 25 countries of the MENA region during the past 15years (2000-2015). The methods and reporting were set according to the 2015 preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) and based on the elements from the international prospective register of systematic reviews (PROSPERO). Our literature search identified 169 studies meeting our predefined inclusion criteria. Studies reporting on RV were conducted in 19 out of the 24 countries of the MENA region. The largest number of studies was reported in Turkey (n=32), Iran (n=31), Saudi Arabia (n=19) and Egypt (n=17). The majority of studies reporting on RV gastroenteritis rates were clinical observational studies. In 115 studies out of 169, RV was reported among in-patients whereas 35 studies reported RV among outpatients. The predominantly reported RV genotype in the region was G1[P8] followed by G2[P4] and G9[P8]. The majority of studies (n=108) were conducted among children less than 5years of age whereas the remaining studies reported on AGE among other age groups and rarely adults. In MENA countries, RV infection was reported all year round with peaks described in cold as well as hot months. This systematic review provides a current update on the epidemiology of RV-associated gastroenteritis in countries of the MENA region and draws attention to the major gaps existing in the continuous monitoring of RV.

Detection and sequencing of rotavirus among sudanese children

INTRODUCTION

Diarrheal diseases are a big public health problem worldwide, particularly among developing countries. The current study was conducted to detect and characterize group A rotavirus among admitted children with gastroenteritis to the pediatric hospitals, Sudan.

METHODS

A total of 755 stool samples were collected from Sudanese children with less than 5 years of age presenting with acute gastroenteritis during the period from April to September 2010. Enzyme-linked immunosorbent assay (ELISA) was used to Detection of Rotavirus antigens. Ribonucleic acid (RNAs) were extracted from rotavirus-positive stool samples using (QIAamp® Viral RNA Mini Kit). (Omniscript® Reverse Transcription kit) was used to convert RNA to complementary Deoxyribonucleic acid (cDNA). The cDNAs were used as template for detection of VP4-P (P for Protease-sensitive) and VP7-G (G for Glycoprotein) genotyping of Rotavirus using nested PCR and sequencing.

RESULTS

Out of the 755 stool samples from children with acute gastroenteritis, 121 were positive for rotavirus A. Among 24 samples that were sequenced; the VP7 predominant G type was G1 (83.3%), followed by G9 (16.7%). Out of these samples, only one VP4 P[8] genotype was detected.

CONCLUSION

As a conclusion the VP7 predominant G type was G1, followed by G9 whereas only one VP4 genotype was detected and showed similarity to P[8] GenBank strain. It appears that the recently approved rotavirus vaccines in Sudan are well matched to the rotavirus genotypes identified in this study, though more studies are needed.

Rotavirus Genotypes and Vaccine Effectiveness from a Sentinel, Hospital-Based, Surveillance Study for Three Consecutive Rotavirus Seasons in Lebanon

Introduction

Globally, rotavirus (RV) is the leading cause of gastroenteritis (GE) in children. Longitudinal data about changes in RV genotype distribution and vaccine effectiveness (VE) are scarce. This study was conducted in Lebanon over 3 consecutive RV seasons to estimate the rate of RVGE hospitalization, identify RV genotypes, determine the seasonal and geographical variations, and calculate RV VE.

Materials and Methods

This prospective, multicenter, hospital-based surveillance study was conducted between 2011 and 2013 and enrolled children (<5 years) admitted for GE. Socio-demographic and clinical data about the current episode of GE at admission were collected. Genotypes were determined from stool samples testing positive for RV by PCR.

Results

Of 1,414 cases included in the final analysis, 83% were <2 years old and 55.6% were boys. Median duration of hospitalization was 4 days and 91.6% of GE cases were severe (Vesikari score ≥11). PCR testing showed that 30.3% of subjects were RV-positive of which 62.1% had fever versus 71.1% of RV-negative subjects (P = 0.001). RV was predominantly detected in the cold season from November till March (69.9%). G and P genotype pairs for all RV-positive stool specimens showed a predominance of G1P[8] in 36% (n = 154) of specimens, G9P[8] in 26.4% (n = 113), and G2P[4] in 17.8% (n = 76). RV-negative subjects were more likely to be RV-vaccinated (21%) compared to the RV-positive subjects (11.3%) (P<0.001), with a vaccine breakthrough rate of 18.8%. The ratio of RV1-vaccinated for each RV5-vaccinated subject was 7.8 and VE against RV disease was 68.4% (95%CI, 49.6%-80.2%).

Conclusion

RV is a major cause of GE requiring hospitalization of children under 5 years of age in Lebanon. A few genotypes predominated over the three RV seasons studied. Mass RV vaccination will likely decrease the burden of hospitalization due to RV. VE is similar to what has been observed for other middle-income countries.

Rotavirus Diarrhea among Children in Taiz, Yemen: Prevalence-Risk Factors and Detection of Genotypes

Diarrheal diseases are a great public health problem; they are among the most causes leading to morbidity and mortality of infants and children particularly in developing countries and even in developed countries. Rotavirus is the most common cause of severe gastroenteritis in infants and young children in both developed and developing countries. The purpose of this study was to determine the incidence rate of Rotavirus infection, its genotypes, and risk factors among children with diarrhea in Taiz, Yemen. 795 fecal samples were collected from children (less than 5 years old), suffering from diarrhea and attending the Yemeni-Swedish Hospital (YSH) in Taiz , Yemen, from November 2006 to February 2008. Rotavirus was detected by enzyme linkage immunosorbent assay (ELISA) on stool specimens of children. Genotypes of Rotavirus were characterized by reverse transcriptase-polymerase chain reaction (RT-PCR) and polyacrylamide gel electrophoresis (PAGE). The results showed that 358 (45.2%) were Rotavirus-positive and the most prevalent genotypes were G2P[4] (55%), followed by G1P[8] (15%). In addition, Rotavirus was found through the whole year; however, higher frequency during the summer season (53.4%) and lower frequency during the winter season (37.1%).

Comparison of different RT-qPCR assays for the detection of human and bovine group A rotaviruses and characterization by sequences analysis of genes encoding VP4 and VP7 capsid proteins

AIMS

The aim of this study was to compare the performance of four RT-qPCR assays for the detection of human and bovine group A rotaviruses and to characterize the positive samples by sequence analysis of VP4 and VP7 genes.

METHODS AND RESULTS

RNA extracted from eight human rotavirus strains, and a panel of 33 human and 25 bovine faecal samples was subjected to different RT-qPCR detection systems. Among these assays, only RT-qPCR primers and probe systems B and C were able to detect all human rotavirus strains from cell culture solutions and faecal samples. However, the results showed that the system C was generally more sensitive by one or two logs than the other RT-qPCR assays tested. With the bovine faecal samples, the most efficient RT-qPCR systems were B and A with the detection in 100 and 92% of samples tested, respectively. Human group A rotavirus G1P[8] and bovine G6P[11] were the most frequently used strains identified in this study. A G3P[9] strain, closely related to a feline rotavirus isolated in the USA, was also discovered in a human rotavirus infection.

CONCLUSION

The RT-qPCR system B was the only TaqMan assay evaluated in this study able to detect rotavirus RNA in all positive human and bovine faecal samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

Utilization of only one RT-qPCR for the detection of human and bovine group A rotaviruses and the possibility of human infection by a feline rotavirus strain.

Characterization of human rotaviruses circulating in Iraq in 2008: atypical G8 and high prevalence of P[6] strains

Fecal samples from 976 children with gastroenteritis were collected and analyzed for group A rotavirus (RVA), in three different cities in Iraq between January 2008 and December 2008. RVA antigen was detected in 394 (40%) of the samples, and 98 samples were available for further genotype analyses using multiplex RT-PCR and sequence analyses for untypeable strains. The G/P-genotype combination was determined for 69 samples, and 19, 2 and 8 samples remained P-untypeable, G-untypeable and G/P-untypeable (UT), respectively. The most prevalent genotype was G2 (40%, 39/98) most often associated with P[6]. G1 was the second most common genotype (16%, 16/98) mainly associated with P[8] and P[UT]. G3, G4 and G9 were detected at a lower prevalence (3%, 11%, 3%, respectively), mainly associated with P[6]. Surprisingly, five G8P[6], and seven G12 RVA strains in combination with P[6] and P[8] were also detected for the first time in Iraq. Overall, a striking high prevalence of 47% of the analyzed samples possessed the P[6] genotype (65% of the P-typed RVA strains). Atypical genotype combinations such as G1P[4], G1P[6], G2P[8] or strains with mixed G-types were detected sporadically. The detection of unusual G8P[6] RVA strains prompted us to further analyze the NSP2, NSP3, NSP4 and NSP5 gene segments of three selected G8P[6] strains, resulting in their designation to the N2, T2, E2 and H2 genotypes, respectively. The VP7, VP4, NSP2, NSP3 and NSP5 gene segments clustered closely with common human RVA strains, whereas the NSP4 gene sequences were found to cluster with animal derived RVA strains, suggesting a potential reassortment event. The high prevalence of RVA strains with the G8, G12 and P[6] genotypes in combination with a DS-1-like genotype constellation in Iraq, needs to be monitored closely as these RVA strains might challenge the effectiveness of current RVA vaccines.

Clinical features and molecular epidemiology of rotavirus and norovirus infections in Libyan children

Rotaviruses and noroviruses are leading viral causes of diarrhoea in children. A cross-sectional study was undertaken among children aged <5 years with acute gastroenteritis at Al-Jala Children's Hospital, Tripoli, Libya, from October 2007 to September 2008. Of 1,090 fecal samples collected, 260 from inpatients and 830 from outpatients, all inpatients and approximately a third of outpatients, selected systematically, were investigated for rotavirus and norovirus infection by ELISA and real-time RT-PCR, respectively. Of 520 fecal samples examined (inpatients = 260, outpatients = 260), 164 (31.5%) had rotavirus and 91 (17.5%) had norovirus detected. Rotavirus was identified more often among inpatients than outpatients (35.8% vs. 27.3% respectively, P = 0.038). Norovirus was detected more commonly among outpatients than inpatients (21.2% vs. 13.8% respectively, P = 0.028). The peak incidence of infection with both viruses was among children aged between 6 and 11 months. The number of rotavirus cases was highest between November and June with a peak detection rate of 50% in January. Norovirus occurred most commonly from May through August with a peak detection rate of 47% in August. The most prevalent rotavirus genotypes were P[8], G9 (n = 116, 65.9%), followed by P[8],G1 (n = 49, 27.8%); a single P[9], G3 strain was detected. There were seven distinct electropherotypes among the G9 strains and all belonged to VP7 Lineage III. Among 91 noroviruses identified, 90 were genogroup II. Of 26 genogroup II noroviruses examined, all were genotype GII.4. Rotaviruses and noroviruses are both important causes of gastrointestinal infection among young children in Libya.

Genotypes of rotavirus strains circulating in Amman, Jordan, in 2006/07 and their significance for the potential effectiveness of future rotavirus vaccination

The prevalence, seasonality and genotypes of rotavirus circulating in Jordan were determined to provide data useful for the implementation of a rotavirus vaccine in the national childhood vaccination program. During 2006/07, rotavirus was detected in 35% of hospitalized children, and 88% of the cases occurred in children aged between 6 and 23 months. Rotavirus infection persisted throughout the year and peaked in winter. Seven genotypes were identified by RT-PCR and sequencing: G1P[8], G9P[8], G2P[4], G1P[4], G3P[8], G4P[8] and G9P[6], which represented 69%, 8.8%, 2.4%, 2.0%, 1.2%, 0.4% and 0.4% of the rotavirus strains, respectively. Thirteen percent and 2.8% of the total strains were partially typed or untypeable, respectively. Eighty-eight percent and 12% of the rotavirus strains possessed a long and short electropherotype, respectively. As more than 90% of the rotavirus strains circulating in Jordan possessed the G1 or P[8]-genotype, it is concluded that the implementation of the rotavirus vaccine in the framework of the national childhood vaccination program of Jordan would most likely be very effective. Continuous monitoring of the currently circulating genotypes in Jordan should be encouraged.

Burden of rotavirus gastroenteritis in the Middle Eastern and North African pediatric population

Background

Rotavirus gastroenteritis (RVGE) is the most common cause of severe childhood diarrhea worldwide. Objectives were to estimate the burden of RVGE among children less than five years old in the Middle East (Bahrain, Iran, Iraq, Israel, Jordan, Kuwait, Oman, Qatar, Saudi Arabia, Syria, UAE, Yemen), North Africa (Algeria, Egypt, Libya, Morocco, Tunisia) and Turkey.

Methods

A comprehensive literature search was conducted in major databases on the epidemiology and burden of rotavirus among children less than five years old between 1999 and 2009. Data from each country was extracted and compared.

Results

The search identified 43 studies. RVGE was identified in 16-61% of all cases of acute gastroenteritis, with a peak in the winter. RVGE-related hospitalization rates ranged from 14% to 45%, compared to 14%-28% for non-RVGE. Annually, RVGE caused up to 112 fatalities per 100,000 in certain countries in the region. Hospitalization costs ranged from $1.8 to $4.6 million annually, depending on the country. The most recent literature available showed that G1P[8] was the most prevalent genotype combination in 8 countries (range 23%-56%). G2P[4] was most prevalent in 4 countries (26%-48%). G9P[8] and G4P[8] were also frequently detected.

Conclusions

RVGE is a common disease associated with significant morbidity, mortality, and economic burden. Given the variety and diverse rotavirus types in the region, use of a vaccine with broad and consistent serotype coverage would be important to help decrease the burden of RVGE in the Middle East and North Africa.

Molecular epidemiology of rotavirus diarrhea among children in Saudi Arabia: first detection of G9 and G12 strains

In anticipation of rotavirus vaccine introduction in Saudi Arabia, this study was undertaken to determine the distribution of the G and P genotypes of rotaviruses in order to examine whether there was any emerging serotype or unusual strain circulating in children in Saudi Arabia. Of 984 stool specimens collected between 17 April 2004 and 16 April 2005, rotavirus was detected by an enzyme-linked immunosorbent assay in 187 (19%) diarrheal children less than 5 years of age. Of these, 160 (86%) were classified into G and P genotypes as follows: G1P[8] (44%), G2P[4] (20%), G9P[8] (11%), G12P[8] (4%), and G3P[8] (4%). RNA polyacrylamide gel electrophoresis identified 94 (50%) specimens as long RNA patterns, 30 (16%) specimens as short RNA patterns, and 1 mixed infection. Only a single long RNA electropherotype was identified for seven specimens containing G12P[8] rotavirus. RNA-RNA hybridization demonstrated that the G12P[8] strains were similar in their genomic constellation to locally cocirculating strains and to a Nepalese G12P[8] strain. The Saudi Arabian G12 VP7 gene had a 99% nucleotide sequence identity with Nepalese and Indian G12 VP7 genes and belonged to the third lineage. This study is the first to describe the distribution of rotavirus G and P types and also the first to identify G9P[8] and G12P[8] strains in the country.

Genotypic characterization of rotaviruses and prevalence of serotype-specific serum antibodies in children in Kuwait

There are no data on the serotypes of rotaviruses prevalent in Kuwait, which has a large expatriate population and hence a focal point for transmission of pathogens. The serotype information will contribute to the fund of knowledge on the world epidemiology of rotavirus serotypes and will predict the outcome of vaccination in Kuwait. Of the 75 rotavirus-positive samples from 172 children (aged <5 years) with severe diarrhoea, 69 were genotyped. The distribution of genotypes was G1 (63.8%) followed by G9 (10.2%), G2 (7.3%), G4 (7.3%) and G3 (4.4%). Among the P types, P[8] was the most common type found across all G types. By fluorescent focus neutralization test, serum antibodies to genotypes G1 (94%), G4 (68%) and G9 (46%) were found in 120 other children. These results show that G1 is the predominant serotype in Kuwait and that a vaccine that contains G1 will be most effective.