Genomic characterization of nontypeable rotaviruses and detection of a rare G8 strain in Delhi, India

Emergence of Intergenogroup Reassortant G9P[4] Strains Following Rotavirus Vaccine Introduction in Ghana

Rotavirus (RVA) is a leading cause of childhood gastroenteritis. RVA vaccines have reduced the global disease burden; however, the emergence of intergenogroup reassortant strains is a growing concern. During surveillance in Ghana, we observed the emergence of G9P[4] RVA strains in the fourth year after RVA vaccine introduction. To investigate whether Ghanaian G9P[4] strains also exhibited the DS-1-like backbone, as seen in reassortant G1/G3/G8/G9 strains found in other countries in recent years, this study determined the whole genome sequences of fifteen G9P[4] and two G2P[4] RVA strains detected during 2015-2016. The results reveal that the Ghanaian G9P[4] strains exhibited a double-reassortant genotype, with G9-VP7 and E6-NSP4 genes on a DS-1-like backbone (G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2). Although they shared a common ancestor with G9P[4] DS-1-like strains from other countries, further intra-reassortment events were observed among the original G9P[4] and co-circulating strains in Ghana. In the post-vaccine era, there were significant changes in the distribution of RVA genotype constellations, with unique strains emerging, indicating an impact beyond natural cyclical fluctuations. However, reassortant strains may exhibit instability and have a limited duration of appearance. Current vaccines have shown efficacy against DS-1-like strains; however, ongoing surveillance in fully vaccinated children is crucial for addressing concerns about long-term effectiveness.

Whole-genome characterization of common rotavirus strains circulating in Vellore, India from 2002 to 2017: emergence of non-classical genomic constellations

Rotaviruses (RVs) are the most common etiological agent of acute gastroenteritis among young children, even after vaccine introduction in low-income countries. A whole-genome classification representing the 11 RV genes, was introduced for surveillance and characterization of RVs. This study characterized the common circulating strains in Vellore, India from 2002 to 2017 to understand rotavirus strain diversity and evolution using Whole genome sequencing (WGS) carried out on Illumina MiSeq. The 89% (92% of Wa-like, 86% of DS-1-like) of strains had classical constellations, while reassortant constellations were seen in 11% (8% of Wa-like, 14% of DS-1-like) of the strains. The rare E6-NSP4 in combination with DS-1 like G1P[8] and the emergence of the OP-354 subtype of P[8] were identified. Phylogenetics of RV strains revealed multiple subtypes circulating in the past 15 years, with strong evidence of animal to human gene transmission among several strains.

Molecular characterization of rotavirus infections in children less than 5 years of age with acute gastroenteritis in Tehran, Iran, 2021-2022: Emergence of uncommon G9P[4] and G9P[8] rotavirus strains

The present study was conducted to monitor the genotypes of circulating species A rotavirus (RVA) in Iran and investigate genetic linkages between specific RVA VP7, VP4, VP6, and NSP4 segments. For this purpose, 48 RVA strains were detected during the 2021-2022 seasons. The two combinations of G9P[4] and G9P[8] RVA strains were predominant. However, several other combinations of RVA also were detected. Based on the distribution of I and E genotypes (46 strains) with respect to G and P, the most common strains were G9P[4]-I2-E2 (19.5%), G9P[4]-I2-E1 (6.5%), G9P[4]-I1-E1 (4.3%), G9P[8]-I1-E1 (19.5%), and G9P[8]-I2-E2 (10.9%), which were followed by several other combinations of G and P RVA strains with different pattern of I-E genotypes and also emerging, rare and uncommon strains. The present study described the continued circulation of G9 strains with the emergence of uncommon G9P[4] and G9P[8] reassortants with three and two different I-E genotypes, respectively, which have not been reported previously in Iran. Our findings indicated that these uncommon strains exhibited a unique genotype pattern comprising a mixture of genogroup 1 and 2 genes and suggest the need for further analysis of rare, uncommon, and emerging strains of RVA at all 11 gene segments to determine intergenogroup and intragenotype reassortments.

Molecular surveillance of rotavirus A associated with diarrheic calves from the Republic of Korea and full genomic characterization of bovine-porcine reassortant G5P[7] strain

Group A rotavirus (RVA) is the most common diarrhea-causing pathogen among humans and animals worldwide. Rotavirus infection in neonatal calves causes major problems in the livestock industry. This study aimed to determine the prevalence and genetic diversity of bovine rotavirus (BoRVA) infections in calves with diarrhea and to perform whole genome analysis of an unusual strain, designated as RVA/Calf-wt/KOR/KNU-GJ2/2020/G5P[7], that was detected in a 2-day-old diarrheic calf. From 459 diarrheic calves aged 1-40 days, fecal samples were collected and BoRVA infections were screened using real-time RT-PCR targeting VP6 gene. BoRVA was detected in 195 (42.4%) samples and was most prevalent in calves aged 1-10 days (47.2%). No significant difference in the BoRVA infection rate was observed between calves born in herds that were (42.1%) and were not (42.6%) vaccinated against BoRVA. A binomial regression analysis revealed that calves aged 1-10 days (95% confidence intervals [CI]:1.18-24.34; P = 0.000) and 11-20 days (95% CI: 0.76-16.83, P = 0.000) had a 5.37- and 3.58-fold higher BoRVA prevalence in comparison to those aged 31-40 days, respectively. The RVA-positive samples were subsequently subjected to amplification of the VP7 and VP4 genes for determining G and P genotypes. Overall, 45 (23.1%, 45/195) and 63 (32.3, 63/195) sequences for VP7 and VP4 were obtained. In this study, four G and three P genotypes were identified. G6 (86.7%) was the most prevalent genotype, followed by G8 (8.9%), G10 (2.2%), and G5 (2.2%). P[5] (92.1%) was the most frequently detected, followed by P[11] (6.3%), and P[7] (1.6%). The G6P[5] (82.2%) is the most common combination found in Korean native calves with diarrhea, whereas G6P[11] (4.4%) and G10P[11] (2.2%) had relatively low prevalence. G8P[5] (8.9%) was identified for the first time in diarrheic calves in the KOR. The uncommon strain KNU-GJ2 exhibited a G5-P[7]-I5-R1-C1-M2-A1-N1-T1-E1-H1 genotype constellation possessing a typical porcine RVA backbone, with the exception of the VP3 gene, which is derived from bovine. Phylogenetically, except for VP3, ten gene segments of KNU-GJ2 were closely related to porcine, porcine-like, and reassortant bovine strains. Interestingly, the VP3-M2 gene of KNU-GJ2 clustered with bovine-like strains as well as reassortant porcine and bovine strains. Comparison of the NSP4s within a species-specific region of amino acids 131-141 demonstrated that KNU-GJ2 belonged to genotype B with porcine RVAs; however, it differed from porcine RVAs by one to three amino acids. The present study is fundamental to understanding the epidemiology and genotypes of circulating RVAs throughout the KOR and underscoring the importance of continuous monitoring and molecular characterization of RVAs circulating within animal populations for future vaccine development.

Prevalence and genotypes distribution of group A rotavirus among outpatient children under 5 years with acute diarrhea in Shanghai, China, 2012-2018

Background

Group A rotavirus (RVA) remains the main causative agent of acute diarrhea among children under five years in countries that have not yet introduced the RVA vaccine worldwide. Long-term and continuous monitoring data on RVA infection in outpatient children were lacking in Shanghai. We investigated the prevalence and distribution of RVA genotypes in outpatient children with acute diarrhea in Shanghai from 2012 to 2018.

Methods

Stool specimens of outpatient children under five years were collected from the Children’s Hospital of Fudan University in Shanghai, China. All the samples enrolled in this study were detected and characterized for the P and G genotypes of RVA were determined using the semi-multiplex RT-PCR technique.

Results

Of 1814 children enrolled with acute diarrhea and having specimens collected, 246 (13.6%) were infected with RVA. The highest frequency of RVA was observed in children younger than two years old (87.0%, 214/246). Year-round RVA transmission was observed and the RVA detection rate peaked every winter and troughed in summer. In this study, 12 different RVA strains were identified in children. G9P[8] (49.2%, 121/246) was detected as the most prevalent genotype, followed by G–P[8] (22.8%, 56/246), G3P[8] (11.4%, 28/246), and G9P- (4.9%, 12/246). Although RVA strains detected in this study varied with the time, G9P[8] has been the most predominant circulating genotype since 2012. Furthermore, 12.2% (30/246) RVA positive samples were co-infected with other diarrhea viruses.

Conclusion

The present analysis showed that RVA was still a major cause of children with acute diarrhea in Shanghai from 2012 to 2018. A great diversity of RVA strains circulated in children with acute diarrhea with G9P[8] being the predominant genotype since 2012. Long-term and continuous monitoring of RVA genotypes is therefore indispensable to refine future vaccine strategy in Shanghai.

Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016-2018

Species A Rotaviruses (RVA) still play a major role in causing acute diarrhea in children under five years old worldwide. Currently, an 11-gene classification system is used to designate the full genotypic constellations of circulating strains. Viral proteins and non-structural proteins in the order VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 are represented by the genotypes Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx, respectively. In Benin, ROTAVAC® vaccine was introduced into the Expanded Programme on Immunization in December 2019. To monitor circulating RVA strains for changes that may affect vaccine performance, in-depth analysis of strains prior to vaccine introduction are needed. Here we report, the whole-gene characterization (11 ORFs) for 72 randomly selected RVA strains of common and unusual genotypes collected in Benin from the 2016-2018 seasons. The sequenced strains were 15 G1P[8], 20 G2P[4], 5 G9P[8], 14 G12P[8], 9 G3P[6], 2 G1P[6], 3 G2P[6], 2 G9P[4], 1 G12P[6], and 1 G1G9P[8]/P[4]. The study strains exhibited two genetic constellations designed as Wa-like G1/G9/G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and DS-1-like G2/G3/G12-P[4]/P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Genotype G9P[4] strains possessed a DS-1-like genetic constellation with an E6 NSP4 gene, G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2. The mixed genotype showed both Wa-like and DS-1-like profiles with a T6 NSP3 gene G1/G9P[8]/[4]-I1/I2-R1/R2-C1/C2-M1/M2-A1/A2-N1/N2-T1/T6-E1/E6-H1/H2. At the allelic level, the analysis of the Benin strains, reference strains (with known alleles), vaccine strains (with known alleles) identified 2-13 and 1-17 alleles for DS-1-like and Wa-like strains, respectively. Most of the study strains clustered into previously defined alleles, but we defined 3 new alleles for the VP7 (G3=1 new allele and G12=2 new alleles) and VP4 (P[4]=1 new allele and P[6]=2 new alleles) genes which formed the basis of the VP7 and VP4 gene clusters, respectively. For the remaining 9 genes, 0-6 new alleles were identified for both Wa-like and DS-1-like strains. This analysis of whole genome sequences of RVA strains circulating in Benin described genetic point mutations and reassortment events as well as novel alleles. Further detailed studies on these new alleles are needed and these data can also provide a baseline for studies on RVA in the post-vaccination period.

Rotavirus in Calves and Its Zoonotic Importance

Rotavirus is a major pathogen responsible for diarrheal disease in calves, resulting in loss of productivity and economy of farmers. However, various facets of diarrheal disease caused by rotavirus in calves in the world are inadequately understood, considering that diarrheal disease caused by rotavirus is a vital health problem in calves that interrupts production benefits with reduced weight gain and increased mortality, and its potential for zoonotic spread. The pathological changes made by rotavirus are almost exclusively limited to the small intestine that leads to diarrhea. It is environmentally distributed worldwide and was extensively studied. Reassortment is one of the important mechanisms for generating genetic diversity of rotaviruses and eventually for viral evolution. So, the primary strategy is to reduce the burden of rotavirus infections by practicing early colostrum's feeding in newborn calves, using vaccine, and improving livestock management. Rotaviruses have a wide host range, infecting many animal species as well as humans. As it was found that certain animal rotavirus strains had antigenic similarities to some human strains, this may be an indication for an animal to play a role as a source of rotavirus infection in humans. Groups A to C have been shown to infect both humans and animals. The most commonly detected strains in both human and animals are G2, G3, G4, and G9, P [6]. Therefore, this review was made to get overview epidemiology status and zoonotic importance of bovine rotavirus.

Genotype constellation of a rotavirus A field strain with an uncommon G8P[11] genotype combination in a rotavirus-vaccinated dairy cattle herd

In this report we describe the genotype constellation of a bovine rotavirus A (RVA) strain with an uncommon G8P[11] genotype combination. The RVA/Cow-wt/BRA/Y136/2017/G8P[11] strain was classified as G8-P[11]-I2-R5-C2-M2-A3-N2-T9-E2-H3. Phylogenetic analysis based on the VP7 gene showed that the Y136 strain and a human G8P[1] strain comprise a putative new (VII) lineage for the G8 genotype. In addition, two other genotypes, R5 (VP1) and T9 (NSP3), were identified in the constellation of Y136 that are rarely found in RVA strains of bovine origin. The immunological pressure caused by regular vaccination of cows might be responsible for the selection of heterologous RVA strains.

10-Year Rotavirus Infection Surveillance: Epidemiological Trends in the Pediatric Population of Perugia Province

Rotavirus (RV) infections are a leading cause of severe gastroenteritis in children, and vaccination is currently recommended in Italy, according to the National Immunization Plan 2017-2019. The objective of this study was to describe the epidemiological and molecular RV surveillance in the pediatric population of Perugia province, Umbria. Between September 2007 and August 2018, 663 RV-positive stool specimens were collected from children <15 years of age presenting with gastroenteritis to the emergency room of the Perugia province hospitals who were then hospitalized. Yearly hospitalization rates were expressed per 100,000 persons, and denominators were extrapolated from the National Institute of Statistics. During the 10-year surveillance, the epidemiological trend was fluctuating but slightly decreasing (Max: 89.7 per 100,000 in 2010/2011; Min: 34.8 per 100,000 in 2017/2018). The hospitalization rate was higher in males and in children under five years of age. Among common genotypes, G1P[8] was prevalent most of the years. The uncommon G12P [8] genotype emerged and was the most common in 2012/2013 (58.2%). Afterwards, its circulation remained high. As the Umbria Region started vaccinating from the 2018 birth cohort, our study reviewed pre-vaccination data and will help to assess the protection induced by vaccination and its effect on circulating strains.

Epidemiology and clinical features of rotavirus, adenovirus, and astrovirus infections and coinfections in children with acute gastroenteritis prior to rotavirus vaccine introduction in Meerut, North India

There are limited reports on the etiology of multiple enteric viruses causing acute gastroenteritis (AGE) in North India. In the present study we have determined the prevalence of three enteric viruses, namely rotavirus, astrovirus (AstV) and adenovirus (AdV) in a total of 312 diarrheic children (<5 years) hospitalized at Lala Lajpat Rai Memorial Medical College, Meerut, Uttar Pradesh from August 2014 to July 2016; and results were compared with data from Delhi. The fecal samples were individually screened for group A rotavirus (RVA), AdV, and AstV using enzyme immunoassay kits. At least one viral agent was detected in 29.2% of 312 fecal specimens. RNA of rotavirus antigen-positive samples was extracted by TRIzol method. Rotavirus G/P genotyping was performed using seminested multiplex reverse transcriptase-polymerase chain reaction. RVA was the most predominant virus (18.3%) followed by AstV (12.5%), and AdV (9.9%). Coinfections were detected in 10.6% cases and the most common coinfection in diarrheic children was RVA combined with AstV (36.4%). Overall, the enteric viruses were found most prevalent in the 6 to 11 months age group (P = .01). Increased duration of vomiting (≥3 days) was significantly (P = .04) associated with AdV infection (61.3%) as compared with AstV (30.76%) and rotavirus (26.31%). G1P[8] was detected throughout as the most prevalent rotavirus strain (10.5%). Unusual RV strains like G2P[6] and G2P[8] were also detected. Of note G3, G4, and G12 rotavirus were detected for the first time in Meerut. This is the first report that demonstrated the important contribution of multiple enteric viruses causing AGE in young children in this part of Uttar Pradesh (Meerut).

Rotavirus Burden, Genetic Diversity and Impact of Vaccine in Children under Five in Tanzania

In Tanzania, rotavirus infections are responsible for 72% of diarrhea deaths in children under five. The Rotarix vaccine was introduced in early 2013 to mitigate rotavirus infections. Understanding the disease burden and virus genotype trends over time is important for assessing the impact of rotavirus vaccine in Tanzania. When assessing the data for this review, we found that deaths of children under five declined after vaccine introduction, from 8171/11,391 (72% of diarrhea deaths) in 2008 to 2552/7087 (36% of diarrhea deaths) in 2013. Prior to vaccination, the prevalence of rotavirus infections in children under five was 18.1–43.4%, 9.8–51%, and 29–41% in Dar es Salaam, Mwanza and Tanga, respectively, and after the introduction of vaccines, these percentages declined to 17.4–23.5%, 16–19%, and 10–29%, respectively. Rotaviruses in Tanzania are highly diverse, and include genotypes of animal origin in children under five. Of the genotypes, 10%, 28%, and 7% of the strains are untypable in Dar es Salaam, Tanga, and Zanzibar, respectively. Mixed rotavirus genotype infection accounts for 31%, 29%, and 12% of genotypes in Mwanza, Tanga and Zanzibar, respectively. The vaccine effectiveness ranges between 53% and 75% in Mwanza, Manyara and Zanzibar. Rotavirus vaccination has successfully reduced the rotavirus burden in Tanzania; however, further studies are needed to better understand the relationship between the wildtype strain and the vaccine strain as well as the zoonotic potential of rotavirus in the post-vaccine era.

Epidemiology and genetic diversity of group A rotavirus in acute diarrhea patients in pre-vaccination era in Himachal Pradesh, India

Acute gastroenteritis due to Group A rotaviruses remains the leading cause of mortality and morbidity in children in developing countries. India introduced its indigenous rotavirus vaccine Rotavac® in 2016 and Himachal Pradesh (HP) the first state to launch it. The present study aimed to evaluate rotavirus strain diversity associated with AGE prior to vaccine introduction in HP. A total of 331 fecal specimens collected from diarrheic children hospitalized at RPGMC Tanda, HP between July-2014 and June-2016 were screened for RVA by EIA. Rotavirus RNA was extracted by TRIZOL method and analyzed by RNA-PAGE. G/P typing was performed using semi-nested multiplex reverse transcriptase PCR. Rotavirus was detected in 45% (n = 149/331) of diarrheic children, with highest rate observed in the 6-11 months age group (47%). Vomiting was found more frequently associated with RV-infection. Among G-types, G12 was found most prevalent (33.1%) followed by G1 (28.4%), G9 (12.2%), G2 (9.5%), G3 (3.4%) and G10 (2.7%). G4 (0.7%) strains were rarely detected. Among P-types, P[6] was the most prevalent (40.5%) followed by P[8] (29.1%) and P[4] (14.2%). Of note, genotypes G3 and P[11] were detected for the first time in HP. Among G/P combinations, G12P[6] was most prevalent (30.4%) followed by G1P[8] (20.3%), G2P[4] (4.7%), G1P[6] (3.4%) and G3P[8] (2.7%). Interestingly, our study observed high percentage of unusual strains (14.2%) namely G9P[4], G2P[6], G2P[8], G12P[4] and G1P[11]. The regionally common strains G3P[6], G4P[6], G9P[6], G9P[8], G10P[6], G10P[8] and G12P[8] strains were very rarely detected. Of interest, RNA migration pattern of G1P[8] was DS-1 like and genomic heterogeneity was observed within G12P[4] strains with both long and short electropherotypes. Our study highlights rich genetic diversity with emergence of rare rotavirus strains circulating in HP and provides baseline data prior to Rotavac® introduction that will help to gauge the impact of the Rotavac® vaccine in HP.

Evidence of zoonotic transmission of VP6 and NSP4 genes into human species A rotaviruses isolated in Pakistan in 2010

Introduction of animal group A rotavirus (RVA) gene segments into the human RVA population is a major factor shaping the genetic landscape of human RVA strains. The VP6 and NSP4 genes of 74 G/P-genotyped RVA isolates collected in Rawalpindi during 2010 were analyzed, revealing the presence of VP6 genotypes I1 (60.8%) and I2 (39.2%) and NSP4 genotypes E1 (60.8%), E2 (28.3%) and E-untypable (10.8%) among the circulating human RVA strains. The typical human RVA combinations I1E1 and I2E2 were found in 59.4% and 24.3% of the cases, respectively, whereas 5.4% of the RVA strains were reassortants, i.e., either I1E2 or I2E1. The phylogeny of the NSP4 gene showed that one G2P[4] and two G1P[6] RVA strains clustered with porcine E1 RVA strains or RVA strains that were considered to be (partially) of porcine origin. In addition, the NSP4 gene segment of the unusual human G6P[1] RVA strains clustered closely with bovine E2 RVA strains, further strengthening the hypothesis of an interspecies transmission event. The study further demonstrates the role of genomic re-assortment and the involvement of interspecies transmission in the evolution of human RVA strains. The VP6 and NSP4 nucleotide sequences analyzed in the study received the GenBank accession numbers KC846908- KC846971 and KC846972-KC847037, respectively.

Prevalence and genotypes of Rotavirus among children under 5 years presenting with diarrhoea in Moshi, Tanzania: a hospital based cross sectional study

Background

Diarrhoea is a main cause of morbidity and mortality in children under 5 responsible for approximately four billion cases and 1.1 million deaths annually. In developing countries, it causes two million deaths each year. The major causative organism responsible is Rotavirus which is responsible for one-third of hospitalizations with approximately 40% mortality.

Results

The prevalence of Rotavirus infection was 26.4% (73/277). The predominant strain of Rotavirus found was G1 21/73 (53.8%), followed by G8 9/73 (23.1%), G12 5/73 (12.8%), G9 3/73(7.7%) and G4 1/73 (2.6%). All serotypes identified were in children who had completed Rotavirus vaccination except for one who had G8 in whom the vaccine was introduced after they had completed immunizations.

Conclusion

The overall prevalence of rotavirus has reduced from 33.2% in 2009 to 26.4% in 2016. We have found G1 to be the predominant serotype as well as other circulating serotypes namely G4, G8, G9 and G12. Despite a reduction in prevalence, there is a need for further rotavirus surveillance in the region.

Electronic supplementary material

The online version of this article (10.1186/s13104-017-2883-3) contains supplementary material, which is available to authorized users.

Molecular characterization of emerging G9P[4] rotavirus strains possessing a rare E6 NSP4 or T1 NSP3 genotype on a genogroup-2 backbone using a refined classification framework

Rotavirus infections associated with unusual strains are an emerging concern in rotavirus vaccination programmes. Recently, an increase in circulation of unusual G9P[4] strains was reported from different regions of India, placing this genotype in third position, after G1P[8] and G2P[4], of the most common rotavirus strains. The aim of the present study was to analyse the complete genomic constellation of three G9P[4] strains (RV09, RV10 and RV11), determine their genetic relatedness to other genogroup-2 strains and understand the evolution of a rare E6 and other NSP4 genotypes. All strains revealed the presence of a genogroup-2 backbone, with RV09 constituting the NSP3 T1 genotype and RV10 and RV11 bearing the NSP4 E6 genotype. A refined criterion adopted to classify the nine internal gene segments of G2P[4] and non-G2P[4] strains with the genogroup-2 backbone into lineages and sub-lineages indicated divergence of >8 % (except NSP1: >5.5 %) for lineages and >3 % for sub-lineages. The VP1 and/or VP3 genes of study strains showed close relationships with animal-like human rotaviruses. The estimated evolutionary rate for the NSP4 E6 genotype was marginally higher (3.78×10-3 substitutions per site per year) than that of genotypes E1 (2.6×10-3 substitutions per site per year) and E2 (3.06×10-3 substitutions per site per year), suggesting a step towards adaptation of E6 on a genogroup-2 backbone. The time and origin of the most recent common ancestor of E6 genotype were estimated to be 1981 and South Asia, respectively. Full-genome and evolutionary analyses performed in this study for G9P[4] strains will help better understand the extent of gene reassortment and origin in unusual rotavirus strains that may remain viable and cause infections in humans.

Distribution of rotavirus VP7 and VP4 genotypes circulating in Tunisia from 2009 to 2014: Emergence of the genotype G12

Group A rotavirus (RVA) represents the most important aetiological agent of diarrhoea in children worldwide. From January 2009 to December 2014, a multi-centre study realized through 11 Tunisian cities was undertaken among children aged <5 years consulting or hospitalized for acute gastroenteritis. A total of 1127 faecal samples were collected. All samples were screened by ELISA for the presence of RVA antigen. RVA-positive samples were further analyzed by PAGE and used for G/P-genotyping by semi-nested multiplex RT-PCR. Globally, 270 specimens (24 %) were RVA-positive, with peaks observed annually between November and March. Nine different electropherotypes could be visualized by PAGE, six with a long profile (173 cases) and two with a short one (seven cases). Mixed profiles were detected in two cases. Among the 267 VP7 genotyped strains, the predominant G- genotype was G1 (39.6 %) followed by G3 (22.2 %), G4 (13 %), G9 (11.5 %), G2 (5.2 %) and G12 (5.2 %). Among the 260 VP4 genotyped strains, P[8] genotype was the predominant (74.5 %) followed by P[6] (10.4 %) and P[4] (5.5 %). A total of 257 strains (95.2 %) could be successfully G- and P-genotyped. G1P[8] was the most prevalent combination (34.4 %), followed by G3P[8] (16.3 %), G9P[8] (10.3 %), G4P[8] (8.9 %), G2P[4] (4 %), G12P[6] (2.6 %) and G12P[8] (1.9 %). Uncommon G/Pgenotype combinations, mixed infections and untypeable strains were also detected. This is the first report, in Tunisia, of multiple detection of an emerging human RVA strain, G12 genotype. This study highlighted the need for maintaining active surveillance of emerging strains in Northern Africa.

Identification of a multi-reassortant G12P[9] rotavirus with novel VP1, VP2, VP3 and NSP2 genotypes in a child with acute gastroenteritis

The G12 rotavirus genotype is globally emerging to cause severe gastroenteritis in children. Common G12 rotaviruses have either a Wa-like or DS-1-like genome constellation, while some G12 strains may have unusual genome composition. In this study, we determined the full-genome sequence of a G12P[9] strain (ME848/12) detected in a child hospitalized with acute gastroenteritis in Italy in 2012. Strain ME848/12 showed a complex genetic constellation (G12-P[9]-I17-R12-C12-M11-A12-N12-T7-E6-H2), likely derived from multiple reassortment events, with the VP1, VP2, VP3 and NSP2 genes being established as novel genotypes R12, C12, M11 and N12, respectively. Gathering sequence data on human and animal rotaviruses is important to trace the complex evolutionary history of atypical RVAs.

Rotavirus diversity among diarrheal children in Delhi, India during 2007-2012

Rotavirus is the leading cause of severe gastroenteritis in young children worldwide and is responsible for around 100,000 deaths in India annually. Vaccination against rotavirus (RV) is a high priority: 'ROTAVAC' an indigenous vaccine will soon be licensed in India. Surveillance to determine the impact of vaccines on emerging RV strains is required. In this study we compared the pattern of RV strains circulating in Delhi over a 5 year period with the strains over the past 12 years. The most commonly detected G genotypes were G1 (22.4%), G2 (17.2%), and G9 (25.2%) with P[4] (25.5%), P[6] (20%) and P[8] (16.9%) specificity. G12 genotype was found to be the fourth common G-type with 14.8% prevalence. Among the G-P combinations; G1P[8], G2P[4], G9P[8] and G12P[6] were detected at 7.2%, 7.2%, 5.2% and 10%, respectively. Of note, G9P[4] and G2P[6] that were rarely detected during 2000-2007 in Delhi, were observed quite frequently with prevalence of 6.5% and 3.4%, respectively. In total, 16 different G-P combinations were detected in the present study demonstrating the rich diversity of rotavirus strains in Delhi. Our data from the 12 year period indicate wide circulation of G1 and G9 genotypes in combination with P[8], G2 with P[4] and G12 with P[6] with high frequency of RV strains having rare G-P combinations in Delhi. Since the indigenous vaccine 'ROTAVAC' has a monovalent formulation, the impact of vaccines on strains and the effect of strain diversity on the efficacy of the vaccine should be monitored.

Disease caused by rotavirus infection

Although rotavirus vaccines are available, rotaviruses remain the major cause of childhood diarrheal disease worldwide. The Rotarix (GlaxoSmithKline Biologicals Rixensart, Belgium) and RotaTeq (Merck and Co., Inc. Whitehouse Station, New Jersey, USA) vaccines are effective for reducing the morbidity and mortality of rotavirus infection. This article aims to assess the epidemiology of rotaviral gastroenteritis and the efficacy and effectiveness of licensed rotavirus vaccines. This review concludes by presenting challenges in the field that require further exploration by and perspectives from basic and translational research in the future.

First report of human rotavirus G8P[4] gastroenteritis in India: evidence of ruminants-to-human zoonotic transmission

Group A rotaviruses are the major cause of childhood gastroenteritis worldwide. Due to close proximity of human and cattle in rural areas of developing countries like India, interspecies transmission or zoonotic transmission is a major source of rapid generation of reassortants and genetic or antigenic variants. Previously, many human group A rotaviruses were found with porcine or bovine characteristics from eastern and north-eastern India. In this study, four unusual human G8P[4] strains were identified which had artiodactyl-like origins. During an ongoing community based surveillance for epidemiological profiling of diarrheal pathogens, these unusual human group A rotavirus G8P[4] strains were detected from the stool samples of 3-14 months old children with acute diarrhea in Sonarpur, eastern India. Analysis of eleven complete and/or partial gene segments of these unusual G8P[4] strains were done by reverse transcription-PCR (RT-PCR) followed by nucleotide sequencing and phylogenetic analysis. The VP7 nucleotide sequences revealed a close phylogenetic relationship to the G8P[7] porcine strain D-1 and bovine strain KJ59-2 from South Korea. Whereas the VP4 gene segments were also related closely to human rotavirus prototype strain DS-1. Other nine gene segments of these G8P[4] rotaviruses were related closely to either animal or animal-derived rotavirus members of the DS-1-like family. These results suggest that origin of these G8P[4] strains might have been resulted from multiple reassortment events between artiodactyls and ruminant-derived reassortant human rotaviruses. To date, this is the first report of G8P[4] rotavirus from India and the first genomic analysis of G8P[4] strains from Asian continent.

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.

Molecular epidemiology and clinical characterization of group A rotavirus infections in Tunisian children with acute gastroenteritis

Rotaviruses are the most common cause of severe viral gastroenteritis in early childhood worldwide. Thus, the objectives of our study were to determine the molecular epidemiology and the clinical features of rotavirus gastroenteritis in Tunisia. Between January 2003 and April 2007, a prospective study was conducted on 788 stool samples collected from children under 12 years of age who were suffering from acute gastroenteritis. Rotavirus was detected by multiplex RT-PCR in 27% (n = 213) of samples, among them 79.3% (n = 169) cases were monoinfections. The frequency of rotavirus infections was significantly higher among inpatients (29%) than among outpatients (13%) (P < 0.001). The seasonal distribution of rotavirus diarrhea showed a winter peak, with an unusual peak from June to September. The mean duration of hospitalization was 6.5 ± 8.1 days and the mean age was 15.8 ± 22.8 months for rotavirus monoinfections. Fever, vomiting, abdominal pain, and dehydration were observed in 88, 98, 13, and 80 cases, respectively, in children with rotavirus monoinfections. G3P[8] (45.6%) and G1P[8] (23.9%) were the most common genotypes found in our study. The determination of rotavirus infection prevalence and the characterization of the rotavirus strains circulating will help us to better understand the molecular biology and epidemiology of the disease in our country.

Rotavirus infections and vaccines: burden of illness and potential impact of vaccination

Rotaviruses are the most common cause of severe gastroenteritis in children. By 5 years of age virtually every child worldwide will have experienced at least one rotavirus infection. This leads to an enormous disease burden, where every minute a child dies because of rotavirus infection and another four are hospitalized, at an annual societal cost in 2007 of $US2 billion. Most of the annual 527 000 deaths are in malnourished infants living in rural regions of low and middle income countries. In contrast, most measurable costs arise from medical expenses and lost parental wages in high income countries. Vaccines are the only public health prevention strategy likely to control rotavirus disease. They were developed to mimic the immunity following natural rotavirus infection that confers protection against severe gastroenteritis and consequently reduces the risk of primary healthcare utilization, hospitalization and death. The two currently licensed vaccines--one a single human strain rotavirus vaccine, the other a multiple strain human-bovine pentavalent reassortant rotavirus vaccine--are administered to infants in a two- or three-dose course, respectively, with the first dose given at 6-14 weeks of age. In various settings they are safe, immunogenic and efficacious against many different rotavirus genotypes. In high and middle income countries, rotavirus vaccines confer 85-100% protection against severe disease, while in low income regions of Africa and Asia, protection is less, at 46-77%. Despite this reduced efficacy in low income countries, the high burden of diarrheal disease in these regions means that proportionately more severe cases are prevented by vaccination than elsewhere. Post-licensure effectiveness studies show that rotavirus vaccines not only reduce rotavirus activity in infancy but they also decrease rates of rotavirus diarrhea in older and unimmunized children. A successful rotavirus vaccination program will rely upon sustained vaccine efficacy against diverse and evolving rotavirus strains and efficient vaccine delivery systems. The potential introduction of rotavirus vaccines into the world's poorest countries with the greatest rates of rotavirus-related mortality is expected to be very cost effective, while rotavirus vaccines should also be cost effective by international standards when incorporated into developed countries immunization schedules. Nonetheless, cost effectiveness in each country still depends largely on the local rotavirus mortality rate and the price of the vaccine in relation to the per capita gross domestic product.