Hospital based surveillance and genetic characterization of rotavirus strains in children (<5 years) with acute gastroenteritis in Kolkata, India, revealed resurgence of G9 and G2 genotypes during 2011-2013

Genomic Analysis of Rwandan G9P[8] Rotavirus Strains Pre- and Post-RotaTeq® Vaccine Reveals Significant Distinct Sub-Clustering in a Post-Vaccination Cohort

Although the introduction of rotavirus vaccines has substantially contributed to the reduction in rotavirus morbidity and mortality, concerns persist about the re-emergence of variant strains that might alter vaccine effectiveness in the long term. The G9 strains re-emerged in Africa during the mid-1990s and have more recently become predominant in some countries, such as Ghana and Zambia. In Rwanda, during the 2011 to 2015 routine surveillance period, G9P[8] persisted during both the pre- and post-vaccine periods. The pre-vaccination cohort was based on the surveillance period of 2011 to 2012, and the post-vaccination cohort was based on the period of 2013 to 2015, excluding 2014. The RotaTeq® vaccine that was first introduced in Rwanda in 2012 is genotypically heterologous to Viral Protein 7 (VP7) G9. This study elucidated the whole genome of Rwandan G9P[8] rotavirus strains pre- and post-RotaTeq® vaccine introduction. Fecal samples from Rwandan children under the age of five years (pre-vaccine n = 23; post-vaccine n = 7), conventionally genotyped and identified as G9P[8], were included. Whole-genome sequencing was then performed using the Illumina® MiSeq platform. Phylogenetic analysis and pair-wise sequence analysis were performed using MEGA6 software. Distinct clustering of three post-vaccination study strains was observed in all 11 gene segments, compared to the other Rwandan G9P[8] study strains. Specific amino acid differences were identified across the gene segments of these three 2015 post-vaccine strains. Important amino acid differences were identified at position N242S in the VP7 genome segment of the three post-vaccine G9 strains compared to the other G9 strains. This substitution occurs at a neutralization epitope site and may slightly affect protein interaction at that position. These findings indicate that the Rwandan G9P[8] strains revealed a distinct sub-clustering pattern among post-vaccination study strains circulating in Rwanda, with changes at neutralization epitopes, which may play a role in neutralization escape from vaccine candidates. This emphasizes the need for continuous whole-genome surveillance to better understand the evolution and epidemiology of the G9P[8] strains post-vaccination.

Epidemiological studies on gastroenteritis in children in the Bannu district, Khyber Pakhtunkhwa, Pakistan

Aims

Gastroenteritis is a digestive disorder among children with symptoms of abdominal cramps, diarrhoea, and vomiting. This study aimed to determine the prevalence of gastroenteritis in children in the Bannu district in 2019, and also contributed for adopting preventive measures to reduce mortality in children.

Subject and methods

A retrospective study was conducted to determine the prevalence of gastroenteritis in children in Bannu. The data were collected from official registers of admission maintained in the children wards in the Women and Children Hospital, Bannu. Patients with symptoms of gastroenteritis at the outpatient department were admitted to one of the children wards.

Results

Overall, 1456 children—897 (61.4%) males and 559 (38.6%) females—suffered from gastroenteritis during the study period. The age group ≤6 months demonstrated the highest share (37.8%), followed by >6 m ≤ 1y (35.5%), >1y ≤ 2y (15.8%), >2y ≤ 5y (7.3%), >5 ≤ 10y (3.2%), and > 10y ≤ 15y (0.4%). Overall, 89.1% of cases were from children ≤2 years old and 96.4% of cases were attributed to children ≤ 5 years of age. April demonstrated the highest percentage of prevalence of 17.7, followed by May (13.5%), November (13%), June (11.7%), September (10.4%), October (9.8%), July (9.5%), August (8.4%), March (3.4%), and February (2.6%). The age group ≤6 m was the dominant group during February through May and was replaced by the age group >6 m ≤ 1y during August through November.

Conclusion

Gastroenteritis showed a reduced prevalence when shifted from lower to higher age groups. Being male and age group ≤6 m showed the highest prevalence of gastroenteritis with the peak of disease in April. Further research is needed to determine the cause-based prevalence of different gastroenteritis cases in the study area.

Demographic Profile and Genotypic Distribution of Rotavirus Gastroenteritis from Rural Haryana, India

OBJECTIVE

To know the prevalence of rotavirus among hospitalized <5 y children, their demographic profile and genotypic distribution of rotavirus strain from tertiary care center of rural Haryana.

METHODS

An observational 3-year study done from June 2016 to June 2019 where children under 5 y of age hospitalized for acute gastroenteritis were enrolled. Various demographic, environmental, and clinical parameters were assessed. Stool samples were collected and sent to CMC, Vellore for rotavirus screening by enzyme immune assay (EIA) and RV-positive samples were genotyped using reverse transcription-polymerase chain reaction (RT-PCR).

RESULTS

Out of 444 stool sample screened, 107 were positive (24.1%) for rotavirus. RV positive cases seen mostly in 6-24 mo age group with moderate to severe dehydration at presentation and peaks in winter months (Dec - Feb). G3P[8] (35.24%) is the most prevalent genotype identified followed by G1P[8] (20.95%), G1P[6] (11.43%), G2P[4] (6.67%) and G12P[8] (2.86%).

CONCLUSION

Continuous surveillance is required to monitor the circulating genotypes in postvaccination phase and assess the effectiveness and impact of the vaccine.

Acute Gastroenteritis in Children Below 5 Years of Age at Tirupati, Andhra Pradesh, India Post Introduction of Rotavirus Vaccine into National Immunization Programme

OBJECTIVE

To identify the burden of rotavirus acute gastroenteritis (AGE) and the genotypes presenting in the authors' area in the period after introduction of rotavirus vaccine in Universal Immunization Programme (UIP).

METHODS

Children aged less than 5 y and presenting to hospital for the treatment of AGE were enrolled into the study from January 2016 to June 2019. Clinical details including age, gender, extent of illness, number of stools, concomitant vomiting and fever, grade of dehydration, and associated illness were recorded. Stool samples were tested for rotavirus using a commercially available ELISA Kit. Genotyping was performed for the rotavirus antigen-positive samples.

RESULTS

Rotavirus positive AGE was seen in 14.2% of the children. High burden of rotavirus gastroenteritis was seen in the age group of 6-23 mo and more cases were observed from December to February months. In our region the prevalent rotavirus genotypes in positive samples are G3 and G1 in G-typing, P[8] and P[4] in P-typing, respectively. G3P[8] and G1P[8] are the most prevalent genotypes identified in our area with a frequency of 35.1% and 25.9%, respectively. Almost all the cases (97.7%) got discharged and only one patient has died.

CONCLUSION

The findings conclude a declining trend in the rotavirus positive AGE cases in the authors' area after introduction of Rotavac vaccine in the UIP.

Rotavirus Diarrhea and its Determinants Among Under-Five Children Admitted in a Tertiary Care Hospital of Southern Haryana, India

OBJECTIVE

To estimate the prevalence of rotavirus diarrhea and its demographic, social, and clinical characteristics among children less than five years of age admitted in a rural tertiary care institute.

METHODS

This prospective hospital-based observational study was carried out during February 2016 to June 2019. Diarrheal admissions of children aged 0-59 mo were screened and those who met the inclusion criteria were included in the study. Sociodemographic and clinical information was collected using a case report form. Stool samples were collected within 48 h of admission and transported in cold chain every month to the referral laboratory situated at Christian Medical College for testing.

RESULTS

Among the children admitted with acute diarrhea, 148 (11.02%) were positive for rotavirus in the study. As per Vesikari scoring system, around three fourth (76.2%) of children were having severe or very severe diarrhea. Severity of diarrhea was more among rotavirus positive cases as assessed by the Vesikari scoring system. The rotavirus diarrhea showed a peak during November to February.

CONCLUSION

Rotavirus diarrhea is an issue of public health importance, particularly due to its association with the severe diarrhea. As evidenced from similar settings in the world, rotavirus vaccine introduction and increased coverage is the most important strategy towards prevention and control of rotavirus diarrhea.

Rotavirus Gastroenteritis Hospitalizations Among Under-5 Children in Northern India

OBJECTIVE

To study epidemiological profile, prevalence, and molecular epidemiology of RVGE in hospitalized under-5 children at a tertiary care teaching rural hospital located in sub-Himalayan belt of Northern India.

METHODS

This was a hospital-based surveillance study done over 4 y (2016-2019) including under-5 children hospitalized with acute gastroenteritis (AGE). Demographic and clinical parameters were recorded in a pre-designed performa. After consent, stool samples were collected and sent to Christian Medical College (CMC), Vellore for RV screening by enzyme immunoassay (EIA). Each EIA-positive sample was further subjected to G and P typing using published methods.

RESULTS

Out of total 851 included children, rotavirus gastroenteritis (RVGE) was detected in 23.03% (196/851) cases by EIA. The highest incidence for RVGE-positive cases (40.43%) was observed in 2016 with gradual decline over next 3 y. Maximum cases of diarrhea were observed in 12-23 mo age group along with highest rotavirus detection. G3P[8] was most common genotype (46.94%) found, followed by G1P[8] (13.78%), G2P[4] (4.59%), G1P[6] (8.16%) and G9P[4] (3.57%). Mixed genotype was seen in 13.78% of total cases.

CONCLUSION

This study summarizes the changing trends in the epidemiology of RVGE in Northern India along with the major circulating genotypes postvaccine introduction.

Genetic diversity of G9 rotavirus strains circulating among diarrheic children in North India: A comparison with 116E rotavirus vaccine strain

The parental rotavirus strain 116E (G9P[11]) used to generate Rotavac® vaccine was isolated in 1986 in New Delhi. Thenceforward, there is no comprehensive report on diversity of G9 rotavirus strains from 116E; therefore, the present study evaluates the VP7 gene sequence diversity of G9 strains (retrieved from GenBank) from different geographical regions (1987-2016). Additionally, 22 recently collected G9 strains from Himachal Pradesh and Delhi (2013-2016) were included in the phylogenetic analysis. Interestingly, unlike 116E which belong to lineage-II all other G9 rotavirus including these 22 samples clustered together in a separate lineage (III). Further, six amino acid substitutions including one novel, K143M (epitope 7-2) different from 116E were detected mostly in the neutralization epitopes of VP7 protein (neutralization escape mutants). Overall, the accumulation of identified substitutions in VP7 epitopes and evolution of G9 strains in India may have impact on Rotavac® efficacy.

Diversity of rotavirus genotypes circulating in children < 5 years of age hospitalized for acute gastroenteritis in India from 2005 to 2016: analysis of temporal and regional genotype variation

Background

From 2016, the Government of India introduced the oral rotavirus vaccine into the national immunization schedule. Currently, two indigenously developed vaccines (ROTAVAC, Bharat Biotech; ROTASIIL, Serum Institute of India) are included in the Indian immunization program. We report the rotavirus disease burden and the diversity of rotavirus genotypes from 2005 to 2016 in a multi-centric surveillance study before the introduction of vaccines.

Methods

A total of 29,561 stool samples collected from 2005 to 2016 (7 sites during 2005–2009, 3 sites from 2009 to 2012, and 28 sites during 2012–2016) were included in the analysis. Stools were tested for rotavirus antigen using enzyme immunoassay (EIA). Genotyping was performed on 65.8% of the EIA positive samples using reverse transcription- polymerase chain reaction (RT-PCR) to identify the G (VP7) and P (VP4) types. Multinomial logistic regression was used to quantify the odds of detecting genotypes across the surveillance period and in particular age groups.

Results

Of the 29,561 samples tested, 10,959 (37.1%) were positive for rotavirus. There was a peak in rotavirus positivity during December to February across all sites. Of the 7215 genotyped samples, G1P[8] (38.7%) was the most common, followed by G2P[4] (12.3%), G9P[4] (5.8%), G12P[6] (4.2%), G9P[8] (4%), and G12P[8] (2.4%). Globally, G9P[4] and G12P[6] are less common genotypes, although these genotypes have been reported from India and few other countries. There was a variation in the geographic and temporal distribution of genotypes, and the emergence or re-emergence of new genotypes such as G3P[8] was seen. Over the surveillance period, there was a decline in the proportion of G2P[4], and an increase in the proportion of G9P[4]. A higher proportion of mixed and partially typed/untyped samples was also seen more in the age group 0–11 months.

Conclusions

This 11 years surveillance highlights the high burden of severe rotavirus gastroenteritis in Indian children < 5 years of age before inclusion of rotavirus vaccines in the national programme. Regional variations in rotavirus epidemiology were seen, including the emergence of G3P[8] in the latter part of the surveillance. Having pre-introduction data is important to track changing epidemiology of rotaviruses, particularly following vaccine introduction.

Detection and molecular characterization of rotavirus of pigs in Kerala, India

Group A rotaviruses (GAR) are an important cause of diarrhoea in infants and newborn animals especially pigs. In this paper, we report the detection, G and P typing and phylogenetic analysis of GAR of pigs in Kerala. A total of 100 fecal samples from diarrhoeic piglets were collected from organized farms in Wayanad, Ernakulam, Thrissur, and Palakkad districts of Kerala. The samples were tested for the presence of GAR employing reverse transcriptase polymerase chain reaction (RT-PCR) targeting VP6 gene. Positive samples were tested by G and P genotyping primers and representative amplicons were sequenced. Of the 100 samples, 12 were positive for GAR. The G and P types detected were G2, G4, G5, G6, G9, P[6] and P[19]. An untypable P type (P21-5 like) was also detected. In some of the samples more than one G type was detected. The nucleotide sequences of G2, G4 and G5 types were similar to those seen in pigs and that of G6 was similar to bovine sequences. G9, P[6] and P[19] sequences showed similarity to human rotavirus sequences. The findings of this study provide the first information on the G and P genotypes of GAR of pigs in Kerala.

A decade-long temporal analyses of human group-A rotavirus among children with gastroenteritis: Prevaccination scenario in West Bengal, eastern India

Despite the significant reduction in the global infantile death toll due to rotaviral diarrhea, India still contributes substantially to rotavirus-related hospitalization as well as mortality rates. The rotavirus surveillance study conducted from 2008 through 2017 among children (≤5 years) with moderate to severe gastroenteritis seeking healthcare facilities at two hospitals in eastern India, revealed a change in the proportion of rotavirus positivity, seasonality, and age-group specificity along with the cycling of different usual and unusual genotypes in this endemic setting. G1 strains predominated during 2008-2010, while G2 and G9 genotypes eventually upsurged during 2011-2013. G1 strains re-established their lead during 2013-2015, while G3 emerged for the first time in eastern India in 2015 and rooted itself as the cardinal strain 2016 onwards. Evolutionary analyses of all the predominant genotypes (G1, G2, G3, and G9) revealed that they were mostly phylogenetically distant to the rotavirus vaccine strains as depicted in the phylogenetic dendrogram. These decade-long epidemiological studies during the pre-vaccination period in West Bengal (eastern India) underscore the cocirculation of multiple rotavirus genotypes in addition to sporadic occurrence of zoonotic strains like G10P[6] and G11P[25].

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.

Burden and Molecular Epidemiology of Rotavirus Causing Diarrhea among Under-Five Children: A Hospital-based Study from Eastern India

Background

Rotavirus (RVA) causes severe gastroenteritis in under-five children, and there are many diverse strains of the virus that are localized to different parts of the world.

Objectives

To study the burden and molecular epidemiology of RVA causing gastroenteritis among children from Eastern India.

Materials and Methods

This hospital-based cross-sectional study included children under-five with gastroenteritis. Demographic and clinical parameters were recorded in a predesigned pro forma. Stool samples collected from these children were initially screened for RVA VP6 antigen by enzyme immunoassay (EIA). Each EIA-positive sample was then subjected to RNA extraction, followed by reverse transcription, and heminested multiplex polymerase chain reaction for genotyping of RVA strains.

Results

Of 320 included children, RVA was detected in 30.62% (98/320) cases by EIA. The highest incidence for RVA-positive cases (34.61%) was observed among children in the age group of 24-36 months, followed by 0-12 months (33.04%). Of the 97 completely typed samples, single genotype was detected in 85 (87.62%) samples with either G (VP7) or P (VP4) types. However, mixed genotypes were detected in 12 (11.21%) samples. G3P[8] (44.09%) was the most common genotype, followed by G1P[8] (32.65%), G2[P4] (5.10%), G1[P6] (3.06%), and G9[P4] (1.02%).

Conclusions

The present study found RVA positivity in 30.62% of children with gastroenteritis, with the highest burden among 24-36 months old. The predominant genotypes were G1, G3, and P[8]. Further large-scale/multicentric studies should be conducted to document the diversity of circulating RVA genotypes in this region for giving inputs for vaccination strategy.

Genetic characterization of group-A rotaviruses among children in eastern India during 2014-2016: Phylodynamics of co-circulating genotypes

BACKGROUND

Group-A human rotaviruses (GARV) are among the major cause of childhood diarrhea worldwide. In lieu of monitoring the circulatory GARV strains and underscoring the burden of GARV related hospitalization, a systematic surveillance was conducted in three hospitals of eastern India. In this hospital-based diarrheal disease surveillance (2014-2016), GARV was the most common cause of acute infantile gastroenteritis. The strains were genotyped and characterized to understand their prevalence and phylodynamics prior to the introduction of vaccine in eastern India.

MATERIALS AND METHODS

A total of 3652 stool samples were screened from children (≤5 years) hospitalized with acute diarrhea during 2014-2016. Initial screening for VP6 antigen was done by ELISA. GARV positive samples were genotyped by multiplex semi-nested PCR and DNA sequencing and phylogenetic analyses were based on the capsid proteins VP4 and VP7.

RESULTS

Of 3652 samples, 1817 (49.8%) were GARV positive. G1, G2, G3 and G9 in conjunction with P[4], P[6]and P[8]genotypes were seen to co-circulate in the population. A sharp deflection from G1 to G3 occurred since 2016; upsurge of G9 strains was seen in alternate years, whereas G2 strains had a low frequency. All the circulating genotypes depicted a low phylogenetic relatedness to the vaccine strains. Differences in antigenic epitopes of VP4 and VP7 proteins in local strains were seen when compared to the vaccine strains. A significant difference in the degree of dehydration, duration of mean hospital stay and frequency of vomiting/24 h between GARV positive and negative children was evident.

CONCLUSION

The study provides a relevant set of base-line data on high burden of rotaviral gastroenteritis and the varied genotypic diversity among children prior to the introduction of GARV vaccine in this endemic region. Continuous monitoring during post-vaccination era will be required to assess the impact of vaccination in this region.

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.

Rotavirus vaccine impact assessment surveillance in India: protocol and methods

INTRODUCTION

Rotavirus infection accounts for 39% of under-five diarrhoeal deaths globally and 22% of these deaths occur in India. Introduction of rotavirus vaccine in a national immunisation programme is considered to be the most effective intervention in preventing severe rotavirus disease. In 2016, India introduced an indigenous rotavirus vaccine (Rotavac) into the Universal Immunisation Programme in a phased manner. This paper describes the protocol for surveillance to monitor the performance of rotavirus vaccine following its introduction into the routine childhood immunisation programme.

METHODS

An active surveillance system was established to identify acute gastroenteritis cases among children less than 5 years of age. For all children enrolled at sentinel sites, case reporting forms are completed and a copy of vaccination record and a stool specimen obtained. The forms and specimens are sent to the referral laboratory for data entry, analysis, testing and storage. Data from sentinel sites in states that have introduced rotavirus vaccine into their routine immunisation schedule will be used to determine rotavirus vaccine impact and effectiveness.

ETHICS AND DISSEMINATION

The Institutional Review Board of Christian Medical College, Vellore, and all the site institutional ethics committees approved the project. Results will be disseminated in peer-reviewed journals and with stakeholders of the universal immunisation programme in India.

Rotavirus gastroenteritis in Indian children < 5 years hospitalized for diarrhoea, 2012 to 2016

Background

In 2016, the Government of India introduced the oral rotavirus vaccine (ROTAVAC, Bharat Biotech, India) in 4 states of India as part of the Universal Immunization Programme, and expanded to 5 more states in 2017. We report four years of data on rotavirus gastroenteritis in hospitalized children < 5 years of age prior to vaccine introduction.

Methods

Children from 7 sites in southern and northern India hospitalized for diarrhoea were recruited between July 2012 and June 2016. Stool samples were screened for rotavirus using enzyme immunoassay (EIA). The EIA positive samples were genotyped by reverse-transcription polymerase chain reaction.

Results

Of the 5834 samples from the 7 sites, 2069 (35.5%) were positive for rotavirus by EIA. Genotyping was performed for 2010 (97.1%) samples. G1P[8](56.3%), G2P[4](9.1%), G9P[4](7.6%), G9P[8](4.2%), and G12P[6](3.7%) were the common genotypes in southern India and G1P[8](36%), G9P[4](11.4%), G2P[4](11.2%), G12P[6](8.4%), and G3P[8](5.9%) in northern India.

Conclusions

The study highlights the high prevalence of rotavirus gastroenteritis in India and the diversity of rotavirus genotypes across different geographical regions. Pre- vaccine surveillance data is necessary to evaluate the potential change in admission rates for gastroenteritis and circulating rotavirus genotypes after vaccine introduction, thus assessing impact.

Electronic supplementary material

The online version of this article (10.1186/s12889-019-6406-0) contains supplementary material, which is available to authorized users.

Molecular characterization of rotavirus diarrhea among children aged under five years in the Philippines, 2013-2015

With the availability of new and existing rotavirus vaccines, credible and reliable data on burden of rotavirus-associated disease are needed to enable evidence-based decision making regarding the introduction of rotavirus vaccines. The national rotavirus surveillance program in the Philippines, a sentinel-based surveillance, was established in 2012 to determine the proportion of laboratory-confirmed rotavirus cases among children under five years with acute gastroenteritis and to describe the geographic distribution and molecular epidemiology of rotavirus in the country. During 2013 to 2015, rotavirus infection was the cause of acute gastroenteritis among children under five years admitted to hospitals or evaluated in emergency rooms, constituting more than one-third of gastroenteritis hospitalizations at the sentinel site hospitals. The predominant genotype observed was G1P[8]. Although a rotavirus surveillance network has been established, findings suggest the need to strengthen the network in the country and to continue monitoring prevalent rotavirus strains to help identify the possible emergence of new strains.

Upsurge and spread of G3 rotaviruses in Eastern India (2014-2016): Full genome analyses reveals heterogeneity within Wa-like genomic constellation

Advent of new strains and shift in predominantly circulating genotypes are characteristics of group- A rotavirus (RVA), one of the major causes of childhood gastroenteritis. During diarrheal disease surveillance at Kolkata, India (2014-2016), a shift in circulating RVA strains from G1P[8] to G3P[8] was seen. Stool samples from children (n = 3048) with acute gastroenteritis were tested of which 38.7% were RVA positive. G1 was the predominant strain (65.3%) in 2014-2015 whereas in late 2015 and 2016, G3 became the preponderant strain (44.6%). In the past decade G3 strains were not observed in this region, we conducted whole genome sequencing of representative strains to gain insight into the phenomenon of emergence and genetic constellation of these circulating human G3 strains. The analyses revealed intergenogroup reassortment in G3P[4] strains (among Wa and DS-1-like genogroup) whereas G3P[8] strains were authentic Wa-like. Phylogenetic analysis revealed Kolkata G3 strains as polymorphic and thus they formed two sub-clusters due to antigenic differences in their VP7 protein. One of the sub-clusters had the wild-type threonine at 87 amino acid position while another sub-cluster had an isoleucine mutation. Presence of additional N-linked glycosylation site at amino acid 283 of VP7 glycoprotein suggests that the major neutralizing epitope on the VP7 (G3) of RotaTeq vaccine differs from the currently circulating G3 strains. The study is important as efficiency of rotavirus vaccine depends on the circulating heterogeneous genotype constellations. Continuous monitoring of circulating RVA strains in endemic settings like India is therefore important in pre- and post-vaccination period to monitor the emergence of new reassortant genotypes in addition to assessing vaccine efficacy.

Molecular characterisation and clinical correlates of rotavirus in children and adults in a tertiary care centre, Chennai, South India

AIMS

This study was undertaken to determine the rate of detection of rotavirus causing diarrhoea among children and adults, identify the common genotypes circulating and determine clinical correlates.

SETTINGS AND DESIGN

This is a cross-sectional study in a tertiary care centre.

MATERIALS AND METHODS

Stool samples were collected from adults and children, transported on ice, aliquoted and stored at - 80°C. Rotavirus antigen detection enzyme-linked immunosorbent assay was performed on all samples. Representative samples were typed by conventional hemi-nested VP7 and VP4 reverse transcription-polymerase chain reaction.

STATISTICAL ANALYSIS USED

Test of proportion, Student's t-test and Chi-square test were used for statistical analysis.

RESULTS

A total of 444 stool samples were collected and tested over 14 months. Among these, 116 were paediatric with a rate of positivity of 36.21% and 328 were adults with rate of positivity of 20.73%. Among children under 5 years (n = 90), the rate of positivity was 41.11%. Vesikari scale was used for clinical assessment. The mean ± standard deviation Vesikari score in rotavirus-infected children and rotavirus-uninfected children was 11.2 ± 3.2 and 8.9 ± 3.6, respectively, and the difference was statistically significant. Nineteen samples were genotyped in children < 5 years, 94.7% were of G1P[8] and 5.3% were of G9P[4] genotype. Genotyping of 14 adult samples, G1P[8](85.7%) was found as the predominant genotype, two samples (14.3%) were partially typed (G9PUT and G12PUT).

CONCLUSIONS

The rate of positivity of rotavirus in children under 5 years was 41.11%. G1P[8] is the most common strain circulating across all age groups.

Genetic analysis of rotavirus G2P[4] strains in Pune, Western India: circulation of a novel reassortant bearing E6 NSP4 genotype

In India, G2P[4] strains are known to be the second most predominant group A rotaviruses causing acute gastroenteritis among children. This study was performed to determine the diversity within VP7(G), VP4(P), VP6(I) and NSP4(E) genes of 16 G2P[4] rotavirus strains detected in children hospitalized for acute gastroenteritis in Pune, Western India during 2009-2013. Fourteen strains showed G2-P[4]-I2-E2 and two strains showed G2-P[4]-I2-E6 genotype constellation. Phylogenetic analysis showed their clustering into G2-IV-a3, P[4]-5bi/ii, I2-3ii and E2-4i/ii or E6 genotypes/lineages. These data reveal inter- and/or intra-genotypic variations in a genogroup-2 constellation of G2P[4] rotavirus strains circulating in Pune, Western India, providing evidence of a novel G2P[4] reassortant bearing a rare NSP4 genotype, E6 during 2009-2013.

Quantification of Rotavirus Diarrheal Risk Due to Hydroclimatic Extremes Over South Asia: Prospects of Satellite-Based Observations in Detecting Outbreaks

Rotavirus is the most common cause of diarrheal disease among children under 5. Especially in South Asia, rotavirus remains the leading cause of mortality in children due to diarrhea. As climatic extremes and safe water availability significantly influence diarrheal disease impacts in human populations, hydroclimatic information can be a potential tool for disease preparedness. In this study, we conducted a multivariate temporal and spatial assessment of 34 climate indices calculated from ground and satellite Earth observations to examine the role of temperature and rainfall extremes on the seasonality of rotavirus transmission in Bangladesh. We extracted rainfall data from the Global Precipitation Measurement and temperature data from the Moderate Resolution Imaging Spectroradiometer sensors to validate the analyses and explore the potential of a satellite-based seasonal forecasting model. Our analyses found that the number of rainy days and nighttime temperature range from 16°C to 21°C are particularly influential on the winter transmission cycle of rotavirus. The lower number of wet days with suitable cold temperatures for an extended time accelerates the onset and intensity of the outbreaks. Temporal analysis over Dhaka also suggested that water logging during monsoon precipitation influences rotavirus outbreaks during a summer transmission cycle. The proposed model shows lag components, which allowed us to forecast the disease outbreaks 1 to 2 months in advance. The satellite data-driven forecasts also effectively captured the increased vulnerability of dry-cold regions of the country, compared to the wet-warm regions.

Species A rotaviruses isolated from hospitalized patients over 5 years of age in Kolkata, India, in 2012/13

In hospital-based diarrhoeal disease surveillance at Infectious Diseases & Beliaghata-General Hospital (May-2012 to April-2013), Kolkata, India, stool samples were collected from patients < 5 years (n = 830) and > 5 years of age (n = 728) hospitalized with diarrhea. Group-A rotavirus (GARV) was identified by ELISA followed by multiplex RT-PCR. In children < 5 years of age, 53.4% of the samples were positive for GARV. In patients > 5 years to 90 years old, only 6.04% (n = 44) tested positive for GARV. G2P[4] strains (n = 16 [36.36%]) were the most prevalent, followed by G9P[4] strains (n = 13 [29.54%]), while P[4]-(n = 30 [68.18%]) was most prevalent among the P genotypes. The GARV strains G2, G9 and P[4] detected in adults clustered together in the phylogenetic tree with the GARV strains identified in children (< 5 years) during the same period. Rotavirus positivity was high among female patients (75%), suggesting that caregivers (mother/grandmother/older-siblings) may get infected through young children or may act as carriers for transmission.

Complex reassortment events of unusual G9P[4] rotavirus strains in India between 2011 and 2013

Rotavirus A (RVA) is the predominant etiological agent of acute gastroenteritis in young children worldwide. Recently, unusual G9P[4] rotavirus strains emerged with high prevalence in many countries. Such intergenogroup reassortant strains highlight the ongoing spread of unusual rotavirus strains throughout Asia. This study was undertaken to determine the whole genome of eleven unusual G9P[4] strains detected in India during 2011-2013, and to compare them with other human and animal global RVAs to understand the exact origin of unusual G9P[4] circulating in India and other countries worldwide. Of these 11 RVAs, four G9P[4] strains were double-reassortants with the G9-VP7 and E6-NSP4 genes on a DS-1-like genetic backbone (G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2). The other strains showed a complex genetic constellation, likely derived from triple reassortment event with the G9-VP7, N1-NSP2 and E6-NSP4 on a DS-1-like genetic backbone (G9-P[4]-I2-R2-C2-M2-A2-N1-T2-E6-H2). Presumably, these unusual G9P[4] strains were generated after several reassortment events between the contemporary co-circulating human rotavirus strains. Moreover, the point mutation S291L at the interaction site between inner and outer capsid proteins of VP6 gene may be important in the rapid spread of this unusual strain. The complex reassortment events within the G9[4] strains may be related to the high prevalence of mixed infections in India as reported in this study and other previous studies.

Epidemiological features and genetic characterization of virus strains in rotavirus associated gastroenteritis in children of Odisha in Eastern India

We have studied the clinical characteristics, severity and seasonality of rotavirus infection and prevalent genotypes in 652 non-rota vaccinated children in Odisha in eastern India. P genotypes were analysed for their association with host blood group antigens. P type of the virus is determined by the VP8* gene, and specific recognition of A - type of Histo - blood group antigen by P[14]VP8* has been reported. VP4, VP7 and VP6 genes of commonly identified G1P[8] strain were compared with genes of the same strain isolated from other parts of India, elsewhere and strains used for Rotarix and Rotateq vaccines. In 54.75% of children with gastroenteritis, rota virus was found. 9.65% of children had moderate, 78.07% severe, and 12.28% very severe disease as assessed using the Vesikari scoring system. The incidence of infection was highest during winter months. There was no association between any blood group and specific P genotypes. G1P[8] was the commonest cause of gastroenteritis, followed by G1P[11], G3P[8], G9P[8], G2P[4], G2P[6], G9P[4], G9P[11] and G1P[6]. Predominant G genotypes identified were G1 (72.9%), G9 (10.81%), G2 (8.10%) and G3 (8.10%). Sequence analysis of the VP7 gene, placed the G1P[8] strain in lineage 1 and of VP6 gene placed nine G1P[8] strains in subgroup II and one in subgroup I. The VP7 gene segment of two Odisha G1P[8] strains were found to cluster relatively close to the VP7 sequences of Rotarix vaccine. Antigenic differences were found with vaccine strains. Ten G1P[8] strains sequenced for the VP4 gene had 91-93% nucleotide and 92-96% amino acid identity with Rotateq vaccine P[8]). Rotarix vaccine VP4 had 89-91% nucleotide and 90-92% amino acid identity. Our findings indicate genetic variability of rotavirus strains circulating in the region and are significant, given the introduction of rota vaccination in the State.

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.

The prevalence and genotype distribution of rotavirus A infection among children with acute gastroenteritis in Kunming, China

The aim of this study was to determine the prevalence of rotavirus A (RVA) infections in children from Kunming, China, and the RVA genotypes present. A total of 16,311 children with acute gastroenteritis were recruited for the study, and 33.1 % (5,394/16,311) were RVA positive. Children under 24 months of age were more susceptible to RVA infection, with an infection rate of 87.4 % (4,712/5,394). The most prevalent genotype was G9P[8] (85/107, 79.4 %), which showed high sequence similarity to G9P[8] strains from other regions of China and neighbouring countries, but not to the licensed vaccine strain LLR. These findings should be useful for the prevention of RVA infections.

Whole genomic analysis of G2P[4] human Rotaviruses in Mymensingh, north-central Bangladesh

Rotavirus A (RVA) is a dominant causative agent of acute gastroenteritis in children worldwide. G2P[4] is one of the most common genotypes among human rotavirus (HRV) strains, and has been persistently prevalent in South Asia including Bangladesh. In the present study, whole genome sequences of a total of 16 G2P[4] HRV strains (8 strains each in 2010 and 2013) detected in Mymensingh, north-central Bangladesh were determined. These strains had typical DS-1-like genotype constellation. Most of gene segments from DS-1 genogroup exhibited high level sequence identities to each other (>98%), while slight diversity was observed for VP1, VP3, and NSP4 genes. By phylogenetic analysis, individual RNA segments were classified into one (V) or two-three lineages (V–VI or V–VII). In terms of lineages (sublineages) of 11 gene segments, the 16 Bangladeshi strains could be further classified into four clades (A-D) containing 8 lineage constellations, revealing the presence of three clades (A-C) with three lineage constellations in 2010, and a single clade (D) with four constellations in 2013. Therefore, co-existence of multiple G2P[4] HRV strains with different lineage constellations, and change in clades for the study period were demonstrated. Although amino acids in the antigenic regions on VP7 and VP4 were mostly identical to those of global G2P[4] strains after 2000, VP4 of clade D RVAs in 2013 had alanine and proline at positions 88 and 114, respectively, which are novel substitutions compared with recent global G2P[4] strains. Replacement of lineage constellations associated with unique amino acid changes in the antigenic region in VP4 suggested continuous genetic evolutionary state for emerging new G2P[4] rotavirus strains in Bangladesh.

Complete genotyping of unusual species A rotavirus G12P[11] and G10P[14] isolates and evidence of frequent in vivo reassortment among the rotaviruses detected in children with diarrhea in Kolkata, India, during 2014

Species A rotaviruses (RVA) are the most important cause of acute gastroenteritis in the young of humans and many animal species globally. G1P[8], G2P[4], G3P[8], G4P[8], G9P[6/8] and G12P[6/8] are the predominantly isolated genotypes throughout the world including India. Unusual genotypes from different host species such as G5, G6, G8, G10 and G11 have also been reported in humans with low frequency. In the present study, among >650 RVA positive stool samples collected from children with diarrhea in Kolkata, India, during 2014, two isolates each of the genotype G12P[11] and G10P[14] were obtained and their genomes completely sequenced. The full genotype constellations were G12-P[11]-I1-R1-C1-M2-A1-N1-T2-E1-H1 and G12-P[11]-I1-R1-C1-M1-A5-N1-T1-E1-H1 for G12P[11] viruses, suggesting several reassortments between Wa- and DS-1-like human RVA strains, including possible reassortment of a simian NSP1 gene. The G10P[14] viruses (G10-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3) were found to contain multiple genes closely related to RVAs of artiodactyl origin, highlighting the role of inter-host species transmissions of RVAs. From the G/P constellation of all RVA isolates, it could be concluded that approximately one quarter had likely arisen from reassortment events in vivo among RVAs of 'usual' genotypes.

Unusual rotavirus genotypes in humans and animals with acute diarrhoea in Northeast India

Rotavirus (RV) infection causes acute infantile diarrhoea in humans and animals and remains a major concern for vaccine development. The close proximity of humans to animals may foster cross-species infection resulting in the emergence of novel/unusual strains by genetic reassortment. In this study, we characterized 500 diarrhoeal samples for group A rotaviruses (RVA) from children (n = 290), piglets (n = 95) and calves (n = 115) in Northeast India during 2012-2013. The data showed that 142/500 (28·4%) faecal samples were positive for RVA with the highest level of infection detected in piglets (57/142, 40·1%) followed by children (51/142, 35·9%) and calves (34/142, 23·9%). Sequence-based G- and P-typing showed G1P[8] (25%) and G1P[7] (35%) were the prevailing genotypes in both humans and animals. Single cases of unusual genotypes, i.e. G9P[8], G5P[8] in humans and G1P[13], G1P[23] and G3P[7] in animals were also identified. Cluster analyses of the sequences showed regional strains were genetically closer to their homologous strains. However, human G5P[8] and porcine G1P[8] strains showed homology to heterologous hosts of their prototype strains. The subsequent global spread of unusual RV strains may result in their establishment over time, presenting challenges to future vaccine evaluation programmes. More studies on emerging genotypes are required to elucidate how RVA strains evolve post-vaccination. This study supports the need for continuous surveillance of RVA infections after detecting from diverse hosts in a common setting.

G2 rotavirus within an emergent VP7 evolutionary lineage circulating in children with acute diarrhea in Guangxi Province of China, 2014

Routine surveillance revealed that the prevalence of P[4] rotaviruses circulating in children with acute diarrhea in Guangxi Province, China, increased in 2014. However, VP7 genotyping for these P[4] rotaviruses was unsuccessful. Exhaustive database searching and sequence analysis indicated that the G genotype of these P[4] rotaviruses was G2, and the VP7 genes clustered with recently emerging G2 strains in several countries within an emergent evolutionary lineage that was distinct from the previously designated lineages I-IV as well as lineage V including porcine rotaviruses. Further studies are essential to monitor the potential global spread of this emerging G2 rotavirus.

Rotavirus Surveillance at a WHO-Coordinated Invasive Bacterial Disease Surveillance Site in Bangladesh: A Feasibility Study to Integrate Two Surveillance Systems

The World Health Organization (WHO) currently coordinates rotavirus diarrhea and invasive bacterial disease (IBD) surveillance at 178 sentinel sites in 60 countries. However, only 78 sites participate in both surveillance systems using a common sentinel site. Here, we explored the feasibility of extending a WHO-IBD surveillance platform to generate data on the burden of rotaviral diarrhea and its epidemiological characteristics to prepare the countries to measure the impact of rotaviral vaccine. A six-month (July to December, 2012) surveillance, managed by IBD team, collected stool samples and clinical data from under-five children with acute watery diarrhea at an IBD sentinel site. Samples were tested for rotavirus antigen by ELISA and genotyped by PCR at the regional reference laboratory (RRL). Specimens were collected from 79% (n = 297) of eligible cases (n = 375); 100% of which were tested for rotavirus by ELISA and 54% (159/297) of them were positive. At RRL, all the cases were confirmed by PCR and genotyped (99%; 158/159). The typing results revealed the predominance of G12 (40%; 64/159) genotype, followed by G1 (31%; 50/159) and G9 (19%; 31/159). All in all, this exploratory surveillance collected the desired demographic and epidemiological data and achieved almost all the benchmark indicators of WHO, starting from enrollment number to quality assurance through a number of case detection, collection, and testing of specimens and genotyping of strains at RRL. The success of this WHO-IBD site in achieving these benchmark indicators of WHO can be used by WHO as a proof-of-concept for considering integration of rotavirus surveillance with WHO-IBD platforms, specifically in countries with well performing IBD site and no ongoing rotavirus surveillance.

Community based case-control study of rotavirus gastroenteritis among young children during 2008-2010 reveals vast genetic diversity and increased prevalence of G9 strains in Kolkata

BACKGROUND

Group A Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children (<5 years) worldwide. Although rotavirus vaccines have been successfully administered in many countries, in India the introduction of rotavirus vaccine in national immunization program was approved in 2014. Since high disease burden and large number of genetic variants have been reported from low income countries including India, monitoring of rotavirus was initiated prior to implementation of the vaccine in the region.

METHODS

A total number of 3,582 stool samples were collected from an urban slum community in Kolkata, among which 1,568 samples were obtained from children of ≤ 5 years of age, with moderate to severe diarrhoea and 2,014 samples were collected from age-sex matched healthy neighbourhood controls. Rotavirus positive samples were typed by multiplex semi-nested PCR and nucleotide sequencing. Circulating strains were phylogenetically analyzed.

RESULTS

Among 1,568 children with diarrhoea, 395 (25.2%), and among 2,014 asymptomatic children, 42 (2%) were rotavirus positive. G1P[8] was identified as the most common strain (32%) followed by G9P[8] (16.9%), G2P[4] (13.5%) and G9P[4] (10.75%). G12 strains with combinations of P[4], P[6] and P[8] comprised 11.9% of total positive strains. The rest (<10%) were rare and uncommon strains like G1P[4], G1P[6], G2P[8] and animal-like strains G4P[6], G6P[14] and G11P[25]. The 42 rotavirus positive samples from asymptomatic children revealed common genotypes like G1, G2 and G9.

CONCLUSION

This community based case-control study showed increased predominance of genotype G9 in Kolkata. It also confirmed co-circulation of a large number of genetic variants in the community. Asymptomatic rotavirus positive children though low in number can also be a source of dispersal of infection in the community. This study provides background information to the policy makers for implementation of rotavirus vaccines in this region.

Analysis of rotavirus genotypes in Korea during 2013: an increase in the G2P[4] genotype after the introduction of rotavirus vaccines

BACKGROUND

Group A rotavirus is the leading cause of acute gastroenteritis in children worldwide. We investigated G and P genotypes of group A rotavirus strains isolated from patients during 2013 and investigated which genotypes were identified from vaccinated patients.

METHODS

From January to December 2013, 2235 fecal specimens were tested for rotavirus antigen, of which 374 specimens (16.7%) showed positive results. Strains from 288 rotavirus-positive specimens were genotyped using PCR and sequencing, and individual patients' corresponding vaccine histories were investigated through the Korean Center for Disease Control website.

RESULTS

G2 (22.6%) and P[4] (24.0%) were the most frequently identified G and P genotypes, respectively; accordingly, G2P[4] (19.8%) was the most prevalent G/P genotype observed in this period. G4P[6] (10.1%) was the second most prevalent G/P genotype and was mostly detected in neonates. Other genotypes, G1P[8], G9P[8], G1P[6], and G3P[6], were also detected. Of 288 rotavirus-positive specimens, 48 specimens were obtained from previously vaccinated patients. G2P[4] was also the genotype most frequently isolated from vaccinated patients. VP7 epitope analysis of G1P[8] and G2P[4] strains showed at least one amino acid differences in comparison with Rotarix and RotaTeq vaccine strains. The genotypic distribution of rotavirus strains in Korea has been shown temporal and geographical differences.

CONCLUSION

This study showed that G2P[4] was the genotype most frequently isolated from both vaccinated and unvaccinated patients in Korea during 2013. However, it is unclear whether the change of predominant genotype is due to the effect of vaccination or due to natural variation.