Rotavirus disease and vaccination: impact on genotype diversity

Analysis of protein determinants of genotype-specific properties of group a rotaviruses using machine learning

Group A rotaviruses (RVAs) are the leading cause of viral diarrhoea across various host species, including mammals and birds. The VP7 and VP4 proteins of these viruses play critical roles in determining genotype specificity, influencing viral infectivity and host adaptation. This study employed machine-learning techniques to classify RVA genotypes based on the molecular and physicochemical properties of these proteins. A dataset of 94 VP7 and 68 VP4 protein sequences was collected from various host species. Seven machine-learning algorithms-Naïve Bayes (NB), logistic regression (LR), decision tree (DT), random forest (RF), k-nearest neighbour (kNN), support vector machine (SVM), and artificial neural network (ANN)-were used for genotype classification. Feature subsets were configured using ranking-based attribute selection, and classification performance was evaluated using accuracy (ACC), precision, recall, Matthews' correlation coefficient (MCC), and the area under the curve (AUC). kNN demonstrated the highest classification accuracy for both VP7 (ACC = 97.87 %) and VP4 (ACC = 100 %), outperforming NB, LR, DT, RF, SVM, and ANN. For VP7 sequences, key properties influencing genotype classification included hydrophobicity, normalised van der Waals volume, and leucine composition. For VP4, polarity, normalised van der Waals volume, and polarizability were the most significant factors. In summary, the genotype-specific molecular features of VP7 and VP4 proteins served as reliable markers for RVA classification. Our findings highlight the potential of machine-learning approaches to predict RVA genotypes based on the physicochemical properties of amino acids, providing valuable insights into the molecular mechanisms that drive viral evolution, host specificity, and immune evasion.

Development of RT-dPCR method and reference material for rotavirus G3P8 and G9P8

The rotavirus (RV) is the predominant causative pathogen associated with acute gastroenteritis in children aged below 5 years, leading to an annual mortality rate of 200,000 infants globally. Despite the development of a vaccine, it exacerbates the medical burden around the world. Here, we have developed reverse transcription digital PCR (RT-dPCR) methods for precise and absolute quantification of nucleic acid in rotavirus G3P8 and G9P8. The pseudovirus reference material (RM) contained the RNA fragment encoding VP4 and VP7. The assigned values with expanded uncertainty were determined as (2432 ± 510) copies/μL and (3406 ± 613) copies/μL. The RM and RT-dPCR methods were employed to validate various digital platforms, revealing the inadequate performance of platform III, which could potentially result in "false-negative" outcomes. The application of RT-dPCR techniques and pseudovirus RM confers advantages in the diagnosis of RV-induced diseases, thereby enhancing the survival rate of young children suffering from acute gastroenteritis.

14 years of rotavirus A surveillance: unusual dominance of equine-like G3P[8] genotype with DS-1-like genotype constellation after the pandemic, Belgium, 2009 to 2023

IntroductionDespite vaccine availability, rotavirus persists as a leading cause of gastroenteritis in children younger than 5 years.AimWe aimed to evaluate temporal changes in rotavirus epidemiology in Belgium between 2009 and 2023, including the period of the COVID-19 pandemic.MethodsWe collected 8,024 rotavirus-positive stool samples throughout Belgium. For 6,352 samples, we determined the G and/or P genotypes through sequencing of the genes encoding the outer capsid proteins VP7 and VP4.ResultsBefore the COVID-19pandemic, we received on average 622 samples per rotavirus epidemiological year, which decreased to 114 and 111 samples during the two pandemic rotavirus epidemiological years, followed by a peak of 1,048 samples in the first post-pandemic year. Notably, the proportion of cases in the age group 2-5-years increased from 20.3% before to 33% after the pandemic (p < 0.001). Over the 14-year study period, the most common genotypes were G2P[4], G3P[8] and G9P[8]. Post-pandemic data show an unusually strong dominance of the equine-like G3P[8] genotype which carried a DS-1-like genotype constellation in the period 2021 to 2023. Additionally, vaccinated individuals were significantly overrepresented among patients infected with the equine-like VP7 carrying G3P[8] rotavirus compared with other genotypes, including typical human VP7 G3P[8].ConclusionDespite the presence of typical yearly genotype fluctuations, several epidemiological changes were associated with the COVID-19 pandemic, including the unusual dominance of an emerging rotavirus strain against which current vaccines may be less effective. It is essential to closely monitor this strain to determine if the phenomenon is temporary.

Detection and characterization of bovine coronavirus and rotavirus in calves in Ethiopia

BACKGROUND

Bovine rotavirus A (BRVA) and bovine coronavirus (BCoV) cause significant diarrhea in young calves, leading to health issues and economic losses in the cattle industry. This study aimed to detect and molecularly characterize BRVA and BCoV in calves from Addis Ababa, Ethiopia. Fecal samples were collected from 105 calves under six months old, both with and without diarrhea. BRVA and BCoV were detected using quantitative real-time Polymerase Chain Reaction (qPCR), followed by genome sequencing for phylogenetic analysis and genotype determination.

RESULTS

BRVA was found in 3.8% of the calves, while BCoV was detected in 2.9%. The identified rotavirus genotypes included G10, found in diarrheic calves, and G8, found in a non-diarrheic calf. All BCoV infections occurred in diarrheic calves. Phylogenetic analysis of the BCoV spike protein 1 (S1) hypervariable region (HVR) and hemagglutinin esterase (HE) gene revealed close relationships with European and Asian strains. The S1 HVR of the current virus sequence PQ249423 was 100% identical at the nucleotide level to previously reported sequences from Ethiopia. Six amino acid substitutions in the HE gene of the current BCoVs were identified compared to the reference Mebus strain of BCoV. Phylogenetic analysis showed that the current G8 BRVA sequences clustered with bovine, caprine, and human rotavirus strains, while the G10 viruses formed a distinct cluster with bovine strains. The G10 viruses showed a 99.37% nucleotide sequence similarity to a previously reported BRVA from Ethiopia, and the G8 virus displayed the highest nucleotide similarity with a caprine isolate from India. Gene segment analysis of the current BRVA viruses indicated varying similarities with human, bovine, caprine, and porcine rotavirus strains, suggesting a potential reassortment event involving artiodactyl, human, and porcine rotavirus.

CONCLUSIONS

This study demonstrates the presence of BRVA and BCoV in Ethiopian dairy calves and provides insights into their genetic diversity. Genetic analysis of BCoV revealed close relationships with strains from Europe and Asia. G10 and G8 were the identified BRVA genotypes, with G8 reported for the first time in Ethiopia. Future research should focus on broader sampling and molecular characterization to understand genetic diversity and devise effective control measures.

Full genome sequence analysis of the predominant and uncommon G9P[4] rotavirus strains circulating in Tehran, Iran, 2021-2022: Evidence for inter and intra-genotype recombination

Group A rotaviruses (RVAs) are a major cause of acute gastroenteritis in children under 5 years of age worldwide. Herein, the genetic sequences of 11 RNA segments from three uncommon G9P[4] RVA strains found in the stool samples of children under 5 years of age in Iran were analyzed using next-generation sequencing (NGS) technology. The genomic constellations of these three uncommon G9P[4] strains indicated the presence of the double and quadruple reassortants of two G9P[4] strains, containing the VP7/NSP2 and VP7/VP2/NSP2/NSP4 genes on a DS-1-like genetic background, respectively. The genome of one strain indicated a Wa-like genetic backbone in a single-reassortant with the VP4 of the DS1-like human strains. With the exception of VP1, VP2, VP7, NSP2, NSP3, and NSP4 genes, which clustered with RVA of human origins belonging to cognate gene sequences of genogroup 1/2 genotypes/lineages, the remaining five genes (VP8/VP4, VP3, VP6, NSP1, NSP5) displayed direct evidence of recombination. It is presumed that the presence of uncommon G9P[4] strains in Iran is not linked to vaccination pressure, but rather to the high prevalence of RVA co-infection or the direct import of these uncommon RVA reassortants strains from other countries (especially those that have implemented RV vaccination).

New Genotype G3 P[8] of Rotavirus Identified in a Mexican Gastroenteric Rabbit

Rotavirus species A (RVA) is a major cause of acute viral gastroenteritis in young humans and diverse animal species. The study of the genetic characteristics of RVAs that infect rabbits (Oryctolagus cuniculus) (lapine strain [LRV]) has been limited, and, to date, the most common and epidemiologically important combinations of G/P genotypes in rabbits have been reported to be G3 P[14] and G3 P[22]. In this study, a rotavirus species A detected from an outbreak of enteritis in a Mexican commercial rabbitry was genotypically characterized. Based on sequence and phylogenetic analysis of the VP7 and VP4 genes, the strain identified in this study (C-3/15) demonstrated a G3 P[8] genotype of rotavirus, which had not previously been reported in rabbits. Moreover, both genes were closely related to human, not lapine, rotaviruses. The G3 genotype has been reported in a wide variety of hosts, including humans and rabbits, whereas the P[8] genotype has only been reported in humans. Because this combination of genotypes has never been identified in rabbits, it is proposed that the finding presented here is possibly the result of an interspecies transmission event. This is the first work to study the molecular characteristics of rotaviruses in rabbits in Mexico, as well as the identification of human G3 and P[8] genotypes in a rabbit with enteric disease.

Identification of Rotavirus Genotypes in Children under Five Years in the United Arab Emirates Using Nanopore Sequencing Technology

Group A rotaviruses (RVA) remain a principal cause of childhood diarrhea in the UAE, despite universal vaccine use. Monitoring genetic diversity is important for identifying prevalent genotypes and escape mutants. Although real-time polymerase chain reaction (RT-PCR) is widely used for RVA genotyping, it may not detect some new strains. This study evaluates nanopore sequencing and RT-PCR for RVA genotyping. Thirty-three RVA strains from children under 5 years presenting with diarrhea were genotyped using both methods. Thirteen strains were genotyped by RT-PCR and confirmed by nanopore sequencing. Fifteen strains were genotyped by nanopore method alone. Most PCR-genotyped strains (56%) had the VP7 G9 genotype, with G3 in five strains and G12 in two. For VP4, P8 (n = 8) and P4 (n = 7) were dominant. The most frequent combinations were G9P[8] (31%) and G9P[4] (25%). Nanopore sequencing of 28 strains revealed G3P[8] (29%) as the most prevalent, followed by G8P[8] (18%). G9P[8] and G2P[4] were present in 14% of samples with G12P[6] being the rarest (7%). Other combinations were detected in 4% the specimens with one nontypeable. Nanopore sequencing was superior to PCR in identifying diverse and emerging genotypes like G8P[8]. This method may enhance surveillance studies and guide preventive measures for RVA gastroenteritis.

Complete genome constellation of a dominant Bovine rotavirus genotype circulating in Bangladesh reveals NSP4 intragenic recombination with human strains

Rotavirus A is a leading cause of non-bacterial gastroenteritis in humans and domesticated animals. Despite the vast diversity of bovine Rotavirus A strains documented in South Asian countries, there are very few whole genomes available for phylogenetic study. A cross-sectional study identified a high prevalence of the G6P[11] genotype of bovine Rotavirus A circulating in the commercial cattle population in Bangladesh. Next-generation sequencing and downstream phylogenetic analysis unveiled all 11 complete gene segments of this strain (BD_ROTA_CVASU), classifying it under the genomic constellation G6P[11]-I2-R2-C2-M2-A13-N2-T6-E2-H3, which belongs to a classical DS-1-like genomic backbone. We found strong evidence of intragenic recombination between human and bovine strains in the Non-structural protein 4 (NSP4) gene, which encodes a multifunctional enterotoxin. Our analyses highlight frequent zoonotic transmissions of rotaviruses in diverse human-animal interfaces, which might have contributed to the evolution and pathogenesis of this dominant genotype circulating in the commercial cattle population in Bangladesh.

Rotavirus infections and their genotype distribution pre- and post-vaccine introduction in Ethiopia: a systemic review and meta-analysis

BACKGROUND

Rotavirus infections are a significant cause of severe diarrhea and related illness and death in children under five worldwide. Despite the global introduction of vaccinations for rotavirus over a decade ago, rotavirus infections still result in high deaths annually, mainly in low-income countries, including Ethiopia, and need special attention. This system review and meta-analysis aimed to comprehensively explore the positive proportion of rotavirus at pre- and post-vaccine introduction periods and genotype distribution in children under five with diarrhea in Ethiopia.

METHODS

The review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. Database sources included PubMed, Scopus, EMBASE, and Epistemonikos, focusing on studies published before November 30, 2023. The search targeted rotavirus infection and genotype distribution in Ethiopia before and after the introduction of the Rota vaccine. Data was managed using EndNote 2020 software and stored in an Excel 2010 sheet. A random-effects model determined the pooled estimate of the rotavirus infection rate at 95% confidence intervals. The Q-and I² statistics were used to assess the study heterogeneity, and a funnel plot (Egger test) was used to determine the possibility of publication bias.

RESULTS

The analysis included data from nine studies conducted in different regions of Ethiopia. The overall prevalence of rotavirus infection was significant, with a prevalence rate of approximately 22.63% (1362/6039). The most common genotypes identified before the Rota vacation introduction were G1, G2, G3, G12, P [4], P [6], P [8], P [9], and P [10]. Meanwhile, G3 and P [8] genotypes were particularly prevalent after the Rota vaccine introduction. These findings highlight the importance of implementing preventive measures, such as vaccination, to reduce the burden of rotavirus infection in this population. The identified genotypes provide valuable insights for vaccine development and targeted interventions.

CONCLUSION

This study contributes to the evidence base for public health interventions and strategies to reduce the impact of rotavirus infection in children under five in Ethiopia. Despite the rollout of the Rota vaccination in Ethiopia, rotavirus heterogeneity is still high, and thus, enhancing vaccination and immunization is essential.

Genomic revelations: investigating rotavirus a presence in wild ruminants and its zoonotic potential

Introduction

Rotaviruses A (RVA) are a major cause of acute viral gastroenteritis in humans worldwide and are responsible for about two million hospitalizations per year. They can also infect other mammals such as pigs, calves, goats, lambs, and horses, in which they are also considered a major cause of viral diarrhea. While RVA is well studied in humans and domestic animals, its occurrence in wild ruminants is not well known. The RVA genome is a double-stranded RNA consisting of 11 segments, and genotyping is based on the VP7 (G) and VP4 (P) segments. Currently, there are 42G genotypes and 58P genotypes. RVA has a high mutation rate, and some combinations of G and P genotypes can infect different animal species, leading to speculation about the potential for zoonotic transmission.

Materials and methods

A total of 432 fecal samples were collected from roe deer, red deer, chamois, mouflon and Alpine ibex in Slovenia between 2017 and 2021. To investigate the presence of RVA in wild ruminants, real-time RT-PCR was used. Positive samples were subjected to next generation sequencing (NGS) using RIP-seq method.

Results and discussion

In total, 7 samples were RVA positive. Complete genomes were determined and phylogenetically analyzed for all 7 RVAs. Four different genotype constellations were present in 7 positive RVA animals: G8-P[14]-I2- R2-C2-M2-A3-N2-T6-E2-H3, G6-P [14]-I2-R2-C2-M2-A11-N2-T6-E2-H3, G10-P [15]-I2-R2-C2-M2-A3-N2-T6-E2-H3 and G10-P [15]-I2-R2-C2-M2-A11- N2-T6-E2-H3. Genotypes G6P[14] and G10P[15] were found in both roe deer and red deer, representing the first confirmed occurrence of RVA in red deer. In addition, genotype G8P[14] was found in chamois, representing the first known case of positive RVA in this species. Some of these genotypes have also been found in humans, indicating the potential for zoonotic transmission.

Reverse vaccinology-based multi-epitope vaccine design against Indian group A rotavirus targeting VP7, VP4, and VP6 proteins

Rotavirus, a primary contributor to severe cases of infantile gastroenteritis on a global scale, results in significant morbidity and mortality in the under-five population, particularly in middle to low-income countries, including India. WHO-approved live-attenuated vaccines are linked to a heightened susceptibility to intussusception and exhibit low efficacy, primarily attributed to the high genetic diversity of rotavirus, varying over time and across different geographic regions. Herein, molecular data on Indian rotavirus A (RVA) has been reviewed through phylogenetic analysis, revealing G1P[8] to be the prevalent strain of RVA in India. The conserved capsid protein sequences of VP7, VP4 and VP6 were used to examine helper T lymphocyte, cytotoxic T lymphocyte and linear B-cell epitopes. Twenty epitopes were identified after evaluation of factors such as antigenicity, non-allergenicity, non-toxicity, and stability. These epitopes were then interconnected using suitable linkers and an N-terminal beta defensin adjuvant. The in silico designed vaccine exhibited structural stability and interactions with integrins (αvβ3 and αIIbβ3) and toll-like receptors (TLR2 and TLR4) indicated by docking and normal mode analyses. The immune simulation profile of the designed RVA multiepitope vaccine exhibited its potential to trigger humoral as well as cell-mediated immunity, indicating that it is a promising immunogen. These computational findings indicate potential efficacy of the designed vaccine against rotavirus infection.

Vaccine-induced strain replacement: theory and real-life implications

The value of preventive medicine is superior to treatment with vaccinations occupying high priority. Nevertheless, heavy pressure has started to form in regard to strains not included in vaccines contributing to the changing epidemiology of pathogen subtypes leading to 'vaccine-induced strain replacement'. Among other mechanisms, increasing fitness of nonvaccine strains and metabolic shifts in the subtypes have been described. Classical examples include pneumococcal infections and viral diseases, such as the human papilloma virus. Recently, it has been described in SARS-CoV-2, leading to the emergence of new subtypes, such as Omicron and Delta variants. The phenomenon has also been reported in Mycobacterium tuberculosis, Neisseria meningitidis and rotavirus. This study addresses the concepts, examples and implications of this phenomenon.

Molecular characterization of rotavirus indicates predominance of G9P[4] genotype among children with acute gastroenteritis: First report after vaccine introduction in Pakistan

Globally, Group A rotavirus (RVA) is the leading cause of acute gastroenteritis in children under 5 years old, with Pakistan having the highest rates of RVA-related morbidity and mortality. The current study aims to determine the genetic diversity of rotavirus and evaluate the impact of Rotarix-vaccine introduction on disease epidemiology in Pakistan. A total of 4749 children, hospitalized with acute gastroenteritis between 2018 and 2020, were tested at four hospitals in Lahore and Karachi. Of the total, 19.3% (918/4749) cases were tested positive for RVA antigen, with the positivity rate varying annually (2018 = 22.7%, 2019 = 14.4%, 2020 = 20.9%). Among RVA-positive children, 66.3% were under 1 year of age. Genotyping of 662 enzyme-linked immuno sorbent assay-positive samples revealed the predominant genotype as G9P[4] (21.4%), followed by G1P[8] (18.9%), G3P[8] (11.4%), G12P[6] (8.7%), G2P[4] (5.7%), G2P[6] (4.8%), and 10.8% had mixed genotypes. Among vaccinated children, genotypes G9P[4] and G12P[6] were more frequently detected, whereas a decline in G2P[4] was observed. Phylogenetic analysis confirmed the continued circulation of indigenous genotypes detected earlier in the country except G9 and P[6] strains. Our findings highlight the predominance of G9P[4] genotype after the vaccine introduction thus emphasizing continual surveillance to monitor the disease burden, viral diversity, and their impact on control of rotavirus gastroenteritis in children.

Rotavirus trends and distribution of genotypes before and during COVID-19 pandemic era: Bangladesh, 2017-2021

Rotavirus gastroenteritis is accountable for an estimated 128 500 deaths among children younger than 5 years worldwide, and the majority occur in low-income countries. Although the clinical trials of rotavirus vaccines in Bangladesh revealed a significant reduction of severe rotavirus disease by around 50%, the vaccines are not yet included in the routine immunization program. The present study was designed to provide data on rotavirus diarrhea with clinical profiles and genotypes before (2017-2019) and during the COVID-19 pandemic period (2020-2021). Fecal samples were collected from 2% of the diarrheal patients at icddr,b Dhaka hospital of all ages between January 2017 and December 2021 and were tested for VP6 rotavirus antigen using ELISA. The clinical manifestations such as fever, duration of diarrhea and hospitalization, number of stools, and dehydration and so on were collected from the surveillance database (n = 3127). Of the positive samples, 10% were randomly selected for genotyping using Sanger sequencing method. A total of 12 705 fecal samples were screened for rotavirus A antigen by enzyme immunoassay. Overall, 3369 (27%) were rotavirus antigen-positive, of whom children <2 years had the highest prevalence (88.6%). The risk of rotavirus A infection was 4.2 times higher in winter than in summer. Overall, G3P[8] was the most prominent genotype (45.3%), followed by G1P[8] (32.1%), G9P[8] (6.8%), and G2P[4] (6.1%). The other unusual combinations, such as G1P[4], G1P[6], G2P[6], G3P[4], G3P[6], and G9P[6], were also present. Genetic analysis on Bangladeshi strains revealed that the selection pressure (dN/dS) was estimated as <1. The number of hospital visits showed a 37% drop during the COVID-19 pandemic relative to the years before the pandemic. Conversely, there was a notable increase in the rate of rotavirus positivity during the pandemic (34%, p < 0.00) compared to the period before COVID-19 (23%). Among the various clinical symptoms, only the occurrence of watery stool significantly increased during the pandemic. The G2P[4] strain showed a sudden rise (19%) in 2020, which then declined in 2021. In the same year, G1P[8] was more prevalent than G3P[8] (40% vs. 38%, respectively). The remaining genotypes were negligible and did not exhibit much fluctuation. This study reveals that the rotavirus burden remained high during the COVID-19 prepandemic and pandemic in Bangladesh. Considering the lack of antigenic variations between the circulating and vaccine-targeted strains, integrating the vaccine into the national immunization program could reduce the prevalence of the disease, the number of hospitalizations, and the severity of cases.

Viral gastroenteritis

Since the discovery of norovirus in 1972 as a cause of what was contemporarily known as acute infectious non-bacterial gastroenteritis, scientific understanding of the viral gastroenteritides has continued to evolve. It is now recognised that a small number of viruses are the predominant cause of acute gastroenteritis worldwide, in both high-income and low-income settings. Although treatment is still largely restricted to the replacement of fluid and electrolytes, improved diagnostics have allowed attribution of illness, enabling both targeted treatment of individual patients and prioritisation of interventions for populations worldwide. Questions remain regarding specific genetic and immunological factors underlying host susceptibility, and the optimal clinical management of patients who are susceptible to severe or prolonged manifestations of disease. Meanwhile, the worldwide implementation of rotavirus vaccines has led to substantial reductions in morbidity and mortality, and spurred interest in vaccine development to diminish the impact of the most prevalent viruses that are implicated in this syndrome.

Genomic analysis of two rare human G3P[9] rotavirus strains in Ningxia, China

G3P (Matthijnssens et al., 2008b [9]) is a rare combination of human rotavirus VP7/VP4 genotypes with a complex evolutionary pattern but limited related studies. Detailed genomic characterisation and genetic evolutionary analyses of G3P (Matthijnssens et al., 2008b [9]) rotaviruses have helped to enhance our understanding of rotavirus diversity. For the first time, we detected two human G3P (Matthijnssens et al., 2008b [9]) Rotavirus A (RVA) strains, RVA/Human-tc/CHN/2020999/2020/G3P (Matthijnssens et al., 2008b [9]) and RVA/Human-wt/CHN/23582009/2023/G3P (Matthijnssens et al., 2008b [9]), in diarrhoea patients from the Ningxia region of China, and carried out a whole-genome analysis of these strains. 2,020,999 and 23,582,009 have identical gene constellations: G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3, and this genotypic constellation was reported first time in China. They are closely related in 11 genome segments. The genotypes of these two strains are different from the human RVA strains L621 and E2451, which are only G3P (Matthijnssens et al., 2008b [9]) strains reported so far in China, but are identical to those of the Thai feline strain Meesuk and the Korean human strain CAU12-2-51.Phylogenetic analysis showed that the VP6, VP1-VP3, and NSP2 genes of the two strains in this study clustered with human/bovine and feline/bovine rotavirus strains to form a sublineage distinct from the common DS-1-like G2 human rotavirus. In contrast, the VP7, VP4, NSP1, and NSP3-NSP5 gene segments were closely associated with human/feline rotavirus and feline rotavirus strains. These findings suggest that the evolutionary origin of the G3P (Matthijnssens et al., 2008b [9]) human rotavirus found in Ningxia, China, is consistent with the Meesuk and CAU12-2-51 strains， may have arisen through reassortment between uncommon human/bovine， feline/bovine rotavirus strains and human/feline， feline rotaviruses. However, VP1-VP2 gene segments did not have the same lineage as strains Meesuk and CAU12-2-51, suggesting that these genes might be derived from additional reassortment event.

Clinical, epidemiological, and genotypic characteristics of rotavirus infection in hospitalized infants and young children in Yunnan Province

Rotaviruses are the most important pathogenic cause of non-bacterial diarrhea in infants and children. Approximately 60% of hospital admissions for acute diarrhea worldwide are caused by rotavirus infection. Rotavirus infection and hospitalization among children in China are a social burden, resulting in economic loss. The prevalence and geographical distribution of rotavirus genotypes is variable, partially due to population migration. Due to the unique geographical conditions and climate in Yunnan Province, several viruses with new genotypes have emerged, and multiple genotypes have become co-epidemic. In this study, rotavirus infection screening and genetic characterization of epidemic strains were performed in 149,492 infants and children admitted to hospitals in six representative prefectures in Yunnan Province between 2019 and 2021. The prevalence of rotavirus infection was 13.39% and was highest in January and lowest in September. G9P[8] was the main epidemic rotavirus genotype. Other epidemic genotypes included G2P[4], G8P[8], G9P[4], G2P[8], G3P[8], G4P[8], G3P[4], and G4P[6]. Phylogenetic analysis revealed that locally epidemic strains were influenced by importation of strains from neighboring provinces and other Asian countries. These findings provide a scientific basis for rotavirus prevention and control and lay a foundation for preliminary studies to establish a rotavirus surveillance network in Yunnan Province.

Classification of group A rotavirus VP7 and VP4 genotypes using random forest

Introduction: Group A rotaviruses are major pathogens in causing severe diarrhea in young children and neonates of many different species of animals worldwide and group A rotavirus sequence data are becoming increasingly available over time. Different methods exist that allow for rotavirus genotyping, but machine learning methods have yet to be explored. Usage of machine learning algorithms such as random forest alongside alignment-based methodology may allow for both efficient and accurate classification of circulating rotavirus genotypes through the dual classification system. Methods: Random forest models were trained on positional features obtained from pairwise and multiple sequence alignment and cross-validated using methods of repeated 10-fold cross-validation thrice and leave one- out cross validation. Models were then validated on unseen data from the testing datasets to observe real-world performance. Results: All models were found to perform strongly in classification of VP7 and VP4 genotypes with high overall accuracy and kappa values during model training (0.975-0.992, 0.970-0.989) and during model testing (0.972-0.996, 0.969-0.996), respectively. Models trained on multiple sequence alignment generally had slightly higher overall accuracy and kappa values than models trained on pairwise sequence alignment method. In contrast, pairwise sequence alignment models were found to be generally faster than multiple sequence alignment models in computational speed when models do not need to be retrained. Models that used repeated 10-fold cross-validation thrice were also found to be much faster in model computational speed than models that used leave-one-out cross validation, with no noticeable difference in overall accuracy and kappa values between the cross-validation methods. Discussion: Overall, random forest models showed strong performance in the classification of both group A rotavirus VP7 and VP4 genotypes. Application of these models as classifiers will allow for rapid and accurate classification of the increasing amounts of rotavirus sequence data that are becoming available.

Complete genome analyses of G12P[8] rotavirus strains from hospitalized children in Surabaya, Indonesia, 2017-2018

Rotavirus A (RVA) is a major viral cause of acute gastroenteritis (AGE) worldwide. G12 RVA strains have emerged globally since 2007. There has been no report of the whole genome sequences of G12 RVAs in Indonesia. We performed the complete genome analysis by the next-generation sequencing of five G12 strains from hospitalized children with AGE in Surabaya from 2017 to 2018. All five G12 strains were Wa-like strains (G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1) and were clustered into lineage-III of VP7 gene phylogenetic tree. STM430 sample was observed as a mixed-infection between G12 and G1 strains: G12/G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. A phylogenetic tree analysis revealed that all five Indonesian G12 strains (SOEP379, STM371, STM413, STM430, and STM433) were genetically close to each other in all 11 genome segments with 98.0%-100% nucleotide identities, except VP3 and NSP4 of STM430, suggesting that these strains have originated from a similar ancestral G12 RVA. The VP3 and NSP4 genome segments of STM430-G12P[8] were separated phylogenetically from those of the other four G12 strains, probably due to intra-genotype reassortment between the G12 and G1 Wa-like strains. The change from G12P[6] lineage-II in 2007 to G12P[8] lineage-III 2017-2018 suggests the evolution and diversity of G12 RVAs in Indonesia over the past approximately 10 years.

M. Eljaro Z, Abu-Awwad F, Bozya Y, Hjaija D, Bhat N, Leader T, Ramlawi A, Marzouqa H. Introducing ROTAVAC® to the occupied Palestinian Territories: Impact on diarrhea incidence, rotavirus prevalence and genotype composition

BACKGROUND

Rotavirus infection remains an important cause of morbidity and mortality in children. The introduction of vaccination programs in more than 100 countries has contributed to a decrease in hospitalizations and mortality. This study investigates the epidemiological impact of the rotavirus vaccine ROTAVAC® in the Palestinian Territories, the first country to switch from ROTARIX® to this new vaccine.

METHODS

Clinical surveillance data was collected fromchildren younger than 5attendingoutpatient clinics throughout Gaza withdiarrhea between 2015 and 2020. The incidence of all-cause diarrhea was assessed using an interrupted time-series approach. Rotavirus prevalence was determined at the Caritas Baby Hospital in the West Bank usingELISA on stool specimen of children younger than 5with diarrhea. Genotyping was performed on 325 randomly selected rotavirus-positive samples from January 2015 through December 2020 using multiplex PCR analysis.

RESULTS

Average monthly diarrhea casesdropped by 16.7% annually fromintroduction of rotavirus vaccination in May 2016 to the beginning of the SARS-CoV-2 epidemic in March 2020 for a total of 53%. Case count declines were maintained afterthe switchto ROTAVAC® in October 2018. Rotavirus positivity in stool samples declined by 67.1% over the same period without change followingthe switch to ROTAVAC®. The distribution of predominant genotypes in rotavirus-positive stool samples changed from a pre-vaccination G1P [8] to G9P[8] and G12P[8] during the ROTARIX® period and G2P[4] after the introduction of ROTAVAC®.

CONCLUSION

ROTAVAC® has shown epidemiological impact on par with ROTARIX® after its introduction to the national immunization schedule in the Palestinian Territories. A molecular genotype shift from a pre-vaccination predominance of G1P[8] to a current predominance of G2P[4] requires more long-term surveillance.

Current Update on Rotavirus in-Silico Multiepitope Vaccine Design

Rotavirus gastroenteritis is one of the leading causes of pediatric morbidity and mortality worldwide in infants and under-five populations. The World Health Organization (WHO) recommended global incorporation of the rotavirus vaccine in national immunization programs to alleviate the burden of the disease. Implementation of the rotavirus vaccination in certain regions of the world brought about a significant and consistent reduction of rotavirus-associated hospitalizations. However, the efficacy of licensed vaccines remains suboptimal in low-income countries where the incidences of rotavirus gastroenteritis continue to happen unabated. The problem of low efficacy of currently licensed oral rotavirus vaccines in low-income countries necessitates continuous exploration, design, and development of new rotavirus vaccines. Traditional vaccine development is a complex, expensive, labor-intensive, and time-consuming process. Reverse vaccinology essentially utilizes the genome and proteome information on pathogens and has opened new avenues for in-silico multiepitope vaccine design for a plethora of pathogens, promising time reduction in the complete vaccine development pipeline by complementing the traditional vaccinology approach. A substantial number of reviews on licensed rotavirus vaccines and those under evaluation are already available in the literature. However, a collective account of rotavirus in-silico vaccines is lacking in the literature, and such an account may further fuel the interest of researchers to use reverse vaccinology to expedite the vaccine development process. Therefore, the main focus of this review is to summarize the research endeavors undertaken for the design and development of rotavirus vaccines by the reverse vaccinology approach utilizing the tools of immunoinformatics.

Rotavirus infections and their genotype distribution in Rwanda before and after the introduction of rotavirus vaccination

Rotavirus vaccination has reduced mortality and hospital admissions due to rotavirus diarrhoea, but its effect on rotavirus infections and the impact of rotavirus genotypes are still unclear. Real-time PCR was used to detect rotavirus and other pathogens in faeces samples from children below five years of age with acute diarrhoea, collected before (n = 827) and after (n = 807, 92% vaccinated) the introduction of vaccination in Rwanda in 2012. Rotavirus was genotyped by targeting VP7 to identify G1, G2, G3, G4, G9 and G12 and VP4 to identify P[4], P[6] and P[8]. In vaccinated children, rotavirus infections were rarer (34% vs. 47%) below 12 months of age, severe dehydration was less frequent, and rotavirus was more often found as a co-infecting agent. (79% vs 67%, p = 0.004). Norovirus genogroup II, astrovirus, and sapovirus were significantly more often detected in vaccinated children. The predominant rotavirus genotypes were G2P[4] and G12P[6] in 2009-2010 (50% and 12%), G9P[8] and G1P[8] in 2011-2012 (51% and 22%), and G12P[8] in 2014-2015 (63%). Rotavirus vaccination in Rwanda has reduced the severity of rotavirus gastroenteritis and rotavirus infection frequency during the first year of life. Rotavirus infections were frequent in vaccinated children with diarrhoea, often as co-pathogen. Rotavirus genotype changes might be unrelated to vaccination because shifts were observed also before its introduction.

Rotavirus genotypes and clinical outcome of natural infection based on vaccination status in the post-vaccine era

Rotavirus (RV) is a leading cause of gastroenteritis in children. In Japan, Rotarix (RV1; GlaxoSmithKline), which is a monovalent vaccine derived from human RV (G1P[8]), has been introduced since November 2011, and RotaTeq (RV5; MSD) which is an pentavalent, human-bovine mono-reassortant vaccine (G1, G2, G3, G4, and P1A[8]), has been introduced since July 2012. Long-term follow-up on vaccine efficacy and RV genotypical change should be carried out in order to control RV infection. The RV gastroenteritis (RVGE) outbreak occurred during the 2018/2019 season in Aichi prefecture, Japan. Therefore, the molecular epidemiology of RV among three different groups of RVGE, which were outpatients who received RV1, those who received RV5, and those without vaccination, was explored. Clinical features of RVGE patients were compared among the three patient groups. Children less than 15 years of age with gastroenteritis who visited any of seven pediatric practices between January and June 2019 were enrolled in the study. G, P, and E genotypes were determined by direct sequencing of reverse transcription-polymerase chain reaction products amplified from stool samples. Among 110 patients, there were 27, 28, and 55 in the RV1-vaccinated, RV5-vaccinated, and unvaccinated groups, respectively. The most frequent genotype was G8P[8] (92/110 patients, 83.6%). Genotype distributions did not significantly differ among the three patient groups (P = .125). Mean Vesikari score was significantly lower among RV1-vaccinated (7.1) and RV5-vaccinated patients (6.4) than among unvaccinated patients (10.2) (P < .001). Even in RVGE patients treated in an outpatient clinic, RV vaccine reduced the severity of the disease in this cohort.

Full genotype constellations analysis of unusual DS-1-like G12P[6] and G6P[8] rotavirus strains detected in Brazil, 2019

Rotavirus A (RVA) is a major cause of acute gastroenteritis (AGE) in children worldwide. We report unusual RVA G12P[6] and G6P[8] strains isolated from fecal samples from Brazilian children hospitalized for AGE. The characterized RVA have genome segments backbone: G12-P[6]/ G6-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 of DS-1-like genogroup. Our study describes the first identification of G6P[8], a DS-1-like genogroup strain. Nucleotide analysis of VP7 and VP4 genes revealed that all G12 Brazilian strains clustered into the sub-lineages IIIB, mostly associated with P[6] lineage I. Additionally, our G6 lineage I strains were closely related to German G6 genotypes, bound with P[8] lineage III, differing from both vaccine strains. The comparative sequence analysis of our strains with vaccine strains revealed amino acid substitutions located in immunodominant regions of VP7 and VP4 proteins. Continuous monitoring of RVA genotypes is essential to evaluate the impact of vaccination on the dynamic nature of RVA evolution.

Suppression of classical nuclear import pathway by importazole and ivermectin inhibits rotavirus replication

BACKGROUND

Rotavirus is the foremost cause of acute gastroenteritis among infants in resource-poor countries, causing severe morbidity and mortality. The currently available rotavirus vaccines are effective in reducing severity of the disease but not the infection rates, thus antivirals as an adjunct therapy are needed to reduce the morbidity in children. Viruses rely on host cellular machinery for nearly every step of the replication cycle. Therefore, targeting host factors that are indispensable for virus replication could be a promising strategy.

OBJECTIVES

To assess the therapeutic potential of ivermectin and importazole against rotaviruses.

METHODS

Antirotaviral activity of importazole and ivermectin was measured against various rotavirus strains (RV-SA11, RV-Wa, RV-A5-13, RV-EW) in vitro and in vivo by quantifying viral protein expression by western blot, analysing viroplasm formation by confocal microscopy, and measuring virus yield by plaque assay.

RESULTS

Importin-β1 and Ran were found to be induced during rotavirus infection. Knocking down importin-β1 severely impaired rotavirus replication, suggesting a critical role for importin-β1 in the rotavirus life cycle. In vitro studies revealed that treatment of ivermectin and importazole resulted in reduced synthesis of viral proteins, diminished production of infectious virus particles, and decrease in viroplasm-positive cells. Mechanistic study proved that both drugs perform antirotavirus activity by inhibiting the function of importin-β1. In vivo investigations in mice also confirmed the antirotavirus potential of importazole and ivermectin at non-toxic doses. Treatments of rotavirus-infected mice with either drug resulted in diminished shedding of viral particles in the stool sample, reduced expression of viral protein in the small intestine and restoration of damaged intestinal villi comapared to untreated infected mice.

CONCLUSIONS

The study highlights the potential of importazole and ivermectin as antirotavirus therapeutics.

Full genome characterization of a human-porcine reassortment G12P[7] rotavirus and its pathogenicity in piglets

In recent years, increasing numbers of cases of acute gastroenteritis caused by Group A rotavirus (RVA) G12 strains have been reported in humans from many countries around the world, but G12 RVA detection in animals is currently less reported. Pigs are an important animal reservoir of zoonotic RVs and a mixing vessel for RVs. In 2020, RVA infection cases in piglets increased in China, which attracted more attention. During an epidemiological survey, a new type of porcine G12P[7] strain (CN127) was detected in pig farms across several provinces. Complete genome analyses revealed that strain CN127 possessed a Wa-like backbone with a genotype constellation of G12-P[7]-I1-C1-M1-R1-A8-N1-T1-E1-H1. The A8 genotype is indicative of its porcine rotavirus origin. Sequence identities and phylogenetic analyses showed that the VP2, VP4, NSP1, NSP4 and NSP5 genes were most closely related to those of porcine rotaviruses, but the VP1, VP6, VP7 and NSP2-3 genes were most closely related to those of human rotaviruses. CN127 likely emerged due to genetic reassortment between porcine and human rotavirus. In vivo experiments showed that CN127 infection caused gastrointestinal tract lesions in piglets and histopathological changes in the lung, liver and mesenteric lymph nodes (MLNs). In the small intestine, RVA antigen was detected in the duodenum and jejunum but not in the ileum. In the extra-intestinal tissues, RVA antigen was detected in the lung but not in the MLNs. Viral RNA was detected in the intestinal and extra-intestinal tissues as well as blood. This study reveals that RVA G12P[7] may become an epidemic strain in China and also provides further evidence that cocirculating human and porcine strains could produce new genotype rotaviruses with high virulence in piglets.

Rotavirus Strain Trends in United States, 2009-2016: Results from the National Rotavirus Strain Surveillance System (NRSSS)

Before the introduction of vaccines, group A rotaviruses (RVA) were the leading cause of acute gastroenteritis in children worldwide. The National Rotavirus Strain Surveillance System (NRSSS) was established in 1996 by the Centers for Disease Control and Prevention (CDC) to perform passive RVA surveillance in the USA. We report the distribution of RVA genotypes collected through NRSSS during the 2009-2016 RVA seasons and retrospectively examine the genotypes detected through the NRSSS since 1996. During the 2009-2016 RVA seasons, 2134 RVA-positive fecal specimens were sent to the CDC for analysis of the VP7 and VP4 genes by RT-PCR genotyping assays and sequencing. During 2009-2011, RVA genotype G3P[8] dominated, while G12P[8] was the dominant genotype during 2012-2016. Vaccine strains were detected in 1.7% of specimens and uncommon/unusual strains, including equine-like G3P[8] strains, were found in 1.9%. Phylogenetic analyses showed limited VP7 and VP4 sequence variation within the common genotypes with 1-3 alleles/lineages identified per genotype. A review of 20 years of NRSSS surveillance showed two changes in genotype dominance, from G1P[8] to G3P[8] and then G3P[8] to G12P[8]. A better understanding of the long-term effects of vaccine use on epidemiological and evolutionary dynamics of circulating RVA strains requires continued surveillance.

Quercetin, a flavonoid, combats rotavirus infection by deactivating rotavirus-induced pro-survival NF-κB pathway

Rotavirus (RV) is the leading cause of acute gastroenteritis and watery diarrhea in children under 5 years accounting for high morbidity and mortality in countries with poor socioeconomic status. Although vaccination against RV has been implemented in more than 100 countries, the efficacy of vaccine has been challenged in low-income settings. The lack of any FDA-approved drug against RV is an additional concern regarding the treatment associated with rotavirus-induced infantile death. With the purpose for the discovery of anti-RV therapeutics, we assessed anti-rotaviral potential of quercetin, a well-characterized antioxidant flavonoid. In vitro study revealed that quercetin treatment resulted in diminished production of RV-SA11 (simian strain) viral particles in a concentration-dependent manner as estimated by the plaque assay. Consistent with this result, Western blot analysis also revealed reduced synthesis of viral protein in quercetin-treated RV-SA11-infected MA104 cells compared to vehicle (DMSO) treated controls. Not surprisingly, infection of other RV strains A5-13 (bovine strain) and Wa (Human strain) was also found to be abridged in the presence of quercetin compared to DMSO. The IC₅₀ of quercetin against three RV strains ranges between 2.79 and 4.36 Mm, and S.I. index is greater than 45. Concurrent to the in vitro results, in vivo study in mice model also demonstrated reduced expression of viral proteins and viral titer in the small intestine of quercetin-treated infected mice compared to vehicle-treated infected mice. Furthermore, the result suggested anti-rotaviral activity of quercetin to be interferon-independent. Mechanistic study revealed that the antiviral action of quercetin is co-related with the inhibition of RV-induced early activation of NF-κB pathway. Overall, this study delineates the strong anti-RV potential of quercetin and also proposes it as future therapeutics against rotaviral diarrhea.

Quantifying mechanisms of coexistence in disease ecology

Pathogen coexistence depends on ecological processes operating at both within and between-host scales, making it difficult to quantify which processes may promote or prevent coexistence. Here, we propose that adapting modern coexistence theory-traditionally applied in plant communities-to pathogen systems provides an exciting approach for examining mechanisms of coexistence operating across different spatial scales. We first overview modern coexistence theory and its mechanistic decomposition; we subsequently adapt the framework to quantify how spatial variation in pathogen density, host resources and immunity, and their interaction may promote pathogen coexistence. We apply this derivation to an example two pathogen, multi-scale model comparing two scenarios with generalist and strain-specific immunity: one with demographic equivalency among pathogens and one with demographic trade-offs among pathogens. We then show how host-pathogen feedbacks generate spatial heterogeneity that promote pathogen coexistence and decompose those mechanisms to quantify how each spatial heterogeneity contributes to that coexistence. Specifically, coexistence of demographically equivalent pathogens occurs due to spatial variation in host resources, immune responses, and pathogen aggregation. With a competition-colonization trade-off, the superior colonizer requires spatial heterogeneity to coexist, whereas the superior competitor does not. Finally, we suggest ways forward for linking theory and empirical tests of coexistence in disease systems.

Multiple reassortment and interspecies transmission events contribute to the diversity of porcine-like human rotavirus C strains detected in South Korea

Globally, rotavirus C (RVC) causes diarrhoeal outbreaks, mainly in swine, with sporadic incidents in human, bovine, and canine populations. In this study, two human RVC strains, RVC/Human-wt/KOR/CAU13-1-77/2013 and RVC/Human-wt/KOR/CAU14-1-242/2014, were isolated in South Korea, and their complete genome sequences were compared with those of other human- and animal-origin RVC strains found worldwide. Genetic analysis revealed that these viruses have a G4-P[2]-I2-R2-C2-M3-A2-N2-T2-E2-H2 genotype constellation. Phylogenetic analysis indicated that these Korean RVC strains belong to the M3 lineage of the VP3 gene in human RVC from Japan and China and porcine RVC from Japan. These results suggest that RVC circulates in northeast Asia in both the human and porcine populations. These results also provide evidence of interspecies RVC reassortment events.

Rotavirus Infection in Children <5 Years of Age in Suzhou, China, 2013-2019: Disease Burden, Genotype Distribution and Seasonality

BACKGROUND

This study aimed to determine the disease burden and strain distribution of rotavirus in children with diarrhea <5 years old in Suzhou, China.

METHODS

The study was conducted among children with diarrhea <5 years old at Suzhou University Affiliated Children's Hospital from 2013 to 2019. Rotavirus antigen was detected in clinical laboratory and then sent to Suzhou Centers for Disease Control and Prevention for further molecular analysis. Group A rotavirus (RVA) was detected through enzyme-linked immunosorbent assays, and G-genotype and P-genotype of RVA were tested using reverse transcription-polymerase chain reaction.

RESULTS

Of a total of 198,130 children with diarrhea, 70,813 (35.7%) were positive for RVA; RVA-related diarrhea was detected in 7798 (20.7%, n = 7798/37,710) inpatients and 63,015 (39.3%, n = 63,015/160,420) outpatients. Most children (92.0%, n = 65,171/70,813) positive for RVA were found as children <3 years old. Children 12-35 months old were reported as the highest prevalence among all age groups. The seasonal peak of RVA was in the autumn and winter. Among all 673 RVA strains genotyped, the G9P[8] strain was reported to be persistently predominant in the pediatric population from 2013 to 2019.

CONCLUSIONS

The burden of diarrhea disease due to rotavirus infection remains high in Suzhou.

Genetic characterization of P[8] rotavirus strains circulated in Iran between 2009 and 2017

Group A rotavirus (RVA) is the most common cause of acute gastroenteritis (AGE) worldwide, which is responsible for causing an estimated 120,000 deaths in children under 5 years of age, which mostly occur in the lower income countries of Asia and Africa. The G1P[8] is a common genotype of RVA that has spread throughout the world, including Iran and this genotype is present in two commonly used RVA vaccines, Rotarix^TM and RotaTeq^TM . In this study, we investigated the genetic diversity, viral evolutionary, and differences between antigenic epitopes of Iran's P[8] strains and two licensed vaccines. The phylogenetic and evolutionary analysis was carried out, using MEGA vs 6.0 and BEAST respectively. Antigenic epitopes of VP8* were compared to determine the differences between strains from Iran and Rotarix^TM and RotaTeq^TM . The P[8]-lineages III and IV was found as the predominant P genotype that circulating in Iran. The TMRCA of P[8]-lineages III and IV was estimated at 1987 and 2009 respectively. The P[8]-lineage III strains showed 12 amino acid changes compared to Rotarix^TM and 10 amino acid changes compared to RotaTeq^TM . The P[8]-lineage IV strains showed 10 amino acid variations for both Rotarix^TM and RotaTeq^TM strains. The results revealed that the P[8] strains circulating in Iran differs from Rotarix^TM and RotaTeq^TM strains. To monitor the long-term effects of vaccines on the emergence of P[8] strains with different lineages, routine and successful monitoring of these strains will be crucial. This article is protected by copyright. All rights reserved.

Effect of rotavirus genetic diversity on vaccine impact

Group A rotaviruses (RVAs) are the leading cause of gastroenteritis, causing 0.2 million deaths and several million hospitalisations globally each year. Four rotavirus vaccines (Rotarix^TM , RotaTeq^TM , Rotavac^® and ROTASIIL^® ) have been pre-qualified by the World Health Organization (WHO), but the two newly pre-qualified vaccines (Rotavac^® and ROTASIIL^® ) are currently only in use in Palestine and India, respectively. In 2009, WHO strongly proposed that rotavirus vaccines be included in the routine vaccination schedule of all countries around the world. By the end of 2019, a total of 108 countries had administered rotavirus vaccines, and 10 countries have currently been approved by Gavi for the introduction of rotavirus vaccine in the near future. With 39% of global coverage, rotavirus vaccines have had a substantial effect on diarrhoeal morbidity and mortality in different geographical areas, although efficacy appears to be higher in high income settings. Due to the segmented RNA genome, the pattern of RVA genotypes in the human population is evolving through interspecies transmission and/or reassortment events for which the vaccine might be less effective in the future. However, despite the relative increase in some particular genotypes after rotavirus vaccine use, the overall efficacy of rotavirus mass vaccination worldwide has not been affected. Some of the challenges to improve the effect of current rotavirus vaccines can be solved in the future by new rotavirus vaccines and by vaccines currently in progress.

Isolation and Characterization of Bovine RVA from Northeast China, 2017-2020

Group A rotaviruses (RVAs) are major enteric pathogens causing infections in calves. To investigate the epidemiological characteristics and genetic diversity of bovine rotavirus (BRV), 233 fecal samples were collected from calves with diarrhea in northeast China. The samples were analyzed for sequences encoding the inner capsid protein VP6 (subgroup) and the outer capsid proteins VP7 and VP4 (G and P type, respectively) using RT-PCR. Ten of the 233 samples (4.3%) were identified as BRV positive and were used for virus isolation and sequence analysis, revealing that all strains analyzed were of the G6P[1] genotype. The isolates exhibited high VP6 sequence identity to the USA cow RVA NCDV strain (>99% amino acid identity) and were further shown to be closely related to Japanese cow RVA BRV101 and Israelian human RVA G6P[1] strains, with >99% amino acid identity to VP7 and VP4 proteins, respectively. Comparative analyses of genome-predicted amino acid sequences between the isolates and the NCDV strains indicated that the antigenicity and infectivity of the strains isolated had changed. In this study, BRV genotypes and the genetic diversity among vaccinated cattle herds were monitored to provide epidemiological data and references for early diagnosis, allowing for early detection of new, potentially pathogenic RVA strains.

Molecular surveillance and genetic divergence of rotavirus A antigenic epitopes in Gabonese children with acute gastroenteritis

BACKGROUND

Rotavirus A (RVA) causes acute gastroenteritis in children <5 years of age in sub-Saharan Africa. In this study, we described the epidemiology and genetic diversity of RVA infecting Gabonese children and examined the antigenic variability of circulating strains in relation to available vaccine strains to maximize the public health benefits of introducing rotavirus vaccine through the Expanded Programme on Immunization (EPI) in Gabon.

METHODS

Stool samples were collected consecutively between April 2018 and November 2019 from all hospitalized children <5 years with gastroenteritis and community controls without gastroenteritis. Children were tested for rotavirus A by quantitative RT-PCR and subsequently sequenced to identify circulating rotavirus A genotypes in the most vulnerable population. The VP7 and VP4 (VP8*) antigenic epitopes were mapped to homologs of vaccine strains to assess structural variability and potential impact on antigenicity.

FINDINGS

Infections were mostly acquired during the dry season. Rotavirus A was detected in 98/177 (55%) hospitalized children with gastroenteritis and 14/67 (21%) of the control children. The most common RVA genotypes were G1 (18%), G3 (12%), G8 (18%), G9 (2%), G12 (25%), with G8 and G9 reported for the first time in Gabon. All were associated either with P[6] (31%) or P[8] (38%) genotypes. Several non-synonymous substitutions were observed in the antigenic epitopes of VP7 (positions 94 and 147) and VP8* (positions 89, 116, 146 and 150), which may modulate the elicited immune responses.

INTERPRETATION

This study contributes to the epidemiological surveillance of rotavirus A required before the introduction of rotavirus vaccination in the EPI for Gabonese children.

Rotavirus research: 2014-2020

Rotaviruses are major causes of acute gastroenteritis in infants and young children worldwide and also cause disease in the young of many other mammalian and of avian species. During the recent 5-6 years rotavirus research has benefitted in a major way from the establishment of plasmid only-based reverse genetics systems, the creation of human and other mammalian intestinal enteroids, and from the wide application of structural biology (cryo-electron microscopy, cryo-EM tomography) and complementary biophysical approaches. All of these have permitted to gain new insights into structure-function relationships of rotaviruses and their interactions with the host. This review follows different stages of the viral replication cycle and summarizes highlights of structure-function studies of rotavirus-encoded proteins (both structural and non-structural), molecular mechanisms of viral replication including involvement of cellular proteins and lipids, the spectrum of viral genomic and antigenic diversity, progress in understanding of innate and acquired immune responses, and further developments of prevention of rotavirus-associated disease.

Rotavirus A infection in pre- and post-vaccine period: Risk factors, genotypes distribution by vaccination status and age of children in Nampula Province, Northern Mozambique (2015-2019)

Mozambique introduced the monovalent rotavirus vaccine (Rotarix^®, GSK Biologicals, Rixensart, Belgium) in September 2015. Previous analysis, showed that Nampula province continues reporting a high frequency of Rotavirus A (RVA) infection and the emergence of G9P[6], G9P[4] and G3P[4] genotypes. This analysis aimed to determine the RVA frequency; risk factors; genotype distribution by vaccination status and age between pre- and post-vaccine periods in children under-five years old with diarrhea in Nampula. A cross-sectional, hospital-based surveillance study was conducted in the Hospital Central de Nampula in Mozambique. Socio-demographic and clinical data were collected to assess factors related to RVA infection in both periods. Stool specimens were screened to detect RVA by ELISA, and positive samples were genotyped. Between 2015 (pre-vaccine period) and 2016–2019 (post-vaccine period), 614 stool specimens were collected and tested for RVA in which 34.9% (67/192) were positive in pre-vaccine period and 21.8% (92/422) in post-vaccine (p = 0.001). In the post-vaccine period, age, year, and contact with different animal species (chicken, duck, or multiple animals) were associated with RVA infection. RVA infection was higher in children partially vaccinated (40.7%, 11/27) followed by the fully vaccinated (29.3%, 56/191) and the unvaccinated (15.3%, 21/137) (p = 0.002). G1P[8] and G9P[4] were common in vaccinated children less than 12 months. The present analysis showed that RVA infection reduced slightly in the post-vaccine period, with a high proportion of infection and genotype diversity in children, under 12 months of age, vaccinated. Further research on factors associated with RVA infection on vaccinated compared to unvaccinated children and vaccination optimization should be done.

Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.

Circulating Rotavirus Genotypes among Children Younger than 5 Years with Acute Gastroenteritis in Zaria, Northwestern Nigeria

Objective This study aimed to determine the circulating rotavirus genotypes among children 0 to 59 months with acute gastroenteritis in Zaria, Northwestern Nigeria.

Methods A cross-sectional hospital-based study was performed from November 2015 to April 2017 on 415 stool samples of children 0 to 59 months with acute gastroenteritis presenting at the pediatric clinics in five selected health care facilities in Zaria, Northwestern Nigeria. The stool samples were tested for group A rotavirus antigen by enzyme-linked immunosorbent assay (ELISA) using the ProSpecT™ Rotavirus Microplate Assay (Thermo Scientific Oxoid, United Kingdom). Rotavirus-positive strains were further characterized using seminested multiplex reverse transcriptase polymerase chain reaction.

Results Of the 415 diarrheal stool samples collected from children with acute gastroenteritis, 12.3% (n = 51) tested positive by ELISA. Five rotavirus G genotypes (G1, G2, G3, G9, and G12) and three P genotypes (P[4], P[6], and P[8]) were detected. Eight genotype combinations were detected with G1P[8], G12P[8], and G3P[6] being the most prevalent (9.8% each) followed by G1P[6], G2P[4], and G9P[8] (5.9% each). G/P mix types representing 25.5% (n = 13) of strains were detected during the study period.

Conclusion This study found a high diversity of rotavirus strains with emerging unusual rotavirus genotypes and a concurrent high proportion of mixed infections. This increased antigenic diversity of rotavirus strains may impact on vaccine effectiveness and rotavirus epidemiology and highlights the importance of continuous surveillance.

Association of Rotavirus Vaccines With Reduction in Rotavirus Gastroenteritis in Children Younger Than 5 Years: A Systematic Review and Meta-analysis of Randomized Clinical Trials and Observational Studies

IMPORTANCE

Rotavirus vaccines have been introduced worldwide, and the clinical association of different rotavirus vaccines with reduction in rotavirus gastroenteritis (RVGE) after introduction are noteworthy.

OBJECTIVE

To evaluate the comparative benefit, risk, and immunogenicity of different rotavirus vaccines by synthesizing randomized clinical trials (RCTs) and observational studies.

DATA SOURCES

Relevant studies published in 4 databases: Embase, PubMed, the Cochrane Library, and Web of Science were searched until July 1, 2020, using search terms including "rotavirus" and "vaccin*."

STUDY SELECTION

Randomized clinical trials and cohort and case-control studies involving more than 100 children younger than 5 years that reported the effectiveness, safety, or immunogenicity of rotavirus vaccines were included.

DATA EXTRACTION AND SYNTHESIS

A random-effects model was used to calculate relative risks (RRs), odds ratios (ORs), risk differences, and 95% CIs. Adjusted indirect treatment comparison was performed to assess the differences in the protection of Rotarix and RotaTeq.

MAIN OUTCOMES AND MEASURES

The primary outcomes were RVGE, severe RVGE, and RVGE hospitalization. Safety-associated outcomes involved serious adverse events, intussusception, and mortality.

RESULTS

A meta-analysis of 20 RCTs and 38 case-control studies revealed that Rotarix (RV1) significantly reduced RVGE (RR, 0.316 [95% CI, 0.224-0.345]) and RVGE hospitalization risk (OR, 0.347 [95% CI, 0.279-0.432]) among children fully vaccinated; RotaTeq (RV5) had similar outcomes (RVGE: RR, 0.350 [95% CI, 0.275-0.445]; RVGE hospitalization risk: OR, 0.272 [95% CI, 0.197-0.376]). Rotavirus vaccines also demonstrated higher protection against severe RVGE. Additionally, no significant differences in the protection of RV1 and RV5 against rotavirus disease were noted in adjusted indirect comparisons. Moderate associations were found between reduced RVGE risk and Rotavac (RR, 0.664 [95% CI, 0.548-0.804]), Rotasiil (RR, 0.705 [95% CI, 0.605-0.821]), and Lanzhou lamb rotavirus vaccine (RR, 0.407 [95% CI, 0.332-0.499]). All rotavirus vaccines demonstrated no risk of serious adverse events. A positive correlation was also found between immunogenicity and vaccine protection (eg, association of RVGE with RV1: coefficient, -1.599; adjusted R2, 99.7%).

CONCLUSIONS AND RELEVANCE

The high protection and low risk of serious adverse events for rotavirus vaccines in children who were fully vaccinated emphasized the importance of worldwide introduction of rotavirus vaccination. Similar protection provided by Rotarix and RotaTeq relieves the pressure of vaccines selection for health care authorities.

Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses

Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.

Novel antigen panel for modern broad-spectrum recombinant rotavirus A vaccine

Purpose

Recombinant rotavirus A vaccines are being developed as an alternative to existing live oral attenuated vaccines. One of the main problems in the production of such vaccines is the genetic diversity of the strains that are in circulation. The goal of this study was to create an antigen panel for modern broad-spectrum recombinant rotavirus A vaccine.

Materials and Methods

The antigens of rotavirus were cloned and expressed in Escherichia coli. Antigenic specificity was investigated by Western blot analysis, which was performed using commercial polyclonal antisera to several RVA strains. Phylogenetic analysis was based on the amino acid sequences of the VP8^* protein fragment of human RVA isolates representing genotypes P[4], P[6], and P[8].

Results

A universal panel of antigens was established, including consensus and conserved sequences of structural proteins VP8^*, VP5^*, and VP7, which are the main targets of neutralizing antibodies. For the first time, a consensus approach was used in the design of extended antigens based on VP8^* (genotypes P[4], P[6], and P[8]) and VP5^* (genotype P[8]) proteins' fragments. In addition, a gene coding the protein (ep-875) containing several copies of conserved short neutralizing epitopes of VP8^*, VP7, and VP5^* was created. Western blot analysis demonstrated that three synthetic VP8^*-based antigens were not recognized by commercial antiserum against rotavirus strains isolated more than 35 years ago, but the specific activity of the VP5^* and ep-875 antigens was confirmed. The problems of serological mismatch of vaccine strains and antigens with currently circulating strains are discussed.

Conclusion

Five antigens representing sequences of structural proteins belonging to different genotypes can be used in various combinations (from mono- to pentavalent mixtures) for the development of an effective broad-spectrum rotavirus vaccine.

Paediatric rotavirus gastroenteritis: A prospective study of regional prevalent genotypes, genotype correlation with disease severity and viral co-infection in County Mayo, Ireland, in the year following rotavirus vaccine introduction in Ireland

Rotavirus A (RV) is the primary cause of gastroenteritis in children worldwide and a leading cause of gastroenteritis in children younger than three years, with a significant burden both globally and in Ireland. Rotavirus vaccine (Rotarix™) was introduced into Ireland in 2016. The aim of this study was to determine the diversity and frequency of, and predominant, RV genotypes, nosocomial acquisition, viral co-infections and severity of RV infection in Ireland in the post-vaccination year, from November 18th 2016 to November 18th 2017. The study included all children up to 3 years of age who had presented to Mayo University Hospital or were admitted with vomiting and diarrhoea, and had their stool tested for rotavirus and other viruses by real-time PCR in the National Virus Reference Laboratory. The Vesikari Scoring System was used to assess disease severity. The results showed that rotavirus was a leading cause of gastroenteritis (37 patients, 24.6 % of a total of 150 patients) and gastroenteritis-related hospitalisation (27 patients were admitted, 21 % of a total of 128 patients). Severe rotaviral gastroenteritis was noted in 78 % of all RV gastroenteritis (37 patients). The RV strain G1P[8], including the vaccine G1P[8] strain (Rotarix™), was the most predominant genotype (47 %), followed by G2P[4] (31 %), G4P[8] (8%), G12P[8] (8%) and G9P[8] (6%). RV co-infection with other viruses was detected in four cases (11 %), of whom three cases (75 %) were severe. Rotarix™ was detected in six vaccinated patients (35 %), 50 % were mild disease. Nosocomial infection was detected in one case. These results indicated that RV remained the leading cause of paediatric gastroenteritis during the post vaccination year in Ireland.

Unexpected Role of Rotavirus G3P[8] Infection in Causing Severe Diarrhea in a Major Tertiary Referral Hospital in the Prevaccine Era

Background: Rotavirus A species is associated with severe gastroenteritis in children. Rotavirus G1P[8] was the most prevalent genotype found in Kuwait in a study conducted between 2005 and 2006. The RotaTeq vaccine was included in the Kuwait national immunization program at the end of 2017. Objectives: Since there is no available data on the rotavirus genotypes circulating before the introduction of the vaccine, we conducted a study to investigate the role of rotaviruses in causing severe diarrhea in children hospitalized in a major tertiary referral hospital in Kuwait during the year 2016. Methods: Viral RNA was isolated from the stool samples of 101 children under five years of age, hospitalized for acute gastroenteritis. Rotavirus VP4 and VP7 dsRNA were detected by RT-PCR, and their partial sequences were analyzed by phylogenic analysis. Results: Rotavirus dsRNA was detected in 24.7% of children with median age of 1 year. The genotype G3P[8] accounted for 47% of cases, followed by G1P[8] (26%), G9P[8] (10.5%), G4P[8] (10.5%), and G9P[4] (5%). Only VP7 nucleotide sequences of rotavirus G3 or G4 type clustered in the same lineage as RotaTeq vaccine, while most VP4 nucleotide sequences of rotavirus P[8] type clustered in a different lineage compared to Rotarix and RotaTeq vaccines. Conclusions: Our findings highlight the role of rotavirus G3P[8] in causing severe diarrhea and invites future investigations to know whether the recent introduction of RotaTeq vaccine in Kuwait selects certain genotypes and subgenomic lineages.

Genotype Diversity before and after the Introduction of a Rotavirus Vaccine into the National Immunisation Program in Fiji

The introduction of the rotavirus vaccine, Rotarix, into the Fiji National Immunisation Program in 2012 has reduced the burden of rotavirus disease and hospitalisations in children less than 5 years of age. The aim of this study was to describe the pattern of rotavirus genotype diversity from 2005 to 2018; to investigate changes following the introduction of the rotavirus vaccine in Fiji. Faecal samples from children less than 5 years with acute diarrhoea between 2005 to 2018 were analysed at the WHO Rotavirus Regional Reference Laboratory at the Murdoch Children's Research Institute, Melbourne, Australia, and positive samples were serotyped by EIA (2005-2006) or genotyped by heminested RT-PCR (2007 onwards). We observed a transient increase in the zoonotic strain equine-like G3P[8] in the initial period following vaccine introduction. G1P[8] and G2P[4], dominant genotypes prior to vaccine introduction, have not been detected since 2015 and 2014, respectively. A decrease in rotavirus genotypes G2P[8], G3P[6], G8P[8] and G9P[8] was also observed following vaccine introduction. Monitoring the rotavirus genotypes that cause diarrhoeal disease in children in Fiji is important to ensure that the rotavirus vaccine will continue to be protective and to enable early detection of new vaccine escape strains if this occurs.

[Synthesis and characterization of human rotavirus A (Reoviridae: Sedoreovirinae: Rotavirus: Rotavirus A) virus-like particles]

INTRODUCTION

Rotavirus infection is the leading cause of acute gastroenteritis among infants. The development of new vaccines against rotavirus A is urgent because the virus has many genotypes, some of which have regional prevalence. Virus-like particles (VLP) is a promising way to create effective and safe vaccine preparations.The purpose of the study is to develop the technology for the production of VLP, containing VP2, VP4, VP6 and VP7 of viral genotypes prevalent on the territory of the Russian Federation, and to give its molecular genetic and virological characteristics.

MATERIAL AND METHODS

The virulent strain Wa G1P[8] of human RV A adapted to MARC-145 cell culture has been used. It was cultured and purified according to the method described by the authors earlier. Standard molecular genetic and cytological methods were used: gene synthesis; cloning into transfer plasmids; recombinant baculoviruses production in Bac-to-Bac expression system; VLP production in the insect cells; centrifugation in sucrose solution; enzyme-linked immunosorbent assay (ELISA); electron microscopy (EM); polyacrylamide gel electrophoresis (SDS-PAGE) and western blot analysis.

RESULTS

VP4 and VP7 of the six most represented in Russia genotypes: G1, G2, G4, G9, P4, P8, as well as VP2 and VP6 were selected for VLP production. Recombinant baculoviruses were obtained with codon frequencies optimized for insect cells. Cabbage loopper (Trichoplusia ni) cell culture was coinfected with different combinations of baculoviruses, and VLP consisting of 2-4 proteins were produced. VLP were purified by centrifugation. The size and morphology of the particles matched the rotavirus A virion (by EM). The presence of rotavirus A proteins in VLP was confirmed by the ELISA, SDS-PAGE and western blot analysis.

CONCLUSION

The technology for the synthesis of three-layer VLP consisting of VP2, VP4, VP6 and VP7 has been developed and optimized. The resulting VLP composition represents 6 serotypes of VP4 and VP7, which are most represented on the territory of Russia, and can be used for vaccine development.

The performance of licensed rotavirus vaccines and the development of a new generation of rotavirus vaccines: a review

Rotavirus, which causes acute gastroenteritis and severe diarrhea, has posed a great threat to children worldwide over the last 30 y. Since no specific drugs and therapies against rotavirus are available, vaccination is considered the most effective method of decreasing the morbidity and mortality related to rotavirus-associated gastroenteritis. To date, six rotavirus vaccines have been developed and licensed by local governments. Notably, Rotarix™ and RotaTeq™ have been recommended as universal agents against rotavirus infection by the World Health Organization; however, lower efficacies were found in less-developed and developing regions with medium and high child mortality than well-developed ones with low child mortality. For now, two promising novel vaccines, Rotavac™ and RotaSiil™ were pre-qualified by the World Health Organization in 2018. Other rotavirus vaccines in the pipeline including neonatal strain (RV3-BB) and several non-replicating rotavirus vaccines with a parenteral delivery strategy are currently undergoing investigation, with the potential to improve the performance of, and eliminate the safety concerns associated with, previous live oral rotavirus vaccines. This paper reviews the important developments in rotavirus vaccines in the last 20 y and discusses problems and challenges that require investigation in the future.

Whole Genome Analysis of African G12P[6] and G12P[8] Rotaviruses Provides Evidence of Porcine-Human Reassortment at NSP2, NSP3, and NSP4

Group A rotaviruses (RVA) represent the most common cause of pediatric gastroenteritis in children <5 years, worldwide. There has been an increase in global detection and reported cases of acute gastroenteritis caused by RVA genotype G12 strains, particularly in Africa. This study sought to characterize the genomic relationship between African G12 strains and determine the possible origin of these strains. Whole genome sequencing of 34 RVA G12P[6] and G12P[8] strains detected from the continent including southern (South Africa, Zambia, Zimbabwe), eastern (Ethiopia, Uganda), central (Cameroon), and western (Togo) African regions, were sequenced using the Ion Torrent PGM method. The majority of the strains possessed a Wa-like backbone with consensus genotype constellation of G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, while a single strain from Ethiopia displayed a DS-1-like genetic constellation of G12-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. In addition, three Ethiopian and one South African strains exhibited a genotype 2 reassortment of the NSP3 gene, with genetic constellation of G12-P[8]-I1-R1-C1-M1-A1-N1-T2-E1-H1. Overall, 10 gene segments (VP1–VP4, VP6, and NSP1–NSP5) of African G12 strains were determined to be genetically related to cognate gene sequences from globally circulating human Wa-like G12, G9, and G1 strains with nucleotide (amino acid) identities in the range of 94.1–99.9% (96.5–100%), 88.5–98.5% (93–99.1%), and 89.8–99.0% (88.7–100%), respectively. Phylogenetic analysis showed that the Ethiopian G12P[6] possessing a DS-1-like backbone consistently clustered with G2P[4] strains from Senegal and G3P[6] from Ethiopia with the VP1, VP2, VP6, and NSP1–NSP4 genes. Notably, the NSP2, NSP3, and NSP4 of most of the study strains exhibited the closest relationship with porcine strains suggesting the occurrence of reassortment between human and porcine strains. Our results add to the understanding of potential roles that interspecies transmission play in generating human rotavirus diversity through reassortment events and provide insights into the evolutionary dynamics of G12 strains spreading across selected sub-Saharan Africa regions.

The origins of G12P[6] rotavirus strains detected in Lebanon

The G12 rotaviruses are an increasingly important cause of severe diarrhoea in infants and young children worldwide. Seven human G12P[6] rotavirus strains were detected in stool samples from children hospitalized with gastroenteritis in Lebanon during a 2011-2013 surveillance study. Complete genomes of these strains were sequenced using VirCapSeq-VERT, a capture-based high-throughput viral-sequencing method, and further characterized based on phylogenetic analyses with global RVA and vaccine strains. Based on the complete genomic analysis, all Lebanese G12 strains were found to have Wa-like genetic backbone G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Phylogenetically, these strains fell into two clusters where one of them might have emerged from Southeast Asian strains and the second one seems to have a mixed backbone between North American and Southeast Asian strains. Further analysis of these strains revealed high antigenic variability compared to available vaccine strains. To our knowledge, this is the first report on the complete genome-based characterization of G12P[6] emerging in Lebanon. Additional studies will provide important insights into the evolutionary dynamics of G12 rotaviruses spreading in Asia.