G1P[8] Rotavirus in children with severe diarrhea in the post-vaccine introduction era in Brazil: Evidence of reassortments and structural modifications of the antigenic VP7 and VP4 regions

Postbiotic Activities of Bifidobacterium adolescentis: Impacts on Viability, Structural Integrity, and Cell Death Markers in Human Intestinal C2BBe1 Cells

Acute diarrheal disease (ADD) caused by rotavirus (RV) contributes significantly to morbidity and mortality in children under five years of age. Currently, there are no specific drugs for the treatment of RV infections. Previously, we reported the anti-rotaviral activity of the protein metabolites derived from Bifidobacterium adolescentis. In this study, our aim was to assess the impact of B. adolescentis-secreted proteins (BaSP), with anti-rotaviral activity on the human intestinal C2BBe1 cell line. We initiated the production of BaSP and subsequently confirmed its anti-rotaviral activity by counting the infectious foci using immunocytochemistry. We then exposed the C2BBe1 cells to various concentrations of BaSP (≤250 µg/mL) for 72 h. Cell viability was assessed using the MTT assay, cell monolayer integrity was monitored through transepithelial electrical resistance (TEER), and cytoskeleton architecture and tight junctions (TJs) were examined using confocal microscopy with F-actin and occludin staining. Finally, we utilized a commercial kit to detect markers of apoptosis and necrosis after 24 h of treatment. The results demonstrated that BaSP does not have adverse effects on C2BBe1 cells. These findings confirm that BaSP inhibits rotavirus infectivity and has the potential to strengthen intestinal defense against viral and bacterial infections via the paracellular route.

Rotavirus and bacterial diarrhoea among children in Ile-Ife, Nigeria: Burden, risk factors and seasonality

BACKGROUND

Diarrhoea is a leading cause of death among under-five children globally, with sub-Saharan Africa alone accounting for 1/3 episodes yearly. Viruses, bacteria and parasites may cause diarrhoea. Rotavirus is the most common viral aetiology of diarrhoea in children less than five years globally. In Nigeria, there is scarce data on the prevalence/importance, burden, clinical/risk factors and seasonality of rotavirus and bacteria and this study aims to determine the role of rotavirus and bacteria on diarrhoea cases in children less than five years in Ile-Ife, Nigeria.

METHODS

Socio-demographic data, environmental/risk factors and diarrhoiec stool samples were collected from children less than five years presenting with acute diarrhoea. Rotavirus was identified using ELISA. Bacteria pathogens were detected using cultural technique and typed using PCR. Diarrhoeagenic E. coli (DEC) isolates were subjected to antimicrobial susceptibility testing. Pathogen positive and negative samples were compared in terms of gender, age-group, seasonal distribution, and clinical/risk factors using chi-square with two-tailed significance. SPSS version 20.0.1 for Windows was used for statistical analysis.

RESULTS

At least one pathogen was detected from 63 (60.6%) children having gastroenteritis while 28 (44.4%) had multiple infections. Rotavirus was the most detected pathogen. Prevalence of rotavirus mono-infection was 22%, multiple infection with bacteria was 45%. Mono-infection prevalence of DEC, Shigella spp., and Salmonella spp. were 5.8% (6/104), 5.8% (6/104), and 2.9% (3/104) and co-infection with RVA were 23.1% (24/104), 21.2% (22/104) and 10.6% (11/104) respectively. All rotaviral infections were observed in the dry season. The pathotypes of DEC detected were STEC and EAEC. Parent earnings and mid-upper arm circumference measurement have statistical correlation with diarrhoea (p = 0.034; 0.035 respectively).

CONCLUSION

In this study, rotavirus was more prevalent than bacteria and occurred only in the dry season. Among bacteria aetiologies, DEC was the most common detected. Differences in seasonal peaks of rotavirus and DEC could be employed in diarrhoea management in Nigeria and other tropical countries to ensure optimal limited resources usage in preventing diarrhoea transmission and reducing indiscriminate use of antibiotics.

Detection and full-genotype determination of rare and reassortant rotavirus A strains in Nizhny Novgorod in the European part of Russia

Reassortant DS-1-like rotavirus A strains have been shown to circulate widely in many countries around the world. In Russia, the prevalence of such strains remains unclear due to the preferred use of the traditional binary classification system. In this work, we obtained partial sequence data from all 11 genome segments and determined the full-genotype constellations of rare and reassortant rotaviruses circulating in Nizhny Novgorod in 2016-2019. DS-1-like G3P[8] and G8P[8] strains were found, reflecting the global trend. Most likely, these strains were introduced into the territory of Russia from other countries but subsequently underwent further evolutionary changes locally. G3P[8], G9P[8], and G12P[8] Wa-like strains of subgenotypic lineages that are unusual for the territory of Russia were also identified. Reassortant G2P[8], G4P[4], and G9P[4] strains with one Wa-like gene (VP4 or VP7) on a DS-1-like backbone were found, and these apparently had a local origin. Feline-like G3P[9] and G6P[9] strains were found to be phylogenetically close to BA222 isolated from a cat in Italy but carried some traces of reassortment with human strains from Russia and other countries. Thus, full-genotype determination of rotavirus A strains in Nizhny Novgorod has clarified some questions related to their origin and evolution.

Genetic heterogeneity of group A rotaviruses: a review of the evolutionary dynamics and implication on vaccination

INTRODUCTION

Human rotavirus remains a major etiology of acute gastroenteritis among under 5-year children worldwide despite the availability of oral vaccines. The genetic instability of rotavirus and the ability to form different combinations from the different G- and P-types reshapes the antigenic landscape of emerging strains which often display limited or no antigen identities with the vaccine strain. As evidence also suggests, the selection of the antigenically distinct novel or rare strains and their successful spread in the human population has raised concerns regarding undermining the effectiveness of vaccination programs.

AREAS COVERED

We review aspects related to current knowledge about genetic and antigenic heterogeneity of rotavirus, the mechanism of genetic diversity and evolution, and the implication of genetic change on vaccination.

EXPERT OPINION

Genetic changes in the segmented genome of rotavirus can alter the antigenic landscape on the virion capsid and further promote viral fitness in a fully vaccinated population. Against this background, the potential risk of the appearance of new rotavirus strains over the long term would be better predicted by a continued and increased close monitoring of the variants across the globe to identify any change associated with disease dynamics.

In Vitro Evaluation of Anti-Rotaviral Activity and Intestinal Toxicity of a Phytotherapeutic Prototype of Achyrocline bogotensis (Kunth) DC

Viruses represent the primary etiologic agents (70-80%) of acute diarrheal disease (ADD), and rotavirus (RV) is the most relevant one. Currently, four rotavirus vaccines are available. However, these vaccines do not protect against emerging viral strains or are not available in low-income countries. To date, there are no approved drugs available against rotavirus infection. In this study, we evaluated the in vitro anti-rotaviral activity and intestinal toxicity of a phytotherapeutic prototype obtained from Achyrocline bogotensis (Kunth) DC. (PPAb); medicinal plant that contains compounds that inhibit the rotavirus replication cycle. Virucidal and viral yield reduction effects exerted by the PPAb were evaluated by immunocytochemistry and flow cytometry. Furthermore, the toxic impact of the PPAb was evaluated in polarized human intestinal epithelial C2BBe1 cells in terms of cytotoxicity, loss of cytoplasmic membrane asymmetry, and DNA fragmentation by MTT and fluorometry. PPAb concentrations under 0.49 mg/mL exerted significant virucidal and viral yield reduction activities, and concentrations under 16 mg/mL neither reduced cell viability, produced DNA fragmentation, nor compromised the C2BBe1cell membrane stability after 24-h incubation. Based on these results, the evaluated phytotherapeutic prototype of Achyrocline bogotensis might be considered as a promising alternative to treat ADD caused by rotavirus.

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.

Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains Before and After Vaccine Introduction Over A Period of 14 Years

Rotavirus G1P[8] strains account for more than half of the group A rotavirus (RVA) infections in children under five years of age, globally. A total of 103 stool samples previously characterized as G1P[8] and collected seven years before and seven years after introducing the Rotarix® vaccine in South Africa were processed for whole-genome sequencing. All the strains analyzed had a Wa-like constellation (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). South African pre- and post-vaccine G1 strains were clustered in G1 lineage-I and II while the majority (84.2%) of the P[8] strains were grouped in P[8] lineage-III. Several amino acid sites across ten gene segments with the exception of VP7 were under positive selective pressure. Except for the N147D substitution in the antigenic site of eight post-vaccine G1 strains when compared to both Rotarix® and pre-vaccine strains, most of the amino acid substitutions in the antigenic regions of post-vaccine G1P[8] strains were already present during the pre-vaccine period. Therefore, Rotarix® did not appear to have an impact on the amino acid differences in the antigenic regions of South African post-vaccine G1P[8] strains. However, continued whole-genome surveillance of RVA strains to decipher genetic changes in the post-vaccine period remains imperative.

Genotype constellations of the rotavirus A strains circulating in Nizhny Novgorod, Russia, 2017-2018

Currently, the full-genome-based classification is widely used to investigate rotavirus A (RVA) strains found in different countries around the world. However, the information on the full genotypes of rotaviruses circulating in Russia is limited. Using partial sequencing, this study determined the full genotype constellations of 15 RVA strains in total commonly detected in Nizhny Novgorod (European part of Russia) in 2017-2018, three from each of the following genotypes G1P[8], G4P[8], and G9P[8] and six from G2P[4]. There were two intergenogroup mono-reassortants possessing an identical genotype constellation of G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 with the DS-1-like NSP4 gene of probably local origin. A variety of subgenotype lineages and their combinations of Wa-like rotaviruses and genetic heterogeneity among G9P[8] and G1P[8] strains were shown on the basis of phylogenetic analysis of each gene. Moreover, two distinct co-circulating variants that differed in all 11 genome segments were found among DS-1-like rotaviruses.

Whole genome and in-silico analyses of G1P[8] rotavirus strains from pre- and post-vaccination periods in Rwanda

Rwanda was the first low-income African country to introduce RotaTeq vaccine into its Expanded Programme on Immunization in May 2012. To gain insights into the overall genetic make-up and evolution of Rwandan G1P[8] strains pre- and post-vaccine introduction, rotavirus positive fecal samples collected between 2011 and 2016 from children under the age of 5 years as part of ongoing surveillance were genotyped with conventional RT-PCR based methods and whole genome sequenced using the Illumina MiSeq platform. From a pool of samples sequenced (n = 158), 36 were identified as G1P[8] strains (10 pre-vaccine and 26 post-vaccine), of which 35 exhibited a typical Wa-like genome constellation. However, one post vaccine strain, RVA/Human-wt/RWA/UFS-NGS:MRC-DPRU442/2012/G1P[8], exhibited a RotaTeq vaccine strain constellation of G1-P[8]-I2-R2-C2-M2-A3-N2-T6-E2-H3, with most of the gene segments having a close relationship with a vaccine derived reassortant strain, previously reported in USA in 2010 and Australia in 2012. The study strains segregated into two lineages, each containing a paraphyletic pre- and post-vaccine introduction sub-lineages. In addition, the study strains demonstrated close relationship amongst each other when compared with globally selected group A rotavirus (RVA) G1P[8] reference strains. For VP7 neutralization epitopes, amino acid substitutions observed at positions T91A/V, S195D and M217T in relation to the RotaTeq vaccine were radical in nature and resulted in a change in polarity from a polar to non-polar molecule, while for the VP4, amino acid differences at position D195G was radical in nature and resulted in a change in polarity from a polar to non-polar molecule. The polarity change at position T91A/V of the neutralizing antigens might play a role in generating vaccine-escape mutants, while substitutions at positions S195D and M217T may be due to natural fluctuation of the RVA. Surveillance of RVA at whole genome level will enhance further assessment of vaccine impact on circulating strains, the frequency of reassortment events under natural conditions and epidemiological fitness generated by such events.

Genetic Characterizations and Molecular Evolution of VP7 Gene in Human Group A Rotavirus G1

Rotavirus group A (RVA) G1 is one leading genotype circulating in humans worldwide, and related molecular information from a global perspective is still limited. Here, we present a comprehensive description of the genetic characterizations and molecular evolution of the RVA G1 VP7 gene. Our results show that RVA G1 can be divided into two lineages and multiple sub-lineages with a relatively high genetic diversity. Vaccine strains are phylogenetic, closer to lineage I. The evolutionary rate of the RVA G1 VP7 gene is 8.869 × 10^-4 substitutions/site/year, and its most recent common ancestor was in 1933. The RVA G1 VP7 gene shows a linear evolution at the nucleotide level and a linear accumulation of difference at the amino acid level. Sub-lineage replacement of G1 VP7 gene is also observed and the effective population size of the G1 VP7 gene has had great change in the past decades and has remained stable in recent years. Altogether, the RVA G1 VP7 gene constantly evolves and there is no clear evidence that the evolution of the RVA G1 VP7 gene was influenced by vaccines. Continuous surveillance is still indispensable to evaluate the molecular epidemiology of RVA, especially in the post-vaccination era.

Uncovering the First Atypical DS-1-like G1P[8] Rotavirus Strains That Circulated during Pre-Rotavirus Vaccine Introduction Era in South Africa

Emergence of DS-1-like G1P[8] group A rotavirus (RVA) strains during post-rotavirus vaccination period has recently been reported in several countries. This study demonstrates, for the first time, rare atypical DS-1-like G1P[8] RVA strains that circulated in 2008 during pre-vaccine era in South Africa. Rotavirus positive samples were subjected to whole-genome sequencing. Two G1P[8] strains (RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1971/2008/G1P[8] and RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1973/2008/G1P[8]) possessed a DS-1-like genome constellation background (I2-R2-C2-M2-A2-N2-T2-E2-H2). The outer VP4 and VP7 capsid genes of the two South African G1P[8] strains had the highest nucleotide (amino acid) nt (aa) identities of 99.6–99.9% (99.1–100%) with the VP4 and the VP7 genes of a locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU1039/2008/G1P[8]. All the internal backbone genes (VP1–VP3, VP6, and NSP1-NSP5) had the highest nt (aa) identities with cognate internal genes of another locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU2344/2008/G2P[6]. The two study strains emerged through reassortment mechanism involving locally circulating South African strains, as they were distinctly unrelated to other reported atypical G1P[8] strains. The identification of these G1P[8] double-gene reassortants during the pre-vaccination period strongly supports natural RVA evolutionary mechanisms of the RVA genome. There is a need to maintain long-term whole-genome surveillance to monitor such atypical strains.