Spread of the emerging equine-like G3P[8] DS-1-like genetic backbone rotavirus strain in Brazil and identification of potential genetic variants

Genetic diversity and evolution of G12P[6] DS-1-like and G12P[9] AU-1-like Rotavirus strains in Brazil

In the early 2000s, the global emergence of rotavirus (RVA) G12P[8] genotype was noted, while G12P[6] and G12P[9] combinations remained rare in humans. This study aimed to characterize and phylogenetically analyze three Brazilian G12P[9] and four G12P[6] RVA strains from 2011 to 2020, through RT-PCR and sequencing, in order to enhance our understanding of the genetic relationship between human and animal-origin RVA strains. G12P[6] strains displayed a DS-1-like backbone, showing a distinct genetic clustering. G12P[6] IAL-R52/2020, IAL-R95/2020 and IAL-R465/2019 strains clustered with 2019 Northeastern G12P[6] Brazilian strains and a 2018 Benin strain, whereas IAL-R86/2011 strain grouped with 2010 Northern G12P[6] Brazilian strains and G2P[4] strains from the United States and Belgium. These findings suggest an African genetic ancestry and reassortments with co-circulating American strains sharing the same DS-1-like constellation. No recent zoonotic reassortment was observed, and the DS-1-like constellation detected in Brazilian G12P[6] strains does not seem to be genetically linked to globally reported intergenogroup G1/G3/G9/G8P[8] DS-1-like human strains. G12P[9] strains exhibited an AU-1-like backbone with two different genotype-lineage constellations: IAL-R566/2011 and IAL-R1151/2012 belonged to a VP3/M3.V Lineage, and IAL-R870/2013 to a VP3/M3.II Lineage, suggesting two co-circulating strains in Brazil. This genetic diversity is not observed elsewhere, and the VP3/M3.II Lineage in G12P[9] strains seems to be exclusive to Brazil, indicating its evolution within the country. All three G12P[9] AU-1-like strains were closely relate to G12P[9] strains from Paraguay (2006-2007) and Brazil (2010). Phylogenetic analysis also highlighted that all South American G12P[9] AU-1-like strains had a common origin and supports the hypothesis of their importation from Asia, with no recent introduction from globally circulating G12P[9] strains or reassortments with local G12 strains P[8] or P[6]. Notably, certain genes in the Brazilian G12P[9] AU-1-like strains share ancestry with feline/canine RVAs (VP3/M3.II, NSP4/E3.IV and NSP2/N3.II), whereas NSP1/A3.VI likely originated from artiodactyls, suggesting a history of zoonotic transmission with human strains. This genomic data adds understanding to the molecular epidemiology of G12P[6] and G12P[9] RVA strains in Brazil, offering insights into their genetic diversity and evolution.

Ten different viral agents infecting and co-infecting children with acute gastroenteritis in Southern Italy: Role of known pathogens and emerging viruses during and after COVID-19 pandemic

Acute gastroenteritis (AGE) represents a world public health relevant problem especially in children. Enteric viruses are the pathogens mainly involved in the episodes of AGE, causing about 70.00% of the cases. Apart from well-known rotavirus (RVA), adenovirus (AdV) and norovirus (NoV), there are various emerging viral pathogens potentially associated with AGE episodes. In this study, the presence of ten different enteric viruses was investigated in 152 fecal samples collected from children hospitalized for gastroenteritis. Real time PCR results showed that 49.3% of them were positive for viral detection with the following prevalence: norovirus GII 19.7%, AdV 15.8%, RVA 10.5%, human parechovirus (HPeV) 5.3%, enterovirus (EV) 3.3%, sapovirus (SaV) 2.6%. Salivirus (SalV), norovirus GI and astrovirus (AstV) 1.3% each, aichivirus (AiV) found in only one patient. In 38.2% of feces only one virus was detected, while co-infections were identified in 11.8% of the cases. Among young patients, 105 were ≤5 years old and 56.0% tested positive for viral detection, while 47 were >5 years old with 40.0% of them infected. Results obtained confirm a complex plethora of viruses potentially implicated in gastroenteritis in children, with some of them previously known for other etiologies but detectable in fecal samples. Subsequent studies should investigate the role of these viruses in causing gastroenteritis and explore the possibility that other symptoms may be ascribed to multiple infections.

Emergence and dissemination of equine-like G3P[8] rotavirus A in Brazil between 2015 and 2021

Rotavirus A (RVA) is a major cause of acute gastroenteritis globally that is classically genotyped by its two immunodominant outer capsid proteins, VP7 (G-) and VP4 (P-). Recent evidence suggests that the reassortant equine-like G3P[8] strain played a substantial role in RVA transmission in Brazil since 2015. To understand its global emergence and dissemination in Brazilian territory, stool samples collected from 11 Brazilian states (n = 919) were genotyped by RT-qPCR and proceeded to sequence the VP7 gene (n = 102, 79 being newly generated) of the G3P[8] samples with pronounced viral loads. Our phylogenetic genotyping showed that G3P[8] became the dominant strain in Brazil between 2017 and 2020, with equine-like variants representing 75%-100% of VP7 samples in this period. A Bayesian discrete phylogeographic analysis strongly suggests that the equine-like G3P[8] strain originated in Asia during the early 2010s and subsequently spread to Europe, the Caribbean, and South America. Multiple introductions were detected in Brazil between 2014 and 2017, resulting in five national clusters. The reconstruction of the effective population size of the largest Brazilian cluster showed an expansion until 2017, followed by a plateau phase until 2019 and subsequent contraction. Our study also supports that most mutations fixed during equine-like G3P[8] evolution were synonymous, suggesting that adaptive evolution was not an important driving force during viral dissemination in humans, potentially increasing its susceptibility to acquired immunity. This research emphasizes the need for comprehensive rotavirus genomic surveillance that allows close monitoring of its ever-shifting composition and informs more effective public health policies.IMPORTANCEOur original article demonstrated the origin and spread in a short time of equine-like G3P[8] in Brazil and the world. Due to its segmented genome, it allows numerous mechanisms including genetic drift and reassortment contribute substantially to the genetic diversity of rotavirus. Although the effectiveness and increasing implementation of vaccination have not been questioned, a matter of concern is its impact on the emergence of escape mutants or even the spread of unusual strains of zoonotic transmission that could drive epidemic patterns worldwide. This research emphasizes the need for comprehensive rotavirus genomic surveillance, which could facilitate the formulation of public policies aimed at preventing and mitigating its transmission.

Human transmission and outbreaks of feline-like G6 rotavirus revealed with whole-genome analysis of G6P[9] feline rotavirus

Group A rotaviruses (RVAs) are generally highly species-specific; however, some strains infect across species. Feline RVAs sporadically infect humans, causing gastroenteritis. In 2012 and 2013, rectal swab samples were collected from 61 asymptomatic shelter cats at a public health center in Mie Prefecture, Japan, to investigate the presence of RVA and any association with human infections. The analysis identified G6P[9] strains in three cats and G3P[9] strains in two cats, although no feline RVA sequence data were available for the former. A whole-genome analysis of these G6P[9] strains identified the genotype constellation G6-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3. The nucleotide identity among these G6P[9] strains exceeded 99.5% across all 11 gene segments, indicating the circulation of this G6P[9] strain among cats. Notably, strain RVA/Human-wt/JPN/KF17/2010/G6P[9], previously detected in a 3-year-old child with gastroenteritis, shares high nucleotide identity (>98%) with Mie20120017f, the representative G6P[9] strain in this study, across all 11 gene segments, confirming feline RVA infection and symptomatic presentation in this child. The VP7 gene of strain Mie20120017f also shares high nucleotide identity with other sporadically reported G6 RVA strains in humans. This suggests that feline-origin G6 strains as the probable source of these sporadic G6 RVA strains causing gastroenteritis in humans globally. Moreover, a feline-like human G6P[8] strain circulating in Brazil in 2022 was identified, emphasizing the importance of ongoing surveillance to monitor potential global human outbreaks of RVA.

Genetic diversity of G9, G3, G8 and G1 rotavirus group A strains circulating among children with acute gastroenteritis in Vietnam from 2016 to 2021

Rotavirus group A (RVA) is the most common cause of severe childhood diarrhea worldwide. The introduction of rotavirus vaccination programs has contributed to a reduction in hospitalizations and mortality caused by RVA. From 2016 to 2021, we conducted surveillance to monitor RVA prevalence and genotype distribution in Nam Dinh and Thua Thien Hue (TT Hue) provinces where a pilot Rotavin-M1 vaccine (Vietnam) implementation took place from 2017 to 2020. Out of 6626 stool samples, RVA was detected in 2164 (32.6%) by ELISA. RT-PCR using type-specific primers were used to determine the G and P genotypes of RVA-positive specimens. Whole genome sequences of a subset of 52 specimens randomly selected from 2016 to 2021 were mapped using next-generation sequencing. From 2016 to 2021, the G9, G3 and G8 strains dominated, with detected frequencies of 39%, 23%, and 19%, respectively; of which, the most common genotypes identified were G9P[8], G3P[8] and G8P[8]. G1 strains re-emerged in Nam Dinh and TT Hue (29.5% and 11.9%, respectively) from 2020 to 2021. G3 prevalence decreased from 74% to 20% in TT Hue and from 21% to 13% in Nam Dinh province between 2017 and 2021. The G3 strains consisted of 52% human typical G3 (hG3) and 47% equine-like G3 (eG3). Full genome analysis showed substantial diversity among the circulating G3 strains with different backgrounds relating to equine and feline viruses. G9 prevalence decreased sharply from 2016 to 2021 in both provinces. G8 strains peaked during 2019-2020 in Nam Dinh and TT Hue provinces (68% and 46%, respectively). Most G8 and G9 strains had no genetic differences over the surveillance period with very high nucleotide similarities of 99.2-99.9% and 99.1-99.7%, respectively. The G1 strains were not derived from the RVA vaccine. Changes in the genotype distribution and substantial diversity among circulating strains were detected throughout the surveillance period and differed between the two provinces. Determining vaccine effectiveness against circulating strains over time will be important to ensure that observed changes are due to natural secular variation and not from vaccine pressure.

Equine Rotavirus A under the One Health Lens: Potential Impacts on Public Health

Group A rotaviruses are a well-known cause of viral gastroenteritis in infants and children, as well as in many mammalian species and birds, affecting them at a young age. This group of viruses has a double-stranded, segmented RNA genome with high genetic diversity linked to point mutations, recombination, and, importantly, reassortment. While initial molecular investigations undertaken in the 1900s suggested host range restriction among group A rotaviruses based on the fact that different gene segments were distributed among different animal species, recent molecular surveillance and genome constellation genotyping studies conducted by the Rotavirus Classification Working Group (RCWG) have shown that animal rotaviruses serve as a source of diversification of human rotavirus A, highlighting their zoonotic potential. Rotaviruses occurring in various animal species have been linked with contributing genetic material to human rotaviruses, including horses, with the most recent identification of equine-like G3 rotavirus A infecting children. The goal of this article is to review relevant information related to rotavirus structure/genomic organization, epidemiology (with a focus on human and equine rotavirus A), evolution, inter-species transmission, and the potential zoonotic role of equine and other animal rotaviruses. Diagnostics, surveillance and the current status of human and livestock vaccines against RVA are also reviewed.

Nonsecretor Phenotype Is Associated With Less Risk of Rotavirus-Associated Acute Gastroenteritis in a Vaccinated Nicaraguan Birth Cohort

BACKGROUND

Histo-blood group antigens (HBGAs) have been associated with rotavirus vaccine take; but the effect of these HBGAs on rotavirus incidence and risk remains poorly explored in vaccinated populations.

METHODS

Rotavirus-associated acute gastroenteritis (AGE) was assessed in 444 Nicaraguan children followed from birth until 3 years of age. AGE episodes were tested for rotavirus by reverse-transcription quantitative polymerase chain reaction, and saliva or blood was used to determine HBGA phenotypes. Cox proportional hazards models were used to estimate the relative hazard of rotavirus AGE by HBGA phenotypes.

RESULTS

Rotavirus was detected in 109 (7%) stool samples from 1689 AGE episodes over 36 months of observation between June 2017 and July 2021. Forty-six samples were successfully genotyped. Of these, 15 (35%) were rotavirus vaccine strain G1P[8], followed by G8P[8] or G8P[nt] (11 [24%]) and equine-like G3P[8] (11 [24%]). The overall incidence of rotavirus-associated AGE was 9.2 per 100 child-years, and was significantly higher in secretor than nonsecretor children (9.8 vs 3.5/100 child-years, P = .002).

CONCLUSIONS

The nonsecretor phenotype was associated with decreased risk of clinical rotavirus vaccine failure in a vaccinated Nicaraguan birth cohort. These results show the importance of secretor status on rotavirus risk, even in vaccinated children.

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

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

Genetic diversity of rotavirus A in Argentina during 2019-2022: detection of G6 strains and insights regarding its dissemination

One of the challenges associated with introducing a vaccine is monitoring its impact through clinical and molecular surveillance. The aims of this study were to analyze the genetic diversity of rotavirus A in Argentina between 2019 and 2022 and to assess the phylogenetic and phylodynamic features of the unusual G6 strains detected. A significant decline in the Wa-like genogroup strains was observed, and G6 strains were detected for the first time in Argentina, in association with P[8] and P[9]. Spatiotemporal analysis showed that the G6-lineage I strains detected recently in Argentina and Brazil might have emerged from European strains. This study provides recent evidence of the genetic diversity of rotaviruses in isolated cases. It is considered important to support continuous surveillance of rotavirus in the post-vaccine scenario, mainly to evaluate potential changes that may occur after the COVID-19 pandemic.

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.

Quadruplex Real-Time TaqMan® RT-qPCR Assay for Differentiation of Equine Group A and B Rotaviruses and Identification of Group A G3 and G14 Genotypes

Equine rotavirus A (ERVA) is the leading cause of diarrhea in foals, with G3P[12] and G14P[12] genotypes being the most prevalent. Recently, equine G3-like RVA was recognized as an emerging infection in children, and a group B equine rotavirus (ERVB) was identified as an emergent cause of foal diarrhea in the US. Thus, there is a need to adapt molecular diagnostic tools for improved detection and surveillance to identify emerging strains, understand their molecular epidemiology, and inform future vaccine development. We developed a quadruplex TaqMan® RT-qPCR assay for differentiation of ERVA and ERVB and simultaneous G-typing of ERVA strains, evaluated its analytical and clinical performance, and compared it to (1) a previously established ERVA triplex RT-qPCR assay and (2) standard RT-PCR assay and Sanger sequencing of PCR products. This quadruplex RT-qPCR assay demonstrated high sensitivity (>90%)/specificity (100%) for every target and high overall agreement (>96%). Comparison between the triplex and quadruplex assays revealed only a slightly higher sensitivity for the ERVA NSP3 target using the triplex format (p-value 0.008) while no significant differences were detected for other targets. This quadruplex RT-qPCR assay will significantly enhance rapid surveillance of both ERVA and ERVB circulating and emerging strains with potential for interspecies transmission.

Rotavirus A during the COVID-19 Pandemic in Brazil, 2020-2022: Emergence of G6P[8] Genotype

Rotavirus A (RVA) remains a leading cause of acute gastroenteritis (AGE) hospitalizations in children worldwide. During the COVID-19 pandemic, a reduction in vaccination coverage in Brazil and elsewhere was observed, and some reports have demonstrated a reduction in AGE notifications during the pandemic. This study aims to investigate the diversity and prevalence of RVA genotypes in children and adults presenting with AGE symptoms in Brazil during the COVID-19 pandemic between 2020 and 2022. RVA was screened using RT-qPCR; then, G and P genotypes were characterized using one-step multiplex RT-PCR. A total of 2173 samples were investigated over the three-year period, and we detected RVA in 7.7% of samples (n = 167), being 15.5% in 2020, 0.5% in 2021, and 13.8% in 2022. Higher RVA prevalence was observed in the Northeastern region (19.3%) compared to the Southeastern (6.1%) and Southern regions (5.5%). The most affected age group was children aged between 0 and 6 months old; however, this was not statistically significant. Genotyping and phylogenetic analysis identified the emergence of G6P[8] during the period; moreover, it was detected in 10.6% of samples in 2020 and in 83.5% in 2022. In contrast, the prevalence of G3P[8], the previous dominant genotype, decreased from 72.3% in 2020 to 11.3% in 2022. We also identified unusual strains, such as G3P[9] and G9P[4], being sporadically detected during the period. This is the first report on the molecular epidemiology and surveillance of RVA during the COVID-19 pandemic period in Brazil. Our study provides evidence for the importance of maintaining high and sustainable levels of vaccine coverage to protect against RVA disease. Furthermore, it highlights the need to maintain nationwide surveillance in order to monitor future trends and changes in the epidemiology of RVA in Brazil.

G6P[8] Rotavirus a Possessing a Wa-like VP3 Gene from a Child with Acute Gastroenteritis Living in the Northwest Amazon Region

The introduction of rotavirus A (RVA) vaccines has considerably reduced the RVA-associated mortality among children under 5 years of age worldwide. The ability of RVA to reassort gives rise to different combinations of surface proteins G (glycoprotein, VP7) and P (protease sensitive, VP4) RVA types infecting children. During the epidemiological surveillance of RVA in the Northwest Amazon region, an unusual rotavirus genotype G6P[8] was detected in feces of a 2-year-old child with acute gastroenteritis (AGE) that had been vaccinated with one dose of Rotarix^® (RV1). The G6P[8] sample had a DS-1-like constellation with a Wa-like VP3 gene mono-reassortment similar to equine-like G3P[8] that has been frequently detected in Brazil previously. The results presented here reinforce the evolutionary dynamics of RVA and the importance of constant molecular surveillance.

Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi

G3 rotaviruses rank among the most common rotavirus strains worldwide in humans and animals. However, despite a robust long-term rotavirus surveillance system from 1997 at Queen Elizabeth Central Hospital in Blantyre, Malawi, these strains were only detected from 1997 to 1999 and then disappeared and re-emerged in 2017, 5 years after the introduction of the Rotarix rotavirus vaccine. Here, we analysed representative twenty-seven whole genome sequences (G3P[4], n = 20; G3P[6], n = 1; and G3P[8], n = 6) randomly selected each month between November 2017 and August 2019 to understand how G3 strains re-emerged in Malawi. We found four genotype constellations that were associated with the emergent G3 strains and co-circulated in Malawi post-Rotarix vaccine introduction: G3P[4] and G3P[6] strains with the DS-1-like genetic backbone genes (G3-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2), G3P[8] strains with the Wa-like genetic backbone genes (G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1), and reassortant G3P[4] strains consisting of the DS-1-like genetic backbone genes and a Wa-like NSP2 (N1) gene (G3-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2). Time-resolved phylogenetic trees demonstrated that the most recent common ancestor for each ribonucleic acid (RNA) segment of the emergent G3 strains was between 1996 and 2012, possibly through introductions from outside the country due to the limited genetic similarity with G3 strains which circulated before their disappearance in the late 1990s. Further genomic analysis revealed that the reassortant DS-1-like G3P[4] strains acquired a Wa-like NSP2 genome segment (N1 genotype) through intergenogroup reassortment; an artiodactyl-like VP3 through intergenogroup interspecies reassortment; and VP6, NSP1, and NSP4 segments through intragenogroup reassortment likely before importation into Malawi. Additionally, the emergent G3 strains contain amino acid substitutions within the antigenic regions of the VP4 proteins which could potentially impact the binding of rotavirus vaccine-induced antibodies. Altogether, our findings show that multiple strains with either Wa-like or DS-1-like genotype constellations have driven the re-emergence of G3 strains. The findings also highlight the role of human mobility and genome reassortment events in the cross-border dissemination and evolution of rotavirus strains in Malawi necessitating the need for long-term genomic surveillance of rotavirus in high disease-burden settings to inform disease prevention and control.

Genetic diversity and Genomic analysis of G3P[6] and equine-like G3P[8] in Children Under-five from Southern Highlands and Eastern Tanzania

Rotavirus group A genomic characterization is critical for understanding the mechanisms of rotavirus diversity, such as reassortment events and possible interspecies transmission. However, little is known about the genetic diversity and genomic relationship of the rotavirus group A strains circulating in Tanzania. The genetic and genomic relationship of RVA genotypes was investigated in children under the age of five. A total of 169 faecal samples were collected from under-five with diarrhea in Mbeya, Iringa and Morogoro regions of Tanzania. The RVA were screened in children under five with diarrhea using reverse transcription PCR for VP7 and VP4, and the G and P genotypes were determined using Sanger dideoxynucleotide cycle sequencing. Whole-genome sequencing was performed on selected genotypes. The overall RVA rate was 4.7% (8/169). The G genotypes were G3 (7/8) and G6 (1/8) among the 8 RVA positives, while the P genotypes were P[6] (4/8) and P[8] (2), and the other two were untypeable. G3P[6] and G3P[8] were the identified genotype combinations. The genomic analysis reveals that the circulating G3P[8] and G3P[6] isolates from children under the age of five with diarrhea had a DS-1-like genome configuration (I2-R2-C2-M2-Ax-N2-T2-E2-H2). The phylogenic analysis revealed that all 11 segments of G3P[6] were closely related to human G3P[6] identified in neighboring countries such as Uganda, Kenya, and other African countries, implying that G3P[6] strains descended from a common ancestor. Whereas, G3P[8] were closely related to previously identified equine-like G3P[P8] from Kenya, Japan, Thailand, Brazil, and Taiwan, implying that this strain was introduced rather than reassortment events. We discovered amino acid differences at antigenic epitopes and N-linked glycosylation sites between the wild type G3 and P[8] compared to vaccine strains, implying that further research into the impact of these differences on vaccine effectiveness is warranted. The phylogenic analysis of VP7 also identified a bovine-like G6. For the first time in Tanzania, we report the emergence of novel equine-like G3 and bovine-like G6 RVA strains, highlighting the importance of rotavirus genotype monitoring and genomic analysis of representative genotypes.

Genomic Constellation of Human Rotavirus G8 Strains in Brazil over a 13-Year Period: Detection of the Novel Bovine-like G8P[8] Strains with the DS-1-like Backbone

Rotavirus (RVA) G8 is frequently detected in animals, but only occasionally in humans. G8 strains, however, are frequently documented in nations in Africa. Recently, an increase in G8 detection was observed outside Africa. The aims of the study were to monitor G8 infections in the Brazilian human population between 2007 and 2020, undertake the full-genotype characterization of the four G8P[4], six G8P[6] and two G8P[8] RVA strains and conduct phylogenetic analysis in order to understand their genetic diversity and evolution. A total of 12,978 specimens were screened for RVA using ELISA, PAGE, RT-PCR and Sanger sequencing. G8 genotype represented 0.6% (15/2434) of the entirely RVA-positive samples. G8P[4] comprised 33.3% (5/15), G8P[6] 46.7% (7/15) and G8P[8] 20% (3/15). All G8 strains showed a short RNA pattern. All twelve selected G8 strains displayed a DS-1-like genetic backbone. The whole-genotype analysis on a DS-1-like backbone identified four different genotype-linage constellations. According to VP7 analysis, the Brazilian G8P[8] strains with the DS-1-like backbone strains were derived from cattle and clustered with newly DS-1-like G1/G3/G9/G8P[8] strains and G2P[4] strains. Brazilian IAL-R193/2017/G8P[8] belonged to a VP1/R2.XI lineage and were grouped with bovine-like G8P[8] strains with the DS-1-like backbone strains detected in Asia. Otherwise, the Brazilian IAL-R558/2017/G8P[8] possess a "Distinct" VP1/R2 lineage never previously described and grouped apart from any of the DS-1-like reference strains. Collectively, our findings suggest that the Brazilian bovine-like G8P[8] strains with the DS-1-like backbone strains are continuously evolving and likely reassorting with local RVA strains rather than directly relating to imports from Asia. The Brazilian G8P[6]-DS-1-like strains have been reassorted with nearby co-circulating American strains of the same DS-1 genotype constellation. However, phylogenetic analyses revealed that these strains have some genetic origin from Africa. Finally, rather than being African-born, Brazilian G8P[4]-DS-1-like strains were likely imported from Europe. None of the Brazilian G8 strains examined here exhibited signs of recent zoonotic reassortment. G8 strains continued to be found in Brazil according to their intermittent and localized pattern, thus, does not suggest that a potential emergence is taking place in the country. Our research demonstrates the diversity of G8 RVA strains in Brazil and adds to the understanding of G8P[4]/P[6]/P[8] RVA genetic diversity and evolution on a global scale.

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.

Complete Genome Sequencing Reveals Unusual Equine Rotavirus A of Bat Origin from India

Rotaviruses are the most common viral agents associated with foal diarrhea. Between 2014 and 2017, the annual prevalence of rotavirus in diarrheic foals ranged between 18 and 28% in Haryana (India). Whole-genome sequencing of two equine rotavirus A (ERVA) isolates (RVA/Horse-wt/IND/ERV4/2017 and RVA/Horse-wt/IND/ERV6/2017) was carried out to determine the genotypic constellations (GCs) of ERVAs. The GCs of both the isolates were G3-P[3]-I8-R3-C3-M3-A9-N3-T3-E3-H6, a unique combination reported for ERVAs so far. Both the isolates carried VP6 of genotype I8, previously unreported from equines. Upon comparison with RVAs of other species, the GC of both isolates was identical to that of a bat rotavirus strain, MSLH14, isolated from China in 2012. The nucleotide sequences of the genes encoding VP3, NSP2, and NSP3 shared >95.81% identity with bat RVA strains isolated from Africa (Gabon). The genes encoding VP1, VP2, VP7, NSP1, and NSP4 shared 94.82% to 97.12% nucleotide identities with the human strains which have zoonotic links to bats (RCH272 and MS2015-1-0001). The VP6 genes of both strains were distinct and had the highest similarity of only 87.08% with that of CMH222, a human strain of bat origin. The phylogenetic analysis and lineage studies revealed that VP7 of both isolates clustered in a new lineage (lineage X) of the G3 genotype with bat, human, and alpaca strains. Similarly, VP4 clustered in a distinct P[3] lineage. These unusual findings highlight the terra incognita of the genomic diversity of equine rotaviruses and support the need for the surveillance of RVAs in animals and humans with a "one health" approach. IMPORTANCE Rotaviruses are globally prevalent diarrheal pathogens in young animals including foals, piglets, calves, goats, sheep, cats, and dogs along with humans. The genome of rotaviruses consists of 11 segments, which enables them to undergo reshuffling by reassortment of segments from multiple species during mixed infections. In this study, the prevalence of equine rotaviruses was 32.11% in organized equine farms of North India. The complete genome analysis of two ERVA isolates revealed an unusual genomic constellation, which was previously reported only in a bat RVA strain. A segment-wise phylogenetic analysis revealed that most segments of both isolates were highly similar either to bat or to bat-like human rotaviruses. The occurrence of unusual bat-like rotaviruses in equines emphasizes the need of extensive surveillance of complete genomes of both animal and human rotaviruses with a "one health" approach.

Diverse human and bat-like rotavirus G3 strains circulating in suburban Bangkok

Although rotavirus vaccines are available in many parts of the world and are effective in reducing the overall incidence of rotavirus infection, it remains a major cause of diarrhea in less-developed countries. Among various rotavirus group A (RVA) strains, the increasingly common genotype G3 (defined by the VP7 gene) has been identified in both humans and animals. Our previous epidemiological surveillance in Bangkok found several unusual non-vaccine-like G3 strains in patients with diarrhea. In this study, we sequenced and characterized the genomes of seven of these G3 strains, which formed combinations with genotypes P[4], P[6], P[9], and P[10] (defined by the VP4 gene). Interestingly, we identified a bat-like RVA strain with the genome constellation G3-P[10]-I3-R3-C3-M3-A9-N3-T3-E3-H6, which has not been previously reported in the literature. The amino acid residues deduced from the nucleotide sequences of our G3 strains differed at the antigenic epitopes to those of the VP7 capsid protein of the G3 strain in RotaTeq vaccine. Although it is not unusual for the segmented genomes of RVA to reassort and give rise to emerging novel strains, the atypical G3 strains identified in this study suggest possible animal-to-human RVA zoonotic spillover even in urban areas.

Molecular characterization of the gastrointestinal eukaryotic virome in elderly people in Belem, Para, Brazil

Acute gastroenteritis is one of the main causes of mortality and morbidity worldwide, affecting mainly children, the immunocompromised and elderly people. Enteric viruses, especially rotavirus A, are considered important etiological agents, while long-term care facilities are considered favorable environments for the occurrence of sporadic cases and outbreaks of acute gastroenteritis. Therefore, it is important to monitor the viral agents present in nursing homes, especially because studies involving the elderly population in Brazil are scarce, resulting in a lack of available virological data. As a result, the causative agent remains unidentified in a large number of reported acute gastroenteritis cases. However, the advent of next-generation sequencing provides new opportunities for viral detection and discovery. The aim of this study was to identify the viruses that circulate among elderly people with and without acute gastroenteritis, living in residential care homes in Belém, Pará, Brazil, between 2017 and 2019. Ninety-three samples were collected and screened by immunochromatography and qPCR. After, the samples were analyzed individually or in pools by next generation sequencing to identify the viruses circulating in this population. In 26 sequenced samples, members of 13 eukaryotic virus families were identified. The most abundantly present virus families were Parvoviridae, Genomoviridae and Smacoviridae. Contigs displaying similarity to pegiviruses were also detected. Furthermore, a near-complete rotavirus A genome was obtained and could be classified as G3P[8] genotype with the equine DS-1-like genetic background. Complete sequences of the VP4 and VP7 genes of a rotavirus C were also detected, belonging to G4P[2]. This study demonstrates the first characterization of the gastrointestinal virome in elderly in Northern Brazil. A diversity of viruses was found to be present in patients with and without diarrhea, reinforcing the need to monitor elderly people residing in long-term care facilities, especially in cases of acute gastroenteritis.

Development of a Real-Time Reverse Transcription-PCR Assay To Detect and Quantify Group A Rotavirus Equine-Like G3 Strains

Since 2013, group A rotavirus strains characterized as novel DS-1-like intergenogroup reassortant "equine-like G3" strains have emerged and spread across 5 continents among human populations in at least 14 countries. Here, we report a novel one-step TaqMan quantitative real-time reverse transcription-PCR assay developed to genotype and quantify the viral load for samples containing rotavirus equine-like G3 strains. Using a universal G forward primer and a newly designed reverse primer and TaqMan probe, we developed and validated an assay with a linear dynamic range of 227 to 2.3 × 10⁹ copies per reaction and a limit of detection of 227 copies. The percent positive agreement, percent negative agreement, and precision of our assay were 100.00%, 99.63%, and 100.00%, respectively. This assay can simultaneously detect and quantify the viral load for samples containing DS-1-like intergenogroup reassortant equine-like G3 strains with high sensitivity and specificity, faster turnaround time, and decreased cost. It will be valuable for high-throughput screening of stool samples collected to monitor equine-like G3 strain prevalence and circulation among human populations throughout the world.

Nosocomial acute gastroenteritis outbreak caused by an equine-like G3P[8] DS-1-like rotavirus and GII.4 Sydney[P16] norovirus at a pediatric hospital in Rio de Janeiro, Brazil, 2019

Worldwide, rotavirus (RVA) and norovirus are considered major etiological agents of acute gastroenteritis (AGE) in pediatric population admitted to hospitals. This study describes the investigation of nosocomial infections caused by emergent RVA and norovirus strains reported at a pediatric hospital in southern Brazil in May 2019. This outbreak affected 30 people among children and adults. Nine stool samples (eight children and one nurse) were obtained and analyzed by RT-qPCR to detect and quantify RVA and norovirus. Positive samples were genotyped by sequencing and subjected to phylogenetic analysis. We detected RVA in 44.4% (4/9) and norovirus in 55.5% (5/9) at high viral loads, ranging from 3.5 × 10⁷ to 6.1 × 10⁷ and 3.2 × 10² to 3.2 × 10⁹ genome copies/g of stool, respectively. Co-infections were not observed. RVA VP4 and VP7 gene sequencing in combination with polyacrylamide gel electrophoresis identified the circulation of equine-like G3P[8] DS-1-like, and the partial sequencing of the other nine genes revealed that strains possessed I2-R2-C2-M2-A2-N1-T2-E2-H2 genotype background. The emergent recombinant norovirus variant, GII.4 Sydney[P16], was identified by ORF1-2 sequencing. Active surveillance and effective prevention measures should be constantly reinforced to avoid the spread of nosocomial viral infections into hospitals, which could severely affect pediatric patients admitted with underlying health conditions.

Molecular analysis of G3P[6] rotavirus in the Amazon region of Brazil: evidence of reassortment with equine-like strains

Aim: To perform a molecular analysis of rotavirus A (RVA) G3P[6] strains detected in 2012 and 2017 in the Amazon region of Brazil. Materials & methods: Eighteen RVA G3P[6] strains were collected from children aged under 10 years hospitalized with acute gastroenteritis, and partial sequencing of each segment genome was performed using Sanger sequencing. Results: Phylogenetic analysis showed that all G3P[6] strains had a DS-1-like genotype constellation. Two strains had the highest nucleotide identities with equine-like G3P[6]/G3P[8] genotypes. Several amino acid alterations in VP4 and VP7 neutralizing epitopes of equine-like RVA G3P[6] strains were observed in comparison with vaccine strains. Conclusion: These findings suggest that equine-like RVA G3P[6] strains have been circulating in the Amazon region of Brazil as a result of direct importation, and support natural RVA evolutionary mechanisms.

Emergence of equine-like G3 strains as the dominant rotavirus among children under five with diarrhea in Sabah, Malaysia during 2018-2019

Rotavirus infection is a dilemma for developing countries, including Malaysia. Although commercial rotavirus vaccines are available, these are not included in Malaysia's national immunization program. A scarcity of data about rotavirus genotype distribution could be partially to blame for this policy decision, because there are no data for rotavirus genotype distribution in Malaysia over the past 20 years. From January 2018 to March 2019, we conducted a study to elucidate the rotavirus burden and genotype distribution in the Kota Kinabalu and Kunak districts of the state of Sabah. Stool specimens were collected from children under 5 years of age, and rotavirus antigen in these samples was detected using commercially available kit. Electropherotypes were determined by polyacrylamide gel electrophoresis of genomic RNA. G and P genotypes were determined by RT-PCR using type specific primers. The nucleotide sequence of the amplicons was determined by Sanger sequencing and phylogenetic analysis was performed by neighbor-joining method. Rotavirus was identified in 43 (15.1%) children with watery diarrhea. The male:female ratio (1.9:1) of the rotavirus-infected children clearly showed that it affected predominantly boys, and children 12-23 months of age. The genotypes identified were G3P[8] (74% n = 31), followed by G1P[8] (14% n = 6), G12P[6](7% n = 3), G8P[8](3% n = 1), and GxP[8] (3% n = 1). The predominant rotavirus circulating among the children was the equine-like G3P[8] (59.5% n = 25) with a short electropherotype. Eleven electropherotypes were identified among 34 strains, indicating substantial diversity among the circulating strains. The circulating genotypes were also phylogenetically diverse and related to strains from several different countries. The antigenic epitopes present on VP7 and VP4 of Sabahan G3 and equine-like G3 differed considerably from that of the RotaTeq vaccine strain. Our results also indicate that considerable genetic exchange is occurring in Sabahan strains. Sabah is home to a number of different ethnic groups, some of which culturally are in close contact with animals, which might contribute to the evolution of diverse rotavirus strains. Sabah is also a popular tourist destination, and a large number of tourists from different countries possibly contributes to the diversity of circulating rotavirus genotypes. Considering all these factors which are contributing rotavirus genotype diversity, continuous surveillance of rotavirus strains is of utmost importance to monitor the pre- and post-vaccination efficacy of rotavirus vaccines in Sabah.

Enteric adenovirus epidemiology from historical fecal samples in Brazil (1998-2005): Pre-rotavirus vaccine era

Human adenovirus (HAdV) is recognized as frequent cause of acute gastroenteritis and enteric viruses can be preserved in frozen stored feces for long periods of times. The purpose of the present study was to investigate enteric HAdV genotypic diversity in archival fecal specimens stored from 1998 to 2005 in order to understand the natural history of HAdV in diarrheal patients in Brazil before rotavirus vaccine introduction. A total of 3346 specimens were tested for HAdV using conventional PCR. Genotypes were identified by sequencing. HAdV was detected in 6.8% (228/3346). Positivity was higher in children ≤ 5 years and males (p < 0.05). HAdV was most frequently observed during winter and spring seasons (p < 0.05). HAdV-F41 was the most prevalent genotype (59.2%;135/228), followed by HAdV-F40 (16.2%;37/228), HAdV-C1 (5.2%;12/228), HAdV-C2 (5.2%;12/228), HAdV-C5 (3.1%;7/228), HAdV-A12 (1.3%;3/228), HAdV-E4 (0.9%;2/228), HAdV-B3 (0.9%;2/228) and HAdV-B21 (0.4%;1/228). In 7.6% (17/228) only species D could be defined. HAdV-E4 strains were phylogenetic analyzed and classified as lineage (a)-like PG II. HAdV prevalence remained stable in Brazilian population, regardless rotavirus vaccine introduction. The predominant HAdV genotypes detected did not change over time, highlighting a high diversity of circulating strains in the country throughout decades. Due to the historical lack of HAdV genotyping surveillance in Brazil, HAdV-E4 epidemiology is virtually unknown in the country. The present study contributed significantly to the understanding of the natural history of HAdV in diarrheal patients in Brazil. The acquired data are important for clinical diagnosis, particularly for studies investigating enteric viruses' prevalence and molecular epidemiology of archival clinical specimens.

Wa-1 Equine-Like G3P[8] Rotavirus from a Child with Diarrhea in Colombia

Rotavirus A (RVA) has been considered the main cause of diarrheal disease in children under five years in emergency services in both developed and developing countries. RVA belongs to the Reoviridae family, which comprises 11 segments of double-stranded RNA (dsRNA) as a genomic constellation that encodes for six structural and five to six nonstructural proteins. RVA has been classified in a binary system with Gx[Px] based on the spike protein (VP4) and the major outer capsid glycoprotein (VP7), respectively. The emerging equine-like G3P[8] DS-1-like strains reported worldwide in humans have arisen an important concern. Here, we carry out the complete genome characterization of a previously reported G3P[8] strain in order to recognize the genetic diversity of RVA circulating among infants in Colombia. A near-full genome phylogenetic analysis was done, confirming the presence of the novel equine-like G3P[8] with a Wa-like backbone for the first time in Colombia. This study demonstrated the importance of surveillance of emerging viruses in the Colombian population; furthermore, additional studies must focus on the understanding of the spread and transmission dynamic of this important RVA strain in different areas of the country.

Prevalence and Distribution of Rotavirus Genotypes Among Children With Acute Gastroenteritis in Areas Other Than Java Island, Indonesia, 2016-2018

Group A rotaviruses (RVAs) are the leading cause of acute gastroenteritis, which is often associated with severe symptoms in children under 5 years old. Genetic reassortments and interspecies transmission commonly occur, resulting in a great diversity of RVA circulating in the world. The aim of this study is to determine the prevalence and distribution of RVA genotypes among children in Indonesia over the years 2016–2018 across representative areas of the country. Stool samples were collected from 202 pediatric patients with acute gastroenteritis in three regions of Indonesia (West Nusa Tenggara, South Sumatra, and West Papua) in 2016–2018. Rotavirus G and P genotypes were determined by reverse transcription PCR (RT-PCR) and direct sequencing analysis. The prevalences of RVA in South Sumatra (55.4%) and West Papua (54.0%) were significantly higher than that in East Java (31.7%) as determined in our previous study. The prevalence in West Nusa Tenggara (42.6%) was the lowest among three regions, but higher than that in East Java. Interestingly, equine-like G3 rotavirus strains were found as predominant strains in South Sumatra in 2016 and in West Papua in 2017–2018. Moreover, the equine-like G3 strains in South Sumatra detected in 2016 were completely replaced by human G1 and G2 in 2018. In conclusion, RVA infection in South Sumatra and West Papua was highly endemic. Equine-like G3 strains were also spread to South Sumatra (West Indonesia) and West Papua (East Indonesia), as well as Java Island. Dynamic change in rotavirus genotypes from equine-like G3 to human genotypes was also observed. Continuous monitoring may be warranted in isolated areas in Indonesia.

Surveillance and molecular characterization of human sapovirus in patients with acute gastroenteritis in Brazil, 2010 to 2017

BACKGROUND

Human sapoviruses (HuSaV) are associated with acute gastroenteritis (AGE), causing sporadic cases and outbreaks in patients worldwide. In Brazil, however, there are few reports describing the prevalence of HuSaV in patients with AGE.

OBJECTIVE

Describing the diversity of HuSaV in Brazil by detecting and molecularly characterizing HuSaV among patients with AGE during an 8-year period (2010-2017).

STUDY DESIGN

A total of 3974 stool samples, testing negative for rotavirus (RVA), norovirus (NoV) and human adenovirus (HAdV), were selected and screened for the presence of HuSaV. Nested RT-PCR were performed for a partial region of VP1, sequenced and genetic analyzed for genotyping the positive samples.

RESULTS

In the current study, the HuSaV prevalence was determined to be 3.7% (149/3974). A higher prevalence, 5.7% (118/2074), was observed in children under 2 years of age. During the surveillance period, 13 outbreaks were detected: 12 outbreaks in children under 3 years old and one outbreak in adults. Among the 149 HuSaV positive cases, 106 samples (71%) were successfully sequenced. The most prevalent genotype found was GI.1 (44.3%), followed by GI.2 (21.7%), GI.3 (3.8%), GI.6 (2.8%), GII.1 (5.7%), GII.2 (8.5%), GII.3 (2.8%), GII.4 (2.8%), GII.5 (5.7%) and GIV.1 (1.9%). Two GIV.1 strains characterized in this study are, to date, the only strains of this genotype reported in Brazil.

CONCLUSIONS

The present study elucidated the circulation of HuSaV in Brazil and highlight that HuSaV has not assumed an epidemiological importance in the country after the introduction of the RVA vaccine.

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.

Molecular and clinical characterization of the equine-like G3 rotavirus that caused the first outbreak in Japan, 2016

Since 2013, equine-like G3 rotavirus (eG3) strains have been detected throughout the world, including in Japan, and the strains were found to be dominant in some countries. In 2016, the first eG3 outbreak in Japan occurred in Tomakomai, Hokkaido prefecture, and the strains became dominant in other Hokkaido areas the following year. There were no significant differences in the clinical characteristics of eG3 and non-eG3 rotavirus infections. The eG3 strains detected in Hokkaido across 2 years from 2016 to 2017 had DS-1-like constellations (i.e. G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2), and the genes were highly conserved (97.5-100 %). One strain, designated as To16-12 was selected as the representative strain for these strains, and all 11 genes of this strain (To16-12) exhibited the closest identity to one foreign eG3 strain (STM050) seen in Indonesia in 2015 and two eG3 strains (IS1090 and MI1125) in another Japanese prefecture in 2016, suggesting that this strain might be introduced into Japan from Indonesia. Sequence analyses of VP7 genes from animal and human G3 strains found worldwide did not identify any with close identity (>92 %) to eG3 strains, including equine RV Erv105. Analysis of another ten genes indicated that the eG3 strain had low similarity to G2P[4] strains, which are considered traditional DS-1-like strains, but high similarity to DS-1-like G1P[8] strains, which first appeared in Asia in 2012. These data suggest that eG3 strains were recently generated in Asia as mono-reassortant strain between DS-1-like G1P[8] strains and unspecified animal G3 strains. Our results indicate that rotavirus surveillance in the postvaccine era requires whole-genome analyses.

Australian Rotavirus Surveillance Program: Annual Report, 2018

Abstract

This report, from the Australian Rotavirus Surveillance Program and collaborating laboratories Australia-wide, describes the rotavirus genotypes identified in children and adults with acute gastroenteritis during the period 1 January to 31 December 2018. During this period, 690 faecal specimens were referred for rotavirus G- and P- genotype analysis, including 607 samples that were confirmed as rotavirus positive. Of these, 457/607 were wild-type rotavirus strains and 150/607 were identified as rotavirus vaccine-like. Genotype analysis of the 457 wild-type rotavirus samples from both children and adults demonstrated that G3P[8] was the dominant genotype nationally, identified in 52% of samples, followed by G2P[4] (17%). The Australian National Immunisation Program, which previously included both RotaTeq and Rotarix vaccines, changed to Rotarix exclusively on 1 July 2017. Continuous surveillance is needed to identify if the change in vaccination schedule could affect rotavirus genotype distribution and diversity in Australia.

Australian Rotavirus Surveillance Program: Annual Report, 2019

Abstract

This report, from the Australian Rotavirus Surveillance Program and collaborating laboratories Australia-wide, describes the rotavirus genotypes identified in children and adults with acute gastroenteritis during the period 1 January to 31 December 2019. During this period, 964 faecal specimens had been referred for rotavirus G- and P- genotype analysis, including 894 samples that were confirmed as rotavirus positive. Of these, 724/894 were wild-type rotavirus strains and 169/894 were identified as vaccine-like. A single sample could not be determined as wild-type or vaccine-like due to poor sequencing. Genotype analysis of the 724 wild-type rotavirus samples from both children and adults demonstrated that G3P[8] was the dominant genotype nationally, identified in 46.7% of samples, followed by G2P[4] in 8.8% of samples. The Australian National Immunisation Program (NIP) changed to the exclusive use of Rotarix as of 1 July 2017. The NIP had previously included two live-attenuated oral vaccines: Rotarix (monovalent, human) and RotaTeq (pentavalent, human-bovine reassortant) in a state-based vaccine selection. Continuous surveillance is imperative to determine the effect of this change in rotavirus vaccine schedule on the genotype distribution and diversity in Australia.

Genomic constellation of human Rotavirus A strains identified in Northern Brazil: a 6-year follow-up (2010-2016)

Surveillance of Rotavirus A (RVA) throughout the national territory is important to establish a more complete epidemiological-molecular scenario of this virus circulation in Brazil. The aim of the present study was to investigate the genetic diversity of RVA strains circulating in Tocantins State (Northern Brazil) during six years of post-vaccination follow-up (2010-2016). A total of 248 stool samples were screened by next generation sequencing and 107 (43.1%) nearly full length RVA genome sequences were obtained; one sample was co-infected with two RVA strains (G2/G8P[4]). Six G and P genotypes combinations were detected: G12P[8] strains (78.6%), as well as the G3P[8] (9.3%) and G1P[8] (0.9%) were associated with a Wa-like genogroup backbone. All G2P[4] (5.6%) and G8P[4] (2.8%) strains, including the mixed G2/G8P[4] infection (0.9%) showed the DS-1-like genetic background. The two G12P[4] strains (1.9%) were associated with distinct genetic backbones: Wa-like and DS-1-like. The phylogenetic analysis revealed the circulation of lineages G1-I, G2-IV, G3-III, G8-I and G12-III, and P[4]-V and P[8]-III of the VP7 and VP4 genes, respectively. Conserved clustering pattern and low genetic diversity were observed regarding VP1-VP3 and VP6, as well as NSP1-5 segments. We identified the same RVA circulation pattern reported in other Brazilian regions in the period of 2010-2016, suggesting that rural and low-income areas may not have a different RVA genotypic distribution compared to other parts of the country. The unique presentation of whole-genome data of RVA strains detected in the Tocantins State provides a baseline for monitoring variations in the genetic composition of RVA in this area.

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.

Rotavirus A in Brazil: Molecular Epidemiology and Surveillance during 2018-2019

Rotavirus A (RVA) vaccines succeeded in lowering the burden of acute gastroenteritis (AGE) worldwide, especially preventing severe disease and mortality. In 2019, Brazil completed 13 years of RVA vaccine implementation (Rotarix™) within the National Immunization Program (NIP), and as reported elsewhere, the use of Rotarix™ in the country has reduced childhood mortality and morbidity due to AGE. Even though both marketed vaccines are widely distributed, the surveillance of RVA causing AGE and the monitoring of circulating genotypes are important tools to keep tracking the epidemiological scenario and vaccines impact. Thus, our study investigated RVA epidemiological features, viral load and G and P genotypes circulation in children and adults presenting AGE symptoms in eleven states from three out of five regions in Brazil. By using TaqMan^®-based one-step RT-qPCR, we investigated a total of 1536 stool samples collected from symptomatic inpatients, emergency department visits and outpatients from January 2018 to December 2019. G and P genotypes of RVA-positive samples were genetically characterized by multiplex RT-PCR or by nearly complete fragment sequencing. We detected RVA in 12% of samples, 10.5% in 2018 and 13.7% in 2019. A marked winter/spring seasonality was observed, especially in Southern Brazil. The most affected age group was children aged >24-60 months, with a positivity rate of 18.8% (p < 0.05). Evaluating shedding, we found a statistically lower RVA viral load in stool samples collected from children aged up to six months compared to the other age groups (p < 0.05). The genotype G3P[8] was the most prevalent during the two years (83.7% in 2018 and 65.5% in 2019), and nucleotide sequencing of some strains demonstrated that they belonged to the emergent equine-like G3P[8] genotype. The dominance of an emergent genotype causing AGE reinforces the need for continuous epidemiological surveillance to assess the impact of mass RVA immunization as well as to monitor the emergence of novel genotypes.

High prevalence of DS-1-like rotavirus infection in Thai adults between 2016 and 2019

Rotavirus infection is the most common cause of viral diarrhea in infants and young children but uncommon and usually asymptomatic in adults. In the winter of 2017–2018, a large-scale outbreak of rotavirus in both children and adults was reported in Thailand. The current study focused on the prevalence, genotyping, and molecular characterization of rotavirus infections in Thai adults from July 2016 to December 2019. In 2,598 stool samples collected from adult residents of Bangkok (aged #x2265; 15 years) with acute gastroenteritis, rotavirus was detected via real-time RT-PCR analysis of the VP6 gene. G, P and I genotypes were determined by direct sequencing of VP7, VP4, and VP6 genes, respectively. Our results showed 8.7% (226/2,598) of stool samples were positive for rotavirus. The incidence of rotavirus was high during the winter season of 2017–2018 (17.7%) compared to another studied periods (4.5% between July 2016- October 2017 and 2.8% between March 2018- December 2019). Nucleotide sequencing of VP7 and VP4 revealed G3P[8] as the predominant strain (33.2%,75/226), followed by G9P[8] (17.3%,39/226), and G2P[4] (15.0%,34/226). Uncommon G and P combinations were additionally detected at low frequencies. VP6 sequencing was conducted to discriminate I genotype between the Wa and DS-1 genogroup. The unusual DS-1-like G3P[8] strain was most prevalent amomg rotavirus strains detected in this study (29.6%, 67/226), and the corresponding VP7 sequences showed high nucleotide identity with unusual DS-1-like globally circulating strains. Our study demonstrates that rotavirus outbreaks in adults are attributable not only to high prevalence of RV infection but also the unusual DS-like genogroup. The collective findings reinforce the importance of investigating rotavirus diagnosis in adults suffering from acute gastroenteritis and taking appropriate preventive measures.

Prevalence and diversity of human rotavirus among Thai adults

Rotavirus infections have become one of the most common causes of infectious gastroenteritis in children. Although rotavirus infections have been intensively studied in infants and young children, the study in adults has been limited. As such, this study assessed the prevalence of rotaviruses and performed the molecular characterization of rotaviruses circulating in Thai adults experiencing acute gastroenteritis between January 2018 and December 2018. Group A human rotaviruses were detected in 100 feces samples by rapid immunochromatography. The peak incidence of infection occurred in February and began to decline in the summer months. From January 2018 to December 2018, there were 1344 acute gastroenteritis adult cases in the Hospital for Tropical Diseases, Bangkok, Thailand. Among these, 310 cases were rotavirus-suspected cases. Only 100 samples tested positive for rotavirus via an immunochromatography test. Twentynine out of the 100 rotavirus-positive samples were further characterized by real-time polymerase chain reaction. The G3[P8] strain was identified as the most prevalent (31.0%) followed by G1P[8], G8P[8] and G9P[8], and G2P[8], which accounted for 20.8%, 17.2%, and 13.8%, respectively. Because of the detection of rare rotavirus genotypes, such as G8, the surveillance of rotavirus epidemiology is crucial in monitoring new emergences of rotavirus strains, leading to a better understanding of the effects of strain variation for further vaccine development.

Full genome characterization of novel DS-1-like G9P[8] rotavirus strains that have emerged in Thailand

The emergence and rapid spread of unusual DS-1-like intergenogroup reassortant rotaviruses having G1/3/8 genotypes have been recently reported from major parts of the world (Africa, Asia, Australia, Europe, and the Americas). During rotavirus surveillance in Thailand, three novel intergenogroup reassortant strains possessing the G9P[8] genotype (DBM2017-016, DBM2017-203, and DBM2018-291) were identified in three stool specimens from diarrheic children. In the present study, we determined and analyzed the full genomes of these three strains. On full-genomic analysis, all three strains were found to share a unique genotype constellation comprising both genogroup 1 and 2 genes: G9-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis demonstrated that each of the 11 genes of the three strains was closely related to that of emerging DS-1-like intergenogroup reassortant, human, and/or locally circulating human strains. Thus, the three strains were suggested to be multiple reassortants that had acquired the G9-VP7 genes from co-circulating Wa-like G9P[8] rotaviruses in the genetic background of DS-1-like intergenogroup reassortant (likely equine-like G3P[8]) strains. To our knowledge, this is the first description of emerging DS-1-like intergenogroup reassortant strains having the G9P[8] genotype. Our observations will add to the growing insights into the dynamic evolution of emerging DS-1-like intergenogroup reassortant rotaviruses through reassortment.

Distribution of rotavirus genotypes in Japan from 2015 to 2018: Diversity in genotypes before and after introduction of rotavirus vaccines

BACKGROUND

Diversity in group A rotavirus (RVA) strains after introduction of RV-vaccines remains an emerging concern worldwide. In this study, we investigated the prevalence and distribution of RVA genotypes in Japanese children with acute gastroenteritis (AGE) from 2015 to 2018. In addition, a comparison of the genotypes in pre-vaccination (2006-2012) and post-vaccination (2012-2018) periods was conducted to understand the impact of these vaccines on genotype distribution.

METHODS

Fecal samples were collected regularly from outpatient clinics in six localities: Hokkaido, Tokyo, Shizuoka, Osaka, Kyoto, and Saga. RVA were screened and genotyped by RT-PCR and sequence-based genotyping.

RESULTS

During the period 2015-2018, RVA was detected in 307 (19.7%) samples out of 1557 specimens: 29.9% (95% CI: 25.8% to 34.3%), 17.9% (95% CI: 14.7% to 21.5%), and 13% (95% CI: 10.3% to 16.0%) were detected RVA-positive in 2015-2016, 2016-2017 and 2017-2018, respectively. The average detection of RVA in pre-vaccination (2006-2012) and post-vaccination (2012-2018) era remained almost similar (18%-20%). The G2P[4]I2 (52.1%, 95% CI: 43.5%-60.6%) remained the most common genotype in 2015-2016, whereas G8P[8]I2 (55.9%, 95% CI: 45.2%-66.2%) dominated in 2016-2017. In 2017-2018, G9P[8]I2 (42.0%, 95% CI: 30.5%-53.9%) prevailed, followed by G9P[8]I1 (23.0%, 95% CI: 14.0%-34.2%). The detection rate of some common genotypes of pre-vaccination era like G1P[8] and G3P[8] has been reduced after introduction of RV-vaccine, whereas genotypes that were sporadic before the introduction of vaccines like G2P[4], G2P[8], G9P[8] and G8P[8] were emerged/reemerged in post-vaccination period.

CONCLUSIONS

Our study presented the diversity in circulating RVA genotypes in Japan before and after introduction of RV-vaccines. Sudden emergence of DS-1-like (I2) unusual strains in post-vaccination era remains alarming. Continuous monitoring of RVA genotypes is therefore indispensable to refine future vaccine strategy.

Genotype distribution of Group A rotavirus in children before and after massive vaccination in Latin America and the Caribbean: Systematic review

BACKGROUND

During the last decade, most of Latin American and the Caribbean (LAC) countries have implemented oral live rotavirus vaccines in their national vaccination programs with remarkable results. However, it has been suggested that massive vaccination could lead to the replacement of circulating genotypes or the emergence of new variants or neutralizing antibodies escape mutants, which may reduce the effectiveness of the vaccine. The objective was to analyze the genetic diversity of Group A rotavirus before and after the introduction of universal vaccination in LAC.

METHODS

We conducted a systematic review of studies published in PubMed, Scielo and LILACS. There were considered only LAC countries with rotavirus massive vaccination strategy which had described circulating genotypes data in children under 5 years of age, either for surveillance or vaccine effectiveness purposes, from 2001 to 2017. Systematic review stages were carried out following the recommendations of PRISMA.

RESULTS

Of the 18 countries that included any of the two licensed rotavirus vaccines in their national schedules since 2006, only 7 (~39%) presented studies of RVA genetic diversity before and after implementation, and met the inclusion criteria. Four of them (Argentina, Brazil, Colombia and Nicaragua) experienced a rapid switch from Wa-like to DS-1-like strains. Also, G1P[8] association, considered the most predominant worldwide in the pre-vaccination era, decreased significantly and was only frequently detected in Venezuela and Nicaragua. No defined pattern of emergence at high frequencies of unusual associations was observed in the post vaccination period, except for some evidence of G9P[4] in Colombia, G3P[6] and G1P[4] in Nicaragua.

CONCLUSIONS

Even though the evidence shows a DS-1-like change trend, data from studies conducted in Latin America and the Caribbean are diverse and still not sufficient to assess the impact of vaccines on viral ecology or if genetic diversity is influenced by natural mechanisms of fluctuation.

High prevalence of equine-like G3P[8] rotavirus in children and adults with acute gastroenteritis in Thailand

Group A rotavirus (RVA) is a major cause of acute gastroenteritis in infants and young children worldwide. This study aims to clarify the distribution of G/P types and genetic characteristics of RVAs circulating in Thailand. Between January 2014 and September 2016, 1867 stool specimens were collected from children and adults with acute gastroenteritis in six provinces in Thailand. RVAs were detected in 514/1867 (27.5%) stool specimens. G1P[8] (44.7%) was the most predominant genotype, followed by G3P[8] (33.7%), G2P[4] (11.5%), G8P[8] (7.0%), and G9P[8] (1.3%). Unusual G3P[9] (0.8%), G3P[10] (0.4%), G4P[6] (0.4%), and G10P[14] (0.2%) were also detected at low frequencies. The predominant genotype, G1P[8] (64.4%), in 2014 decreased to 6.1% in 2016. In contrast, the frequency of G3P[8] markedly increased from 5.5% in 2014 to 65.3% in 2015 and 89.8% in 2016. On polyacrylamide gel electrophoresis, most (135/140; 96.4%) of the G3P[8] strains exhibited a short RNA profile. Successful determination of the nucleotide sequences of the VP7 genes of 98 G3P[8] strains with a short RNA profile showed that they are all equine-like G3P[8] strains. On phylogenetic analysis of genome segments of two representative Thai equine-like G3P[8] strains, it was noteworthy that they possessed distinct NSP4 genes, one bovine-like and the other human-like. Thus, we found that characteristic equine-like G3P[8] strains with a short RNA electropherotype are becoming highly prevalent in children and adults in Thailand.

Whole genome characterization and evolutionary analysis of OP354-like P[8] Rotavirus A strains isolated from Ghanaian children with diarrhoea

In 2010, the rare OP354-like P[8]b rotavirus subtype was detected in children less than 2 years old in Ghana. In this follow-up study, to provide insight into the evolutionary history of the genome of Ghanaian P[8]b strains RVA/Human-wt/GHA/GHDC949/2010/G9P[8] and RVA/Human-wt/GHA/GHM0094/2010/G9P[8] detected in an infant and a 7-month old child hospitalised for acute gastroenteritis, we sequenced the complete genome using both Sanger sequencing and Illumina MiSeq technology followed by phylogenetic analysis of the near-full length sequences. Both strains possessed the Wa-like/genotype 1 constellation G9P[8]b-I1-R1-C1-M1-A1-N1-T1-E1-H1. Sequence comparison and phylogenetic inference showed that both strains were identical at the lineage level throughout the 11 genome segments. Their VP7 sequences belonged to the major sub-lineage of the G9-lineage III whereas their VP4 sequences belonged to P[8]b cluster I. The VP7 and VP4 genes of the study strains were closely related to a Senegalese G9P[8]b strain detected in 2009. In the remaining nine genome segments, both strains consistently clustered together with Wa-like RVA strains possessing either P[8]a or P[8]b mostly of African RVA origin. The introduction of a P[8]b subtype VP4 gene into the stable Wa-like strain backbone may result in strains that might propagate easily in the human population, with a potential to become an important public health concern, especially because it is not certain if the monovalent rotavirus vaccine (Rotarix) used in Ghana will be efficacious against such strains. Our analysis of the full genomes of GHM0094 and GHDC949 adds to knowledge of the genetic make-up and evolutionary dynamics of P[8]b rotavirus strains.

Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains

Recent increase in the detection of unusual G1P[8], G3P[8], G8P[8], and G9P[4] Rotavirus A (RVA) strains bearing the DS-1-like constellation of the non-G, non-P genes (hereafter referred to as the genotype 2 backbone) requires better understanding of their evolutionary relationship. However, within a genotype, there is lack of a consensus lineage designation framework and a set of common sequences that can serve as references. Phylogenetic analyses were carried out on over 8,500 RVA genotype 2 genes systematically retrieved from the rotavirus database within the NCBI Virus Variation Resource. In line with previous designations, using pairwise comparison of cogent nucleotide sequences and stringent bootstrap support, reference lineages were defined. This study proposes a lineage framework and provides a dataset ranging from 34 to 145 sequences for each genotype 2 gene for orderly lineage designation of global genotype 2 genes of RVAs detected in human and animals. The framework identified five to 31 lineages depending on the gene. The least number of lineages (five to seven) were observed in genotypes A2 (NSP1), T2 (NSP3) and H2 (NSP5) which are limited to human RVA whereas the most number of lineages (31) was observed in genotype E2 (NSP4). Sharing of the same lineage constellations of the genotype 2 backbone genes between recently-emerging, unusual G1P[8], G3P[8], G8P[8] and G9P[4] reassortants and many contemporary G2P[4] strains provided strong support to the hypothesis that unusual genotype 2 strains originated primarily from reassortment events in the recent past involving contemporary G2P[4] strains as one parent and ordinary genotype 1 strains or animal RVA strains as the other. The lineage framework with selected reference sequences will help researchers to identify the lineage to which a given genotype 2 strain belongs, and trace the evolutionary history of common and unusual genotype 2 strains in circulation.

Emergence of G12P[6] rotavirus strains among hospitalised children with acute gastroenteritis in Belém, Northern Brazil, following introduction of a rotavirus vaccine

Species A rotavirus still remains a major cause of acute gastroenteritis in infants and young children. Globally, six genotypes (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]) account for >90% of circulating strains; however, genotype G12 in combination with P[6] or P[9] has been detected at increasing rates. We sought to broaden our knowledge about the rotavirus strains circulating during the early post-vaccine-introduction period. Stool samples were obtained from children hospitalised for acute gastroenteritis in Belém, Northern Brazil, from May 2008 to May 2011 and examined by reverse transcription polymerase chain reaction and nucleotide sequencing. A total of 122 out of the original 1076 rotavirus strains were judged to be non-typeable in the first analysis and were therefore re-examined. G2P[4] was the most prevalent genotype (58.0%), followed by G1P[8] (16.9%), and G12P[6] (7.5%). G12P[6] strains were identified at similar rates during the first (2.5%) and second (3.9%) years, and the rate jumped to 15.6% in the third year. Analysis of VP7 sequences of the G12P[6] strains showed that they belonged to lineage III. In addition, co-circulating G12P[6] strains displaying long and short RNA patterns were found to belong to the Wa-like and DS-1-like constellation, respectively. Additional unusual circulating strains G12P[9] and G3P[9] were also identified. This hospital-based study showed a high prevalence of G12P[6] strains in the third year of surveillance. Our results highlight the need for continuous longitudinal monitoring of circulating rotavirus strains after introduction of rotavirus vaccines in Brazil and elsewhere.

Molecular Epidemiology and Clinical Features of Rotavirus Infection Among Pediatric Patients in East Java, Indonesia During 2015-2018: Dynamic Changes in Rotavirus Genotypes From Equine-Like G3 to Typical Human G1/G3

Group A rotavirus (RVA) is the most important cause of severe gastroenteritis among children worldwide, and effective RVA vaccines have been introduced in many countries. Here we performed a molecular epidemiological analysis of RVA infection among pediatric patients in East Java, Indonesia, during 2015-2018. A total of 432 stool samples were collected from hospitalized pediatric patients with acute gastroenteritis. None of the patients in this cohort had been immunized with an RVA vaccine. The overall prevalence of RVA infection was 31.7% (137/432), and RVA infection was significantly more prevalent in the 6- to 11-month age group than in the other age groups (P < 0.05). Multiplex reverse transcription-PCR (RT-PCR) revealed that the most common G-P combination was equine-like G3P[8] (70.8%), followed by equine-like G3P[6] (12.4%), human G1P[8] (8.8%), G3P[6] (1.5%), and G1P[6] (0.7%). Interestingly, the equine-like strains were exclusively detected until May 2017, but in July 2017 they were completely replaced by a typical human genotype (G1 and G3), suggesting that the dynamic changes in RVA genotypes from equine-like G3 to typical human G1/G3 in Indonesia can occur even in the country with low RVA vaccine coverage rate. The mechanism of the dynamic changes in RVA genotypes needs to be explored. Infants and children with RVA-associated gastroenteritis presented more frequently with some dehydration, vomiting, and watery diarrhea, indicating a greater severity of RVA infection compared to those with non-RVA gastroenteritis. In conclusion, a dynamic change was found in the RVA genotype from equine-like G3 to a typical human genotype. Since severe cases of RVA infection were prevalent, especially in children aged 6 to 11 months or more generally in those less than 2 years old, RVA vaccination should be included in Indonesia's national immunization program.