Genotype G1P Research Articles

Emergence of non-classical genotype constellations of G9P[8] rotavirus strains in diarrheic children in Sabah, Malaysia

G9P[8] has been the predominant rotavirus A (RVA) genotype in Malaysia since the 2000s. However, the overall genetic makeup and evolution of Malaysian G9P[8] strains are still unknown. Therefore, this study aimed to evaluate and characterize the complete genomes of three G9P[8] RVA strains isolated from diarrheic children under five years old in Sabah. Contrary to the classical Wa-like constellation, these strains contained a DS-1-like genotype. Two strains, namely L202 and L234, were genotype G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1, while one (KN102) was genotype G9-P[8]-I1-R1-C1-M1-A2-N1-T1-E1-H1. Phylogenetic analysis revealed that the NSP4 genes of L202 and L234 strains were closer to that of G9P[8]-E2 strains from Japan, suggesting they might share a common ancestor. The findings from this study provide new insights into the genetic characteristics of circulating G9P[8] strains in Sabah, which are important for rotavirus surveillance and potential vaccine development in the region.

Unusual BA222-like strains of Rotavirus A (Sedoreoviridae: Rotavirus: Rotavirus A): molecular and genetic analysis based on all genome segments.

Rotavirus infection is the major cause of severe dehydrating diarrhea requiring hospitalization in young children worldwide. Due to their segmented genome, rotaviruses are capable of gene reassortment, which makes the emergence and spread of genetically novel strains possible. The purpose of this study was to search for unusual rotaviruses circulating in Nizhny Novgorod in 2021‒2023 and their molecular genetic characterization based on all genome segments. Rotavirus-positive stool samples of children were examined by PCR genotyping and electrophoresis in PAAG. cDNA fragments of each of the 11 genes (VP1‒VP4, VP6, VP7, NSP1‒NSP5), 570 to 850 nucleotide pairs in length were sequenced for the selected strains. The phylogenetic analysis was performed in the MEGA X program. In the study period 2021‒2023, 11 G[P] combinations with a predominance of G3P[8] (59.5%) were identified. Six atypical Rotavirus А (RVA) strains were identified: 2 strains of the G2P[4] genotype (G2-P[4]-I2-R2-C2-M2-A3-N2-T3-E2-H3, G2-P[4]-I2-R2-C2-M2-A3-N2-T3-E3-H2) and 4 G3P[9] strains (all strains had the genotype G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3). Phylogenetic analysis based on all genes showed an evolutionary relationship between rotaviruses similar to rotaviruses of cats and dogs (BA222-like) and unusual strains of the G2P[4] genotype, for which a mixed combination of genotypes was identified and characterized for the first time. The results obtained expand the understanding of the diversity of reassortant RVAs, as well as complement the data on the genotypic structure of the rotavirus population in Nizhny Novgorod. The wide genetic diversity of reassortant RVA can help rotaviruses overcome the immunological pressure provided by natural and vaccine-induced immunity. In this regard, to control the emergence of new variants and assess changes in the virulence of rotaviruses after reassortment processes, continuous molecular monitoring for circulating RVA is necessary.

Genetic and antigenic characterization of two diarrhoeicdominant rotavirus A genotypes G3P[12] and G14P[12] circulating in the global equine population.

Equine rotavirus species A (ERVA) G3P[12] and G14P[12] are two dominant genotypes that cause foal diarrhoea with a significant economic impact on the global equine industry. ERVA can also serve as a source of novel (equine-like) rotavirus species A (RVA) reassortants with zoonotic potential as those identified previously in 2013-2019 when equine G3-like RVA was responsible for worldwide outbreaks of severe gastroenteritis and hospitalizations in children. One hurdle to ERVA research is that the standard cell culture system optimized for human rotavirus replication is not efficient for isolating ERVA. Here, using an engineered cell line defective in antiviral innate immunity, we showed that both equine G3P[12] and G14P[12] strains can be rapidly isolated from diarrhoeic foals. The genome sequence analysis revealed that both G3P[12] and G14P[12] strains share the identical genotypic constellation except for VP7 and VP6 segments in which G3P[12] possessed VP7 of genotype G3 and VP6 of genotype I6 and G14P[12] had the combination of VP7 of genotype G14 and VP6 of genotype I2. Further characterization demonstrated that two ERVA genotypes have a limited cross-neutralization. The lack of an in vitro broad cross-protection between both genotypes supported the increased recent diarrhoea outbreaks due to equine G14P[12] in foals born to dams immunized with the inactivated monovalent equine G3P[12] vaccine. Finally, using the structural modelling approach, we provided the genetic basis of the antigenic divergence between ERVA G3P[12] and G14P[12] strains. The results of this study will provide a framework for further investigation of infection biology, pathogenesis and cross-protection of equine rotaviruses.

Genetic characterization and evidence for multiple reassortments of rotavirus A G3P[3] in dogs and cats in Thailand

Rotavirus A (RVA) causes gastroenteritis in humans and animals. The zoonotic potential of RVA has been reported and raises major concerns, especially in animal-human interface settings. The study aimed to characterize and investigate the genetic diversity among RVAs in dogs and cats in Thailand. We collected 572 rectal swab samples from dogs and cats in Bangkok animal hospitals from January 2020 to June 2021. The one-step RT-PCR assay detected RVAs in 1.92% (11/572) of the samples, with 2.75% (8/290) in dogs and 1.06% (3/282) in cats. Two canine RVA and one feline RVA were subjected to whole genome sequencing. Our results showed that all three viruses were identified as RVA genotype G3P[3]. The genetic constellation of RVAs is unique for different species. For canine RVAs is G3-P [3]-I3-R3-C3-M3-A9-N2-T3-E3-H6, while Feline RVA is G3-P [3]-I8-R3-C3-M3-A9-N3-T3-E3-H6. Notably, both canine and feline RVAs contained the AU-1 genetic constellation with multiple reassortments. The results of phylogenetic, genetic, and bootscan analyses showed that canine RVAs may have reassorted from dog, human, and cat RVAs. While feline RVA was closely related to RVAs in humans, bats, and simians. This study provided genetic characteristics and diversity of RVAs in dogs and cats and suggested possible multiple reassortments, suggesting the zoonotic potential of the viruses. Thus, public health awareness should be raised regarding the zoonotic potential of RVAs in dogs and cats. Further studies on RVAs on a larger scale in dogs and cats in Thailand are needed.

Phylodynamic characteristics of reassortant DS-1-like G3P[8]-strains of rotavirus type A isolated in Nizhny Novgorod (Russia).

Since 2013, there has been an increase in reports of the spread of a double intergroup reassortant strain of rotavirus type A (RVA) with the genotype G3P[8] and other genes belonging to the second genogroup I2-R2-C2-M2-A2-N2-T2-E2-H2. In our study, we provide a molecular genetic characterization of rotaviruses with genotype G3P[8]-I2 isolated in Nizhny Novgorod. In our study, we used RT-PCR, Sanger sequencing, RNA-PAGE methods. Phylogenetic and phylodynamic analysis were performed using the Bayesian approach. According to our study, there was a significant increase in the proportion of G3P[8] from 15% during the period of 2020-2021 to 53% during the period of 2021-2022 in Nizhny Novgorod, Russia. Phylogenetic analysis based on the VP4 gene revealed that DS-1-like RVAs isolated in Nizhny Novgorod belong to different clusters of the P[8]-3.1 lineage, with a level of variation ranging from 1.1% to 1.3%. Based on the VP6 gene, the equine-like RVAs identified by us carry genetic variants belonging to three distinct clusters of the lineage I2-V, with a variation level ranging from 2.0% to 4.5%. These data indicate the genotypic diversity of circulating DS-1-like G3 RVAs. Phylogenetic analysis of the VP7 gene allowed us to assign the isolates identified in our study to the G3-1 lineage. We estimated that the circulation of the most recent common ancestor of the spreading strains dates back to 2002. Additionally, we determined the typical level of mutations in the VP7 gene, which amounted to 2.14*10-3 substitutions/per site/per year.

Gastroenteritis Outbreak of Rotavirus G3P[8] in a Secondary School in Pathum Thani Province, Thailand, 2022

On 14 Sep 2022, the Division of Epidemiology was notified of a cluster of food poisoning in a secondary school. We conducted an investigation to describe the epidemiological characteristics of the outbreak, identify the causative agent, source of illness, and possible risks, and provide control measures. An electronic-based questionnaire was distributed to school members. Students and staff were interviewed. Inspection of the school canteen, water supply system, toilets, and hand-washing facilities as well as observation of personal and food hygiene practices among food handlers were done. A retrospective cohort study was conducted. The overall attack rate was 40.4% (684/1,695). Most cases were students (95.9%). Thirteen out of twenty-eight rectal swabs were positive for rotavirus, with two being identified as genotype G3P[8]. Being exposed to foods or drinks from the school canteen was a significant risk factor (adjusted odds ratio (AOR) 2.35, 95% CI 1.23–4.52), and bringing a drink to school was protective (AOR 0.67, 95% CI 0.50–0.88). Although rotavirus was not detected in the environment, contamination of groundwater used for cooking and drinking was evident. We recommend routine water quality testing and installation of groundwater treatment to ensure the safety of the water supply.

Increase in rotavirus prevalence with the emergence of genotype G9P[8] in replacement of genotype G12P[6] in Sabah, Malaysia.

Rotaviruses are major causative agents of acute diarrhea in children under 5 years of age in Malaysia. However, a rotavirus vaccine has not been included in the national vaccination program. To date, only two studies have been carried out in the state of Sabah, Malaysia, although children in this state are at risk of diarrheal diseases. Previous studies showed that 16%-17% of cases of diarrhea were caused by rotaviruses and that equine-like G3 rotavirus strains are predominant. Because the prevalence of rotaviruses and their genotype distribution vary over time, this study was conducted at four government healthcare facilities from September 2019 through February 2020. Our study revealed that the proportion of rotavirus diarrhea increased significantly to 37.2% (51/137) after the emergence of the G9P[8] genotype in replacement of the G12P[8] genotype. Although equine-like G3P[8] strains remain the predominant rotaviruses circulating among children, the Sabahan G9P[8] strain belonged to lineage VI and was phylogenetically related to strains from other countries. A comparison of the Sabahan G9 strains with the G9 vaccine strains used in the RotaSiil and Rotavac vaccines revealed several mismatches in neutralizing epitopes, indicating that these vaccines might not be effective in Sabahan children. However, a vaccine trial may be necessary to understand the precise effects of vaccination.

An Intermittent Gastroenteritis Outbreak of Rotavirus Genotype G9P[8] in a Hotel in Songkhla Province, Thailand, April–May 2019

A series of acute gastroenteritis outbreaks occurred among participants of two seminars at a hotel in Songkhla Province during 26–29 Apr 2019 and 8–10 May 2019. Investigations were done to determine the causes of the outbreaks and recommend control measures. A case was defined as a participant who developed diarrhea, vomiting, nausea or abdominal pain between 26–30 April (Seminar 1) or 8–13 May (Seminar 2). Samples of the drinking and cooking water used during the seminars were taken and rectal swabs from cases and food handlers were collected for bacterial culture and viral reverse transcription polymerase chain reaction tests. A retrospective cohort study was conducted to identify risk factors. Of 349 participants interviewed, 237 were cases, giving an attack rate of 67.9%. The ages of the cases ranged from 11–57 years (median 15 years). The most common symptoms were watery diarrhea (94.1%), abdominal pain (81.0%) and nausea (57.8%). Rotavirus was detected in five cases, three food handlers and a sample of water used for cooking. All were of the same genotype G9P[8]. Implicated dishes included spicy seafood salad (adjusted odds ratio (AOR) 4.5, 95% confidence interval (CI) 1.7–11.8), shrimp in sauce (AOR 2.9, 95% CI 1.0-8.2), roast duck with vegetables (AOR 2.9, 95% CI 1.2–7.3) and water from a cooler (AOR 2.0, 95% CI 1.0–3.9). Contaminated water and infected food handlers were probable sources of cross-contamination. After the hotel’s water system was repaired and the food handlers were educated on safe food handling practices and good personal hygiene, no other outbreaks associated with the hotel were reported.

Rotaviruses in Wild Ungulates from Germany, 2019–2022

Rotavirus A (RVA) is an important cause of diarrhea in humans and animals. However, RVA in wild animals has only scarcely been investigated so far. Here, the presence of RVA in wild ungulates hunted between 2019 and 2022 in Brandenburg, Germany, was investigated using real-time RT-PCR and sequencing of RT-PCR products. By analyzing intestinal contents, RVA-RNA was detected in 1.0% (2/197) of wild boar (Sus scrofa), 1.3% (2/152) of roe deer (Capreolus capreolus), and 2.1% (2/95) of fallow deer (Dama dama) but not in 28 red deer (Cervus elaphus) samples. Genotyping identified G3P[13] strains in wild boar, which were closely related to previously described pig and wild boar strains. Genotype G10P[15] strains, closely related to strains from roe deer, sheep, or cattle, were found in roe deer. The strains of fallow deer represented genotype G3P[3], clustering in a group containing different strains from several hosts. The results indicated a low prevalence of RVA in wild ungulates in Germany. Associations of specific genotypes with certain ungulate species seem to exist but should be confirmed by analyses of more samples in the future.

Variability of genes encoding nonstructural proteins of rotavirus А (Reoviridae: Rotavirus: Rotavirus A) genotype G9P[8] during the period of dominance in the territory of Nizhny Novgorod (central part of Russia) (2011-2020)

In Russia, rotavirus A is the main cause of severe viral gastroenteritis in young children. The molecular features that allow a rotavirus of a particular genotype to gain an evolutionary advantage remain unclear, therefore, the study of the genetic diversity of rotaviruses based on genes encoding nonstructural proteins (NSPs) responsible for the reproduction of the virus in the cell is an urgent task. To study the genetic diversity of rotaviruses of genotype G9P[8], which dominated Nizhny Novgorod in 20112020, based on genes encoding nonstructural proteins. Rotavirus-positive samples were subjected to PCR-genotyping and sequencing of NSP1 NSP5 genes. Phylogenetic analysis was carried out in the MEGA X program. In the period 20112020, G9P[8] rotaviruses with four variants of the NSP2 gene were co-circulating in Nizhny Novgorod. New alleles were noted in 2012 (N1-a-III), 2016 (N1-a-IV) and in 2019 (N1-a-II). The appearance of new variants of other genes occurred in 2014 (E1-3, NSP4), 2018 (T1-a3-III, NSP3) and in 2019 (A1-b-II, NSP1). NSP2 gene had the most variable amino acid sequence (16 substitutions), 2 to 7 substitutions were observed in NSP1, NSP3 and NSP4, NSP5 was conservative. The results obtained are consistent with the literature data and indicate the participation of NSP genes in maintaining the heterogeneity of the rotavirus population. Until 2018, the genetic diversity of rotaviruses in Nizhny Novgorod was determined by the circulation of strains carrying several alleles of the NSP2 gene and conservative genes NSP1, NSP3NSP5. By the end of the study period, new variants of the genotype G9P[8] were formed in the population, carrying previously unknown combinations of alleles of nonstructural genes.

1218. Genotypic Investigation of a Rotavirus Cluster at a Pediatric Hospital in 2022

Abstract Background Rotavirus group A (RVA) was the most common cause of infectious gastroenteritis among young children before introduction of rotavirus vaccine in the United States in 2006. Following widespread vaccination, U.S. hospital acquired (HA) rotavirus cases are rare. We describe a cluster of rotavirus infections in a pediatric hospital with a genotype uncommon among U.S. children. Methods Patient cases of HA gastrointestinal (GI) illness were detected through hospital-wide microbiology surveillance, performed by Infection Prevention and Control (IPC) practitioners per state requirements. Cluster procedures were implemented on a unit when 3 cases were identified by symptoms and/or laboratory tests within 48 hours. Due to the current rarity of rotavirus clusters, the hospital partnered with Centers for Disease Control and Prevention (CDC) laboratories to sequence strains in addition to instituting local control measures. RVA strains were genotyped by using the genotype specific qRT-PCR assays for VP7 and VP4 genes. Next Generation Sequencing (NGS) was performed for RVA strain characterization on Illumina MiSeq. Genotypes for all 10 RVA were determined by NCBI’s BLASTN program. Results Epidemiologic surveillance identified a rotavirus cluster of 10 patients aged 10 months to 10 years old, of whom 50% had received rotavirus vaccine. Symptoms included emesis and diarrhea. Cases could not be attributed to vaccine related shedding. All patients had epidemiologic links by contiguous bed spaces or shared care teams. Sequencing was conclusive for 9 of the 10 stool samples to be a G9P[4] genotype, which is rarely detected amongst U.S. children. Local control measures of increased education and cleaning, isolation of positive patients in single rooms, use of soap and water instead of alcohol-based hand sanitizer on room exit, and furlough of symptomatic healthcare workers halted transmission. Conclusion Routine surveillance of HA GI illness identified a cluster; RVA strain genotyping and characterization identified unusual rotavirus genotype G9P[4] as the cause. Partnership between IPC practitioners and laboratorians with CDC demonstrated the need to enhance infection prevention measures to halt transmission and identified a rare rotavirus strain as the likely cause of the cluster. Disclosures Courtney E. Comar, PhD, Pfizer: Stocks/Bonds|Viatris: Stocks/Bonds.

Viral Gastroenteritis Prevalence in Iranian Pediatric Population: A Systematic Review

Background: Viral gastroenteritis infection, a prevalent condition in adolescents and children, is still a rigid and serious problem among humans. This disease is responsible for up to three million fatalities nationwide. noroviruses, rotaviruses, astroviruses, adenoviruses, and sapoviruses are the most common and well-known pathogens associated with viral gastroenteritis agents. In this systematic review, we extracted all original articles and data on viral gastroenteritis that were performed on the Iranian pediatric population. Methods: To investigate the viral agent pathogens of gastroenteritis in Iran, 48 articles on the identification of viral gastroenteritis were gathered from the existing data. Viral gastroenteritis was detected in fourteen provinces, including the southern and northern parts of Iran. The seasonal distribution in Iran was analyzed as well. Finally, all the data from 1978-2021, along with their detailed information, were summarized, including the number of patients, the number of positive cases, applied technics, and the region of the studied cases in Iran. Results: Based on the results, most of the viral detection was associated with Rotavirus, the major pathogen responsible for gastroenteritis disease, followed by Adenovirus, Norovirus, Parechovirus, Bocavirus, Astrovirus, Aichivirus, Sapovirus, and three case reports of SARS-CoV-2 that were associated with viral gastroenteritis. Conclusion: Different studies conducted over Iran, including the northern, southern, and central regions, were obtained based on the data. Most studies had been merely dedicated to rotavirus, which had the highest prevalence of all other viral gastroenteritis. Our review clearly demonstrated that Rotavirus genotype G1P [8] is the dominating sereotype among the other studied gastroenteritis viral agents in Iran in which the most frequency rate was during the winter (44.26%), while the least frequency rate was observed during summer (8.96%).

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

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

Genome Sequence of a Wa-Like G3P[8] Rotavirus from a 12-Month-Old Child with Diarrhea in Manipur, India.

ABSTRACTRotavirus A (RVA) was detected in the stool of a 12-month-old child with diarrhea, mild fever, and vomiting. A viral metagenomic approach identified a Wa-like genotype G3P[8] strain named RVA/Human-wt/IND/RM25112/2016.

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

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

Лонгітудинальне спостереження за ротавірусною інфекцією у дітей віком до 5 років, яких госпіталізували в два центри України в 2006–2015 роках

Актуальність. В Україні щорічно реєструється більше 50 тисяч захворювань на гостру кишкову інфекцію (ГКІ) у дітей. Статистичні дані щодо ротавірусної інфекції не відповідають дійсності через низьку можливість лабораторної діагностики в лікувальних закладах. Мета дослідження: визначити рівень навантаження ротавірусної інфекції, провести аналіз і дати характеристику ротавірусної інфекції дітей віком до 5 років, яких госпіталізували в два інфекційні стаціонари (Київ, Одеса), за період спостереження 2006–2015 роки. Матеріал та методи. Дослідження проводилося за стандартним протоколом, затвердженим Всесвітньою організацією охорони здоров’я. Визначення тяжкості перебігу захворювання проводилося за допомогою бальної шкали оцінки тяжкості клінічних проявів ротавірусного гастроентериту Vesikari. Результати. За період з грудня 2006 по грудень 2015 року було взято під спостереження 20 932 дитини віком до 5 років, яких госпіталізували в інфекційні відділення м. Києва і м. Одеси з діагнозом «гострий гастроентерит/гостра кишкова інфекція» і які відповідали критеріям включення в дослідження. Обстежено на ротавірус 18 384 (87,33 %) дитини віком до 5 років, тобто переважна більшість дітей, які надходили в стаціонар з ГКІ. Протягом усіх років спостереження причиною майже половини госпіталізацій дітей до 5-річного віку була ротавірусна інфекція. Звернуло на себе увагу, що в окремі роки в Києві частота госпіталізацій через ротавірусну інфекцію збільшувалася, навіть до 70 %. В Україні серед 6 країн Європейського регіону, що входять до глобальної мережі епіднагляду за ротавірусною інфекцією (Global Rotavirus Surveillance Network), спостерігалася найвища частота ротавірусної діареї серед госпіталізованих дітей до 5 років. При середній частоті в регіоні 24 % в Україні вона досягала 41 %. У всі роки спостереження половина випадків ротавірусної інфекції, що була причиною госпіталізації, припадала на перші 2 роки життя. У всі роки в обох центрах визначалися переважно 4 генотипи ротавірусів: G1P[8], G2P[4], G3P[8], G4P[8]. Генотип G9P[8] займав досить значні позиції в Києві, але були роки, коли він зовсім не визначався як в Києві, так і в Одесі. Цей генотип ротавірусу описано в складі типових комбінацій G та Р ротавірусів, що уражають людину у близько 90 % усіх випадків ротавірусної інфекції на багатьох територіях земної кулі. Відмічалася зміна лідерства окремих генотипів описаних вище ротавірусів за роками. При ротавірусній інфекції вірогідно більшою є частота епізодів діареї та блювання, тривалість блювання у днях також є довшою, ніж при ротанегативних ГКІ. Явища дегідратації також були тяжчими у групі ротавіруспозитивних дітей. Висновки. Ротавірусна інфекція впродовж 10 років спостереження в Україні незмінно залишалася основною причиною госпіталізації дітей віком до 5 років з ГКІ. ГКІ ротавірусної етіології характеризуються значно більш тяжкими проявами, ніж ГКІ, при яких ротавірус було виключено. Суттєвих змін у генотипах за цей період не було, лише періодично спостерігалася зміна домінуючого штаму. Отримані дані обґрунтовують введення універсальної вакцинації проти ротавірусної інфекції в Україні.

Detection of a novel species A, DS-1-like, G4P[6] rotavirus strain from a Brazilian child with gastroenteritis.

Rotaviruses belonging to species A (RVA) remain among the most common causes of severe gastroenteritis in children aged <5 years, leading to substantial morbidity and mortality worldwide. Genome reassortment events between two human strains or human and animal strains represent one of the mechanisms which appear to generate the broad genetic variability of circulating. According to a nucleotide, sequence-based classification system, RVA strains are currently classified into three genotype constellations includingWa-like (genogroup I), DS-1-like (genogroup II), and AU-like (genogroup III). The present study reports the detection of an unusual RVA G4P[6] strain (coded as strain HSE005),which might have originated from a natural reassortment event between human and animal RVA strains. Molecular characterization of this isolate showed that it belonged to genogroup II, genotype G4P[6]. In addition, two genes (VP3 and NSP4) of this strain denoted evidence of reassortment events involving strains of distinct zoonotic evolutionary origins. Therefore, we propose that a new G4P[6] strain was identified, highlighting a possible first zoonotic transmission including a reassortment event that involved the VP3 gene.

Molecular monitoring of the rotavirus (Reoviridae: Sedoreovirinae: Rotavirus: Rotavirus A) strains circulating in Nizhny Novgorod (2012-2020): detection of the strains with the new genetic features

The pentavalent rotavirus vaccine has been registered in Russia, however, the vaccination coverage remains low, and an annual increase in the incidence of rotavirus infection is unavoidable. In this regard, molecular monitoring of rotaviruses in order to search for new variants possessing epidemic potential is an urgent task. PCR genotyping and VP4 and VP7 genes sequencing were used to characterize rotaviruses circulating in Nizhny Novgorod in 2012-2020. The phylogenetic analysis of the strains was carried out using the BEAST software package. The spectrum included 17 genotypes with predominance of G9P[8] (37,4%). Detected in this study genotypes G1P[4], G1P[9], G2P[8], G4P[4], G4P[6], G8P[8], and G9P[4] were not previously identified in Nizhny Novgorod. The circulation of DS-1-like strains possessing genotypes G1P[8], G3P[8], G8P[8], or G9P[8] and a short RNA pattern had been shown. Rotaviruses of the common genotypes were genetically heterogeneous and belonged to different phylogenetic lineages and/or sublineages (P[4]-IV-a; P[4]-IV-b; P[8]-3.1; P[8]-3.3; P[8]-3.4 and P[8]-3.6; G1-I; G1-II; G2-IVa-1; G2-IVa-3; G3-1; G3-3; G4-I-c; G9-III; G9-VI). These results extend the available data on the genotypic structure of rotavirus populations in Russia and show the genetic diversity of viral strains. G3P[8] DS-1-like viruses were representatives of the G3-1 lineage, new for the territory of Russia, and had the largest number of amino acid substitutions in the VP7 antigenic epitopes. The emergence and spread of strains with new genetic features may allow rotavirus to overcome the immunological pressure formed by natural and vaccine-induced immunity, and maintain or increase the incidence of rotavirus infection.

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

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

Epidemiological, molecular, and clinical features of rotavirus infections among pediatrics in Qatar.

Acute gastroenteritis (AGE) remains a major cause of diarrhea in developing and developed countries. Rotavirus (RV) is a leading cause of severe pediatric diarrhea worldwide. Here we report on the prevalence of circulating genotypes in association with demographics and clinical manifestations outcomes in Qatar. A total of 231 RV-positive fecal samples were collected from children suffering from AGE during 3years study period between June 2016 and June 2019. The age of the subjects ranged between 2months and 14years (median of 16months). The VP4 and VP7 were amplified and sequenced. Phylogenetic analyses were performed using MEGA7.0. Pearson's chi-squared test was used to determine significant differences for comparisons of general categorical variables. RV infections were most common in children between 1 and 3years of age (49%), followed by those < 1year and > 3years of age (33% and 28%, respectively). RV infections were more frequent in males than females, with a ratio of 1.4:1. RV infections occurred throughout the year, with a noticeable increase in summer (42.8%) and a drop in winter (20.1%). RV genotypes G3P[8] (30.8%), G2P[8] (12.3%), G4P[8] (11.7%), and G1P[8] (10.4%) were the common genotypes during the study period. The G3P[8] strain detected in our study revealed similarities to the equine-like G3P[8] (10.3%; 24/231) (KT988229.1), Wa-like genomic constellation (9%; 21/231) (MF563894.1), and DS-1-like strains (6.4%; 15/231) (LC386081.1). Based on the Vesikari score system, severe clinical illness including diarrhea and vomiting (average frequency: 4 to 5 times/day) was recorded for G3P[8] group, followed by G9P[8], G4P[8], and G1P[8]. Higher incidence for G3P[8], G2P[8], G4P[8], and G1P[8] were reported in Qatari subjects compared to other nationalities. The multinational status of a small country explains the wide diversity of circulating RV genotypes in Qatar. The highest prevalence and severe illnesses were recorded to G3P[8], which is different from other surrounding countries/global levels.