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

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

Paediatric viral gastroenteritis and regional predominant viral pathogens in the post-rotavirus vaccination year: prospective Irish regional study

Acute gastroenteritis harbours a significant global burden. Rotavirus is the primary cause of gastroenteritis in children worldwide. We aim to determine the predominant enteric viral pathogens detected in the post-rotavirus vaccine period (2016-2017) in our region in county Mayo (west of Ireland), United Kingdom. All children up to 3 years old, who presented to Mayo University Hospital with vomiting and diarrhoea, from November 18th, 2016, to November 18th, 2017, had their stools tested by real-time reverse transcription polymerase chain reaction for viral pathogens. A total of 150 stool samples were tested, and 90 (60%) tested positive for a single viral pathogen. Rotavirus was the leading cause of gastroenteritis (37 patients, 24.6%; including 6 rotavirus vaccinated infants), followed by human adenovirus F (19 patients, 13%), norovirus (18 patients, 12%), sapovirus (9 patients, 6%) and astrovirus (7 patients, 5%). Rotavirus remained the predominant cause of gastroenteritis in the first year post-rotavirus vaccination, similar to the national Irish data from the pre vaccination years (July 2014-June 2015).

Molecular Epidemiology of Rotavirus A Strains Pre- and Post-Vaccine (Rotarix®) Introduction in Mozambique, 2012-2019: Emergence of Genotypes G3P[4] and G3P[8]

Group A rotavirus (RVA) remains the most important etiological agent associated with severe acute diarrhea in children. Rotarix^® monovalent vaccine was introduced into Mozambique’s Expanded Program on Immunization in September 2015. In the present study, we report the diversity and prevalence of rotavirus genotypes, pre- (2012–2015) and post-vaccine (2016–2019) introduction in Mozambique, among diarrheic children less than five years of age. Genotyping data were analyzed for five sentinel sites for the periods indicated. The primary sentinel site, Mavalane General Hospital (HGM), was analyzed for the period 2012–2019, and for all five sites (country-wide analyses), 2015–2019. During the pre-vaccine period, G9P[8] was the most predominant genotype for both HGM (28.5%) and the country-wide analysis (46.0%). However, in the post-vaccine period, G9P[8] was significantly reduced. Instead, G3P[8] was the most common genotype at HGM, while G1P[8] predominated country-wide. Genotypes G9P[4] and G9P[6] were detected for the first time, and the emergence of G3P[8] and G3P[4] genotypes were observed during the post-vaccine period. The distribution and prevalence of rotavirus genotypes were distinct in pre- and post-vaccination periods, while uncommon genotypes were also detected in the post-vaccine period. These observations support the need for continued country-wide surveillance to monitor changes in strain diversity, due to possible vaccine pressure, and consequently, the effect on vaccine effectiveness.

Group A Rotavirus Detection and Genotype Distribution before and after Introduction of a National Immunisation Programme in Ireland: 2015-2019

Immunisation against rotavirus infection was introduced into Ireland in December 2016. We report on the viruses causing gastroenteritis before (2015–2016) and after (2017–2019) implementation of the Rotarix vaccine, as well as changes in the diversity of circulating rotavirus genotypes. Samples from patients aged ≤ 5 years (n = 11,800) were received at the National Virus Reference Laboratory, Dublin, and tested by real-time RT-PCR for rotavirus, Rotarix, norovirus, sapovirus, astrovirus, and enteric adenovirus. Rotavirus genotyping was performed either by multiplex or hemi-nested RT-PCR, and a subset was characterised by sequence analysis. Rotavirus detection decreased by 91% in children aged 0–12 months between 2015/16 and 2018/19. Rotarix was detected in 10% of those eligible for the vaccine and was not found in those aged >7 months. Rotavirus typically peaks in March–May, but following vaccination, the seasonality became less defined. In 2015–16, G1P[8] was the most common genotype circulating; however, in 2019 G2P[4] was detected more often. Following the introduction of Rotarix, a reduction in numbers of rotavirus infections occurred, coinciding with an increase in genotype diversity, along with the first recorded detection of an equine-like G3 strain in Ireland.

Rotavirus contamination of surface waters from the northwest of Argentina

Fecal pollution of water is a serious concern because it is associated with the transmission of pathogens. The aim of this study was to analyze the occurrence of group A rotavirus (RVA) in surface waters from the Arias-Arenales River in Salta, a northern city in Argentina, and to define possible sources of fecal viral pollution. A total of 116 water samples were analyzed and RVA was detected in 3.4% (95% CI: 0.1-7.0%), with concentrations ranging from 1.9 × 10⁵ to 3.8 × 10⁶ genome copies per liter. RVA strains were characterized as G1P[8], G4P[8] and G9P[8], which are common genotypes circulating in the local population. The Arias-Arenales River presented unusual and sporadic contamination by RVA, originated from stormwater discharges and a variety of non-identified sources, and support the essential need of viral indicators for enhanced monitoring of water quality.

Molecular characterization of group A rotavirus among children aged under 5 years in Tunisia, 2015-2017

The aim of the present study was to report the molecular characterization of human group A rotaviruses (RVAs) circulating in Tunisia. Stool specimens were collected from children under 5 years of age who had been hospitalized or were consulting for gastroenteritis in Tunisian hospitals between 2015 and 2017. All samples were screened by reverse-transcription polymerase chain reaction (RT-PCR) for the detection of the VP6 gene specific for RVA. RVA-positive samples were further analysed for G/P genotyping by semi-nested multiplex RT-PCR. Among 454 tested samples, 72 (15.8 %) were positive for RVA. G1P[8] was the most prevalent detected strain (41.7%), followed by G9P[8] (32.8%), G2P[4] (7.5%), G12P[8] (7.5%), G1P[6] (3.0%), G2P[8] (1.5%) and G3P[8] (1.5%), with mixed infections in 4.5 % of cases. In the absence of a national anti-rotavirus vaccination strategy, RVAs remain the primary aetiological agent for gastroenteritis in Tunisian children.

Study of Complete Genome Sequences of Rotavirus A Epidemics and Evolution in Japan in 2012-2014

A comprehensive molecular epidemiological study using next-generation sequencing technology was conducted on 333 rotavirus A (RVA)-positive specimens collected from six sentinel hospitals across Japan over three consecutive seasons (2012–2014). The majority of the RVA isolates were grouped into five genotype constellations: Wa-like G1P[8], DS-1-like G1P[8], G2P[4], G3P[8] and G9P[8]. Phylogenetic analysis showed that the distribution of strains varied by geographical locations and epidemic seasons. The VP7 genes of different G types were estimated to evolve at 7.26 × 10^-4–1.04 × 10^-3 nucleotide substitutions per site per year. The Bayesian time-scaled tree of VP7 showed that the time to the most recent common ancestor of epidemic strains within a region was 1–3 years, whereas that of the epidemic strains across the country was 2–6 years. This study provided, for the first time, the timeframe during which an epidemic strain spread locally and within the country and baseline information needed to predict how rapidly RVAs spread.

Viruses Associated With Foodborne Infections

Foodborne pathogens cause acute and chronic health outcomes of very different durations, severity and mortality, resulting in high costs and burdens to society. The issues of food safety and food poisoning are being increasingly emphasised, particularly in developed countries. Infection/contamination with many agents i.e., bacterial, parasitic and viral entities can result in foodborne illness. This article will focus mainly on viral agents of infection.

A range of different viruses can cause food poisoning/foodborne infection, and infection can result in a myriad of symptoms, ranging from mild, acute disease to chronic, debilitating disease and even death. Due to the inherent differences between bacteria and viruses, namely the fact that viruses do not replicate in food, while bacteria do, viruses are frequently difficult to detect. This is compounded by the fact that many of the viruses associated with enteric disease do not replicate in cell culture. These factors can lead to a lag between reporting, detection and analysis of foodborne viruses versus bacterial agents. Despite these constraints, it is now evident that there are both well-established and emerging viruses implicated in foodborne infections, and the role of molecular detection and characterisation is becoming increasingly important.

A Multiplex PCR/LDR Assay for Viral Agents of Diarrhea with the Capacity to Genotype Rotavirus

Rotavirus and noroviruses are major causes of diarrhea. Variable rotavirus vaccination efficacy in Africa and Asia is multifactorial, including the diversity of circulating strains and viral co-infection. We describe a multiplexed assay that detects and genotypes viruses from stool specimens. It includes a one-step reverse transcriptase PCR reaction, a ligase detection reaction (LDR), then hybridization of fluorescent products to micro-beads. In clinical samples it detects rotavirus, caliciviruses (sapovirus and norovirus), mixed infections, and genotypes or genogroups of rotaviruses and noroviruses, respectively. The assay also has the capacity to detect hepatitis A. The assay was validated on reference isolates and 296 stool specimens from the US and Ghana. The assay was 97% sensitive and 100% specific. The genogroup was concordant in 100% of norovirus, and the genotype in 91% and 89% of rotavirus G- and P-types, respectively. Two rare rotavirus strains, G6P[6] and G6P[8], were detected in stool specimens from Ghana. The high-throughput assay is sensitive, specific, and may be of utility in the epidemiological surveillance for rare and emerging viral strains post-rotavirus vaccine implementation.

High genetic diversity of species A rotaviruses detected in swine farms in Chile

Rotavirus A is one of the main causative agents of diarrhoea in lactating and weaned pigs worldwide. Its impact in the swine industry is well documented. However, in Chile, the current epidemiological status of rotavirus on porcine farms is unknown. This study evaluated the current epidemiologic status of rotavirus A infection in Chile using on-farm detection techniques, electrophoretic confirmation, genotyping and phylogenetic clustering by analysis of partial sequences of VP4 and VP7 genes. Rotavirus A was detected in four out of five farms with an overall prevalence of 17.7 % in diarrhoeic pigs. The average age of diarrhoea onset was at 32±6.2 days, corresponding to weaning pigs, and rotavirus was not detected in lactating piglets. Molecular characterization indicated that genotypes G5, G3, P[7] and P[13] are currently the most widely represented on these pigs farms. The phylogenetic analysis showed that farms shared similar G types (VP7), which might denote a common origin. Meanwhile, [P] types (VP4) showed considerable genetic diversity, and this might represent a high rate of reassortment of this genetic segment in rotavirus circulating in the researched area. These findings demonstrate the importance of considering both the geographical and production factors to accurately determine rotavirus prevalence status at the national level, and have relevant implications in determining effective strategies for rotavirus infection control on porcine farms.

Molecular characterization of two rare human G8P[14] rotavirus strains, detected in Italy in 2012

Since 2007, the Italian Rotavirus Surveillance Program (RotaNet-Italy) has monitored the diversity and distribution of genotypes identified in children hospitalized with rotavirus acute gastroenteritis. We report the genomic characterization of two rare human G8P[14] rotavirus strains, identified in two children hospitalized with acute gastroenteritis in the southern Italian region of Apulia during rotavirus strain surveillance in 2012. Both strains showed a G8-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3 genomic constellation (DS-1-like genomic background). Phylogenetic analysis of each genome segment revealed a mixed configuration of genes of animal and zoonotic human origin, indicating that genetic reassortment events generated these unusual human strains. Eight out of 11 genes (VP1, VP2, VP3, VP6, VP7, NSP3, NSP4 and NSP5) of the Italian G8P[14] strains exhibited close identity with a Spanish sheep strain, whereas the remaining genes (VP4, NSP1 and NSP2) were more closely related to human strains. The amino acid sequences of the antigenic regions of outer capsid proteins VP4 and VP7 were compared with vaccine and field strains, showing high conservation between the amino acid sequences of Apulia G8P[14] strains and human and animal strains bearing G8 and/or P[14] proteins, and revealing many substitutions with respect to the RotaTeq™ and Rotarix™ vaccine strains. Conversely, the amino acid analysis of the four antigenic sites of VP6 revealed a high degree of conservation between the two Apulia strains and the human and animal strains analyzed. These results reinforce the potential role of interspecies transmission and reassortment in generating novel rotavirus strains that might not be fully contrasted by current vaccines.

Identification of G and P genotype-specific motifs in the predicted VP7 and VP4 amino acid sequences

Equine rotavirus (ERV) strain L338 (G13P[18]) has a unique G and P genotype. However, the evolutionary relationship of L338 with other ERVs is still unknown. Here whole genome analysis of the L338 ERV strain was independently performed. Its genotype constellations were determined as G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11, confirming previous genotype assignments. The L338 strain only shared the P[18] and I6 genotypes with other ERVs. The nucleotide sequences of the other 9 RNA segments were different from those of cogent genes of all other group A rotavirus (RVA) strains including ERVs and formed unique phylogenetic lineages. The L338 evolutionary footprints were tentatively identified in both VP7 and VP4 amino acid sequences: two regions were found in VP7 and twelve in VP4. The conserved regions shared between L338 and other group A rotavirus strains (RVAs) indicated that L338 was more closely related genomically to animal and human RVAs other than ERVs, suggesting that L338 may not be an endogenous equine RV but have emerged as an interspecies reassortant with other RVA strains. Furthermore, genotype-specific motifs of all 27 G and 37 P types were identified in regions 7-1a (aa 91-100) of VP7 and regions 8-1 (aa146-151) and 8-3 (aa113-118 and 125-135) of VP4 (VP8*).