An unusual outbreak of rotavirus G8P[8] gastroenteritis in adults in an urban community, Singapore, 2016

Rotavirus Sickness Symptoms: Manifestations of Defensive Responses from the Brain

Rotavirus is infamous for being extremely contagious and for causing diarrhea and vomiting in infants. However, the symptomology is far more complex than what could be expected from a pathogen restricted to the boundaries of the small intestines. Other rotavirus sickness symptoms like fever, fatigue, sleepiness, stress, and loss of appetite have been clinically established for decades but remain poorly studied. A growing body of evidence in recent years has strengthened the idea that the evolutionarily preserved defensive responses that cause rotavirus sickness symptoms are more than just passive consequences of illness and rather likely to be coordinated events from the central nervous system (CNS), with the aim of maximizing the survival of the individual as well as the collective group. In this review, we discuss both established and plausible mechanisms of different rotavirus sickness symptoms as a series of CNS responses coordinated from the brain. We also consider the protective and the harmful nature of these events and highlight the need for further and deeper studies on rotavirus etiology.

Driving forces of continuing evolution of rotaviruses

Rotaviruses are non-enveloped double-stranded RNA virus that causes acute diarrheal diseases in children (< 5 years). More than 90% of the global rotavirus infection in humans was caused by Rotavirus group A. Rotavirus infection has caused more than 200000 deaths annually and predominantly occurs in the low-income countries. Rotavirus evolution is indicated by the strain dynamics or the emergence of the unprecedented strain. The major factors that drive the rotavirus evolution include the genetic shift that is caused by the reassortment mechanism, either in the intra- or the inter-genogroup. However, other factors are also known to have an impact on rotavirus evolution. This review discusses the structure and types, epidemiology, and evolution of rotaviruses. This article also reviews other supplemental factors of rotavirus evolution, such as genetic reassortment, mutation rate, glycan specificity, vaccine introduction, the host immune responses, and antiviral drugs.

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.

Efficacy of washing produce in removing human coronavirus OC43 and murine norovirus

AIMS

Fresh produce is often a vehicle for the transmission of foodborne pathogens such as human norovirus. Thus, it is recommended to wash the surface of produce before consumption, and one of the most common ways to wash produce is by rinsing under running tap water. This study determined the effectiveness of removal of human coronavirus-OC43 (HCoV-OC43), as a surrogate for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and murine norovirus-1 (MNV-1), as a surrogate for human norovirus, from contaminated lettuce, apples and cucumbers.

METHODS AND RESULTS

The produce surfaces were artificially inoculated in conjunction with faecal material to represent natural contamination. Rinsing under tap water for 10 s at 40 ml/s removed 1.94 ± 0.44, 1.42 ± 0.00 and 1.42 ± 0.42 log of HCoV-OC43 from apple, cucumber and lettuce respectively. The same washing technique removed 1.77 ± 0.17, 1.42 ± 0.07 and 1.79 ± 0.14 log of MNV-1 from apple, cucumber and lettuce respectively. This washing technique was effective at reducing a significant amount of viral contamination, however, it was not enough to eliminate the entire contamination. There was no significant difference in the reduction of viral load between the two viruses, nor between the three surfaces tested in this study.

CONCLUSIONS

Our data suggest that washing under tap water would be an efficient way of reducing the risk of foodborne viral transmission only if the level of contamination is less than 2 log PFU.

SIGNIFICANCE AND IMPACT OF STUDY

This study demonstrates that running tap water was effective at reducing the amount of infectious HCoV-OC43 and MNV on produce surfaces, and washing produce continues to be an important task to perform prior to consumption to avoid infection by foodborne viruses, particularly for foods which are eaten raw.

Genetic characterization of two G8P[8] rotavirus strains isolated in Guangzhou, China, in 2020/21: evidence of genome reassortment

Background

The G8 rotavirus genotype has been detected frequently in children in many countries and even became the predominant strain in sub-Saharan African countries, while there are currently no reports from China. In this study we described the genetic characteristics and evolutionary relationship between rotavirus strains from Guangzhou in China and the epidemic rotavirus strains derived from GenBank, 2020–2021.

Methods

Virus isolation and subsequent next-generation sequencing were performed for confirmed G8P[8] specimens. The genetic characteristics and evolutionary relationship were analyzed in comparison with epidemic rotavirus sequences obtained from GenBank.

Results

The two Guangzhou G8 strains were DS-1-like with the closest genetic distance to strains circulating in Southeast Asia. The VP7 genes of the two strains were derived from a human, not an animal G8 rotavirus. Large genetic distances in several genes suggested that the Guangzhou strains may not have been transmitted directly from Southeast Asian countries, but have emerged following reassortment events.

Conclusions

We report the whole genome sequence information of G8P[8] rotaviruses recently detected in China; their clinical and epidemiological significance remains to be explored further.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07542-9.

The burden of rotavirus-associated acute gastroenteritis in the elderly: assessment of the epidemiology in the context of universal childhood vaccination programs

INTRODUCTION

Rotaviruses (RVs) cause acute gastroenteritis (AGE) in infants and young children worldwide and also in older adults (≥60 years), however the burden among this age group is not well understood. Herd immunity through pediatric RV vaccination may reduce the burden of RVGE across all ages, however the impact of pediatric vaccination on burden in older adults is poorly understood.

AREAS COVERED

This systematic review was undertaken to identify studies related to the following objectives: understand the burden of RV in older adults, RV seroprevalence, and the impact of pediatric vaccination on this burden and highlight evidence gaps to guide future research. Of studies identified, 59 studies from two databases were included in this analysis following a review by two reviewers.

EXPERT OPINION

RV is an understudied disease in older adults. We found that 0-62% of patients with AGE tested positive for RV, with results varying by setting, country, and patient age. Results also suggest that pediatric vaccination benefits older adults through herd protection. Several studies showed a reduction in RV incidence after vaccination. However, there was variety in results and lack of consistency in outcomes reported. Further studies targeting older adults are needed to better characterize RV burden.

Human Coronaviruses Do Not Transfer Efficiently between Surfaces in the Absence of Organic Materials

Human coronaviruses, including SARS-CoV-2, are known to spread mainly via close contact and respiratory droplets. However, other potential means of transmission may be present. Fomite-mediated transmission occurs when viruses are deposited onto a surface and then transfer to a subsequent individual. Surfaces can become contaminated directly from respiratory droplets or from a contaminated hand. Due to mask mandates in many countries around the world, the former is less likely. Hands can become contaminated if respiratory droplets are deposited on them (i.e., coughing or sneezing) or through contact with fecal material where human coronaviruses (HCoVs) can be shed. The focus of this paper is on whether human coronaviruses can transfer efficiently from contaminated hands to food or food contact surfaces. The surfaces chosen were: stainless steel, plastic, cucumber and apple. Transfer was first tested with cellular maintenance media and three viruses: two human coronaviruses, 229E and OC43, and murine norovirus-1, as a surrogate for human norovirus. There was no transfer for either of the human coronaviruses to any of the surfaces. Murine norovirus-1 did transfer to stainless steel, cucumber and apple, with transfer efficiencies of 9.19%, 5.95% and 0.329%, respectively. Human coronavirus OC43 transfer was then tested in the presence of fecal material, and transfer was observed for stainless steel (0.52%), cucumber (19.82%) and apple (15.51%) but not plastic. This study indicates that human coronaviruses do not transfer effectively from contaminated hands to contact surfaces without the presence of fecal material.

Indirect impact of rotavirus vaccination on viral causes of acute gastroenteritis in the elderly

BACKGROUND

Rotavirus is considered a childhood infection causing acute gastroenteritis however, it also causes disease in adults which may be underestimated due to less frequent testing in this age-group.

OBJECTIVES

To determine if paediatric rotavirus vaccination, introduced into Ireland in December 2016, affected the viral aetiology in those aged ≥65 yrs presenting with gastroenteritis in the pre- and post-vaccination years. Additionally, rotavirus genotypes in this age-group will be described.

METHODS

Faecal samples from 2015 to 2019 for the investigation of gastroenteritis were tested by real-time (RT-) PCR for norovirus, adenovirus, rotavirus, Rotarix, astrovirus and sapovirus. Rotaviruses were genotyped by multiplex real-time RT-PCR or hemi-nested RT-PCR and a proportion confirmed by sequencing.

RESULTS

22,593 samples from adults aged ≥65 yrs were tested and 2566 (11 %) had ≥1 virus detected. Of 2566 positive samples, norovirus was detected in 82 %, rotavirus 9 %, sapovirus 6 %, astrovirus 3 % and adenovirus 1 %. Rotavirus and norovirus infections decreased between pre and post-vaccine year groups p < 0.001, whereas sapovirus, astrovirus and adenovirus remained unchanged. Between 2015-16 and 2018-19, G2P[4] increased and G4P[8] decreased, p < 0.001. In 2015-2019 there were 37 rotavirus outbreaks. Five geriatric outbreaks were genotyped and caused by G4P[8] (n = 1), G1P[8] (n = 1), G2P[4] (n = 2) and G12P[8] (n = 1).

CONCLUSION

Rotavirus causes acute gastroenteritis in older people. Paediatric vaccination may have contributed to a decline in infections in the elderly; nevertheless, rotavirus continued to circulate in older people following vaccine introduction. Genotype distribution changed between the pre- and post-vaccine era however genotypes in outbreak and endemic settings were comparable.

Persistence of Pathogens on Inanimate Surfaces: A Narrative Review

For the prevention of infectious diseases, knowledge about transmission routes is essential. In addition to respiratory, fecal-oral, and sexual transmission, the transfer of pathogens via surfaces plays a vital role for human pathogenic infections-especially nosocomial pathogens. Therefore, information about the survival of pathogens on surfaces can have direct implications on clinical measures, including hygiene guidelines and disinfection strategies. In this review, we reviewed the existing literature regarding viral, bacterial, and fungal persistence on inanimate surfaces. In particular, the current knowledge of the survival time and conditions of clinically relevant pathogens is summarized. While many pathogens persist only for hours, common nosocomial pathogens can survive for days to weeks under laboratory conditions and thereby potentially form a continuous source of transmission if no adequate inactivation procedures are performed.

Rotavirus disease and genotype diversity in older children and adults in Australia

Background

Rotavirus is a major cause of gastroenteritis in children <5 years of age. The disease burden in older children, adults, and the elderly is underappreciated. This study describes rotavirus disease and genotypic diversity in the Australian population comprising children ≥5 years of age and adults.

Methods

Rotavirus positive fecal samples were collected from laboratories Australia-wide participating in the Australian Rotavirus Surveillance Program between 2010 and 2018. Rotavirus samples were genotyped using a heminested multiplex reverse-transcription polymerase chain reaction. Notification data from the National Notifiable Diseases Surveillance System were also analyzed.

Results

Rotavirus disease was highest in children aged 5–9 years and adults ≥85 years. G2P[4] was the dominant genotype in the population ≥5 years of age. Genotype distribution fluctuated annually and genotypic diversity varied among different age groups. Geographical differences in genotype distribution were observed based on the rotavirus vaccine administered to infants <1 year of age.

Conclusions

This study revealed a substantial burden of rotavirus disease in the population ≥5 years of age, particularly in children 5–9 years and the elderly. This study highlights the continued need for rotavirus surveillance across the population, despite the implementation of efficacious vaccines.

Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain

RNA viruses form a dynamic distribution of mutant swarms (termed "quasispecies") due to the accumulation of mutations in the viral genome. The genetic diversity of a viral population is affected by several factors, including a bottleneck effect. Human-to-human transmission exemplifies a bottleneck effect, in that only part of a viral population can reach the next susceptible hosts. In the present study, two lineages of the rhesus rotavirus (RRV) strain of rotavirus A were serially passaged five times at a multiplicity of infection (MOI) of 0.1 or 0.001, and three phenotypes (infectious titer, cell binding ability, and specific growth rate) were used to evaluate the impact of a bottleneck effect on the RRV population. The specific growth rate values of lineages passaged under the stronger bottleneck (MOI of 0.001) were higher after five passages. The nucleotide diversity also increased, which indicated that the mutant swarms of the lineages under the stronger bottleneck effect were expanded through the serial passages. The random distribution of synonymous and nonsynonymous substitutions on rotavirus genome segments indicated that almost all mutations were selectively neutral. Simple simulations revealed that the presence of minor mutants could influence the specific growth rate of a population in a mutant frequency-dependent manner. These results indicate a stronger bottleneck effect can create more sequence spaces for minor sequences.IMPORTANCE In this study, we investigated a bottleneck effect on an RRV population that may drastically affect the viral population structure. RRV populations were serially passaged under two levels of a bottleneck effect, which exemplified human-to-human transmission. As a result, the genetic diversity and specific growth rate of RRV populations increased under the stronger bottleneck effect, which implied that a bottleneck created a new space in a population for minor mutants originally existing in a hidden layer, which includes minor mutations that cannot be distinguished from a sequencing error. The results of this study suggest that the genetic drift caused by a bottleneck in human-to-human transmission explains the random appearance of new genetic lineages causing viral outbreaks, which can be expected according to molecular epidemiology using next-generation sequencing in which the viral genetic diversity within a viral population is investigated.

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.

Emergence of Rare Bovine-Human Reassortant DS-1-Like Rotavirus A Strains with G8P[8] Genotype in Human Patients in the Czech Republic

Group A Rotaviruses (RVA) are the leading cause of acute gastroenteritis in children and a major cause of childhood mortality in low-income countries. RVAs are mostly host-specific, but interspecies transmission and reassortment between human and animal RVAs significantly contribute to their genetic diversity. We investigated the VP7 and VP4 genotypes of RVA isolated from 225 stool specimens collected from Czech patients with gastroenteritis during 2016–2019. The most abundant genotypes were G1P[8] (42.7%), G3P[8] (11.1%), G9P[8] (9.8%), G2P[4] (4.4%), G4P[8] (1.3%), G12P[8] (1.3%), and, surprisingly, G8P[8] (9.3%). Sequence analysis of G8P[8] strains revealed the highest nucleotide similarity of all Czech G8 sequences to the G8P[8] rotavirus strains that were isolated in Vietnam in 2014/2015. The whole-genome backbone of the Czech G8 strains was determined with the use of next-generation sequencing as DS-1-like. Phylogenetic analysis of all segments clustered the Czech isolates with RVA strains that were formerly described in Southeast Asia, which had emerged following genetic reassortment between bovine and human RVAs. This is the first time that bovine–human DS-1-like G8P[8] strains were detected at a high rate in human patients in Central Europe. Whether the emergence of this unusual genotype reflects the establishment of a new RVA strain in the population requires the continuous monitoring of rotavirus epidemiology.

Utility of Spatial Point-Pattern Analysis Using Residential and Workplace Geospatial Information to Localize Potential Outbreak Sources

Identifying the source of an outbreak facilitates its control. Spatial methods are not optimally used in outbreak investigation, due to a mix of the complexities involved (e.g., methods requiring additional parameter selection), imperfect performance, and lack of confidence in existing options. We simulated 30 mock outbreaks and compared 5 simple methods that do not require parameter selection but could select between mock cases’ residential and workplace addresses to localize the source. Each category of site had a unique spatial distribution; residential and workplace address were visually and statistically clustered around the residential neighborhood and city center sites respectively, suggesting that the value of workplace addresses is tied to the location where an outbreak might originate. A modification to centrographic statistics that we propose—the center of minimum geometric distance with address selection—was able to localize the mock outbreak source to within a 500 m radius in almost all instances when using workplace in combination with residential addresses. In the sensitivity analysis, when given sufficient workplace data, the method performed well in various scenarios with only 10 cases. It was also successful when applied to past outbreaks, except for a multisite outbreak from a common food supplier.

Whole genome characterization of feline-like G3P[8] reassortant rotavirus A strains bearing the DS-1-like backbone genes detected in Vietnam, 2016

While conducting rotavirus gastroenteritis surveillance in Vietnam, two G3P[8] rotavirus A specimens possessing an identical short RNA electropherotype were detected. They were RVA/Human-wt/VNM/0232/2016/G3P[8] and RVA/Human-wt/VNM/0248/2016/G3P[8], and recovered from 9 and 23 months old boys, respectively. The patients developed diarrhoea within one-week interval in March 2016 but in places >100 km apart in northern Vietnam. Whole genome sequencing of the two G3P[8] rotavirus A strains revealed that their genomic RNA sequences were identical across the 11 genome segments, suggesting that they derived from a single clone. The backbone gene constellation was I2-R2-C2-M2-A2-N2-T2-E2-H2. The backbone genes and the VP4 gene had a virtually identical nucleotide sequences with identities ranging from 99.2 to 100% to the corresponding genes of RVA/Human-wt/VNM/1149/2014/G8P[8]; the prototype of recently-emerging bovine-like G8P[8] reassortant strains in Vietnam. On the other hand, the VP7 gene was 98.8% identical with that of RVA/Human-wt/CHN/E2451/2011/G3P[9], and they were clustered together in the lineage represented by RVA/Cat-tc/JPN/FRV-1/1986/G3P[9]. The observations led us to hypothesise that one of the bovine-like G8P[8] strains bearing the DS-1-like backbone genes reassorted with a locally circulating FRV-1-like strain to gain the G3 VP7 gene and to emerge as a thus-far undescribed feline-like G3P[8] reassortant strain. The identification of feline-like G3P[8] strains bearing the DS-1-like backbone genes exemplifies the strength and necessity of the whole genome sequencing approach in monitoring, describing and understanding the evolutionary changes that are occurring in emerging strains and their interactions with co-circulating strains.