Genomic characterization of G3P[6], G4P[6] and G4P[8] human rotaviruses from Wuhan, China: Evidence for interspecies transmission and reassortment events

Prevalence and genetic diversity of porcine rotavirus A from diarrheic piglets in Northern Thailand

BACKGROUND

Rotavirus A (RVA) is an important pathogen causing acute viral gastroenteritis in young children and various animals. RVA is also recognized as a common cause of gastroenteritis in piglets. Epidemiological studies of porcine RVA (PoRVA) conducted in different settings worldwide reported that the prevalence of PoRVA infection ranged from 9.4% to 74.0% with the predominance of G4P[6], G4P[7], and G5P[7] genotypes. In Thailand, long-term epidemiological surveillance of PoRVA infection is limited. Continuous monitoring of PoRVA infection is required to gain a better understanding the prevalence and evolution of PoRVA. In this study, the prevalence and genetic diversity of PoRVA were investigated by screening of 1,260 stool samples collected from 0 to 5-week-old piglets with acute diarrhea during 2016 to 2023 by using real-time RT-PCR. The G- and P-genotypes of RVA were identified by characterization of the partial VP7 and VP4 genes by using multiplex-PCR, nucleotide sequencing, and phylogenetic analysis.

RESULTS

A total of 303 out of 1,260 (24.0%) samples were positive for PoRVA. Overall, the G5P[23] (28.7%) and G4P[23] (28.4%) were detected as the co-predominant PoRVA genotypes, followed by G5P[13] (9.9%), G3P[23] (9.6%), G9P[23] (8.2%), G4P[13] (7.9%), G9P[13] (3.3%), G3P[13] (1.7%), G4P[6] (1.7%), and G2P[23] (0.3%) genotypes. Additionally, a rare G2P[27] (0.3%) genotype re-emerged approximately 22 years after the initial detection in 2000 in Chiang Mai, Thailand.

CONCLUSION

Our results revealed the prevalence of wide variety of PoRVA genotypes circulating in piglets with acute diarrhea in Thailand over a study period of seven years. Of these, G5P[23] and G4P[23] emerged as the most predominant genotypes, which were substantially different from previous reports in the same geographical area. The findings offer valuable contribution to a better understanding of molecular epidemiology and evolution of PoRVA in piglets with acute diarrhea.

Complete genome constellation of a dominant Bovine rotavirus genotype circulating in Bangladesh reveals NSP4 intragenic recombination with human strains

Rotavirus A is a leading cause of non-bacterial gastroenteritis in humans and domesticated animals. Despite the vast diversity of bovine Rotavirus A strains documented in South Asian countries, there are very few whole genomes available for phylogenetic study. A cross-sectional study identified a high prevalence of the G6P[11] genotype of bovine Rotavirus A circulating in the commercial cattle population in Bangladesh. Next-generation sequencing and downstream phylogenetic analysis unveiled all 11 complete gene segments of this strain (BD_ROTA_CVASU), classifying it under the genomic constellation G6P[11]-I2-R2-C2-M2-A13-N2-T6-E2-H3, which belongs to a classical DS-1-like genomic backbone. We found strong evidence of intragenic recombination between human and bovine strains in the Non-structural protein 4 (NSP4) gene, which encodes a multifunctional enterotoxin. Our analyses highlight frequent zoonotic transmissions of rotaviruses in diverse human-animal interfaces, which might have contributed to the evolution and pathogenesis of this dominant genotype circulating in the commercial cattle population in Bangladesh.

Detection of Porcine-Human Reassortant and Zoonotic Group A Rotaviruses in Humans in Poland

Group A rotaviruses (RVAs) are widespread in humans and many animal species and represent the most epidemiologically important rotavirus group. The aim of the study was the identification of the genotype pattern of human RVA strains circulating in Poland, assessment of their phylogenetic relationships to pig RVAs and identification of reassortant and zoonotic virus strains. Human stool samples which were RVA positive (n = 166) were collected from children and adults at the age of 1 month to 74 years with symptoms of diarrhoea. Identification of the G and P genotypes of human RVAs as well as the complete genotype of reassortant and zoonotic virus strains was performed by the use of an RT-PCR method. The G (G1-G4, G8 or G9) and/or P (P[4], P[6], P[8] or P[9]) genotypes were determined for 148 (89.2%) out of 166 RVA strains present in human stool. G1P[8] RVA strains prevailed, and G4P[8] (20.5%), G9P[8] (15.7%) and G2P[4] (13.3%) human RVA strains were also frequently identified. The full genome analysis of human G4P[6] as well as pig G1P[8] and G5P[6] RVAs revealed the occurrence of porcine-human reassortants and zoonotic RVAs. Detection of G4P[6] in pigs confirms their role as a reservoir of zoonotic RVAs.

Isolation, characterization and whole-genome analysis of G9 group a rotaviruses in China: Evidence for possible Porcine-Human interspecies transmission

Group A rotaviruses (RVAs) are major causes of severe gastroenteritis in infants and young animals. To enhance our understanding of the relationship between human and animals RVAs, complete genome data are necessary. We screened 92 intestinal and stool samples from diarrheic piglets by RT‒PCR targeting the VP6 gene, revealing a prevalence of 10.9%. RVA was confirmed in two out of 5 calf samples. We successfully isolated two porcine samples using MA104 cell line. The full-length genetic constellation of the two isolates were determined to be G9-P[23]-I5-R1-C1-M1-A8-N1-T7-E1-H1, with close similarity to human Wa-like and porcine strains. Sequence analysis revealed the majority of genes were closely related to porcine and human RVAs. Phylogenetic analysis revealed that these isolates might have their ancestral origin from pigs, although some of their gene segments were related to human strains. This study reveals evidence of reassortment and possible interspecies transmission between pigs and humans in China.

Emergence of a Novel G4P[6] Porcine Rotavirus with Unique Sequence Duplication in NSP5 Gene in China

Rotavirus is a major causative agent of diarrhoea in children, infants, and young animals around the world. The associated zoonotic risk necessitates the serious consideration of the complete genetic information of rotavirus. A segmented genome makes rotavirus prone to rearrangement and the formation of a new viral strain. Monitoring the molecular epidemiology of rotavirus is essential for its prevention and control. The quantitative RT-PCR targeting the NSP5 gene was used to detect rotavirus group A (RVA) in pig faecal samples, and two pairs of universal primers and protocols were used for amplifying the G and P genotype. The genotyping and phylogenetic analysis of 11 genes were performed by RT-PCR and a basic bioinformatics method. A unique G4P[6] rotavirus strain, designated S2CF (RVA/Pig-tc/CHN/S2CF/2023/G4P[6]), was identified in one faecal sample from a piglet with severe diarrhoea in Guangdong, China. Whole genome sequencing and analysis suggested that the 11 segments of the S2CF strain showed a unique Wa-like genotype constellation and a typical porcine RVA genomic configuration of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Notably, 4 of the 11 gene segments (VP4, VP6, VP2, and NSP5) clustered consistently with human-like RVAs, suggesting independent human-to-porcine interspecies transmission. Moreover, a unique 344-nt duplicated sequence was identified for the first time in the untranslated region of NSP5. This study further reveals the genetic diversity and potential inter-species transmission of porcine rotavirus.

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.

Recent Molecular Characterization of Porcine Rotaviruses Detected in China and Their Phylogenetic Relationships with Human Rotaviruses

Porcine rotavirus A (PoRVA) is an enteric pathogen capable of causing severe diarrhea in suckling piglets. Investigating the prevalence and molecular characteristics of PoRVA in the world, including China, is of significance for disease prevention. In 2022, a total of 25,768 samples were collected from 230 farms across China, undergoing porcine RVA positivity testing. The results showed that 86.52% of the pig farms tested positive for porcine RVA, with an overall positive rate of 51.15%. Through the genetic evolution analysis of VP7, VP4 and VP6 genes, it was revealed that G9 is the predominant genotype within the VP7 segment, constituting 56.55%. VP4 genotypes were identified as P[13] (42.22%), P[23] (25.56%) and P[7] (22.22%). VP6 exhibited only two genotypes, namely I5 (88.81%) and I1 (11.19%). The prevailing genotype combination for RVA was determined as G9P[23]I5. Additionally, some RVA strains demonstrated significant homology between VP7, VP4 and VP6 genes and human RV strains, indicating the potential for human RV infection in pigs. Based on complete genome sequencing analysis, a special PoRVA strain, CHN/SD/LYXH2/2022/G4P[6]I1, had high homology with human RV strains, revealing genetic reassortment between human and porcine RV strains in vivo. Our data indicate the high prevalence, major genotypes, and cross-species transmission of porcine RVA in China. Therefore, the continuous monitoring of porcine RVA prevalence is essential, providing valuable insights for virus prevention and control, and supporting the development of candidate vaccines against porcine RVA.

Full genome-based characterization of an Asian G3P[6] human rotavirus strain found in a diarrheic child in Japan: Evidence for porcine-to-human zoonotic transmission

Human rotavirus strains having the unconventional G3P[6] genotype have been sporadically detected in diarrheic patients in different parts of the world. However, the full genomes of only three human G3P[6] strains from Asian countries (China, Indonesia, and Vietnam) have been sequenced and characterized, and thus the exact origin and evolution of G3P[6] strains in Asia remain to be elucidated. Here, we sequenced and characterized the full genome of a G3P[6] strain (RVA/Human-wt/JPN/SO1199/2020/G3P[6]) found in a stool sample from a 3-month-old infant admitted with acute gastroenteritis in Japan. On full genomic analysis, strain SO1199 was revealed to have a unique Wa-like genogroup configuration: G3-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1. VP6 genotype I5 and NSP1 genotype A8 are commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis demonstrated that all 11 genes of strain SO1199 were closely related to those of porcine and/or porcine-like human rotaviruses and thus appeared to be of porcine origin. Thus, strain SO1199 was shown to possess a porcine-like genomic backbone and thus is likely to be the result of interspecies transmission of a porcine rotavirus strain. Of note is that all 11 genes of strain SO1199 were phylogenetically located in clusters, distinct from those of the previously identified porcine-like human G3P[6] strains from around the world including Asia, suggesting the occurrence of independent porcine-to-human zoonotic transmission events. To our knowledge, this is the first report on full genome-based characterization of a human G3P[6] strain that has emerged in Japan. Our findings revealed the diversity of unconventional human G3P[6] strains in Asia, and provide important insights into the origin and evolution of G3P[6] strains.

Metatranscriptomic assessment of diarrhoeic faeces reveals diverse RNA viruses in rotavirus group A infected piglets and calves from India

RNA viruses are a major group contributing to emerging infectious diseases and neonatal diarrhoea, causing morbidity and mortality in humans and animals. Hence, the present study investigated the metatranscriptomic-derived faecal RNA virome in rotavirus group A (RVA)-infected diarrheic piglets and calves from India. The viral genomes retrieved belonged to Astroviridae in both species, while Reoviridae and Picornaviridae were found only in piglets. The nearly complete genomes of porcine RVA (2), astrovirus (AstV) (6), enterovirus G (EVG) (2), porcine sapelovirus (PSV) (2), Aichivirus C (1), and porcine teschovirus (PTV) (1) were identified and characterised. In the piglet, AstVs of PAstV2 (MAstV-26) and PAstV4 (MAstV-31) lineages were predominant, followed by porcine RVA, EVG, PSV, Aichivirus C, teschovirus (PTV-17) in decreasing order of sequence reads. In contrast, AstV accounted for the majority of reads in bovines and belonged to MAstV-28 and a proposed MAstV-35. Both RVA G4P[6] strains exhibited prototype Gottfried strains like a genotypic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Ten out of eleven genes were of porcine origin, while the VP7 gene clustered with G4-lineage-1, consisting of human strains, suggesting a natural porcine-human reassortant. In the recombination analysis, multiple recombination events were detected in the PAstV4 and PAstV2 genomes, pointing out that these viruses were potential recombinants. Finally, the study finds diverse RNA virome in Indian piglets and calves for the first time, which may have contributed to diarrhoea. In the future, the investigation of RNA virome in animals will help in revealing pathogen diversity in multifactorial diseases, disease outbreaks, monitoring circulating viruses, viral discovery, and evaluation of their zoonotic potential.

Prevalence and Genomic Characterization of Rotavirus A from Domestic Pigs in Zambia: Evidence for Possible Porcine-Human Interspecies Transmission

Rotavirus is a major cause of diarrhea globally in animals and young children under 5 years old. Here, molecular detection and genetic characterization of porcine rotavirus in smallholder and commercial pig farms in the Lusaka Province of Zambia were conducted. Screening of 148 stool samples by RT-PCR targeting the VP6 gene revealed a prevalence of 22.9% (34/148). Further testing of VP6-positive samples with VP7-specific primers produced 12 positives, which were then Sanger-sequenced. BLASTn of the VP7 positives showed sequence similarity to porcine and human rotavirus strains with identities ranging from 87.5% to 97.1%. By next-generation sequencing, the full-length genetic constellation of the representative strains RVA/pig-wt/ZMB/LSK0137 and RVA/pig-wt/ZMB/LSK0147 were determined. Genotyping of these strains revealed a known Wa-like genetic backbone, and their genetic constellations were G4-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1 and G9-P[13]-I5-R1-C1-M1-A8-N1-T1-E1-H1, respectively. Phylogenetic analysis revealed that these two viruses might have their ancestral origin from pigs, though some of their gene segments were related to human strains. The study shows evidence of reassortment and possible interspecies transmission between pigs and humans in Zambia. Therefore, the "One Health" surveillance approach for rotavirus A in animals and humans is recommended to inform the design of effective control measures.

Development of a droplet digital PCR assay for detection of group A porcine rotavirus

Group A porcine rotavirus (PoRVA) is an important pathogen of acute enteritis in piglets, which has caused severe economic losses in the pig industry worldwide. A convenient, sensitive and specific diagnosis method is an urgent requirement for the surveillance of the PoRVA circulating in clinical samples. In this study, a novel and convenient droplet digital PCR (ddPCR) for the detection of PoRVA was developed using the conserved region of the VP6 gene. The detection limit of ddPCR was 1.81 ± 0.14 copies/rection, ~10 times greater sensitivity than TaqMan real-time quantitative PCR (qPCR). Both ddPCR and qPCR assays exhibited good linearity and repeatability, and the established ddPCR method was highly specific for PoRVA. The results of clinical sample testing showed that the positivity rate of ddPCR (5.6%) was higher than that of qPCR (4.4%). Therefore, the newly developed ddPCR assay could be widely used in clinical diagnosis of PoRVA infections.

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

INTRODUCTION

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

AREAS COVERED

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

EXPERT OPINION

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

Genomic characterization of an African G4P[6] human rotavirus strain identified in a diarrheic child in Kenya: Evidence for porcine-to-human interspecies transmission and reassortment

Human rotavirus strains having the unconventional G4P[6] genotype have been sporadically identified in diarrheic patients in different parts of the world. However, the whole genome of only one human G4P[6] strain from Africa (central Africa) has been sequenced and analyzed, and thus the exact origin and evolutionary pattern of African G4P[6] strains remain to be elucidated. In this study, we characterized the full genome of an African G4P[6] strain (RVA/Human-wt/KEN/KCH148/2019/G4P[6]) identified in a stool specimen from a diarrheic child in Kenya. Full genome analysis of strain KCH148 revealed a unique Wa-like genogroup constellation: G4-P[6]-I1-R1-C1-M1-A1-N1-T7-E1-H1. NSP3 genotype T7 is commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis showed that 10 of the 11 genes of strain KCH148 (VP7, VP4, VP6, VP1-VP3, NSP1, and NSP3-NSP5) appeared to be of porcine origin, the remaining NSP2 gene appearing to be of human origin. Therefore, strain KCH148 was found to have a porcine rotavirus backbone and thus is likely to be of porcine origin. Furthermore, strain KCH148 is assumed to have been derived through interspecies transmission and reassortment events involving porcine and human rotavirus strains. To our knowledge, this is the first report on full genome-based characterization of a human G4P[6] strain from east Africa. Our observations demonstrated the diversity of human G4P[6] strains in Africa, and provide important insights into the origin and evolutionary pattern of zoonotic G4P[6] strains on the African continent.

Serological Humoral Immunity Following Natural Infection of Children with High Burden Gastrointestinal Viruses

Acute gastroenteritis (AGE) is a major cause of morbidity and mortality worldwide, resulting in an estimated 440,571 deaths of children under age 5 annually. Rotavirus, norovirus, and sapovirus are leading causes of childhood AGE. A successful rotavirus vaccine has reduced rotavirus hospitalizations by more than 50%. Using rotavirus as a guide, elucidating the determinants, breath, and duration of serological antibody immunity to AGE viruses, as well as host genetic factors that define susceptibility is essential for informing development of future vaccines and improving current vaccine candidates. Here, we summarize the current knowledge of disease burden and serological antibody immunity following natural infection to inform further vaccine development for these three high-burden viruses.

Full genome-based characterization of G4P[6] rotavirus strains from diarrheic patients in Thailand: Evidence for independent porcine-to-human interspecies transmission events

The exact evolutionary patterns of human G4P[6] rotavirus strains remain to be elucidated. Such strains possess unique and strain-specific genotype constellations, raising the question of whether G4P[6] strains are primarily transmitted via independent interspecies transmission or human-to-human transmission after interspecies transmission. Two G4P[6] rotavirus strains were identified in fecal specimens from hospitalized patients with severe diarrhea in Thailand, namely, DU2014-259 (RVA/Human-wt/THA/DU2014-259/2014/G4P[6]) and PK2015-1-0001 (RVA/Human-wt/THA/PK2015-1-0001/2015/G4P[6]). Here, we analyzed the full genomes of the two human G4P[6] strains, which provided the opportunity to study and confirm their evolutionary origin. On whole genome analysis, both strains exhibited a unique Wa-like genotype constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The NSP1 genotype A8 is commonly found in porcine rotavirus strains. Furthermore, on phylogenetic analysis, each of the 11 genes of strains DU2014-259 and PK2015-1-0001 appeared to be of porcine origin. On the other hand, the two study strains consistently formed distinct clusters for nine of the 11 gene segments (VP4, VP6, VP1-VP3, and NSP2-NSP5), strongly indicating the occurrence of independent porcine-to-human interspecies transmission events. Our observations provide important insights into the origin of zoonotic G4P[6] strains, and into the dynamic interaction between porcine and human rotavirus strains.

New approach of genetic characterization of group A rotaviruses by the nanopore sequencing method

Nanopore sequencing of virus genomes represented by segmented RNA (e.g. rotaviruses) requires the development of specific approaches. Due to the massive use of rotavirus vaccines, the relevance of monitoring the genetic diversity of circulating strains of group A rotaviruses (RVA) increased. The WHO recommended method of multiplex type-specific PCR does not allow genotyping of all clinically significant strains of RVA and identifying inter-strain differences within the genotype. We have described a new principle of amplification of RVA gene segments using six primers for reverse transcription and one universal primer for PCR for nanopore sequencing. The amplification of RVA genome was tested on clinical samples and three phylogenetically distant laboratory RVA strains, Wa (G1P[8]), DS-1 (G2P[4]) and 568 (G3P[3]). The developed protocol of sample preparation and nanopore sequencing allowed obtaining full-length sequences for gene segments of RVA, including the diagnostically significant segments 9 (VP7), 4 (VP4) and 6 (VP6) with high accuracy and coverage. The accuracy of sequencing of the rotavirus genome exceeded 99.5 %, and the genome coverage varied for different strains from 59.0 to 99.6 % (on average 86 %). The developed approach of nanopore sequencing of RVA genome could be a prospective tool for epidemiological studies and surveillance of rotavirus infection.

Isolation and Characterization of Coronavirus and Rotavirus Associated with Calves in Central Part of Oromia, Ethiopia

BACKGROUND

Coronavirus and rotavirus are most commonly associated etiologies for calves' diarrhoea, resulting in loss of productivity and economy of farmers. However, various facets of diarrheal disease caused by coronavirus and rotavirus in calves in Ethiopia are inadequately understood. A cross-sectional study was conducted with the aim of isolation and molecular characterization of coronavirus and rotavirus from calves in the central part of Oromia (Bishoftu, Sebata, Holeta, and Addis Ababa), Ethiopia, from November 2018 to May 2019. The four study areas were purposively selected and faecal samples were collected by simple random sampling for diagnosis of coronavirus and rotavirus infection by using the antigen detection enzyme-linked immunosorbent assay (Ag-ELISA) kit. In addition, this study was carried out to have insight in prevalence and associated risk factors of coronavirus and rotavirus infection in calves.

RESULT

During the study, 83 diarrheic and 162 nondiarrheic faecal samples collected from calves less than 4 weeks of age were screened for coronavirus and rotavirus. Of the 83 diarrheic samples, 1 sample (1.2%) was positive for coronavirus antigen and 6 samples (7.2%) were found to be positive for rotavirus antigen by Ag-ELISA. All the nondiarrheic samples were negative for both coronavirus and rotavirus Ag. The overall prevalence of coronavirus and rotavirus infection in calves was estimated at 0.4% (1/245) and 2.45% (6/245), respectively. All samples (7) of ELISA test positive of both coronavirus and rotavirus were propagated in Madin-Darby bovine kidney (MDBK) cells. After 3 subsequent passages, progressive cytopathic effect (CPE), i.e., rounding, detachment, and the destruction of monolayer cell of five samples (1 sample of coronavirus and 4 samples of rotavirus) (71.4%) were observed. At the molecular stage, reverse transcriptase polymerase chain reaction (RT-PCR) technique was used to determine the presence of coronavirus and rotavirus nucleic acid by using specific primers. The 5 samples that were coronavirus and rotavirus antigen positive by ELISA and develop CPE on cell culture were also positive on RT-PCR technique. The prevalence of infection peaked at 1st and 2nd weeks of age in male calves.

CONCLUSION

Diarrheal disease caused by coronavirus and rotavirus has a great health problem in calves that interrupts production benefits with reduced weight gain and increased mortality and its potential for zoonotic spread. So, the present findings show coronavirus and rotavirus infection in calves in Ethiopia that needs to be addressed by practising early colostrum feeding in newborn calves, using vaccine, or improving livestock management.

Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia

A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 is often observed in porcine strains. Phylogenetic analyses showed that VP6, VP7, NSP2, NSP4, and NSP5 genes were closely related to cognate gene sequences of porcine strains (e.g., RVA/Pig-wt/CHN/DZ-2/2013/G5P[X] for VP7) from the NCBI database, while VP1, VP3, VP4, and NSP3 were closely related to porcine-like human strains (e.g., RVA/Human-wt/CHN/E931/2008/G4P[6] for VP1, and VP3). On the other hand, the origin of the VP2 was not clear from our analyses, as it was not only close to both porcine (e.g., RVA/Pig-tc/CHN/SWU-1C/2018/G9P[13]) and porcine-like human strains (e.g., RVA/Human-wt/LKA/R1207/2009/G4P[6]) but also to three human strains (e.g., RVA/Human-wt/USA/1476/1974/G1P[8]). The VP7 gene was located in lineage II that comprised only porcine strains, which suggests the occurrence of independent porcine-to-human reassortment events. The study strain may have collectively been derived through interspecies transmission, or through reassortment event(s) involving strains of porcine and porcine-like human origin. The results of this study underline the importance of whole-genome characterisation of rotavirus strains and provide insights into interspecies transmissions from porcine to humans.

Generation of Simian Rotavirus Reassortants with VP4- and VP7-Encoding Genome Segments from Human Strains Circulating in Africa Using Reverse Genetics

Human rotavirus A (RVA) causes acute gastroenteritis in infants and young children. The broad use of two vaccines, which are based on RVA strains from Europe and North America, significantly reduced rotavirus disease burden worldwide. However, a lower vaccine effectiveness is recorded in some regions of the world, such as sub-Saharan Africa, where diverse RVA strains are circulating. Here, a plasmid-based reverse genetics system was used to generate simian RVA reassortants with VP4 and VP7 proteins derived from African human RVA strains not previously adapted to cell culture. We were able to rescue 1/3 VP4 mono-reassortants, 3/3 VP7 mono-reassortants, but no VP4/VP7 double reassortant. Electron microscopy showed typical triple-layered virus particles for the rescued reassortants. All reassortants stably replicated in MA-104 cells; however, the VP4 reassortant showed significantly slower growth compared to the simian RVA or the VP7 reassortants. The results indicate that, at least in cell culture, human VP7 has a high reassortment potential, while reassortment of human VP4 from unadapted human RVA strains with simian RVA seems to be limited. The characterized reassortants may be useful for future studies investigating replication and reassortment requirements of rotaviruses as well as for the development of next generation rotavirus vaccines.

Full genome characterization of human G3P[6] and G3P[9] rotavirus strains in Lebanon

Rotaviruses are the most common infectious agents causing severe diarrheal diseases in young children globally. Three rare human rotavirus strains, two G3P[9] and one G3P[6], were detected in stool samples of children under 5 years of age hospitalized for gastroenteritis in Lebanon during the course of a surveillance study. Complete genomes of these strains were sequenced using VirCapSeq-VERT, a capture based high-throughput sequencing method. Genomic sequences were further characterized by using phylogenetic analyses with global RVA G3P[6]/P[9] strains, other vaccine and reference strains. Genetic analysis revealed that the G3P[6] strain emerged as a DS-1/Wa-like mono-reassortant strain with a potential Ethiopian origin. The two G3P[9] strains possessed a mixed DS-1/Wa/AU-1-like origin indicating that these may have evolved via multiple reassortment events involving feline, human and bovine rotaviruses. Furthermore, analysis of these strains revealed high antigenic variability compared to the vaccine strains. Additional studies are essential to fully understand the evolutionary dynamics of G3P[6]/P[9] strains spreading worldwide and their implications on vaccine effectiveness.

Molecular epidemiology of group A rotavirus in outpatient diarrhea infants and children in Chongqing, China, 2011-2015

Human group A rotavirus (RVA) is the leading cause of acute viral gastroenteritis in children under 5 years old worldwide. The aim of this study was to investigate the genotype distribution of RVA in the Midwest of China. Sentinel-based surveillance of acute diarrhea was conducted at Children's Hospital of Chongqing Medical University from 2011 to 2015. RVA was tested by using enzyme-linked immunosorbent assays. The partial VP4 genes and VP7 genes of rotavirus were amplified and sequenced, and genotyping and phylogenetic analyses were performed. Among the 2236 stool specimens collected from children with acute gastroenteritis, 681 (30.46%) were positive for RVA. The majority of children (89.28%) who tested positive for RVA were children aged ≤2 years. The seasonal peak of RVA was in the winter. As for genotype, four strain combinations, G9P[8], G3P[8], G1P[8], and G2P[4] contributed to 75.62% (515/681) of the RVA-associated diarrhea cases. After a marked increase in G9P[8] (30.77%) in 2013, G9P[8] became the predominant genotype in 2014 and 2015, whilst the prevalence of G1P[8] was decreased to 2.72% in 2015. Unusual G-P combinations (eg, G1P[4], G9P[4], G4P[6], G3P[4], G2P[8]) were also detected sporadically over the study period. Phylogenetic tree analysis results showed that the VP7 sequences of G9 strains were clustered into two main lineages, and 77.34% of them were clustered into lineage VI, with the highest nucleotide similarity to the strain JS12-17(China). VP4 gene sequences of P[8] strains were almost P[8]-lineage 3. Substantial temporal variation in the circulation of various genotypes of rotavirus in Chongqing was observed during 2011-2015, and highlights the need for continuous surveillance of RVA infection for better understanding and control of RVA infection.

Whole-genome analysis of rotavirus G4P[6] strains isolated from Korean neonates: association of Korean neonates and rotavirus P[6] genotypes

Background

Group A rotaviruses are the major causative agents of pediatric gastroenteritis worldwide. Several studies have reported the predominance of G4P[6] rotavirus genotypes in Korean neonates, which is uncommon in other countries. Therefore, the purposes of this study were to determine the genotype constellations of complete genomes of G4P[6] rotavirus strains isolated from Korean neonates using next-generation sequencing, to compare these sequences with other G4P[6] strains in other countries, and to determine the reason for the predominance of G4P[6] genotypes in Korean neonates.

Results

Twenty rotavirus G4P[6] strains, isolated from January 2013 to January 2016, were selected for whole-genome sequencing. Eleven rotavirus genes were amplified using specific primer sets, and sequencing was carried out using an Ion S5 XL next-generation sequencing platform. Genotypes of each gene were determined, and phylogenetic analyses were performed to investigate genetic distances between genes of rotaviruses in this study and those of other rotavirus G4P[6] strains whose whole-genome sequences were previously published. All 20 rotavirus strains in this study had the same genotype: G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, representing the Wa-like genotype constellation. BLAST searches of 20 G4P[6] rotavirus strains revealed that all G4 sequences in this study showed the highest nucleotide identity to G4 sequences of G4P[6] rotavirus strains isolated in Korea in 2008 (GenBank accession number: FJ603447). Additionally, P[6] gene sequences in this study showed the highest nucleotide identity to P[6] sequences of G4P[6] strains detected in Korea in 2002 (AY158093). Phylogenetic and nucleotide sequence analyses showed that G4P[6] strains in this study and previously reported G4P[6] strains in Korea were mostly detected in neonates and had similar G4 and P[6] sequences compared with other G4P[6] strains detected in other countries.

Conclusions

This study showed that the whole-genome constellation of rotavirus G4P[6] strains from Korean neonates resembled a Wa-like genotype constellation. Additionally, rotavirus genotypes detected in Korean neonates had unique P[6] sequences, which may be the cause of Korean neonatal rotavirus infection.

Electronic supplementary material

The online version of this article (10.1186/s13099-019-0318-5) contains supplementary material, which is available to authorized users.

Rotavirus A in wild and domestic animals from areas with environmental degradation in the Brazilian Amazon

Acute gastroenteritis is one of the main causes of mortality in humans and young animals. Domestic and mainly wild animals such as bats, small rodents and birds are highly diversified animals in relation to their habitats and ecological niches and are widely distributed geographically in environments of forest fragmentation in some areas of the Amazon, being considered important sources for viruses that affect humans and other animals. Due to the anthropical activities, these animals changed their natural habitat and adapted to urbanized environments, thus representing risks to human and animal health. Although the knowledge of the global diversity of enteric viruses is scarce, there are reports demonstrating the detection of rotavirus in domestic animals and animals of productive systems, such as bovines and pigs. The present study investigated the prevalence of Rotavirus A in 648 fecal samples of different animal species from the northeastern mesoregion of the state of Pará, Brazil, which is characterized as an urbanized area with forest fragments. The fecal specimens were collected from October 2014 to April 2016 and subjected to a Qualitative Real-Time Polymerase Chain Reaction (RT-qPCR), using the NSP3 gene as a target. It was observed that 27.5% (178/648) of the samples presented positive results for RVA, with 178 samples distributed in birds (23.6%), canines (21.35%), chiropterans (17.98%), bovines (14.6%), horses (8.43%), small rodents (6.74%), pigs (3.93%) and felines (3.37%), demonstrating the circulation of RVA in domestic animals and suggesting that such proximity could cause transmissions between different species and the occurrence of rearrangements in the genome of RVA as already described in the literature, associated to the traces of environmental degradation in the studied areas.

Detection of an animal-derived G4P[6] group A rotavirus strain in a symptomatic child, in Italy

During 2017, a G4P[6] group A rotavirus strain was identified in the feces of an Italian child hospitalized for acute gastroenteritis in Southern Italy. Nucleotide sequencing of the 11 genomic segments, revealed the G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 genotype constellation. Phylogenetic analyses of the gene segments investigated revealed high nucleotide sequence identities with G4P[6] RVA strains detected previously in pigs and in humans. The human strains related to the Italian G4P[6] were mainly reported from Asia, and were detected after an inter-species transmission event from swine. This study reports the genotyping and phylogenetic analysis of a G4P[6] RVA strain presenting a genomic constellation never detected before in Italy. In addition, this strain was able to cause AGE symptoms in a healthy child, successively hospitalized. The molecular characterization suggested zoonotic origin and inter-species transmission of this strain from swine, living open the possibility of its importation from abroad.

Complete genome sequence analysis of rare G4P[6] rotavirus strains from human and pig reveals the evidence for interspecies transmission

Two rare human rotavirus strains, RVA/Human-wt/THA/CMH-N016-10/2010/G4P[6] and RVA/Human-wt/THA/CMH-N014-11/2011/G4P[6], were detected during the surveillance of group A rotavirus (RVA) in Chiang Mai, Thailand. Complete genome sequences of both strains were analyzed in comparison with that of the representative porcine G4P[6] RVA strain (RVA/Pig-wt/THA/CMP-011-09/2009/G4P[6]) detected in the same geographical area. Human RVA strain CMH-N016-10 containing the genotype constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1 was identical to that of porcine RVA strain CMP-011-09. Another human RVA strain (CMH-N014-11) was also contained the genotype constellation of ten segments identical to those of CMH-N016-10 and of porcine RVA strain CMP-011-09 except for genotype I of VP6 gene which contained I5 instead of I1. The genotype constellation of CMH-N014-11, G4-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1 was a novel genotype constellation that has not been reported previously in both human and pig. Phylogenetic analysis of all 11 genome segments revealed that both strains of human RVA were more closely related to porcine and porcine-like human than to human RVA reference strains, particularly those reported from Thailand and other Asian countries with very high nucleotide sequence identities ranging from 91.1-100% except for NSP4 gene from 86.1-92.2%. Based on complete genome constellation and overall phylogenetic analyses suggested that these two human G4P[6] strains may have probably originated from porcine RVA strains of independent ancestor. This study provided an evidence for direct interspecies transmission of porcine RVA from pig to human.

Human-porcine reassortant rotavirus generated by multiple reassortment events in a Sri Lankan child with diarrhea

A human-porcine reassortant rotavirus, strain R1207, was identified from 74 group A rotaviruses detected in 197 (37.6%) stool samples collected from patients who attended a tertiary care hospital in Ragama, Sri Lanka. This is the first report of a human-porcine reassortant rotavirus in Sri Lanka. The patient was a 12-month-old boy who had been hospitalized with fever and acute diarrhea with a duration of 6 days. The family had pigs at home before the birth of this boy. However, the neighbors still practice pig farming. The genotype constellation of R1207 was G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. This is based on the assignment of all the eleven gene segments a full genome-based genotyping system. R1207 showed a 4-2-3-2 genomic electrophoretic migration pattern, which is characteristic of group A rotaviruses. Our analyses revealed that five (NSP2, NSP4, VP1, VP2, and VP7) of the 11 genes were closely related to the respective genes of porcine strains. Although the remaining six genes (NSP1, NSP3, NSP5, VP3, VP4, and VP6) were related to human strains, with the exception of the gene sequence of NSP1, all of these human strains were human-porcine reassortants. With a genogroup 1 genetic backbone, this strain was possibly formed via multiple genetic reassortments. We do not know whether this strain is circulating in pigs, as no data are available on porcine rotaviruses in Sri Lanka. Surveillance should be strengthened to determine the epidemiology of this genotype of rotavirus in Sri Lanka and to assess whether the infection was limited or sustained by ongoing human-to-human transmission.

Specificity and affinity of neuraminic acid exhibited by canine rotavirus strain K9 carbohydrate-binding domain (VP8*)

The outer capsid spike protein VP4 of rotaviruses is a major determinant of infectivity and serotype specificity. Proteolytic cleavage of VP4 into 2 domains, VP8* and VP5*, enhances rotaviral infectivity. Interactions between the VP4 carbohydrate-binding domain (VP8*) and cell surface glycoconjugates facilitate initial virus-cell attachment and subsequent cell entry. Our saturation transfer difference nuclear magnetic resonance (STD NMR) and isothermal titration calorimetry (ITC) studies demonstrated that VP8*_64-224 of canine rotavirus strain K9 interacts with N-acetylneuraminic and N-glycolylneuraminic acid derivatives, exhibiting comparable binding epitopes to VP8* from other neuraminidase-sensitive animal rotaviruses from pigs (CRW-8), cattle (bovine Nebraska calf diarrhoea virus, NCDV), and Rhesus monkeys (Simian rhesus rotavirus, RRV). Importantly, evidence was obtained for a preference by K9 rotavirus for the N-glycolyl- over the N-acetylneuraminic acid derivative. This indicates that a VP4 serotype 5A rotavirus (such as K9) can exhibit a neuraminic acid receptor preference that differs from that of a serotype 5B rotavirus (such as RRV) and the receptor preference of rotaviruses can vary within a particular VP4 genotype.

Whole genome characterisation of a porcine-like human reassortant G26P[19] Rotavirus A strain detected in a child hospitalised for diarrhoea in Nepal, 2007

A rare G26 Rotavirus A strain RVA/Human-wt/NPL/07N1760/2007/G26P[19] was detected in a child hospitalised for acute diarrhoea in Kathmandu, Nepal. The complete genome of 07N1760 was determined in order to explore its evolutionary history as well as examine its relationship to a Vietnamese strain RVA/Human-wt/VNM/30378/2009/G26P[19], the only G26 strain whose complete genotype constellation is known. The genotype constellation of 07N1760 was G26-P[19]-I12-R1-C1-M1-A8-N1-T1-E1-H1, a unique constellation identical to that of the Vietnamese 30378 except the VP6 gene. Phylogenetic analysis revealed that both strains were unrelated at the lineage level despite their similar genotype constellation. The I12 VP6 gene of 07N1760 was highly divergent from the six currently deposited I12 sequences in the GenBank. Except for its NSP2 gene, the remaining genes of 07N1760 shared lineages with porcine and porcine-like human RVA genes. The NSP2 gene belonged to a human RVA N1 lineage which was distinct from typical porcine and porcine-like human lineages. In conclusion, the Nepali G26P[19] strain 07N1760 was a porcine RVA strain which derived an NSP2 gene from a human Wa-like RVA strain by intra-genotype reassortment probably after transmission to the human host.

Development and Validation of Monoclonal Antibody-Based Antigen Capture ELISA for Detection of Group A Porcine Rotavirus

Porcine rotavirus-A (PoRVA) is one of the common causes of mild to severe dehydrating diarrhea, leading to losses in weaning and postweaning piglets. A rapid, highly specific, and sensitive antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) was developed for detection of PoRVA, by using VP6 (a highly conserved and antigenic protein of group-A rotavirus)-directed rabbit polyclonal antibodies (capture antibody) and murine monoclonal antibodies (detector antibody). The detection limit of AC-ELISA was found to be equal to that of conventional reverse transcription-polymerase chain reaction (RT-PCR; about 10^2.5 TCID₅₀/mL). For validation of the in-house AC-ELISA, 295 porcine fecal/diarrhea samples, collected from different provinces of China, were evaluated and compared with conventional RT-PCR and TaqMan RT-quantitative PCR (qPCR). The sensitivity and specificity of this in-house AC-ELISA relative to RT-qPCR were found to be 91.67% and 100%, respectively, with the strong agreement (kappa = 0.972) between these two techniques. Total detection rate with AC-ELISA, conventional RT-PCR, and RT-qPCR were found to be 11.2%, 11.5%, and 12.2%, respectively, without any statistical significant difference. Moreover, AC-ELISA failed to detect any cross-reactivity with porcine epidemic diarrhea virus, transmissible gastroenteritis virus, pseudorabies virus, and porcine circovirus-2. These results suggested that our developed method was rapid, highly specific, and sensitive, which may help in large-scale surveillance, timely detection, and preventive control of rotavirus infection in porcine farms.

Genotypic and epitope characteristics of group A porcine rotavirus strains circulating in Canada

Surveillance of Rotavirus A (RVA) infections in North America swine populations are limited and not performed over a significant time period to properly assess the diversity of RVA strains in swine. The VP7 (G) and VP4 (P) genes of 32 Canadian RVA strains, circulating between 2009 and 2015 were sequenced, identifying the G3P[13], G5P[7], G9P[7], G9[13], and G9[19] genotype combinations. The Canadian RVA strains were compared to the RVA strains present in the swine ProSystems RCE rotavirus vaccine. The comparison revealed multiple amino acid differences in the G and P antigenic epitopes, regardless of the G and P genotypes but specifically in the Canadian G3, P[13] and P[19] genotypes. Our study further contributes to the characterization of RVA's evolution and disease mitigation among swine, which may optimize target vaccine design, thereby minimizing RVA disease in this economically important animal population.

Porcine Rotaviruses: Epidemiology, Immune Responses and Control Strategies

Rotaviruses (RVs) are a major cause of acute viral gastroenteritis in young animals and children worldwide. Immunocompetent adults of different species become resistant to clinical disease due to post-infection immunity, immune system maturation and gut physiological changes. Of the 9 RV genogroups (A–I), RV A, B, and C (RVA, RVB, and RVC, respectively) are associated with diarrhea in piglets. Although discovered decades ago, porcine genogroup E RVs (RVE) are uncommon and their pathogenesis is not studied well. The presence of porcine RV H (RVH), a newly defined distinct genogroup, was recently confirmed in diarrheic pigs in Japan, Brazil, and the US. The complex epidemiology, pathogenicity and high genetic diversity of porcine RVAs are widely recognized and well-studied. More recent data show a significant genetic diversity based on the VP7 gene analysis of RVB and C strains in pigs. In this review, we will summarize previous and recent research to provide insights on historic and current prevalence and genetic diversity of porcine RVs in different geographic regions and production systems. We will also provide a brief overview of immune responses to porcine RVs, available control strategies and zoonotic potential of different RV genotypes. An improved understanding of the above parameters may lead to the development of more optimal strategies to manage RV diarrheal disease in swine and humans.

Epidemiological survey of enteric viruses in wild boars in the Czech Republic: First evidence of close relationship between wild boar and human rotavirus A strains

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Prevalence of enteric RNA-viruses in free-living wild boars was studied.

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Most frequent were teschovirus A, sapelovirus A, RVC; less prevalent RVA and EV-G.

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No PRRSV or members of family Coronaviridae were detected.

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We found close relationship between wild boar and domestic pig or human RVA strains.

Population of wild boar is increasing in the whole Europe, the animals migrate close to human habitats which greatly increases the possibility of natural transmission between domestic animals or humans and wild boars. The aim of the study was to estimate in population of free-living wild boar in the Czech Republic the prevalence of enteric viral pathogens, namely rotavirus groups A and C (RVA and RVC), porcine reproductive and respiratory syndrome virus (PRRSV), and members of family Coronaviridae (transmissible gastroenteritis virus – TGEV, porcine epidemic diarrhea virus − PEDV, porcine respiratory coronavirus – PRCV, and porcine hemagglutination encephalomyelitis virus – PHEV) and Picornaviridae,(teschovirus A – PTV, sapelovirus A – PSV, and enterovirus G – EV-G). In our study, stool samples from 203 wild boars culled during hunting season 2014–2015 (from October to January) were examined by RT-PCR. RVA was detected in 2.5% of tested samples. Nucleotide analysis of VP7, VP4, and VP6 genes revealed that four RVA strains belong to G4P[25]I1, G4P[6]I5, G11P[13]I5, and G5P[13]I5 genotypes and phylogenetic analysis suggested close relation to porcine and human RVAs. The prevalence of RVC in wild boar population reached 12.8%, PTV was detected in 20.2%, PSV in 8.9%, and EV-G in 2.5% of samples. During our study no PRRSV or coronaviruses were detected. Our study provides the first evidence of RVC prevalence in wild boars and indicates that wild boars might contribute to the genetic variability of RVA and also serve as an important reservoir of other enteric viruses.

Comparison of electron microscopy, ELISA, real time RT-PCR and insulated isothermal RT-PCR for the detection of Rotavirus group A (RVA) in feces of different animal species

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Agreement between molecular tests for Rotavirus group A (RVA) detection was 80–92%.

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The agreement between all assays was 81–100% in samples containing high viral loads.

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The sensitivity of RVA RT-iiPCR was 3–4 copies of in vitro transcribed dsRNA.

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The field-deployable RT-iiPCR system holds promise for on-site detection of RVA.

There is no gold standard for detection of Rotavirus Group A (RVA), one of the main causes of diarrhea in neonatal animals. Sensitive and specific real-time RT-PCR (rtRT-PCR) assays are available for RVA but require submission of the clinical samples to diagnostic laboratories. Patient-side immunoassays for RVA protein detection have shown variable results, particularly with samples from unintended species. A sensitive and specific test for detection of RVA on the farm would facilitate rapid management decisions. The insulated isothermal RT-PCR (RT-iiPCR) assay works in a portable machine to allow sensitive and specific on-site testing. The aim of this investigation was to evaluate a commercially available RT-iiPCR assay for RVA detection in feces from different animal species. This assay was compared to an in-house rtRT-PCR assay and a commercially available rtRT-PCR kit, as well as an ELISA and EM for RVA detection. All three PCR assays targeted the well-conserved NSP5 gene. Clinical fecal samples from 108 diarrheic animals (mainly cattle and horses) were tested. The percentage of positive samples by ELISA, EM, in-house rtRT-PCR, commercial rtRT-PCR, and RT-iiPCR was 29.4%, 31%, 36.7%, 51.4%, 56.9%, respectively. The agreement between different assays was high (81.3–100%) in samples containing high viral loads. The sensitivity of the RT-iiPCR assay appeared to be higher than the commercially available rtRT-PCR assay, with a limit of detection (95% confidence index) of 3–4 copies of in vitro transcribed dsRNA. In conclusion, the user-friendly, field-deployable RT-iiPCR system holds substantial promise for on-site detection of RVA.

Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans

Rotaviruses are an important cause of severe diarrheal illness in children globally. We characterized rotaviruses sampled in humans, insectivores (shrews) and rodents from urban and rural regions of Zhejiang province, China. Phylogenetic analyses revealed seven genotypic constellations of human rotaviruses with six different combinations of G and P genotypes – G3P[8] (50.06%), G9P[8] (36.16%), G1P[8] (8.92%), G2P[4] (4.63%), G3P[3] (0.12%), and G3P[9] (0.12%). In rodents and shrews sampled from the same locality we identified a novel genotype constellation (G32-P[46]-I24-R18-C17-M17-A28-N17-T19-E24-H19), a novel P genotype (P[45]), and two different AU-1-like rotaviruses associated with a G3P[3] genotype combination. Of particular note was a novel rotavirus from a human patient that was closely related to viruses sampled from rodents in the same region, indicative of a local species jump. In sum, these data are suggestive of the cross-species transmission of rodent rotaviruses into humans and for reassortment among human and animal rotaviruses.

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Rotaviruses are an important cause of severe diarrheal illness.

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Although rotaviruses are associated with a diverse range of animals, relatively little attention has been directed toward rotaviruses in rodents.

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However, as rodents often live in close proximity to humans and domestic animals, rodents may play an important role in the cross-species transmission of rotaviruses among animals and perhaps directly or indirectly to humans.

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Our data suggest the direct spill-over of rodent rotaviruses in human populations, as well as the reassortment between human and zoonotic rotaviruses.

Epidemiology of rotavirus A diarrhea in Chókwè, Southern Mozambique, from February to September, 2011

Acute diarrhea disease caused by Rotaviruses A (RVA) is still the leading cause of morbidity and mortality in children ≤5 years old in developing countries. An exploratory cross-sectional study was conducted between February and September, 2011 to determine the proportion of acute diarrhea caused by RVA. A total of 254 stool specimens were collected from children ≤5 years old with acute diarrhea, including outpatients (222 children) and inpatients (32 children), in three local health centers in Chókwè District, Gaza Province, South of Mozambique. RVA antigens were detected using enzyme immunoassay (EIA); the RVA G (VP7) and P (VP4) genotypes were determined by RT-PCR or analysis sequencing. Sixty (24%) out of 254 fecal specimens were positive for RVA by EIA; being 58 (97%) from children ≤2 years of age. RVA prevalence peaks in June and July (coldest and drier months) and the G[P] binary combination observed were G12P[8] (57%); G1P[8] (9%); G12P[6] (6%); and 2% for each of the following genotypes: G1P[6], G2P[6] G4P[6], and G9P[8]. Non-Typeable (NT) G and/or P genotypes were observed as follows: G12P [NT] (6%); G1P [NT], G3P[NT] and GNTP[NT] (4%). Considering the different GP combinations, G12 represented 67% of the genotypes. This is the first data showing the diversity of RVA genotypes in Mozambique highlighting the epidemiological importance of these viruses in acute diarrhea cases in children ≤2 years old. In addition, these findings will provide a baseline data before the introduction of the RVA monovalent (Rotarix(®) ) vaccine in the National Immunization Program in September 2015. J. Med. Virol. 88:1751-1758, 2016. © 2016 Wiley Periodicals, Inc.

Zoonotic transmission of rotavirus: surveillance and control

Group A rotavirus (Rotavirus A, RVA) is the main cause of acute dehydrating diarrhea in humans and numerous animal species. RVA shows vast diversity and a variety of human strains share genetic and antigenic features with animal origin RVA strains. This finding suggests that interspecies transmission is an important mechanism of rotavirus evolution and contributes to the diversity of human RVA strains. RVA is responsible for half a million deaths and several million hospitalizations worldwide. Globally, two rotavirus vaccines are available for routine use in infants. These vaccines show a great efficacy profile and induce protective immunity against various rotavirus strains. However, little is known about the long-term evolution and epidemiology of RVA strains under selective pressure related to vaccine use. Continuous strain surveillance in the post-vaccine licensure era is needed to help better understand mechanisms that may affect vaccine effectiveness.

Diversity of group A rotavirus on a UK pig farm

Group A rotaviruses (GARV) are a significant cause of enteritis in young pigs. The aim of this study was to extend our understanding of the molecular epidemiology of porcine GARV in the UK by investigating the genetic diversity of GARV on a conventional farrow-to-finish farm. Faecal samples were obtained from six batches of pigs in 2009 and 8 batches in 2010, when the pigs were 2, 3 (time point omitted in 2009), 4, 5, 6 and 8 weeks of age. Presence of rotavirus was detected by reverse transcriptase-polymerase chain reaction (RT-PCR) in 89% and 80% of samples from 2009 and 2010, respectively. A combination of multiplex PCRs and sequencing identified four VP7 genotypes (G2, G3, G4 and G5) and three VP4 genotypes (P[6], P[7] and P[32]) present in almost every combination over the 2 years. The predominant genotype combination was G5P[32] in 2009 and G4P[32] in 2010. Conservation among the P[32] sequences between 2009 and 2010 suggests that reassortment may have led to the different genotype combinations. There were significant changes in the predominant VP7 genotype prior to weaning at 4 weeks, and post weaning when pigs were moved to a different building. Phylogenetic analysis indicated that introduction of new viruses onto the farm was limited. Taken together, these findings suggest that genetically diverse GARV strains persist within the farm environment.