Zoonotic transmission of rotavirus: surveillance and control

Association between circulating rotavirus genotypes and histo-blood group antigens in the children hospitalized with acute gastroenteritis in Iran

Rotaviruses are the dominant cause of severe acute gastroenteritis in children under 5 years of age. Previous studies showed that some children are less susceptible to rotavirus gastroenteritis. It has been shown that this resistance depends on the rotavirus genotype and also human histo-blood group antigens (HBGAs), which works as a receptor for rotavirus surface protein (VP4). The present study aimed to evaluate the human genetic susceptibility to rotavirus gastroenteritis in Iran and to obtain a comparative analysis between rotavirus gastroenteritis and secretor or Lewis status in case and control groups in the Iranian population. The study was performed on fecal specimens from 108 children with acute rotavirus gastroenteritis from 2015 to 2017. A total of 50 fecal specimens from children with acute gastroenteritis of unknown etiology were also used as a control group. After the genotyping of positive rotavirus cases and human HBGAs by Sanger sequencing, the phylogenetic tree analysis showed that all rotavirus strains from Iran belonged to P[II]. The most common genotype was P[8] (n = 102; 94.4%), while the remaining belonged to P[4] (n = 3; 2.8%) and P[6] (n = 3; 2.8%) genotypes. The P[8] genotype was found to be associated with secretor and Lewis positive status (p < .05).

Genomic Analysis of an Indian G8P[1] Caprine Rotavirus-A Strain Revealing Artiodactyl and DS-1-Like Human Multispecies Reassortment

The surveillance studies for the presence of caprine rotavirus A (RVA) are limited in India, and the data for the whole-genome analysis of the caprine RVA is not available. This study describes the whole-genome-based analysis of a caprine rotavirus A strain, RVA/Goat-wt/IND/K-98/2015, from a goat kid in India. The genomic analysis revealed that the caprine RVA strain K-98, possess artiodactyl-like and DS-1 human-like genome constellation G8P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The three structural genes (VP2, VP4, and VP7) were close to caprine host having nucleotide-based identity range between 97.5 and 98.9%. Apart from them, other gene segments showed similarity with either bovine or human like genes, ultimately pointing toward a common evolutionary origin having an artiodactyl-type backbone of strain K-98. Phylogenetically, the various genes of the current study isolate also clustered inside clades comprising Human-Bovine-Caprine isolates from worldwide. The current findings add to the knowledge on caprine rotaviruses and might play a substantial role in designing future vaccines or different alternative strategies combating such infections having public health significance. To the best of our knowledge, this is the first report on the whole-genome characterization of a caprine RVA G8P[1] strain from India. Concerning the complex nature of the K-98 genome, whole-genome analyses of more numbers of RVA strains from different parts of the country are needed to comprehend the genomic nature and genetic diversity among caprine RVA.

Emerging and Neglected Viruses of Zoonotic Importance in Croatia

Several arboviruses have emerged in Croatia in recent years. Tick-borne encephalitis is endemic in continental counties; however, new natural micro-foci have been detected. Two autochthonous dengue cases were reported in 2010. West Nile virus emerged in 2012, followed by emergence of Usutu virus in 2013. Although high seroprevalence rates of Toscana virus have been detected among residents of Croatian littoral, the virus remains neglected, with only a few clinical cases of neuroinvasive infections reported. Lymphocytic choriomeningitis virus is a neglected neuroinvasive rodent-borne virus. So far, there are no reports on human clinical cases; however, the seroprevalence studies indicate the virus presence in the Croatian mainland. Puumala and Dobrava hantaviruses are widely distributing rodent-borne viruses with sporadic and epidemic occurrence. Hepatitis E virus is an emerging food-borne virus in Croatia. After the emergence in 2012, cases were regularly recorded. Seropositivity varies greatly by region and population group. Rotaviruses represent a significant healthcare burden since rotavirus vaccination is not included in the Croatian national immunization program. Additionally, rotaviruses are widely distributed in the Croatian ecosystem. A novel coronavirus, SARS-CoV-2, emerged in February 2020 and spread rapidly throughout the country. This review focuses on emerging and neglected viruses of zoonotic importance detected in Croatia.

Genomic analysis reveals G3P[13] porcine rotavirus A interspecific transmission to human from pigs in a swine farm with diarrhoea outbreak

Rotavirus A (RVA) is a major diarrhoea-causing pathogen in young animals and children. The zoonotic potential of RVA has received extensive attention in recent years. In May 2018, an outbreak of diarrhoea among piglets occurred on a swine farm in Sichuan province, PR China. RVA was detected in 95.7 % (22/23) of piglet samples, 60 % (9/15) of sow samples and 100 % (3/3) of pig-breeder faecal samples. The predominant RVA genotype on this swine farm was G3P[13], and G3P[13] RVA was also detected in the three breeder faecal samples. Three G3P[13] RVA strains were isolated from a piglet faecal sample, a sow faecal sample and a pig-breeder faecal sample, and were named SCLS-X1, SCLS-3 and SCLS-R3, respectively. The complete sequences of 11 gene segments of these three isolates were derived. Phylogenetic analysis showed that ten gene segments (VP7, VP4, VP1-VP3 and NSP1-NSP5) of pig-breeder isolate SCLS-R3 were closely related to pig isolates SCLS-X1 and SCLS-3 from this farm. Only the VP6 gene shared higher homology with human RVA strain I321. Therefore, a G3P[13] porcine RVA strain most likely infected pig breeders. These results provided the first complete epidemiological link demonstrating interspecies transmission of G3P[13] RVA from pigs to human. Our data contribute to an improved understanding of the genetic evolution and interspecies transmission of RVA.

Phylogenetic analysis of open reading frame of 11 gene segments of novel human-bovine reassortant RVA G6P[1] strain in Pakistan

Multiple Rotavirus A (RVA) strains are linked with gastrointestinal infections in children that fall in age bracket of 0 to 60 months. However, the problem is augmented with emergence of unique strains that reassort with RVA strains of animal origin. The study describes the sequence analysis of a rare G6P[1] rotavirus strain isolated from a less than 1 year old child, during rotavirus surveillance in Rawalpindi district, Pakistan in 2010. Extracted RNA from fecal specimen was subjected to high throughput RT-PCR for structural and nonstructural gene segments. The complete rotavirus genome of one isolate RVA/Human-wt/PAK/PAK99/2010/G6P[1] was sequenced for phylogenetic analysis to elucidate the evolutionary linkages and origin. Full genome examination of novel strain RVA/Human-wt/PAK/PAK99/2010/G6P[1] revealed the unique genotype assemblage: G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H1. The evolutionary analyses of VP7, VP4, NSP1 and NSP3 gene segments revealed that PAK99 clustered with bovine, or cattle-like rotavirus strains from other closely related species, in the genotypes G6, P[1], A3 and T6 respectively. Gene segments VP6, VP1, VP2, VP3, NSP2 and NSP4 all possessed the DS-1-like bovine genotype 2 and bovine (-like) RVA strains instead of RVA strains having human origin. However, the NSP5 gene was found to cluster closely with contemporary human Wa-like rotavirus strains of H1 genotype. This is the first report on bovine-human (Wa-like reassortant) genotype constellation of G6P[1] strain from a human case in Pakistan (and the second description worldwide). Our results emphasize the significance of incessant monitoring of circulating RVA strains in humans and animals for better understanding of RV evolution.

Occurrence and genetic diversity of rotavirus A in faeces of diarrheic calves submitted to a veterinary laboratory in Spain

A total of 237 faecal specimens from diarrheic calves younger than two months were collected and submitted for diagnosis of enteropathogens over a two-year period (2017-2018) to a veterinary laboratory. Samples originated from 193 dairy and beef farms in 29 provinces distributed throughout Spain, and were tested for the occurrence of three target enteric pathogens by reverse transcription real-time PCR (RT-qPCR): bovine rotavirus A (RVA), Cryptosporidium parvum and bovine coronavirus (BCoV). RT-PCR and nucleotide sequencing analysis were used to determine the G (VP7 gene) and P (VP4 gene) genotypes of 26 specimens positive for RVA. A total of 188 specimens (79.3 %) were positive for at least one of the three target enteric pathogens, and 101 samples (42.6 %) harbored mixed infections. The individual prevalence was 57.8 %, 50.6 % and 23.6 % for C. parvum, RVA and BCoV, respectively. Molecular analysis of selected RVA strains revealed the presence of the G6, G10, G3, P[5] and P[11] genotypes, with the combinations G6P[5] and G6P[11] being the most prevalent. Alignments of nucleotide sequences of the VP7 and VP4 markers showed a high frequency of single nucleotide polymorphisms (SNPs), with up to 294 SNPs found in 869bp of sequence at the G6 genotype (0.338 SNPs/nt), which reveals the extensive genetic diversity of RVA strains. Phylogenetic analysis of the VP7 gene of the G6 strains revealed four distinct lineages, with most strains clustering in the G6-IV lineage. The discrepancies between the RVA genotypes circulating in the sampled cattle farms and the genotypes contained in commercial vaccines currently available in Spain are discussed. We believe that this is the first study on the molecular characterization of rotavirus infecting cattle in Spain.

Rotavirus A, C, and H in Brazilian pigs: potential for zoonotic transmission of RVA

Rotaviruses (RVs) have been identified as one of the main infectious causes of diarrhea in young pigs. We determined the prevalence of rotavirus A (RVA), C (RVC), and H (RVH) in pigs on a Brazilian farm. Samples were screened by reverse-transcription (RT)-PCR, and samples positive for RVA were genotyped by PCR amplification and sequencing analysis. Of the 329 fecal samples analyzed, 102 (30.9%) were positive for RV, 25 (7.6%) contained RVA only, 32 (9.7%) contained RVC only, and 31 (9.4%) contained RVH only. Co-circulation, the presence of ≥ 2 RVs in a sample, was detected in 14 (4.2%) samples. Of the 15 animals with diarrhea, 6 (40%) were positive for RV, and of the 314 asymptomatic animals, 96 (30.6%) were positive for RV; there was no statistically significant difference between the 2 groups (p = 0.441). Genotyping of RVA strains showed co-circulation of genotypes G1, G3, G9-P[8]-I1, and I2-E1. Phylogenetic analysis showed that some of the RVA genotypes found in pigs had high percentages of identity when compared with reference strains from humans, which suggests interspecies transmission. Because RVs may be zoonotic, excretion of RVs into the environment can result in transmission to agricultural workers causing interspecies infections and allowing the emergence of new reassorted viruses.

Molecular characterization identifies intra-host recombination and zoonotic potential of canine rotavirus among dogs from Thailand

From September 2016 to January 2019, we collected 710 rectal swabs from both healthy and sick dogs from small animal hospitals in 5 provinces of Thailand. The samples were tested for canine rotavirus group A (CRV) by using one-step RT-PCR specific to the VP6 gene. Our results showed that 0.70% (5/710) were positive for CRV. The five CRVs were then characterized by whole-genome sequencing. Our results showed that the genotype of Thai CRVs is G3P[3], which is the predominant genotype reported in dogs. The Thai CRVs posed a novel genetic constellation 'G3-P[3]-I3-R3-C3-M3-A9-N2-T3-E3-H6', which has never been reported in CRVs from dogs but has been reported in rotaviruses from humans. Based on phylogenetic analysis, the Thai CRVs are the result of multiple reassortments in which gene segments might have originated from human and bat rotaviruses and suggests the zoonotic potential of the virus.

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.

Whole genome and in-silico analyses of G1P[8] rotavirus strains from pre- and post-vaccination periods in Rwanda

Rwanda was the first low-income African country to introduce RotaTeq vaccine into its Expanded Programme on Immunization in May 2012. To gain insights into the overall genetic make-up and evolution of Rwandan G1P[8] strains pre- and post-vaccine introduction, rotavirus positive fecal samples collected between 2011 and 2016 from children under the age of 5 years as part of ongoing surveillance were genotyped with conventional RT-PCR based methods and whole genome sequenced using the Illumina MiSeq platform. From a pool of samples sequenced (n = 158), 36 were identified as G1P[8] strains (10 pre-vaccine and 26 post-vaccine), of which 35 exhibited a typical Wa-like genome constellation. However, one post vaccine strain, RVA/Human-wt/RWA/UFS-NGS:MRC-DPRU442/2012/G1P[8], exhibited a RotaTeq vaccine strain constellation of G1-P[8]-I2-R2-C2-M2-A3-N2-T6-E2-H3, with most of the gene segments having a close relationship with a vaccine derived reassortant strain, previously reported in USA in 2010 and Australia in 2012. The study strains segregated into two lineages, each containing a paraphyletic pre- and post-vaccine introduction sub-lineages. In addition, the study strains demonstrated close relationship amongst each other when compared with globally selected group A rotavirus (RVA) G1P[8] reference strains. For VP7 neutralization epitopes, amino acid substitutions observed at positions T91A/V, S195D and M217T in relation to the RotaTeq vaccine were radical in nature and resulted in a change in polarity from a polar to non-polar molecule, while for the VP4, amino acid differences at position D195G was radical in nature and resulted in a change in polarity from a polar to non-polar molecule. The polarity change at position T91A/V of the neutralizing antigens might play a role in generating vaccine-escape mutants, while substitutions at positions S195D and M217T may be due to natural fluctuation of the RVA. Surveillance of RVA at whole genome level will enhance further assessment of vaccine impact on circulating strains, the frequency of reassortment events under natural conditions and epidemiological fitness generated by such events.

Genetic characterisation of novel G29P[14] and G10P[11] rotavirus strains from African buffalo

We report the first description of rotavirus A strains in African buffalo (Syncerus caffer). Following RNA extraction from stool samples, cDNA was prepared, followed either by sequence-independent amplification and 454 pyrosequencing or direct sequencing on an Illumina MiSeq platform. RVA/Buffalo-wt/ZAF/4426/2002/G29P[14] exhibited a novel G29P[14] combination and an artiodactyl backbone: I2-R2-C2-M2-A11-N2-T6-E2-H3. RVA/Buffalo-wt/ZAF/1442/2007/G10P[11] also exhibited an artiodactyl backbone: I2-R2-C2-M2-A13-N2-T6-E2-H3. Characterisation of these genome constellations indicate that the two buffalo strains are moderately diverse from each other and related to South African bovine RVA strains. The detection of RVA in buffalo contribute to our understanding of the host range of rotavirus in animals.

Evidence for zoonotic transmission of species A rotavirus from goat and cattle in nomadic herds in Morocco, 2012-2014

Species A rotaviruses (RVAs) are a leading cause of diarrhea in children and in the young of a large variety of mammalian and avian host species. The purpose of this study was to identify RVA in nomadic goats and calves during severe diarrhea outbreaks in 2012 and 2014 in Bouaarfa, Morocco, and to characterize the complete genomic constellation of two bovine and caprine strains (S18 and S19) and their genetic relatedness with the human strain ma31 detected in 2011 in Morocco. Partial nucleotide sequencing of VP4 and VP7 genes for the twenty-two positive samples revealed three circulating genotypes: G6P[14], G10P[14], and G10P[5] with predominance of G6P[14] genotype. Full-genome sequencing for both strains S18 and S19 presented, respectively, the following genomic constellations: G6-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3 and G10-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3. Phylogenetic analyses and the analysis of the VP8* antigenic epitopes for S18, S19 and ma31 revealed a shared similarity with bovine, caprine, ovine and human strains from Morocco and other countries. The VP2 and NSP1 genes of the S19 strain were closely related to those of the cognate genes of the human ma31 strain, while the VP4 gene of S18 strain was closely related to the cogent gene of the ma31 strain. Our findings revealed cases of zoonotic transmission and confirmed the risk of emergence of new genotypes in some environments such as nomadic regions, where close physical proximity between human and livestock is common. The present study is novel in reporting whole-genome analyses of RVA isolates obtained from nomadic livestock in Morocco.

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

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

First isolation and whole-genome characterization of a G9P[14] rotavirus strain from a diarrheic child in Egypt

An unusual group A rotavirus (RVA) strain (RVA/Human-tc/EGY/AS997/2012/G9[14]) was isolated for the first time in a faecal sample from a 6-month-old child who was hospitalized for treatment of acute gastroenteritis in Egypt in 2012. Whole-genome analysis showed that the strain AS997 had a unique genotype constellation: G9-P[14]-I2-R2-C2-M2-A11-N2-T1-E2-H1. Phylogenetic analysis indicated that the strain AS997 had the consensus P[14] genotype constellation with the G9, T1 and H1 reassortment. This suggests either a mixed gene configuration originated from a human Wa-like strain and a P[14]-containing animal virus, or that this P[14] could have been acquired via reassortment of human strains only. The study shows the possible roles of interspecies transmission and multiple reassortment events leading to the generation of novel rotavirus genotypes and underlines the importance of whole-genome characterization of rotavirus strains in surveillance studies.

Porcine rotavirus C strains carrying human-like NSP4 and NSP5

BACKGROUND

Rotavirus C (RVC) is an enteric pathogen that affects humans and animals around the world.

METHODS

In this study, we characterized the genetic diversity of RVC strains detected in asymptomatic Brazilian pigs by sequencing the NSP4, NSP5 and VP6 genes.

RESULTS

The results of reverse transcription polymerase chain reaction showed that 53 of 579 samples (9.2%) contained RVC. Positive samples were genotyped by sequencing gene segments NSP4, and NSP5. Most of the RCV strains encountered were classified into typically porcine genotypes: E1-H1. In two strains, BP182 and BP208, the NSP4 gene grouped with E2-RVC human strains with 94.2%-96.5% nucleotide identity, although the NSP5 gene was porcine-like (H1). In strain SD67, the NSP5 gene grouped with human H2-RVC with 92.5%-98.7% nucleotide identity and the NSP4 gene grouped with porcine strains (E1). Two strains (BP208 and SD67) were also genotyped by sequencing gene segment VP6. The VP6 gene grouped with porcine strains, I6 (89.3%-90.2% nucleotide identity) and I5 (88.7%-90.5% nucleotide identity), for strains BP208 and SD67, respectively.

CONCLUSIONS

These results are indicative of genomic reassortment between RVC strains of human and porcine origin. In recent years, the incidence of RVC infection among humans has increased significantly. It is important to measure the frequency of interspecies transmission in order to monitor the evolution of these viruses and to identify rearranged strains that may lead to an epidemic.

Intragenic recombination influences rotavirus diversity and evolution

Because of their replication mode and segmented dsRNA genome, homologous recombination is assumed to be rare in the rotaviruses. We analyzed 23,627 complete rotavirus genome sequences available in the NCBI Virus Variation database, and found 109 instances of homologous recombination, at least eleven of which prevailed across multiple sequenced isolates. In one case, recombination may have generated a novel rotavirus VP1 lineage. We also found strong evidence for intergenotypic recombination in which more than one sequence strongly supported the same event, particularly between different genotypes of segment 9, which encodes the glycoprotein, VP7. The recombined regions of many putative recombinants showed amino acid substitutions differentiating them from their major and minor parents. This finding suggests that these recombination events were not overly deleterious, since presumably these recombinants proliferated long enough to acquire adaptive mutations in their recombined regions. Protein structural predictions indicated that, despite the sometimes substantial amino acid replacements resulting from recombination, the overall protein structures remained relatively unaffected. Notably, recombination junctions appear to occur nonrandomly with hot spots corresponding to secondary RNA structures, a pattern seen consistently across segments. In total, we found strong evidence for recombination in nine of eleven rotavirus A segments. Only segments 7 (NSP3) and 11 (NSP5) did not show strong evidence of recombination. Collectively, the results of our computational analyses suggest that, contrary to the prevailing sentiment, recombination may be a significant driver of rotavirus evolution and may influence circulating strain diversity.

Rotavirus Burden, Genetic Diversity and Impact of Vaccine in Children under Five in Tanzania

In Tanzania, rotavirus infections are responsible for 72% of diarrhea deaths in children under five. The Rotarix vaccine was introduced in early 2013 to mitigate rotavirus infections. Understanding the disease burden and virus genotype trends over time is important for assessing the impact of rotavirus vaccine in Tanzania. When assessing the data for this review, we found that deaths of children under five declined after vaccine introduction, from 8171/11,391 (72% of diarrhea deaths) in 2008 to 2552/7087 (36% of diarrhea deaths) in 2013. Prior to vaccination, the prevalence of rotavirus infections in children under five was 18.1–43.4%, 9.8–51%, and 29–41% in Dar es Salaam, Mwanza and Tanga, respectively, and after the introduction of vaccines, these percentages declined to 17.4–23.5%, 16–19%, and 10–29%, respectively. Rotaviruses in Tanzania are highly diverse, and include genotypes of animal origin in children under five. Of the genotypes, 10%, 28%, and 7% of the strains are untypable in Dar es Salaam, Tanga, and Zanzibar, respectively. Mixed rotavirus genotype infection accounts for 31%, 29%, and 12% of genotypes in Mwanza, Tanga and Zanzibar, respectively. The vaccine effectiveness ranges between 53% and 75% in Mwanza, Manyara and Zanzibar. Rotavirus vaccination has successfully reduced the rotavirus burden in Tanzania; however, further studies are needed to better understand the relationship between the wildtype strain and the vaccine strain as well as the zoonotic potential of rotavirus in the post-vaccine era.

Rotavirus Species B Encodes a Functional Fusion-Associated Small Transmembrane Protein

Rotavirus is an important cause of diarrheal disease in young mammals. Rotavirus species A (RVA) causes most human rotavirus diarrheal disease and primarily affects infants and young children. Rotavirus species B (RVB) has been associated with sporadic outbreaks of human adult diarrheal disease. RVA and RVB are predicted to encode mostly homologous proteins but differ significantly in the proteins encoded by the NSP1 gene. In the case of RVB, the NSP1 gene encodes two putative protein products of unknown function, NSP1-1 and NSP1-2. We demonstrate that human RVB NSP1-1 mediates syncytium formation in cultured human cells. Based on sequence alignment, NSP1-1 proteins from species B, G, and I contain features consistent with fusion-associated small transmembrane (FAST) proteins, which have previously been identified in other genera of the Reoviridae family. Like some other FAST proteins, RVB NSP1-1 is predicted to have an N-terminal myristoyl modification. Addition of an N-terminal FLAG peptide disrupts NSP1-1-mediated fusion. NSP1-1 from a human RVB mediates fusion of human cells but not hamster cells and, thus, may serve as a species tropism determinant. NSP1-1 also can enhance RVA replication in human cells, both in single-cycle infection studies and during a multicycle time course in the presence of fetal bovine serum, which inhibits rotavirus spread. These findings suggest potential yet untested roles for NSP1-1 in RVB species tropism, immune evasion, and pathogenesis.IMPORTANCE While species A rotavirus is commonly associated with diarrheal disease in young children, species B rotavirus has caused sporadic outbreaks of adult diarrheal disease. A major genetic difference between species A and B rotaviruses is the NSP1 gene, which encodes two proteins for species B rotavirus. We demonstrate that the smaller of these proteins, NSP1-1, can mediate fusion of cultured human cells. Comparison with viral proteins of similar function provides insight into NSP1-1 domain organization and fusion mechanism. These comparisons suggest that there is a fatty acid modification at the amino terminus of the protein, and our results show that an intact amino terminus is required for NSP1-1-mediated fusion. NSP1-1 from a human virus mediates fusion of human cells, but not hamster cells, and enhances species A rotavirus replication in culture. These findings suggest potential, but currently untested, roles for NSP1-1 in RVB host species tropism, immune evasion, and pathogenesis.

Full-length genome analysis of the first human G8P[14] rotavirus strain from Morocco suggests evidence of zoonotic transmission

An unusual group A rotavirus (RVA) strain MAR/ma31/2011/G8P[14] was detected for the first time in Morocco in a stool sample from hospitalized child aged 18 months suffering from acute gastroenteritis and fever in 2011. Complete genome sequencing of the ma31 strain was done using the capillary sequencing technology. The analysis revealed the G8-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3 constellation and the backbone genes: I2-R2-C2-M2-A11-N2-T6-E2-H3 are commonly found in RVA strains from artiodactyls such as cattle. The constellation was shared with another Italian zoonotic G8P[14] strains (BA01 and BA02), two Hungarian human strains (182-02 and BP1062) and a sheep RVA strain OVR762. Phylogenetic analysis of each genome segment of ma31 revealed a mixed gene configuration originated from animals and human. Comparison of the antigenic regions of VP7 and VP4 amino acid sequences between ma31 strain and selected animal and human strains bearing G8 and or P[14], showed a high level of conservation, while many substitutions was observed in comparison with RotaTeq™ and Rotarix™ vaccine strains. In contrast, alignment analysis of the four antigenic sites of VP6 revealed a high degree of conservation. These findings reveal a typical zoonotic origin of the strain and confirm a high potential for RVA zoonotic transmission between bovine and humans, allowing the generation of novel rotavirus genotypes.

Whole-genome characterization of G12 rotavirus strains detected in Mozambique reveals a co-infection with a GXP[14] strain of possible animal origin

A high prevalence of G12 rotavirus strains has previously been reported in southern Mozambique. In this study, the full genomes of five Mozambican G12 strains were determined directly from stool using an Illumina Miseq platform. One sample (0060) contained an intergenogroup co-infection of a G12P[8] Wa-like strain and a GXP[14] DS-1-like strain. The sequences of seven genome segments, detected for the GXP[14] strain, clustered with a diverse group of mostly animal strains, suggesting co-infection with a strain of possible animal origin. The stool samples contained G12P[6] rotavirus strains with Wa-like backbones. Phylogenetic analyses of the VP4 and VP7 encoding segments of the G12P[6] strains suggested that they were reassortants containing backbones that are similar to that of the G12P[8] strain. The study confirms previous observations of interspecies transmission and emphasizes the importance of whole-genome sequencing in order to evaluate rotavirus co-infections and reassortants.

Genetic diversity and zoonotic potential of rotavirus A strains in the southern Andean highlands, Peru

Interspecies transmission is an important mechanism of evolution and contributes to rotavirus A (RVA) diversity. In order to evaluate the detection frequency, genetic diversity, epidemiological characteristics and zoonotic potential of RVA strains in faecal specimens from humans and animals cohabiting in the same environment in the department of Cusco, Peru, by molecular analysis, 265 faecal specimens were obtained from alpacas, llamas, sheep and shepherd children, and tested for RVA by RT-PCR. Genotyping was performed by multiplex PCR and sequence analysis. Rotavirus A was detected in 20.3% of alpaca, 47.5% of llama, 100% of sheep and 33.3% of human samples. The most common genetic constellations were G3-P[40]-I8-E3-H6 in alpacas, G1/G3-P[8]-I1-E1-H1 in llamas, G1/G3/G35-P[1]/P[8]-I1-E1-H1 in sheep and G3-P[40]-I1/I8-E3-H1 in humans. The newly described genotypes P[40] and P[50] were identified in all host species, including humans. Genotyping showed that the majority of samples presented coinfection with two or more RVA strains. These data demonstrate the great genetic diversity of RVA in animals and humans in Cusco, Peru. Phylogenetic analysis suggested that the strains represent zoonotic transmission among the species studied. Due to the characteristics of the human and animal populations in this study (cohabitation of different host species in conditions of poor sanitation and hygiene), the occurrence of zoonoses is a real possibility.

Detection of potentially pathogenic enteric viruses in environmental samples from Kenya using the bag-mediated filtration system

Enteric virus environmental surveillance via a highly sensitive method is critical, as many enteric viruses have low infectious doses and can persist in the environment for extended periods. This study determined the potential of the novel bag-mediated filtration system (BMFS) to recover human enteric viruses and pepper mild mottle virus (PMMoV) from wastewater and wastewater-impacted surface waters, examined PMMoV use as a fecal contamination indicator in Kenya, and identified potential BMFS process controls. From April 2015 to April 2016, BMFS samples were collected from seven sites in Kenya (n = 59). Enteroviruses and PMMoV were detected in 100% of samples, and human adenovirus, human astrovirus, hepatitis A virus, norovirus GI, norovirus GII, sapovirus, and human rotavirus were detected in the majority of samples. The consistent detection of enteroviruses and PMMoV suggests that these viruses could be used as indicators in similarly fecally contaminated sites and BMFS process controls. As contamination of surface water sources remains a global issue, enteric virus environmental surveillance is necessary. This study demonstrates an effective way to sample large volumes of wastewater and wastewater-impacted surface waters for the detection of multiple enteric viruses simultaneously.

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.

RA-839, a selective agonist of Nrf2/ARE pathway, exerts potent anti-rotaviral efficacy in vitro

Acute watery diarrhea due to Rotavirus (RV) infection is associated with high infantile morbidity and mortality in countries with compromised socio-economic backgrounds. Although showing promising trends in developed countries, the efficacy of currently licensed RV vaccines is sub-optimal in socio-economically poor settings with high disease burden. Currently, there are no approved anti-rotaviral drugs adjunct to classical vaccination program. Interestingly, dissecting host-rotavirus interaction has yielded novel, non-mutable host determinants which can be subjected to interventions by selective small molecules. The present study was undertaken to evaluate the anti-RV potential of RA-839, a recently discovered small molecule with potent and highly selective agonistic activity towards cellular redox stress-sensitive Nuclear factor erytheroid-derived-2-like 2 (Nrf2)/Antioxidant Response Element (ARE) pathway. In vitro studies revealed that RA-839 inhibits RV RNA and protein expression, viroplasm formation, yield of virion progeny and virus-induced cytopathy independent of RV strains, RV-permissive cell lines and without bystander cytotoxicity. Anti-RV potency of RA-839 was subsequently identified to be independent of stochastic Interferon (IFN) stimulation but to be dependent on RA-839's ability to stimulate Nrf2/ARE signaling. Interestingly, anti-rotaviral effects of RA-839 were also mimicked by 2-Cyano-3, 12-dioxo-oleana-1, 9(11)-dien-28-oic acid methyl ester (CDDO-Me) and Hemin, two classical pharmacological activators of Nrf2/ARE pathway. Overall, this study highlights that RA-839 is a potent antagonist of RV propagation in vitro and can be developed as anti-rotaviral therapeutics.

Viral gastroenteritis

Enteric viruses, particularly rotaviruses and noroviruses, are a leading cause of gastroenteritis worldwide. Rotaviruses primarily affect young children, accounting for almost 40% of hospital admissions for diarrhoea and 200 000 deaths worldwide, with the majority of deaths occurring in developing countries. Two vaccines against rotavirus were licensed in 2006 and have been implemented in 95 countries as of April, 2018. Data from eight high-income and middle-income countries showed a 49-89% decline in rotavirus-associated hospital admissions and a 17-55% decline in all-cause gastroenteritis-associated hospital admissions among children younger than 5 years, within 2 years of vaccine introduction. Noroviruses affect people of all ages, and are a leading cause of foodborne disease and outbreaks of gastroenteritis worldwide. Prevention of norovirus infection relies on frequent hand hygiene, limiting contact with people who are infected with the virus, and disinfection of contaminated environmental surfaces. Norovirus vaccine candidates are in clinical trials; whether vaccines will provide durable protection against the range of genetically and antigenically diverse norovirus strains remains unknown. Treatment of viral gastroenteritis is based primarily on replacement of fluid and electrolytes.

Inactivation Mechanisms of Human and Animal Rotaviruses by Solar UVA and Visible Light

Two rotavirus (RV) strains (sialidase-resistant Wa and sialidase-sensitive OSU) were irradiated with simulated solar UVA and visible light in sensitizer-free phosphate buffered solution (PBS) (lacking exogenous reactive oxygen species (ROS)) or secondary effluent wastewater (producing ROS). Although light attenuated for up to 15% through the secondary effluent wastewater (SEW), the inactivation efficacies increased by 0.7 log₁₀ for Wa and 2 log₁₀ for OSU compared to those in sensitizer-free phosphate buffered solution (PBS) after 4 h of irradiation. A binding assay using magnetic beads coated with porcine gastric mucin containing receptors for rotaviruses (PGM-MB) was developed to determine if inactivation influenced RV binding to its receptors. The linear correlation between the reduction in infectivity and the reduction in binding after irradiation in sensitizer-free solution suggests that the main mechanism of RV inactivation in the absence of exogenous ROS was due to damage to VP8*, the RV protein that binds to host cell receptors. For a given reduction in infectivity, greater damage in VP8* was observed with sialidase-resistant Wa compared to sialidase-sensitive OSU. The lack of correlation between the reduction in infectivity and the reduction in binding, in SEW, led us to include RNase treatment before the binding step to quantify virions with intact protein capsids and exclude virions that can bind to the receptors but have their capsid permeable after irradiation. This assay showed a linear correlation between the reduction in RV infectivity and RV-receptor interactions, suggesting that RV inactivation in SEW was due to compromised capsid proteins other than the VP8* protein. Thus, rotavirus inactivation by UVA and visible light irradiation depends on both the formation of ROS and the stability of viral proteins.

Detection and molecular characterization of two rare G8P[14] and G3P[3] rotavirus strains collected from children with acute gastroenteritis in Japan

This study describes the detection and molecular characterization of two rare G8P[14] and G3P[3] rotavirus strains, which were collected from children with acute gastroenteritis in 2014 in Japan. Among 247 rotaviruses, one G8P[14] (strain 12,597) and one G3P[3] (strain 12,638) rotaviruses were detected. The genotypes of 11 gene segments of these two rotavirus strains (RVA/Human-wt/JPN/12597/2014/G8P[14] and RVA/Human-wt/JPN/12638/2014/G3P[3]) were characterized. The genotype constellation of strain 12,597 was assigned to G8-P[14]-I2-R2-C2-M2-A3-N2-T9-E2-H3, and this strain possessed a rare T9 genotype of NSP3 gene which has never been reported previously in combination with G8 genotype of VP7 gene. Molecular characterization and phylogenetic analysis suggested that the strain 12,597 had the consensus G8P[14] backbone that originated from the rotaviruses of animal origins such as cows, deer, dogs, and cats. The genotype constellation of strain 12,638 was identified as G3-P[3]-I3-R3-C3-M3-A9-N2-T3-E3-H6. The VP7 and VP4 genotypes of strain 12,638 was similar to those of the Cat97-like strains, but the VP1, VP2, and VP3 were closely related to those of the AU-1-like strain. Interestingly, the NSP1 to NSP3 genes shared highest identities with those of a bat rotavirus (RVA/Bat-wt/ZMB/LUS12-14/2012/G3P[3] strain). These findings indicated that the strain 12,638 was an intra-genotype reassortant strain among the AU-1-like strains, the Cat97-like strains and the bat strain. Interestingly, the strains 12,597 and 12,638 possessed the same N2 genotype of NSP2 gene. The results of this study support the possible roles of interspecies transmission and multiple reassortment events for generating the genetic diversity of rotavirus in human.

Characterisation of a rare, reassortant human G10P[14] rotavirus strain detected in Honduras

BACKGROUND

Although first detected in animals, the rare rotavirus strain G10P[14] has been sporadically detected in humans in Slovenia, Thailand, United Kingdom and Australia among other countries. Earlier studies suggest that the strains found in humans resulted from interspecies transmission and reassortment between human and bovine rotavirus strains.

OBJECTIVES

In this study, a G10P[14] rotavirus genotype detected in a human stool sample in Honduras during the 2010-2011 rotavirus season, from an unvaccinated 30-month old boy who reported at the hospital with severe diarrhea and vomiting, was characterised to determine the possible evolutionary origin of the rare strain.

METHODS

For the sample detected as G10P[14], 10% suspension was prepared and used for RNA extraction and sequence independent amplification. The amplicons were sequenced by next-generation sequencing using the Illumina MiSeq 150 paired end method. The sequence reads were analysed using CLC Genomics Workbench 6.0 and phylogenetic trees were constructed using PhyML version 3.0.

FINDINGS

The next generation sequencing and phylogenetic analyses of the 11-segmented genome of the G10P[14] strain allowed classification as G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. Six of the genes (VP1, VP2, VP3, VP6, NSP2 and NSP4) were DS-1-like. NSP1 and NSP5 were AU-1-like and NSP3 was T6, which suggests that multiple reassortment events occurred in the evolution of the strain. The phylogenetic analyses and genetic distance calculations showed that the VP7, VP4, VP6, VP1, VP3, NSP1, NSP3 and NSP4 genes clustered predominantly with bovine strains. NSP2 and VP2 genes were most closely related to simian and human strains, respectively, and NSP5 was most closely related to a rhesus strain.

MAIN CONCLUSIONS

The genetic characterisation of the G10P[14] strain from Honduras suggests that its genome resulted from multiple reassortment events which were possibly mediated through interspecies transmissions.

Whole genome analysis of selected human and animal rotaviruses identified in Uganda from 2012 to 2014 reveals complex genome reassortment events between human, bovine, caprine and porcine strains

Rotaviruses of species A (RVA) are a common cause of diarrhoea in children and the young of various other mammals and birds worldwide. To investigate possible interspecies transmission of RVAs, whole genomes of 18 human and 6 domestic animal RVA strains identified in Uganda between 2012 and 2014 were sequenced using the Illumina HiSeq platform. The backbone of the human RVA strains had either a Wa- or a DS-1-like genetic constellation. One human strain was a Wa-like mono-reassortant containing a DS-1-like VP2 gene of possible animal origin. All eleven genes of one bovine RVA strain were closely related to those of human RVAs. One caprine strain had a mixed genotype backbone, suggesting that it emerged from multiple reassortment events involving different host species. The porcine RVA strains had mixed genotype backbones with possible multiple reassortant events with strains of human and bovine origin.Overall, whole genome characterisation of rotaviruses found in domestic animals in Uganda strongly suggested the presence of human-to animal RVA transmission, with concomitant circulation of multi-reassortant strains potentially derived from complex interspecies transmission events. However, whole genome data from the human RVA strains causing moderate and severe diarrhoea in under-fives in Uganda indicated that they were primarily transmitted from person-to-person.

Identification and characterization of a human G9P[23] rotavirus strain from a child with diarrhoea in Thailand: evidence for porcine-to-human interspecies transmission

An unusual rotavirus strain with the G9P[23] genotype (RVA/Human-wt/THA/KKL-117/2014/G9P[23]) was identified in a stool specimen from a 10-month-old child hospitalized with severe diarrhoea. In this study, we sequenced and characterized the complete genome of strain KKL-117. On full-genomic analysis, strain KKL-117 was found to have the following genotype constellation: G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. The non-G/P genotype constellation of this strain (I5-R1-C1-M1-A8-N1-T1-E1-H1) is commonly shared with rotavirus strains from pigs. Furthermore, phylogenetic analysis indicated that each of the 11 genes of strain KKL-117 appeared to be of porcine origin. Our observations provide important insights into the dynamic interactions between human and porcine rotavirus strains.

Dynamics of Virus Distribution in a Defined Swine Production Network Using Enteric Viruses as Molecular Markers

Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively.

IMPORTANCE

Using rotaviruses and astroviruses as markers of enteric contamination in a swine network has revealed the potential role of abattoirs and livestock transporters as a reservoir and vectors of enteric pathogens. The results from this study highlight the importance of tightening biosecurity measures. For instance, implementing sanitary vacancy between animal batches and emphasizing washing, disinfection, and drying procedures on farms and for transportation vehicles, as well as giving limited access and circulation of vehicles throughout the production premises, are some examples of measures that should be applied properly. The results also emphasize the need to closely monitor the dynamics of enteric contamination in the swine industry in order to better understand and potentially prevent the spread of infectious diseases. This is especially relevant when a virulent and economically damaging agent is involved, as seen with the recent introduction of the porcine epidemic diarrhea virus in the country.

Novel G9 rotavirus strains co-circulate in children and pigs, Taiwan

Molecular epidemiologic studies collecting information of the spatiotemporal distribution of rotavirus VP7 (G) and VP4 (P) genotypes have shown evidence for the increasing global importance of genotype G9 rotaviruses in humans and pigs. Sequence comparison of the VP7 gene of G9 strains identified different lineages to prevail in the respective host species although some of these lineages appear to be shared among heterologous hosts providing evidence of interspecies transmission events. The majority of these events indicates the pig-to-human spillover, although a reverse route of transmission cannot be excluded either. In this study, new variants of G9 rotaviruses were identified in two children with diarrhea and numerous pigs in Taiwan. Whole genome sequence and phylogenetic analyses of selected strains showed close genetic relationship among porcine and human strains suggesting zoonotic origin of Taiwanese human G9 strains detected in 2014-2015. Although the identified human G9P[19] and G9P[13] rotaviruses represented minority strains, the repeated detection of porcine-like rotavirus strains in Taiwanese children over time justifies the continuation of synchronized strain surveillance in humans and domestic animals.

Whole genome sequencing of a rare rotavirus from archived stool sample demonstrates independent zoonotic origin of human G8P[14] strains in Hungary

Genotype P[14] rotaviruses in humans are thought to be zoonotic strains originating from bovine or ovine host species. Over the past 30 years only few genotype P[14] strains were identified in Hungary totaling<0.1% of all human rotaviruses whose genotype had been determined. In this study we report the genome sequence and phylogenetic analysis of a human genotype G8P[14] strain, RVA/Human-wt/HUN/182-02/2001/G8P[14]. The whole genome constellation (G8-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3) of this strain was shared with another Hungarian zoonotic G8P[14] strain, RVA/Human-wt/HUN/BP1062/2004/G8P[14], although phylogenetic analyses revealed the two rotaviruses likely had different progenitors. Overall, our findings indicate that human G8P[14] rotavirus detected in Hungary in the past originated from independent zoonotic events. Further studies are needed to assess the public health risk associated with infections by various animal rotavirus strains.

Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection

Coordinated and synchronous surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus (RV) is an important cause of viral gastroenteritis in humans and animals. In this study, we document the RV diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of sixty human rotaviruses (all group A) and thirty-one porcine rotaviruses (thirteen group A, seven group B, six group C, and five group H). Phylogenetic analyses showed the co-circulation of multiple distinct RV group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C, and H, none of which have been previously reported in Vietnam. Furthermore, the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event.

Full genome characterization of the first G3P[24] rotavirus strain detected in humans provides evidence of interspecies reassortment and mutational saturation in the VP7 gene

During the 2008-2009 rotavirus season of the Centers for Disease Control and Prevention New Vaccine Surveillance Network, one case of paediatric acute gastroenteritis associated with a rotavirus G14P[24] strain was identified. This was the first detection of the genotype G14 and P[24] in humans, and the first detection of the G14P[24] combination. To gain an insight into the origins and the evolution of this strain, we determined the complete ORF sequences of all 11 genes. A majority of the genes identified were similar to the simian strain TUCH, except for the VP1 and VP7 genes that clustered only distantly with the bovine and equine strains, respectively. In addition, this strain carried AU-1-like NSP2 and NSP4 genes. Using codon-partitioning and protein-based phylogenetic approaches, we determined that the VP7 genotype of strain 2009727118 was actually G3; therefore, the proposed full genomic classification of the 2009727118 strain is G3-P[24]-I9-R2-C3-M3-A9-N3-T3-E3-H6. These findings indicate the possibility that the 2009727118 strain originated by interspecies transmission and multiple reassortment events involving human, bovine and equine rotaviruses, resulting in the introduction of some genes into the genome of simian rotaviruses. Additionally, we found evidence of mutational saturation in the third codon position of the VP7 ORF which presented an issue with homoplasy in phylogenetic analyses.