Full genomic characterization and phylogenetic analysis of a zoonotic human G8P[14] rotavirus strain detected in a sample from Guatemala

Gautam, Rashi; Mijatovic-Rustempasic, Slavica; Roy, Sunando; Esona, Mathew D.; López, Beatriz; Mencos, Yolanda; Rey-Benito, Gloria; Bowen, Michael D.

doi:10.1016/j.meegid.2015.05.004

Cited by 29 publications

(19 citation statements)

References 37 publications

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“…The closest genome segment relatives based on nucleic acid similarity, however, have been isolated from humans (Table 2), possibly pointing towards a bovine-human zoonotic transmission of this virus (54). The same genomic constellation has been found recently when unusual G8P[14] RVA isolates were recovered from human strain collections in Hungary (55) and Guatemala (56), and isolated from children in Slovenia (57) and Italy (58). Cook and colleagues calculated that there would be approximately 5000 zoonotic human infections per year in the UK from livestock transmission, but many would be asymptomatic (59).…”

Section: Discussionsupporting

confidence: 68%

Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses

Adriaenssens

Farkas

Harrison

et al. 2018

Preprint

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13Detection of viruses in the environment is heavily dependent on PCR-based 14 approaches that require reference sequences for primer design. While this strategy 15 can accurately detect known viruses, it will not find novel genotypes, nor emerging 16 and invasive viral species. In this study, we investigated the use of viromics, i.e. 17 high-throughput sequencing of the biosphere viral fraction, to detect human/animal 18 pathogenic RNA viruses in the Conwy river catchment area in Wales, UK. Using a 19 combination of filtering and nuclease treatment, we extracted the viral fraction from 20 wastewater, estuarine river water and sediment, followed by RNASeq analysis on 21 the Illumina HiSeq platform for the discovery of RNA virus genomes. We found a 22 the range of potentially pathogenic viruses that are present in the environment and 37 identify prevalent genotypes. The ultimate goal is to trace the fate of these 38 pathogenic viruses from origin to the point where they are a threat to human health, 39 informing reference-based detection methods and water quality management. 40Recent reviews have proposed the use of viral metagenomics or viromic approaches 58 as an alternative method to test for the presence of pathogenic viruses in the 59 environment (2, 9, 10). Provided the entire viral community is sampled and 60 4 sequenced, novel genotypes or even entirely novel viruses can be detected. 61Potential new viral markers for faecal contamination have already been revealed, 62 such as pepper mild mottle virus and crAssphage (11, 12), among the huge diversity 63 of human viruses found in sludge samples (13). 64In this pilot study, we have used viromics to investigate the presence of human 65 pathogenic RNA viruses in wastewater, estuarine surface water and sediment in a 66 single catchment. The water and sediment samples were collected at, and 67 downstream of, the wastewater treatment plant (Lanrwst, Wales, UK), at the estuary 68 of the river Conwy (Wales, UK) near Morfa beach (Figure 1). To our knowledge, this 69 is the first study to use unamplified environmental viral RNA for sequencing library 70 construction, sequence dataset production and subsequent analysis. Because we 71 used a directional library sequencing protocol on RNA, rather than amplifying to 72 cDNA, we were able to distinguish single-stranded from double-stranded RNA 73 genome fragments. 74

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Section: Discussionsupporting

confidence: 68%

Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses

Adriaenssens

Farkas

Harrison

et al. 2018

Preprint

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“…Zoonotic rotavirus infections in humans are not uncommon, and there are a growing number of reports describing the interspecies transmission of rotavirus among animals and from animals to humans (Ben Hadj Fredj et al, 2013., Gautam et al, 2015, Martella et al, 2010Medici et al, 2015. Like influenza viruses, zoonotic rotaviruses can become increasingly "humanized" by reassortment with co-infecting human viruses (Cowley et al, 2013, Jeong et al, 2014, Matthijnssens et al, 2009, Theuns et al, 2015.…”

Section: Introductionmentioning

confidence: 99%

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

Lin²,

Huang

et al. 2016

Virology

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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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“…In human RVAs, 6 G-genotypes (G1-4, G9 and G12) and 3 P genotypes (P[4], P [6] and P[8]) are commonly associated with human infections (Santos & Hoshino, 2005). In addition, several G-genotypes (G5, G6, G8, G10, G11 and G20) and Pgenotypes (Ben Hadj Fredj et al, 2013b;Gautam et al, 2015;Gentsch et al, 2005;Santos & Hoshino, 2005;Solberg et al, 2009;Tacharoenmuang et al, 2015). At least 73 G/P-genotype combinations of RVAs infecting humans have been described (Matthijnssens et al, 2009 (B anyai et al, 2012;Gómez et al, 2014;Matthijnssens et al, 2010;Rahman et al, 2007;Santos & Hoshino, 2005;Stupka et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Distribution of rotavirus VP7 and VP4 genotypes circulating in Tunisia from 2009 to 2014: Emergence of the genotype G12

Moussa

Fredj

Fodha

et al. 2016

Journal of Medical Microbiology

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Group A rotavirus (RVA) represents the most important aetiological agent of diarrhoea in children worldwide. From January 2009 to December 2014, a multi-centre study realized through 11 Tunisian cities was undertaken among children aged <5 years consulting or hospitalized for acute gastroenteritis. A total of 1127 faecal samples were collected. All samples were screened by ELISA for the presence of RVA antigen. RVA-positive samples were further analyzed by PAGE and used for G/P-genotyping by semi-nested multiplex RT-PCR. Globally, 270 specimens (24 %) were RVA-positive, with peaks observed annually between November and March. Nine different electropherotypes could be visualized by PAGE, six with a long profile (173 cases) and two with a short one (seven cases). Mixed profiles were detected in two cases. Among the 267 VP7 genotyped strains, the predominant G-genotype was G1 (39.6 %) followed by G3 (22.2 %), G4 (13 %), G9 (11.5 %), G2 (5.2 %) and G12 (5.2 %). Among the 260 VP4 genotyped strains, P[8] genotype was the predominant (74. 9 %). Uncommon G/Pgenotype combinations, mixed infections and untypeable strains were also detected. This is the first report, in Tunisia, of multiple detection of an emerging human RVA strain, G12 genotype. This study highlighted the need for maintaining active surveillance of emerging strains in Northern Africa.

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Full genomic characterization and phylogenetic analysis of a zoonotic human G8P[14] rotavirus strain detected in a sample from Guatemala

Cited by 29 publications

References 37 publications

Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses

Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses

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

Distribution of rotavirus VP7 and VP4 genotypes circulating in Tunisia from 2009 to 2014: Emergence of the genotype G12

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