Discovery of Cucumis melo endornavirus by deep sequencing of human stool samples in Brazil

Costa, Antônio Charlys da; Leal, Élcio; Gill, Danielle Elise; Milagres, Flavio Augusto de Pádua; Komninakis, Shirley Vasconcelos; Brustulin, Rafael; Teles, Maria da Aparecida Rodrigues; Lobato, Márcia Cristina Alves Brito Sayão; Chagas, Rogério Togisaki das; Abrão, Maria de Fátima Neves dos Santos; Soares, Cassia Vitória de Deus Alves; Deng, Xutao; Delwart, Eric; Sabino, Éster Cerdeira; Luchs, Adriana

doi:10.1007/s11262-019-01648-0

Cited by 13 publications

(13 citation statements)

References 23 publications

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“…The samples described above were initially sent to the Public Health Laboratory of Tocantins (LACEN-TO) and stored at −20 °C, and the frozen faecal specimens were then taken to USP's Institute of Tropical Medicine (IMT/USP) to identify common enteric viruses, including RVAs, NoVs, HAstVs [32], and HSaVs [33], as well as rare [34][35][36] or potential new viruses [37][38][39][40][41][42], through NGS investigation.…”

Section: Study Populationmentioning

confidence: 99%

Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics

Tahmasebi

Luchs

Tardy

et al. 2020

Journal of General Virology

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Human enteric adenovirus species F (HAdV-F) is one of the most common pathogens responsible for acute gastroenteritis worldwide. Brazil is a country with continental dimensions where continuous multiregional surveillance is vital to establish a more complete picture of the epidemiology of HAdV-F. The aim of the current study was to investigate the molecular epidemiology of HAdV-F using full-genome data in rural and low-income urban areas in northern Brazil. This will allow a genetic comparison between Brazilian and global HAdV-F strains. The frequency of HAdV-F infections in patients with gastroenteritis and molecular typing of positive samples within this period was also analysed. A total of 251 stool samples collected between 2010 and 2016 from patients with acute gastroenteritis were screened for HAdV-F using next-generation sequencing techniques. HAdV-F infection was detected in 57.8 % (145/251) of samples. A total of 137 positive samples belonged to HAdV-F41 and 7 to HAdV-F40. HAdV-F40/41 dual infection was found in one sample. Detection rates did not vary significantly according to the year. Single HAdV-F infections were detected in 21.9 % (55/251) of samples and mixed infections in 37.4 % (94/251), with RVA/HAdV-F being the most frequent association (21.5 %; 54/251). Genetic analysis indicated that the HAdV-F strains circulating in Brazil were closely related to worldwide strains, and the existence of some temporal order was not observed. This is the first large-scale HAdV-F study in Brazil in which whole-genome data and DNA sequence analyses were used to characterize HAdV-F strains. Expanding the viral genome database could improve overall genotyping success and assist the National Center for Biotechnology Information (NCBI)/GenBank in standardizing the HAdV genome records by providing a large set of annotated HAdV-F genomes.

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Section: Study Populationmentioning

confidence: 99%

Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics

Tahmasebi

Luchs

Tardy

et al. 2020

Journal of General Virology

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“…Further, complexity is compounded by MRV-3 infection in association with other pathogens in human and animals. Pertaining to our study, gastroenteritis symptoms was observed in patient TO-151/BR, and may be associated to one (or more) of the enteric viruses (i.e., Rotavirus A, Adenovirus and Norovirus), which was detected in the fecal sample (see the number of reads in the figure S10) 14,15,17,18 . Alternatively, presence of MRV-3 in feces may be due to dietary consumption of infected porcine meat 34 .…”

Section: Resultsmentioning

confidence: 63%

“…This study was part of surveillance program carried out in the state of Tocantins, north Brazil, from 2010 to 2016 and details regarding the selection of patients were described previously 14–18 . Briefly, a total of 251 fecal specimens were collected between 2010 and 2016 and screened for enteric pathogens (i.e., rotavirus and norovirus), bacteria (i.e., Escherichia coli and Salmonella sp.…”

Section: Methodsmentioning

confidence: 99%

First identification of mammalian orthoreovirus type 3 by gut virome analysis in diarrheic child in Brazil

Rosa

Ribeiro

Villanova

et al. 2019

Sci Rep

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Diarrhea remains one of the most common causes of deaths in children. Although many studies have investigated the prevalence of enteric pathogens around the globe some diarrheal episodes remain unexplained. It is possible that some yet-unidentified viral agents could be related to these cases of gastroenteritis. By using viral metagenomics techniques, we screened 251 fecal samples of children between 0.5 to 2.5-year-old with acute diarrhea not associated with common pathogens. These children live in rural areas and have different levels of contact with animals such as pigs, cows and bats. Here we report a complete genome of one mammalian orthoreovirus (MRV) type 3, denoted TO-151/BR, detected in a female child in the state of Tocantins (north of Brazil). Brazilian TO-151/BR strain was classified as MRV-3 based on S1 phylogeny and was closely related to porcine Asian strains. Phylogenetic analyses showed that other segments were more similar to MRV-3s of different geographic locations and hosts, including human and bats, highlighting genome reassortment and lack of host-specific barriers. This is the first report of MRV-3 in South America and a hypothesis of a silent long-term circulation of this virus in Brazil has been raised.

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“…Some of these viruses, such as cowpea mosaic virus (CPMV) and pepper mild mottle virus (PMMoV), have been shown to be stable and infectious under simulated gastric conditions (Zhang et al 2006;Berardi et al 2018). Several studies have shown that plant viruses are common in human feces and, in some cases, their infectivity has been confirmed and their genome assembled (Zhang et al 2006;Colson et al 2010;da Costa et al 2019). The presence of these viruses is likely the result of consumption of virusinfected plant products (Colson et al 2010;da Costa et al 2019).…”

Section: Resultsmentioning

confidence: 99%

“…Several studies have shown that plant viruses are common in human feces and, in some cases, their infectivity has been confirmed and their genome assembled (Zhang et al 2006;Colson et al 2010;da Costa et al 2019). The presence of these viruses is likely the result of consumption of virusinfected plant products (Colson et al 2010;da Costa et al 2019).…”

Section: Resultsmentioning

confidence: 99%

Effect of two digestive enzymes and pH on the dsRNA of endornaviruses of bell pepper and melon under in vitro conditions

et al. 2019

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Purpose The objective of this investigation was to determine the in vitro effect of two common digestive enzymes, amylase and pepsin, and pH on the integrity of the RI dsRNA of bell pepper endornavirus (BPEV) and Cucumis melo endornavirus (CmEV) evaluated by gel electrophoresis and reverse-transcription PCR (RT-PCR). Methods We conducted experiments on the in vitro effect of two common digestive enzymes, amylase and pepsin, and pH on the structural integrity of the replicative intermediate (RI) dsRNA of bell pepper endornavirus (BPEV) and Cucumis melo endornavirus (CmEV), evaluated by gel electrophoresis and reverse-transcription polymerase chain reaction. Result The effect of the amylase, pepsin, and pH treatments on the dsRNA of both viruses was similar. Amylase did not appear to affect the structural integrity of the dsRNA. In contrast, gel electrophoresis analysis of pepsin-treated dsRNA samples showed an abnormal electrophoretic migration and evidence of partial dsRNA degradation. DsRNAs from both fruits were partially degraded when exposed to a pH value of 2.0 and completely degraded at a pH value of 1.0. Conclusion The results of this investigation suggest that when exposed to pepsin and pH values lower than 2.0, the RI of BPEV and CmEV lose their structural integrity. Therefore, when consuming endornavirus-infected bell pepper or melon, our digestive organs are exposed to both fragmented and full RI dsRNA of these two viruses.

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Discovery of Cucumis melo endornavirus by deep sequencing of human stool samples in Brazil

Cited by 13 publications

References 23 publications

Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics

Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics

First identification of mammalian orthoreovirus type 3 by gut virome analysis in diarrheic child in Brazil

Effect of two digestive enzymes and pH on the dsRNA of endornaviruses of bell pepper and melon under in vitro conditions

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