Near full length genome of a recombinant (E/D) cosavirus strain from a rural area in the central region of Brazil

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

doi:10.1038/s41598-018-30214-1

Cited by 17 publications

(9 citation statements)

References 14 publications

(17 reference statements)

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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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“…Cosaviruses were first detected in stool samples of patients presenting acute flaccid paralysis and their healthy contacts [4,5]. They were also detected in patients with diarrhea in the work of da Costa et al [6], but the etiological role of cosaviruses remains unclear to date [7].…”

Section: Introductionmentioning

confidence: 99%

Detection and Characterization of Human Enteroviruses, Human Cosaviruses, and a New Human Parechovirus Type in Healthy Individuals in Osun State, Nigeria, 2016/2017

Osundare

Opaleye

Akindele

et al. 2019

Viruses

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Human enteroviruses and human parechoviruses are associated with a broad range of diseases and even severe and fatal conditions. For human cosaviruses, the etiological role is yet unknown. Little is known about the circulation of non-polio enteroviruses, human parechoviruses, and human cosaviruses in Nigeria. A total of 113 stool samples were collected from healthy individuals in Osun State between February 2016 and May 2017. RT-PCR assays targeting the 5′ non-coding region (5′ -NCR) were used to screen for human enteroviruses, human parechoviruses, and human cosaviruses. For human enteroviruses, species-specific RT-PCR assays targeting the VP1 regions were used for molecular typing. Inoculation was carried out on RD-A, CaCo-2, HEp-2C, and L20B cell lines to compare molecular and virological assays. Ten samples tested positive for enterovirus RNA with 11 strains detected, including CV-A13 (n = 3), E-18 (n = 2), CV-A20 (n = 1), CV-A24 (n = 1), EV-C99 (n = 1), and EV-C116 (n = 2). Three samples tested positive for human parechovirus RNA, and full genome sequencing on two samples allowed assignment to a new Parechovirus A type (HPeV-19). Thirty-three samples tested positive for cosavirus with assignment to species Cosavirus D and Cosavirus A based on the 5′-NCR region. Screening of stool samples collected from healthy individuals in Nigeria in 2016 and 2017 revealed a high diversity of circulating human enteroviruses, human parechoviruses, and human cosaviruses. Molecular assays for genotyping showed substantial benefits compared with those of cell-culture assays.

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“…These patients have also been found to have other pathogenic viruses, such as noroviruses, sapoviruses, and adenoviruses (Table 1). Detailed description of viruses found in all 251 patients enrolled in this study was summarized in previous publications [32][33][34][35][36][37][38][39][40].…”

Section: Viral Diversitymentioning

confidence: 99%

Multiple clades of Husavirus in South America revealed by next generation sequencing

et al. 2021

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Husavirus (HuV) is an unclassified virus of the order Picornavirales that has already been identified worldwide in various locations. The genetic, epidemiological, and pathogenic characteristics are, however, little understood. In children with acute gastroenteritis, this study used next-generation sequencing to recognize unknown sources of viruses. In particular, 251 fecal samples obtained from individuals were sequenced in southern, northeastern, and northern Brazil. all samples were also analyzed using culture methods and parasitological tests to classify other enteric pathogens such as bacteria, parasites, and viruses. 1.9% of the samples tested positive for HuV, for a total of 5 positive children, with a mean age of 2 year, with three males and two females. Detailed molecular characterization of full genomes showed that Brazilian HuVs’ nucleotide divergence is less than 11%. The genetic gap between Brazilian sequences and the closest HuV reported previously, on the other hand, is 18%. The study showed that Brazilian sequences are closely related to the HuV defined in Viet Nam in 2013, further characterization based on phylogenetics. At least two divergent clades of HuV in South America were also seen in the phylogenetic study.

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Near full length genome of a recombinant (E/D) cosavirus strain from a rural area in the central region of Brazil

Cited by 17 publications

References 14 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

Detection and Characterization of Human Enteroviruses, Human Cosaviruses, and a New Human Parechovirus Type in Healthy Individuals in Osun State, Nigeria, 2016/2017

Multiple clades of Husavirus in South America revealed by next generation sequencing

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