Viral species richness and composition in young children with loose or watery stool in Ethiopia

Aiemjoy, Kristen; Altan, Eda; Aragie, Solomon; Fry, Dionna M.; Phan, Tung Gia; Deng, Xutao; Chanyalew, Melsew; Tadesse, Zerihun; Callahan, E. Kelly; Delwart, Eric; Keenan, Jeremy D.

doi:10.1186/s12879-019-3674-3

Cited by 20 publications

(27 citation statements)

References 46 publications

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“…The richness of eukaryotic virus species found in this work was higher than in previous studies in healthy children, in which less than 9 different virus species were found per individual samples [5,7,41,43,45]. We identified on average 15 (±9 s.d.)…”

Section: Discussioncontrasting

confidence: 78%

“…virus species per sample, which is higher even when compared to previous reports in rural or small village communities [41,43,45]. In general, we also identified a greater number of enteric viruses compared to previous studies carried out not only in healthy infants, but also in sick children [32,45]. Several factors may influence these results and should be considered in future studies.…”

Section: Discussionsupporting

confidence: 55%

“…In our study, members of the Anelloviridae family were highly abundant, containing different species of torque teno mini virus and unclassified species in up to 80% of the samples. In previous studies, viruses from this family have been identified as the most abundant and frequent in healthy children [6,29,31,33,41–45], being more abundant during the first year of life [5,29,42], after which the abundances decrease. Their presence has been associated with a reduced host immune status; a higher abundance have been reported in patient with lung transplantation [46,47], AIDs [48], pulmonary diseases [49,50], cancer [51], among others; although their role in the pathogenesis of these diseases remains unclear [52].…”

Section: Discussionmentioning

confidence: 99%

“…Viruses in the Caliciviridae family have been found at a low frequency (7%) in healthy infants in metropolitan areas of the USA [5], while they were absent in an urban city but frequent (45%-60%) in rural communities of Venezuela [43] and Ethiopia [41]. In case-control studies they have been more frequently identified in sick as compared to healthy children [32,45,54]. In this context, it is remarkable that these viruses were present in up to 72% of the infant samples we studied and in the absence of gastrointestinal symptoms.…”

Section: Discussionmentioning

confidence: 99%

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The gut virome of healthy children during the first year of life is diverse and dynamic

Arias

Taboada

Morán

et al. 2020

Preprint

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In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infant’s immune system or on the health of the infants later in life, remains to be investigated.

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Section: Discussioncontrasting

confidence: 78%

Section: Discussionsupporting

confidence: 55%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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The gut virome of healthy children during the first year of life is diverse and dynamic

Arias

Taboada

Morán

et al. 2020

Preprint

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“…The results showed that rotavirus was the primary (40%) virus causing diarrhoea among children in Kuwait [33,34]. Concerning norovirus, other studies have also demonstrated that norovirus GII is the predominant genogroup known to cause gastroenteritis in children [35][36][37][38].…”

Section: Discussionmentioning

confidence: 94%

Analysis of viral diversity in stool samples from infants and children with acute gastroenteritis in Kuwait using Metagenomics approach

Mohammad

Madi

Al‐Nakib

2020

Virol J

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Background: Current molecular target-dependent methods are used to detect only known viruses. However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait. Methods: We have investigated 84 stool samples from infants and children aged one month to ten years old with signs and symptoms of gastroenteritis who attended Mubarak Al-Kabeer and Al-Amiri hospitals in Kuwait from January to December 2017. A metagenomics approach using NGS to characterise viruses in clinical samples was used. Also, the commercial Real-Time PCR assay was used to detect viruses causing gastroenteritis. Results: Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. The analysis of viral sequences verified that single infection of human adenovirus was the leading cause of gastroenteritis among infants and children, which was detected in 23.2% of the patients, followed by a mixed infection of human adenovirus and other viruses, which was detected in 20.9% of patients. Also, the newly discovered viruses known to cause gastroenteritis were detected, such as astrovirus MLB2, primate bocaparvovirus-1, Aichivirus A, cardiovirus, parechovirus A, astrovirus VA4, cosavirus-F, and bufavirus-3. Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples. Conclusion: Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples.

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A Comprehensive Review on Human Aichi Virus

Rivadulla

Romalde

2020

Virol. Sin.

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Although norovirus, rotavirus, adenovirus and Astrovirus are considered the most important viral agents transmitted by food and water, in recent years other viruses, such as Aichi virus (AiV), have emerged as responsible for gastroenteritis outbreaks associated with different foods. AiV belongs to the genus Kobuvirus of the family Picornaviridae. It is a virus with icosahedral morphology that presents a single stranded RNA genome with positive sense (8280 nucleotides) and a poly (A) chain. AiV was first detected from clinical samples and in recent years has been involved in acute gastroenteritis outbreaks from different world regions. Furthermore, several studies conducted in Japan, Germany, France, Tunisia and Spain showed a high prevalence of AiV antibodies in adults (between 80% and 99%), which is indicative of a large exposure to this virus. The aim of this review is to bring together all the discovered information about the emerging pathogen human Aichi virus (AiV), discussing the possibles routes of transmission, new detection techniques and future research. Although AiV is responsible for a low percentage of gastroenteritis outbreaks, the high seroprevalence shown by human populations indicates an evident role as an enteric agent. The low percentage of AiV detection could be explained by the fact that the pathogen is more associated to subclinical infections. Further studies will be needed to clarify the real impact of AiV in human health and its importance as a causative gastroenteritis agent worldwide.

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Viral species richness and composition in young children with loose or watery stool in Ethiopia

Cited by 20 publications

References 46 publications

The gut virome of healthy children during the first year of life is diverse and dynamic

The gut virome of healthy children during the first year of life is diverse and dynamic

Analysis of viral diversity in stool samples from infants and children with acute gastroenteritis in Kuwait using Metagenomics approach

A Comprehensive Review on Human Aichi Virus

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