Complex virome in feces from Amerindian children in isolated Amazonian villages

Siqueira, Juliana D.; Domínguez-Bello, María Gloria; Contreras, Mónica; Lander, Orlana; Caballero-Arias, Hortensia; Deng, Xutao; Noya-Alarcón, Óscar; Delwart, Eric

doi:10.1038/s41467-018-06502-9

Cited by 51 publications

(54 citation statements)

References 74 publications

(68 reference statements)

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“…[5] and suggest that infants come more in contact with these viruses a few months after birth, from an unknown source. Viruses in the Picornaviridae family have also been frequently found in healthy children [9,41,43,44]. In our study, this family was identified in 80% of the infant samples, with parechovirus A and enterovirus A being the most common species.…”

Section: Discussionsupporting

confidence: 54%

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: Discussionsupporting

confidence: 54%

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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“…We show here that children from both connected and highly isolated villages in northern Colombia carry diverse human viruses in their nasal mucosa and that extreme geographic and cultural isolation did not result in a general reduction in viral diversity. A recent study of fecal viromes in children also showed that extreme isolation in Venezuelan Amazon villages did not reduce the diversity of their enteric human viruses (4). The genetically very close similarities between the human viruses reported here or in the prior enteric virome study (4) and genomes in GenBank (derived from much larger, interconnected, populations) points to frequent virus introduction into such villages despite their high degree of geographic isolation.…”

Section: Discussionsupporting

confidence: 58%

“…Coincident with the arrival of Europeans, native Amerindian populations underwent strong population bottlenecks, possibly due to imported airborne epidemics (such as smallpox, measles, and, more recently, influenza viruses) to which they had no prior exposure (2,3). A recent study of feces collected from children in isolated villages in the Venezuelan Amazon region showed that extreme geographic isolation did not result in a reduction in enteric human virus diversity (4). To determine whether reduced rates of outside contact coincide with a reduction in the diversity of human viruses in the respiratory tract, we compared the nasal mucosal viromes of children in two highly isolated Amerindian Kogi villages in a tropical forest of northern Colombia and in one largely Hispanic village alongside a coastal highway.…”

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confidence: 99%

Effect of Geographic Isolation on the Nasal Virome of Indigenous Children

Altan

Dib

Gulloso³

et al. 2019

J Virol

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The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels of geographic isolation. Metagenomic analysis was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families Anelloviridae, Papillomaviridae, Picornaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, and Paramyxoviridae were detected in decreasing proportions of children. The number of papillomavirus infections detected was greater among Hispanic children most exposed to outside contacts, while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ among the villages. Closely related variants of rhinovirus A or B were identified in 2 to 4 children from each village, reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including members of the families Parvoviridae, Partitiviridae, Dicistroviridae, and Iflaviridae and circular Rep-encoding single-stranded DNA (CRESS-DNA) virus, were also detected in nasal swabs, possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high levels of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages, indicating ongoing exposure to globally circulating viruses. IMPORTANCE Extreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population sizes may also result in rapid local viral extinction due to a lack of seronegative subjects to maintain transmission chains for rapidly cleared viruses. We compared the viruses in the nasal passages of young children in three villages with increasing levels of geographic isolation. We found that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each village, likely reflecting recent viral introductions and transmission clusters among epidemiologically linked members of these very small communities. We conclude that, despite their geographic isolation, remote indigenous villages show evidence of ongoing exposure to globally circulating viruses.

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“…In addition, depending on the tissue, it may be difficult to determine the exact virus host (i.e., intestinal tissue sample) due to 'contamination' from the diet of the animal. Indeed, previous studies have shown the detection of viruses in gut and fecal samples of humans and animals that are likely derived from their diet [40][41][42]. Due to their detection in multiple animals we are confident that the field vole and the rabbit were the likely hosts for the paramyxovirus and the rotavirus A, respectively.…”

Section: Discussionmentioning

confidence: 69%

Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits

Tsoleridis

Chappell

Monchâtre-Leroy

et al. 2019

Viruses

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The advent of unbiased metagenomic virus discovery has revolutionized studies of virus biodiversity and evolution. Despite this, our knowledge of the virosphere, including in mammalian species, remains limited. We used unbiased metagenomic sequencing to identify RNA viruses in European field voles and rabbits. Accordingly, we identified a number of novel RNA viruses including astrovirus, rotavirus A, picorna-like virus and a narmovirus (paramyxovirus). In addition, we identified a sobemovirus and a novel luteovirus that likely originated from the rabbit diet. These newly discovered viruses were often divergent from those previously described. The novel astrovirus was most closely related to a virus sampled from the rodent-eating European roller bird (Coracias garrulous). PCR screening revealed that the novel narmovirus in the UK field vole had a prevalence of approximately 4%, and shared common ancestry with other rodent narmoviruses sampled globally. Two novel rotavirus A sequences were detected in a UK field vole and a French rabbit, the latter with a prevalence of 5%. Finally, a highly divergent picorna-like virus found in the gut of the French rabbit virus was only~35% similar to an arilivirus at the amino acid level, suggesting the presence of a novel viral genus within the Picornaviridae.

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Complex virome in feces from Amerindian children in isolated Amazonian villages

Cited by 51 publications

References 74 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

Effect of Geographic Isolation on the Nasal Virome of Indigenous Children

Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits

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