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Genetic Diversity and Evolution | Spotlight

Effect of Geographic Isolation on the Nasal Virome of Indigenous Children

Eda Altan, Juan Carlos Dib, Andres Rojas Gulloso, Duamaco Escribano Juandigua, Xutao Deng, Roberta Bruhn, Kristen Hildebrand, Pamela Freiden, Janie Yamamoto, Stacey Schultz-Cherry, Eric Delwart
Julie K. Pfeiffer, Editor
Eda Altan
aVitalant Research Institute, San Francisco, California, USA
bDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
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  • ORCID record for Eda Altan
Juan Carlos Dib
cUniversidad del Norte, Barranquilla, Atlantico, Colombia
dFundación Salud Para el Trópico-Tropical Health Foundation, Santa Marta, Magdalena, Colombia
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Andres Rojas Gulloso
dFundación Salud Para el Trópico-Tropical Health Foundation, Santa Marta, Magdalena, Colombia
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Duamaco Escribano Juandigua
dFundación Salud Para el Trópico-Tropical Health Foundation, Santa Marta, Magdalena, Colombia
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Xutao Deng
aVitalant Research Institute, San Francisco, California, USA
bDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
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Roberta Bruhn
aVitalant Research Institute, San Francisco, California, USA
bDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
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Kristen Hildebrand
eDepartment of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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Pamela Freiden
eDepartment of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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Janie Yamamoto
aVitalant Research Institute, San Francisco, California, USA
bDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
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Stacey Schultz-Cherry
eDepartment of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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Eric Delwart
aVitalant Research Institute, San Francisco, California, USA
bDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
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Julie K. Pfeiffer
University of Texas Southwestern Medical Center
Roles: Editor
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DOI: 10.1128/JVI.00681-19
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  • FIG 1
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    FIG 1

    View of isolated indigenous village of Seywiaka (top) and the most isolated indigenous village of Umandita (bottom).

  • FIG 2
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    FIG 2

    Distribution and levels of reads for human viruses within villages. To display the amounts of viral reads in each sample, a bubble chart was generated based on the number of reads for named viruses (BLASTx E scores of <10−10) per 1 million total reads (reads per million [RPM]), with log10 transformation. For example, 10 and 1,000 viral reads in 106 total reads yield values of 1 and 3, respectively.

  • FIG 3
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    FIG 3

    Phylogenetic analysis of VP4-VP2 region of rhinoviruses inferred using the maximum likelihood method, based on the general time reversible model. A discrete gamma distribution was used to model evolutionary rate differences among sites. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. There were a total of 518 positions in the final data set. Evolutionary analyses were conducted in MEGA6. ●, Calabazo nonindigenous (CNI); ▲, Seywiaka indigenous (SI); ■, Umandita indigenous (UI).

  • FIG 4
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    FIG 4

    Distribution and levels of anellovirus (top) and papillomavirus (bottom) reads within villages. The bubble charts were generated based on the number of reads for named viruses (BLASTx E scores of <10−10) per 1 million total reads (reads per million [RPM]), with log10 transformation.

  • FIG 5
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    FIG 5

    Phylogenetic analysis of the major capsid (L1) protein of papillomaviruses inferred using the maximum likelihood method, based on the general time reversible model. A discrete gamma distribution was used to model evolutionary rate differences among sites. There were a total of 1,693 positions in the final data set. Evolutionary analyses were conducted in MEGA6. ●, Calabazo nonindigenous (CNI); ▲, Seywiaka indigenous (SI); ■, Umandita indigenous (UI).

  • FIG 6
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    FIG 6

    Distribution and levels of reads for viral groups not known to infect vertebrates, or with unknown tropism, within villages. The bubble chart was generated based on the number of reads for named viruses (BLASTx E scores of <10−10) per 1 million total reads (reads per million [RPM]), with log10 transformation.

Tables

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  • TABLE 1

    Age and gender of children analyzed

    VillageNo. of children
    2–5 yr of age6–9 yr of ageGirlBoy
    Calabazo1110813
    Seywiaka129912
    Umandita138174
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Effect of Geographic Isolation on the Nasal Virome of Indigenous Children
Eda Altan, Juan Carlos Dib, Andres Rojas Gulloso, Duamaco Escribano Juandigua, Xutao Deng, Roberta Bruhn, Kristen Hildebrand, Pamela Freiden, Janie Yamamoto, Stacey Schultz-Cherry, Eric Delwart
Journal of Virology Aug 2019, 93 (17) e00681-19; DOI: 10.1128/JVI.00681-19

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Effect of Geographic Isolation on the Nasal Virome of Indigenous Children
Eda Altan, Juan Carlos Dib, Andres Rojas Gulloso, Duamaco Escribano Juandigua, Xutao Deng, Roberta Bruhn, Kristen Hildebrand, Pamela Freiden, Janie Yamamoto, Stacey Schultz-Cherry, Eric Delwart
Journal of Virology Aug 2019, 93 (17) e00681-19; DOI: 10.1128/JVI.00681-19
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    • ABSTRACT
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KEYWORDS

Colombia
nasal virome
next-generation sequencing
children
metagenomics
papillomavirus
rhinovirus

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