Non-random patterns in viral diversity

Simon J. Anthony; Ariful Islam; Christine Johnson; Isamara Navarrete-Macias; Eliza Liang; Komal Jain; Peta L. Hitchens; Xiaoyu Che; Alexander Soloyvov; Allison L. Hicks; Rafael Ojeda-Flores; Carlos Zambrana-Torrelio; Werner Ulrich; Melinda K. Rostal; Alexandra Petrosov; Joel Garcia; Najmul Haider; Nathan Wolfe; Tracey Goldstein; Stephen S. Morse; Mahmudur Rahman; Jonathan H. Epstein; Jonna K. Mazet; Peter Daszak; W. Ian Lipkin

doi:10.1038/ncomms9147

Non-random patterns in viral diversity

Simon J. Anthony, Ariful Islam, Christine Johnson, Isamara Navarrete-Macias, Eliza Liang, Komal Jain, Peta L. Hitchens, Xiaoyu Che, Alexander Soloyvov, Allison L. Hicks, Rafael Ojeda-Flores, Carlos Zambrana-Torrelio, Werner Ulrich, Melinda K. Rostal, Alexandra Petrosov, Joel Garcia, Najmul Haider, Nathan Wolfe, Tracey Goldstein, Stephen S. MorseMahmudur Rahman, Jonathan H. Epstein, Jonna K. Mazet, Peter Daszak, W. Ian Lipkin

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Abstract

It is currently unclear whether changes in viral communities will ever be predictable. Here we investigate whether viral communities in wildlife are inherently structured (inferring predictability) by looking at whether communities are assembled through deterministic (often predictable) or stochastic (not predictable) processes. We sample macaque faeces across nine sites in Bangladesh and use consensus PCR and sequencing to discover 184 viruses from 14 viral families. We then use network modelling and statistical null-hypothesis testing to show the presence of non-random deterministic patterns at different scales, between sites and within individuals. We show that the effects of determinism are not absolute however, as stochastic patterns are also observed. In showing that determinism is an important process in viral community assembly we conclude that it should be possible to forecast changes to some portion of a viral community, however there will always be some portion for which prediction will be unlikely.

Original language	English
Article number	8147
Journal	Nature Communications
Volume	6
Number of pages	7
ISSN	2041-1723
DOIs	https://doi.org/10.1038/ncomms9147
Publication status	Published - 2015

Keywords

Biological sciences
Ecology
Microbiology
Virology

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Anthony, S. J., Islam, A., Johnson, C., Navarrete-Macias, I., Liang, E., Jain, K., Hitchens, P. L., Che, X., Soloyvov, A., Hicks, A. L., Ojeda-Flores, R., Zambrana-Torrelio, C., Ulrich, W., Rostal, M. K., Petrosov, A., Garcia, J., Haider, N., Wolfe, N., Goldstein, T., ... Lipkin, W. I. (2015). Non-random patterns in viral diversity. Nature Communications, 6, Article 8147. https://doi.org/10.1038/ncomms9147

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title = "Non-random patterns in viral diversity",

abstract = "It is currently unclear whether changes in viral communities will ever be predictable. Here we investigate whether viral communities in wildlife are inherently structured (inferring predictability) by looking at whether communities are assembled through deterministic (often predictable) or stochastic (not predictable) processes. We sample macaque faeces across nine sites in Bangladesh and use consensus PCR and sequencing to discover 184 viruses from 14 viral families. We then use network modelling and statistical null-hypothesis testing to show the presence of non-random deterministic patterns at different scales, between sites and within individuals. We show that the effects of determinism are not absolute however, as stochastic patterns are also observed. In showing that determinism is an important process in viral community assembly we conclude that it should be possible to forecast changes to some portion of a viral community, however there will always be some portion for which prediction will be unlikely.",

keywords = "Biological sciences, Ecology, Microbiology, Virology",

author = "Anthony, {Simon J.} and Ariful Islam and Christine Johnson and Isamara Navarrete-Macias and Eliza Liang and Komal Jain and Hitchens, {Peta L.} and Xiaoyu Che and Alexander Soloyvov and Hicks, {Allison L.} and Rafael Ojeda-Flores and Carlos Zambrana-Torrelio and Werner Ulrich and Rostal, {Melinda K.} and Alexandra Petrosov and Joel Garcia and Najmul Haider and Nathan Wolfe and Tracey Goldstein and Morse, {Stephen S.} and Mahmudur Rahman and Epstein, {Jonathan H.} and Mazet, {Jonna K.} and Peter Daszak and Lipkin, {W. Ian}",

year = "2015",

doi = "10.1038/ncomms9147",

language = "English",

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journal = "Nature Communications",

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Anthony, SJ, Islam, A, Johnson, C, Navarrete-Macias, I, Liang, E, Jain, K, Hitchens, PL, Che, X, Soloyvov, A, Hicks, AL, Ojeda-Flores, R, Zambrana-Torrelio, C, Ulrich, W, Rostal, MK, Petrosov, A, Garcia, J, Haider, N, Wolfe, N, Goldstein, T, Morse, SS, Rahman, M, Epstein, JH, Mazet, JK, Daszak, P & Lipkin, WI 2015, 'Non-random patterns in viral diversity', Nature Communications, vol. 6, 8147. https://doi.org/10.1038/ncomms9147

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T1 - Non-random patterns in viral diversity

AU - Anthony, Simon J.

AU - Islam, Ariful

AU - Johnson, Christine

AU - Navarrete-Macias, Isamara

AU - Liang, Eliza

AU - Jain, Komal

AU - Hitchens, Peta L.

AU - Che, Xiaoyu

AU - Soloyvov, Alexander

AU - Hicks, Allison L.

AU - Ojeda-Flores, Rafael

AU - Zambrana-Torrelio, Carlos

AU - Ulrich, Werner

AU - Rostal, Melinda K.

AU - Petrosov, Alexandra

AU - Garcia, Joel

AU - Haider, Najmul

AU - Wolfe, Nathan

AU - Goldstein, Tracey

AU - Morse, Stephen S.

AU - Rahman, Mahmudur

AU - Epstein, Jonathan H.

AU - Mazet, Jonna K.

AU - Daszak, Peter

AU - Lipkin, W. Ian

PY - 2015

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N2 - It is currently unclear whether changes in viral communities will ever be predictable. Here we investigate whether viral communities in wildlife are inherently structured (inferring predictability) by looking at whether communities are assembled through deterministic (often predictable) or stochastic (not predictable) processes. We sample macaque faeces across nine sites in Bangladesh and use consensus PCR and sequencing to discover 184 viruses from 14 viral families. We then use network modelling and statistical null-hypothesis testing to show the presence of non-random deterministic patterns at different scales, between sites and within individuals. We show that the effects of determinism are not absolute however, as stochastic patterns are also observed. In showing that determinism is an important process in viral community assembly we conclude that it should be possible to forecast changes to some portion of a viral community, however there will always be some portion for which prediction will be unlikely.

AB - It is currently unclear whether changes in viral communities will ever be predictable. Here we investigate whether viral communities in wildlife are inherently structured (inferring predictability) by looking at whether communities are assembled through deterministic (often predictable) or stochastic (not predictable) processes. We sample macaque faeces across nine sites in Bangladesh and use consensus PCR and sequencing to discover 184 viruses from 14 viral families. We then use network modelling and statistical null-hypothesis testing to show the presence of non-random deterministic patterns at different scales, between sites and within individuals. We show that the effects of determinism are not absolute however, as stochastic patterns are also observed. In showing that determinism is an important process in viral community assembly we conclude that it should be possible to forecast changes to some portion of a viral community, however there will always be some portion for which prediction will be unlikely.

KW - Biological sciences

KW - Ecology

KW - Microbiology

KW - Virology

U2 - 10.1038/ncomms9147

DO - 10.1038/ncomms9147

M3 - Journal article

C2 - 26391192

SN - 2041-1723

VL - 6

JO - Nature Communications

JF - Nature Communications

M1 - 8147

ER -

Non-random patterns in viral diversity

Abstract

Keywords

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