Non-random patterns in viral diversity

Simon J. Anthony; Ariful Islam; Christine K 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 A Mazet; Peter Daszak; W. Ian Lipkin

doi:10.1038/ncomms9147

Non-random patterns in viral diversity

Simon J. Anthony, Ariful Islam, Christine K 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 A Mazet, Peter Daszak, W. Ian Lipkin

Medicine and Epidemiology

Research output: Contribution to journal › Article › peer-review

37 Scopus citations

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 (US)
Article number	8147
Journal	Nature Communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms9147
State	Published - Sep 22 2015

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)
Chemistry(all)
Physics and Astronomy(all)

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Anthony, S. J., Islam, A., Johnson, C. K., 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, [8147]. https://doi.org/10.1038/ncomms9147

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

In: Nature Communications, Vol. 6, 8147, 22.09.2015.

Research output: Contribution to journal › Article › peer-review

Anthony, SJ, Islam, A, Johnson, CK, 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, JA, Daszak, P & Lipkin, WI 2015, 'Non-random patterns in viral diversity', Nature Communications, vol. 6, 8147. https://doi.org/10.1038/ncomms9147

Anthony, Simon J. ; Islam, Ariful ; Johnson, Christine K ; Navarrete-Macias, Isamara ; Liang, Eliza ; Jain, Komal ; Hitchens, Peta L. ; Che, Xiaoyu ; Soloyvov, Alexander ; Hicks, Allison L. ; Ojeda-Flores, Rafael ; Zambrana-Torrelio, Carlos ; Ulrich, Werner ; Rostal, Melinda K. ; Petrosov, Alexandra ; Garcia, Joel ; Haider, Najmul ; Wolfe, Nathan ; Goldstein, Tracey ; Morse, Stephen S. ; Rahman, Mahmudur ; Epstein, Jonathan H. ; Mazet, Jonna A ; Daszak, Peter ; Lipkin, W. Ian. / Non-random patterns in viral diversity. In: Nature Communications. 2015 ; Vol. 6.

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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.",

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Non-random patterns in viral diversity

Abstract

ASJC Scopus subject areas

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